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17,600
|
Kozea/cairocffi
|
cairocffi/context.py
|
Context.tag_begin
|
def tag_begin(self, tag_name, attributes=None):
"""Marks the beginning of the ``tag_name`` structure.
Call :meth:`tag_end` with the same ``tag_name`` to mark the end of the
structure.
The attributes string is of the form "key1=value2 key2=value2 ...".
Values may be boolean (true/false or 1/0), integer, float, string, or
an array.
String values are enclosed in single quotes ('). Single quotes and
backslashes inside the string should be escaped with a backslash.
Boolean values may be set to true by only specifying the key. eg the
attribute string "key" is the equivalent to "key=true".
Arrays are enclosed in '[]'. eg "rect=[1.2 4.3 2.0 3.0]".
If no attributes are required, ``attributes`` can be omitted, an empty
string or None.
See cairo's Tags and Links Description for the list of tags and
attributes.
Invalid nesting of tags or invalid attributes will cause the context to
shutdown with a status of ``CAIRO_STATUS_TAG_ERROR``.
See :meth:`tag_end`.
:param tag_name: tag name
:param attributes: tag attributes
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
if attributes is None:
attributes = ''
cairo.cairo_tag_begin(
self._pointer, _encode_string(tag_name),
_encode_string(attributes))
self._check_status()
|
python
|
def tag_begin(self, tag_name, attributes=None):
"""Marks the beginning of the ``tag_name`` structure.
Call :meth:`tag_end` with the same ``tag_name`` to mark the end of the
structure.
The attributes string is of the form "key1=value2 key2=value2 ...".
Values may be boolean (true/false or 1/0), integer, float, string, or
an array.
String values are enclosed in single quotes ('). Single quotes and
backslashes inside the string should be escaped with a backslash.
Boolean values may be set to true by only specifying the key. eg the
attribute string "key" is the equivalent to "key=true".
Arrays are enclosed in '[]'. eg "rect=[1.2 4.3 2.0 3.0]".
If no attributes are required, ``attributes`` can be omitted, an empty
string or None.
See cairo's Tags and Links Description for the list of tags and
attributes.
Invalid nesting of tags or invalid attributes will cause the context to
shutdown with a status of ``CAIRO_STATUS_TAG_ERROR``.
See :meth:`tag_end`.
:param tag_name: tag name
:param attributes: tag attributes
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
if attributes is None:
attributes = ''
cairo.cairo_tag_begin(
self._pointer, _encode_string(tag_name),
_encode_string(attributes))
self._check_status()
|
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Marks the beginning of the ``tag_name`` structure.
Call :meth:`tag_end` with the same ``tag_name`` to mark the end of the
structure.
The attributes string is of the form "key1=value2 key2=value2 ...".
Values may be boolean (true/false or 1/0), integer, float, string, or
an array.
String values are enclosed in single quotes ('). Single quotes and
backslashes inside the string should be escaped with a backslash.
Boolean values may be set to true by only specifying the key. eg the
attribute string "key" is the equivalent to "key=true".
Arrays are enclosed in '[]'. eg "rect=[1.2 4.3 2.0 3.0]".
If no attributes are required, ``attributes`` can be omitted, an empty
string or None.
See cairo's Tags and Links Description for the list of tags and
attributes.
Invalid nesting of tags or invalid attributes will cause the context to
shutdown with a status of ``CAIRO_STATUS_TAG_ERROR``.
See :meth:`tag_end`.
:param tag_name: tag name
:param attributes: tag attributes
*New in cairo 1.16.*
*New in cairocffi 0.9.*
|
[
"Marks",
"the",
"beginning",
"of",
"the",
"tag_name",
"structure",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/context.py#L2198-L2240
|
17,601
|
Kozea/cairocffi
|
cairocffi/context.py
|
Context.tag_end
|
def tag_end(self, tag_name):
"""Marks the end of the ``tag_name`` structure.
Invalid nesting of tags will cause @cr to shutdown with a status of
``CAIRO_STATUS_TAG_ERROR``.
See :meth:`tag_begin`.
:param tag_name: tag name
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
cairo.cairo_tag_end(self._pointer, _encode_string(tag_name))
self._check_status()
|
python
|
def tag_end(self, tag_name):
"""Marks the end of the ``tag_name`` structure.
Invalid nesting of tags will cause @cr to shutdown with a status of
``CAIRO_STATUS_TAG_ERROR``.
See :meth:`tag_begin`.
:param tag_name: tag name
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
cairo.cairo_tag_end(self._pointer, _encode_string(tag_name))
self._check_status()
|
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",",
"_encode_string",
"(",
"tag_name",
")",
")",
"self",
".",
"_check_status",
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")"
] |
Marks the end of the ``tag_name`` structure.
Invalid nesting of tags will cause @cr to shutdown with a status of
``CAIRO_STATUS_TAG_ERROR``.
See :meth:`tag_begin`.
:param tag_name: tag name
*New in cairo 1.16.*
*New in cairocffi 0.9.*
|
[
"Marks",
"the",
"end",
"of",
"the",
"tag_name",
"structure",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/context.py#L2242-L2258
|
17,602
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
_make_read_func
|
def _make_read_func(file_obj):
"""Return a CFFI callback that reads from a file-like object."""
@ffi.callback("cairo_read_func_t", error=constants.STATUS_READ_ERROR)
def read_func(_closure, data, length):
string = file_obj.read(length)
if len(string) < length: # EOF too early
return constants.STATUS_READ_ERROR
ffi.buffer(data, length)[:len(string)] = string
return constants.STATUS_SUCCESS
return read_func
|
python
|
def _make_read_func(file_obj):
"""Return a CFFI callback that reads from a file-like object."""
@ffi.callback("cairo_read_func_t", error=constants.STATUS_READ_ERROR)
def read_func(_closure, data, length):
string = file_obj.read(length)
if len(string) < length: # EOF too early
return constants.STATUS_READ_ERROR
ffi.buffer(data, length)[:len(string)] = string
return constants.STATUS_SUCCESS
return read_func
|
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"-",
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"."
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450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L24-L33
|
17,603
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
_make_write_func
|
def _make_write_func(file_obj):
"""Return a CFFI callback that writes to a file-like object."""
if file_obj is None:
return ffi.NULL
@ffi.callback("cairo_write_func_t", error=constants.STATUS_WRITE_ERROR)
def write_func(_closure, data, length):
file_obj.write(ffi.buffer(data, length))
return constants.STATUS_SUCCESS
return write_func
|
python
|
def _make_write_func(file_obj):
"""Return a CFFI callback that writes to a file-like object."""
if file_obj is None:
return ffi.NULL
@ffi.callback("cairo_write_func_t", error=constants.STATUS_WRITE_ERROR)
def write_func(_closure, data, length):
file_obj.write(ffi.buffer(data, length))
return constants.STATUS_SUCCESS
return write_func
|
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|
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"-",
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] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L36-L45
|
17,604
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
_encode_filename
|
def _encode_filename(filename): # pragma: no cover
"""Return a byte string suitable for a filename.
Unicode is encoded using an encoding adapted to what both cairo and the
filesystem want.
"""
# Don't replace unknown characters as '?' is forbidden in Windows filenames
errors = 'ignore' if os.name == 'nt' else 'replace'
if not isinstance(filename, bytes):
if os.name == 'nt' and cairo.cairo_version() >= 11510:
# Since 1.15.10, cairo uses utf-8 filenames on Windows
filename = filename.encode('utf-8', errors=errors)
else:
try:
filename = filename.encode(sys.getfilesystemencoding())
except UnicodeEncodeError:
# Use plain ASCII filenames as fallback
filename = filename.encode('ascii', errors=errors)
# TODO: avoid characters forbidden in filenames?
return ffi.new('char[]', filename)
|
python
|
def _encode_filename(filename): # pragma: no cover
"""Return a byte string suitable for a filename.
Unicode is encoded using an encoding adapted to what both cairo and the
filesystem want.
"""
# Don't replace unknown characters as '?' is forbidden in Windows filenames
errors = 'ignore' if os.name == 'nt' else 'replace'
if not isinstance(filename, bytes):
if os.name == 'nt' and cairo.cairo_version() >= 11510:
# Since 1.15.10, cairo uses utf-8 filenames on Windows
filename = filename.encode('utf-8', errors=errors)
else:
try:
filename = filename.encode(sys.getfilesystemencoding())
except UnicodeEncodeError:
# Use plain ASCII filenames as fallback
filename = filename.encode('ascii', errors=errors)
# TODO: avoid characters forbidden in filenames?
return ffi.new('char[]', filename)
|
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|
[
"Return",
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"string",
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] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L48-L70
|
17,605
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
Surface.create_similar_image
|
def create_similar_image(self, content, width, height):
"""
Create a new image surface that is as compatible as possible
for uploading to and the use in conjunction with this surface.
However, this surface can still be used like any normal image surface.
Initially the surface contents are all 0
(transparent if contents have transparency, black otherwise.)
Use :meth:`create_similar` if you don't need an image surface.
:param format: the :ref:`FORMAT` string for the new surface
:param width: width of the new surface, (in device-space units)
:param height: height of the new surface (in device-space units)
:type format: str
:type width: int
:type height: int
:returns: A new :class:`ImageSurface` instance.
"""
return Surface._from_pointer(
cairo.cairo_surface_create_similar_image(
self._pointer, content, width, height),
incref=False)
|
python
|
def create_similar_image(self, content, width, height):
"""
Create a new image surface that is as compatible as possible
for uploading to and the use in conjunction with this surface.
However, this surface can still be used like any normal image surface.
Initially the surface contents are all 0
(transparent if contents have transparency, black otherwise.)
Use :meth:`create_similar` if you don't need an image surface.
:param format: the :ref:`FORMAT` string for the new surface
:param width: width of the new surface, (in device-space units)
:param height: height of the new surface (in device-space units)
:type format: str
:type width: int
:type height: int
:returns: A new :class:`ImageSurface` instance.
"""
return Surface._from_pointer(
cairo.cairo_surface_create_similar_image(
self._pointer, content, width, height),
incref=False)
|
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Create a new image surface that is as compatible as possible
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However, this surface can still be used like any normal image surface.
Initially the surface contents are all 0
(transparent if contents have transparency, black otherwise.)
Use :meth:`create_similar` if you don't need an image surface.
:param format: the :ref:`FORMAT` string for the new surface
:param width: width of the new surface, (in device-space units)
:param height: height of the new surface (in device-space units)
:type format: str
:type width: int
:type height: int
:returns: A new :class:`ImageSurface` instance.
|
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450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L209-L232
|
17,606
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
Surface.create_for_rectangle
|
def create_for_rectangle(self, x, y, width, height):
"""
Create a new surface that is a rectangle within this surface.
All operations drawn to this surface are then clipped and translated
onto the target surface.
Nothing drawn via this sub-surface outside of its bounds
is drawn onto the target surface,
making this a useful method for passing constrained child surfaces
to library routines that draw directly onto the parent surface,
i.e. with no further backend allocations,
double buffering or copies.
.. note::
As of cairo 1.12,
the semantics of subsurfaces have not been finalized yet
unless the rectangle is in full device units,
is contained within the extents of the target surface,
and the target or subsurface's device transforms are not changed.
:param x:
The x-origin of the sub-surface
from the top-left of the target surface (in device-space units)
:param y:
The y-origin of the sub-surface
from the top-left of the target surface (in device-space units)
:param width:
Width of the sub-surface (in device-space units)
:param height:
Height of the sub-surface (in device-space units)
:type x: float
:type y: float
:type width: float
:type height: float
:returns:
A new :class:`Surface` object.
*New in cairo 1.10.*
"""
return Surface._from_pointer(
cairo.cairo_surface_create_for_rectangle(
self._pointer, x, y, width, height),
incref=False)
|
python
|
def create_for_rectangle(self, x, y, width, height):
"""
Create a new surface that is a rectangle within this surface.
All operations drawn to this surface are then clipped and translated
onto the target surface.
Nothing drawn via this sub-surface outside of its bounds
is drawn onto the target surface,
making this a useful method for passing constrained child surfaces
to library routines that draw directly onto the parent surface,
i.e. with no further backend allocations,
double buffering or copies.
.. note::
As of cairo 1.12,
the semantics of subsurfaces have not been finalized yet
unless the rectangle is in full device units,
is contained within the extents of the target surface,
and the target or subsurface's device transforms are not changed.
:param x:
The x-origin of the sub-surface
from the top-left of the target surface (in device-space units)
:param y:
The y-origin of the sub-surface
from the top-left of the target surface (in device-space units)
:param width:
Width of the sub-surface (in device-space units)
:param height:
Height of the sub-surface (in device-space units)
:type x: float
:type y: float
:type width: float
:type height: float
:returns:
A new :class:`Surface` object.
*New in cairo 1.10.*
"""
return Surface._from_pointer(
cairo.cairo_surface_create_for_rectangle(
self._pointer, x, y, width, height),
incref=False)
|
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Create a new surface that is a rectangle within this surface.
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Nothing drawn via this sub-surface outside of its bounds
is drawn onto the target surface,
making this a useful method for passing constrained child surfaces
to library routines that draw directly onto the parent surface,
i.e. with no further backend allocations,
double buffering or copies.
.. note::
As of cairo 1.12,
the semantics of subsurfaces have not been finalized yet
unless the rectangle is in full device units,
is contained within the extents of the target surface,
and the target or subsurface's device transforms are not changed.
:param x:
The x-origin of the sub-surface
from the top-left of the target surface (in device-space units)
:param y:
The y-origin of the sub-surface
from the top-left of the target surface (in device-space units)
:param width:
Width of the sub-surface (in device-space units)
:param height:
Height of the sub-surface (in device-space units)
:type x: float
:type y: float
:type width: float
:type height: float
:returns:
A new :class:`Surface` object.
*New in cairo 1.10.*
|
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"onto",
"the",
"target",
"surface",
"making",
"this",
"a",
"useful",
"method",
"for",
"passing",
"constrained",
"child",
"surfaces",
"to",
"library",
"routines",
"that",
"draw",
"directly",
"onto",
"the",
"parent",
"surface",
"i",
".",
"e",
".",
"with",
"no",
"further",
"backend",
"allocations",
"double",
"buffering",
"or",
"copies",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L234-L277
|
17,607
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
Surface.set_fallback_resolution
|
def set_fallback_resolution(self, x_pixels_per_inch, y_pixels_per_inch):
"""
Set the horizontal and vertical resolution for image fallbacks.
When certain operations aren't supported natively by a backend,
cairo will fallback by rendering operations to an image
and then overlaying that image onto the output.
For backends that are natively vector-oriented,
this method can be used to set the resolution
used for these image fallbacks,
(larger values will result in more detailed images,
but also larger file sizes).
Some examples of natively vector-oriented backends are
the ps, pdf, and svg backends.
For backends that are natively raster-oriented,
image fallbacks are still possible,
but they are always performed at the native device resolution.
So this method has no effect on those backends.
.. note::
The fallback resolution only takes effect
at the time of completing a page
(with :meth:`show_page` or :meth:`copy_page`)
so there is currently no way to have
more than one fallback resolution in effect on a single page.
The default fallback resoultion is
300 pixels per inch in both dimensions.
:param x_pixels_per_inch: horizontal resolution in pixels per inch
:type x_pixels_per_inch: float
:param y_pixels_per_inch: vertical resolution in pixels per inch
:type y_pixels_per_inch: float
"""
cairo.cairo_surface_set_fallback_resolution(
self._pointer, x_pixels_per_inch, y_pixels_per_inch)
self._check_status()
|
python
|
def set_fallback_resolution(self, x_pixels_per_inch, y_pixels_per_inch):
"""
Set the horizontal and vertical resolution for image fallbacks.
When certain operations aren't supported natively by a backend,
cairo will fallback by rendering operations to an image
and then overlaying that image onto the output.
For backends that are natively vector-oriented,
this method can be used to set the resolution
used for these image fallbacks,
(larger values will result in more detailed images,
but also larger file sizes).
Some examples of natively vector-oriented backends are
the ps, pdf, and svg backends.
For backends that are natively raster-oriented,
image fallbacks are still possible,
but they are always performed at the native device resolution.
So this method has no effect on those backends.
.. note::
The fallback resolution only takes effect
at the time of completing a page
(with :meth:`show_page` or :meth:`copy_page`)
so there is currently no way to have
more than one fallback resolution in effect on a single page.
The default fallback resoultion is
300 pixels per inch in both dimensions.
:param x_pixels_per_inch: horizontal resolution in pixels per inch
:type x_pixels_per_inch: float
:param y_pixels_per_inch: vertical resolution in pixels per inch
:type y_pixels_per_inch: float
"""
cairo.cairo_surface_set_fallback_resolution(
self._pointer, x_pixels_per_inch, y_pixels_per_inch)
self._check_status()
|
[
"def",
"set_fallback_resolution",
"(",
"self",
",",
"x_pixels_per_inch",
",",
"y_pixels_per_inch",
")",
":",
"cairo",
".",
"cairo_surface_set_fallback_resolution",
"(",
"self",
".",
"_pointer",
",",
"x_pixels_per_inch",
",",
"y_pixels_per_inch",
")",
"self",
".",
"_check_status",
"(",
")"
] |
Set the horizontal and vertical resolution for image fallbacks.
When certain operations aren't supported natively by a backend,
cairo will fallback by rendering operations to an image
and then overlaying that image onto the output.
For backends that are natively vector-oriented,
this method can be used to set the resolution
used for these image fallbacks,
(larger values will result in more detailed images,
but also larger file sizes).
Some examples of natively vector-oriented backends are
the ps, pdf, and svg backends.
For backends that are natively raster-oriented,
image fallbacks are still possible,
but they are always performed at the native device resolution.
So this method has no effect on those backends.
.. note::
The fallback resolution only takes effect
at the time of completing a page
(with :meth:`show_page` or :meth:`copy_page`)
so there is currently no way to have
more than one fallback resolution in effect on a single page.
The default fallback resoultion is
300 pixels per inch in both dimensions.
:param x_pixels_per_inch: horizontal resolution in pixels per inch
:type x_pixels_per_inch: float
:param y_pixels_per_inch: vertical resolution in pixels per inch
:type y_pixels_per_inch: float
|
[
"Set",
"the",
"horizontal",
"and",
"vertical",
"resolution",
"for",
"image",
"fallbacks",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L342-L382
|
17,608
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
Surface.get_font_options
|
def get_font_options(self):
"""Retrieves the default font rendering options for the surface.
This allows display surfaces to report the correct subpixel order
for rendering on them,
print surfaces to disable hinting of metrics and so forth.
The result can then be used with :class:`ScaledFont`.
:returns: A new :class:`FontOptions` object.
"""
font_options = FontOptions()
cairo.cairo_surface_get_font_options(
self._pointer, font_options._pointer)
return font_options
|
python
|
def get_font_options(self):
"""Retrieves the default font rendering options for the surface.
This allows display surfaces to report the correct subpixel order
for rendering on them,
print surfaces to disable hinting of metrics and so forth.
The result can then be used with :class:`ScaledFont`.
:returns: A new :class:`FontOptions` object.
"""
font_options = FontOptions()
cairo.cairo_surface_get_font_options(
self._pointer, font_options._pointer)
return font_options
|
[
"def",
"get_font_options",
"(",
"self",
")",
":",
"font_options",
"=",
"FontOptions",
"(",
")",
"cairo",
".",
"cairo_surface_get_font_options",
"(",
"self",
".",
"_pointer",
",",
"font_options",
".",
"_pointer",
")",
"return",
"font_options"
] |
Retrieves the default font rendering options for the surface.
This allows display surfaces to report the correct subpixel order
for rendering on them,
print surfaces to disable hinting of metrics and so forth.
The result can then be used with :class:`ScaledFont`.
:returns: A new :class:`FontOptions` object.
|
[
"Retrieves",
"the",
"default",
"font",
"rendering",
"options",
"for",
"the",
"surface",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L397-L411
|
17,609
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
Surface.set_device_scale
|
def set_device_scale(self, x_scale, y_scale):
"""Sets a scale that is multiplied to the device coordinates determined
by the CTM when drawing to surface.
One common use for this is to render to very high resolution display
devices at a scale factor, so that code that assumes 1 pixel will be a
certain size will still work. Setting a transformation via
cairo_translate() isn't sufficient to do this, since functions like
cairo_device_to_user() will expose the hidden scale.
Note that the scale affects drawing to the surface as well as using the
surface in a source pattern.
:param x_scale: the scale in the X direction, in device units.
:param y_scale: the scale in the Y direction, in device units.
*New in cairo 1.14.*
*New in cairocffi 0.9.*
"""
cairo.cairo_surface_set_device_scale(self._pointer, x_scale, y_scale)
self._check_status()
|
python
|
def set_device_scale(self, x_scale, y_scale):
"""Sets a scale that is multiplied to the device coordinates determined
by the CTM when drawing to surface.
One common use for this is to render to very high resolution display
devices at a scale factor, so that code that assumes 1 pixel will be a
certain size will still work. Setting a transformation via
cairo_translate() isn't sufficient to do this, since functions like
cairo_device_to_user() will expose the hidden scale.
Note that the scale affects drawing to the surface as well as using the
surface in a source pattern.
:param x_scale: the scale in the X direction, in device units.
:param y_scale: the scale in the Y direction, in device units.
*New in cairo 1.14.*
*New in cairocffi 0.9.*
"""
cairo.cairo_surface_set_device_scale(self._pointer, x_scale, y_scale)
self._check_status()
|
[
"def",
"set_device_scale",
"(",
"self",
",",
"x_scale",
",",
"y_scale",
")",
":",
"cairo",
".",
"cairo_surface_set_device_scale",
"(",
"self",
".",
"_pointer",
",",
"x_scale",
",",
"y_scale",
")",
"self",
".",
"_check_status",
"(",
")"
] |
Sets a scale that is multiplied to the device coordinates determined
by the CTM when drawing to surface.
One common use for this is to render to very high resolution display
devices at a scale factor, so that code that assumes 1 pixel will be a
certain size will still work. Setting a transformation via
cairo_translate() isn't sufficient to do this, since functions like
cairo_device_to_user() will expose the hidden scale.
Note that the scale affects drawing to the surface as well as using the
surface in a source pattern.
:param x_scale: the scale in the X direction, in device units.
:param y_scale: the scale in the Y direction, in device units.
*New in cairo 1.14.*
*New in cairocffi 0.9.*
|
[
"Sets",
"a",
"scale",
"that",
"is",
"multiplied",
"to",
"the",
"device",
"coordinates",
"determined",
"by",
"the",
"CTM",
"when",
"drawing",
"to",
"surface",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L413-L435
|
17,610
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
Surface.get_mime_data
|
def get_mime_data(self, mime_type):
"""Return mime data previously attached to surface
using the specified mime type.
:param mime_type: The MIME type of the image data.
:type mime_type: ASCII string
:returns:
A CFFI buffer object, or :obj:`None`
if no data has been attached with the given mime type.
*New in cairo 1.10.*
"""
buffer_address = ffi.new('unsigned char **')
buffer_length = ffi.new('unsigned long *')
mime_type = ffi.new('char[]', mime_type.encode('utf8'))
cairo.cairo_surface_get_mime_data(
self._pointer, mime_type, buffer_address, buffer_length)
return (ffi.buffer(buffer_address[0], buffer_length[0])
if buffer_address[0] != ffi.NULL else None)
|
python
|
def get_mime_data(self, mime_type):
"""Return mime data previously attached to surface
using the specified mime type.
:param mime_type: The MIME type of the image data.
:type mime_type: ASCII string
:returns:
A CFFI buffer object, or :obj:`None`
if no data has been attached with the given mime type.
*New in cairo 1.10.*
"""
buffer_address = ffi.new('unsigned char **')
buffer_length = ffi.new('unsigned long *')
mime_type = ffi.new('char[]', mime_type.encode('utf8'))
cairo.cairo_surface_get_mime_data(
self._pointer, mime_type, buffer_address, buffer_length)
return (ffi.buffer(buffer_address[0], buffer_length[0])
if buffer_address[0] != ffi.NULL else None)
|
[
"def",
"get_mime_data",
"(",
"self",
",",
"mime_type",
")",
":",
"buffer_address",
"=",
"ffi",
".",
"new",
"(",
"'unsigned char **'",
")",
"buffer_length",
"=",
"ffi",
".",
"new",
"(",
"'unsigned long *'",
")",
"mime_type",
"=",
"ffi",
".",
"new",
"(",
"'char[]'",
",",
"mime_type",
".",
"encode",
"(",
"'utf8'",
")",
")",
"cairo",
".",
"cairo_surface_get_mime_data",
"(",
"self",
".",
"_pointer",
",",
"mime_type",
",",
"buffer_address",
",",
"buffer_length",
")",
"return",
"(",
"ffi",
".",
"buffer",
"(",
"buffer_address",
"[",
"0",
"]",
",",
"buffer_length",
"[",
"0",
"]",
")",
"if",
"buffer_address",
"[",
"0",
"]",
"!=",
"ffi",
".",
"NULL",
"else",
"None",
")"
] |
Return mime data previously attached to surface
using the specified mime type.
:param mime_type: The MIME type of the image data.
:type mime_type: ASCII string
:returns:
A CFFI buffer object, or :obj:`None`
if no data has been attached with the given mime type.
*New in cairo 1.10.*
|
[
"Return",
"mime",
"data",
"previously",
"attached",
"to",
"surface",
"using",
"the",
"specified",
"mime",
"type",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L504-L523
|
17,611
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
Surface.write_to_png
|
def write_to_png(self, target=None):
"""Writes the contents of surface as a PNG image.
:param target:
A filename,
a binary mode file-like object with a :meth:`~file.write` method,
or :obj:`None`.
:returns:
If :obj:`target` is :obj:`None`,
return the PNG contents as a byte string.
"""
return_bytes = target is None
if return_bytes:
target = io.BytesIO()
if hasattr(target, 'write'):
write_func = _make_write_func(target)
_check_status(cairo.cairo_surface_write_to_png_stream(
self._pointer, write_func, ffi.NULL))
else:
_check_status(cairo.cairo_surface_write_to_png(
self._pointer, _encode_filename(target)))
if return_bytes:
return target.getvalue()
|
python
|
def write_to_png(self, target=None):
"""Writes the contents of surface as a PNG image.
:param target:
A filename,
a binary mode file-like object with a :meth:`~file.write` method,
or :obj:`None`.
:returns:
If :obj:`target` is :obj:`None`,
return the PNG contents as a byte string.
"""
return_bytes = target is None
if return_bytes:
target = io.BytesIO()
if hasattr(target, 'write'):
write_func = _make_write_func(target)
_check_status(cairo.cairo_surface_write_to_png_stream(
self._pointer, write_func, ffi.NULL))
else:
_check_status(cairo.cairo_surface_write_to_png(
self._pointer, _encode_filename(target)))
if return_bytes:
return target.getvalue()
|
[
"def",
"write_to_png",
"(",
"self",
",",
"target",
"=",
"None",
")",
":",
"return_bytes",
"=",
"target",
"is",
"None",
"if",
"return_bytes",
":",
"target",
"=",
"io",
".",
"BytesIO",
"(",
")",
"if",
"hasattr",
"(",
"target",
",",
"'write'",
")",
":",
"write_func",
"=",
"_make_write_func",
"(",
"target",
")",
"_check_status",
"(",
"cairo",
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"cairo_surface_write_to_png_stream",
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"_pointer",
",",
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"(",
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"_pointer",
",",
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"target",
")",
")",
")",
"if",
"return_bytes",
":",
"return",
"target",
".",
"getvalue",
"(",
")"
] |
Writes the contents of surface as a PNG image.
:param target:
A filename,
a binary mode file-like object with a :meth:`~file.write` method,
or :obj:`None`.
:returns:
If :obj:`target` is :obj:`None`,
return the PNG contents as a byte string.
|
[
"Writes",
"the",
"contents",
"of",
"surface",
"as",
"a",
"PNG",
"image",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L630-L653
|
17,612
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
ImageSurface.create_from_png
|
def create_from_png(cls, source):
"""Decode a PNG file into a new image surface.
:param source:
A filename or
a binary mode file-like object with a :meth:`~file.read` method.
If you already have a byte string in memory,
use :class:`io.BytesIO`.
:returns: A new :class:`ImageSurface` instance.
"""
if hasattr(source, 'read'):
read_func = _make_read_func(source)
pointer = cairo.cairo_image_surface_create_from_png_stream(
read_func, ffi.NULL)
else:
pointer = cairo.cairo_image_surface_create_from_png(
_encode_filename(source))
self = object.__new__(cls)
Surface.__init__(self, pointer) # Skip ImageSurface.__init__
return self
|
python
|
def create_from_png(cls, source):
"""Decode a PNG file into a new image surface.
:param source:
A filename or
a binary mode file-like object with a :meth:`~file.read` method.
If you already have a byte string in memory,
use :class:`io.BytesIO`.
:returns: A new :class:`ImageSurface` instance.
"""
if hasattr(source, 'read'):
read_func = _make_read_func(source)
pointer = cairo.cairo_image_surface_create_from_png_stream(
read_func, ffi.NULL)
else:
pointer = cairo.cairo_image_surface_create_from_png(
_encode_filename(source))
self = object.__new__(cls)
Surface.__init__(self, pointer) # Skip ImageSurface.__init__
return self
|
[
"def",
"create_from_png",
"(",
"cls",
",",
"source",
")",
":",
"if",
"hasattr",
"(",
"source",
",",
"'read'",
")",
":",
"read_func",
"=",
"_make_read_func",
"(",
"source",
")",
"pointer",
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"cairo_image_surface_create_from_png_stream",
"(",
"read_func",
",",
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"NULL",
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":",
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"Surface",
".",
"__init__",
"(",
"self",
",",
"pointer",
")",
"# Skip ImageSurface.__init__",
"return",
"self"
] |
Decode a PNG file into a new image surface.
:param source:
A filename or
a binary mode file-like object with a :meth:`~file.read` method.
If you already have a byte string in memory,
use :class:`io.BytesIO`.
:returns: A new :class:`ImageSurface` instance.
|
[
"Decode",
"a",
"PNG",
"file",
"into",
"a",
"new",
"image",
"surface",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L742-L762
|
17,613
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
PDFSurface.add_outline
|
def add_outline(self, parent_id, utf8, link_attribs, flags=None):
"""Add an item to the document outline hierarchy.
The outline has the ``utf8`` name and links to the location specified
by ``link_attribs``. Link attributes have the same keys and values as
the Link Tag, excluding the ``rect`` attribute. The item will be a
child of the item with id ``parent_id``. Use ``PDF_OUTLINE_ROOT`` as
the parent id of top level items.
:param parent_id:
the id of the parent item or ``PDF_OUTLINE_ROOT`` if this is a
top level item.
:param utf8: the name of the outline.
:param link_attribs:
the link attributes specifying where this outline links to.
:param flags: outline item flags.
:return: the id for the added item.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
if flags is None:
flags = 0
value = cairo.cairo_pdf_surface_add_outline(
self._pointer, parent_id, _encode_string(utf8),
_encode_string(link_attribs), flags)
self._check_status()
return value
|
python
|
def add_outline(self, parent_id, utf8, link_attribs, flags=None):
"""Add an item to the document outline hierarchy.
The outline has the ``utf8`` name and links to the location specified
by ``link_attribs``. Link attributes have the same keys and values as
the Link Tag, excluding the ``rect`` attribute. The item will be a
child of the item with id ``parent_id``. Use ``PDF_OUTLINE_ROOT`` as
the parent id of top level items.
:param parent_id:
the id of the parent item or ``PDF_OUTLINE_ROOT`` if this is a
top level item.
:param utf8: the name of the outline.
:param link_attribs:
the link attributes specifying where this outline links to.
:param flags: outline item flags.
:return: the id for the added item.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
if flags is None:
flags = 0
value = cairo.cairo_pdf_surface_add_outline(
self._pointer, parent_id, _encode_string(utf8),
_encode_string(link_attribs), flags)
self._check_status()
return value
|
[
"def",
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"None",
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"self",
".",
"_check_status",
"(",
")",
"return",
"value"
] |
Add an item to the document outline hierarchy.
The outline has the ``utf8`` name and links to the location specified
by ``link_attribs``. Link attributes have the same keys and values as
the Link Tag, excluding the ``rect`` attribute. The item will be a
child of the item with id ``parent_id``. Use ``PDF_OUTLINE_ROOT`` as
the parent id of top level items.
:param parent_id:
the id of the parent item or ``PDF_OUTLINE_ROOT`` if this is a
top level item.
:param utf8: the name of the outline.
:param link_attribs:
the link attributes specifying where this outline links to.
:param flags: outline item flags.
:return: the id for the added item.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
|
[
"Add",
"an",
"item",
"to",
"the",
"document",
"outline",
"hierarchy",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L873-L903
|
17,614
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
PDFSurface.set_metadata
|
def set_metadata(self, metadata, utf8):
"""Sets document metadata.
The ``PDF_METADATA_CREATE_DATE`` and ``PDF_METADATA_MOD_DATE``
values must be in ISO-8601 format: YYYY-MM-DDThh:mm:ss. An optional
timezone of the form "[+/-]hh:mm" or "Z" for UTC time can be appended.
All other metadata values can be any UTF-8 string.
:param metadata: the metadata item to set.
:param utf8: metadata value.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
cairo.cairo_pdf_surface_set_metadata(
self._pointer, metadata, _encode_string(utf8))
self._check_status()
|
python
|
def set_metadata(self, metadata, utf8):
"""Sets document metadata.
The ``PDF_METADATA_CREATE_DATE`` and ``PDF_METADATA_MOD_DATE``
values must be in ISO-8601 format: YYYY-MM-DDThh:mm:ss. An optional
timezone of the form "[+/-]hh:mm" or "Z" for UTC time can be appended.
All other metadata values can be any UTF-8 string.
:param metadata: the metadata item to set.
:param utf8: metadata value.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
cairo.cairo_pdf_surface_set_metadata(
self._pointer, metadata, _encode_string(utf8))
self._check_status()
|
[
"def",
"set_metadata",
"(",
"self",
",",
"metadata",
",",
"utf8",
")",
":",
"cairo",
".",
"cairo_pdf_surface_set_metadata",
"(",
"self",
".",
"_pointer",
",",
"metadata",
",",
"_encode_string",
"(",
"utf8",
")",
")",
"self",
".",
"_check_status",
"(",
")"
] |
Sets document metadata.
The ``PDF_METADATA_CREATE_DATE`` and ``PDF_METADATA_MOD_DATE``
values must be in ISO-8601 format: YYYY-MM-DDThh:mm:ss. An optional
timezone of the form "[+/-]hh:mm" or "Z" for UTC time can be appended.
All other metadata values can be any UTF-8 string.
:param metadata: the metadata item to set.
:param utf8: metadata value.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
|
[
"Sets",
"document",
"metadata",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L905-L923
|
17,615
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
PDFSurface.set_thumbnail_size
|
def set_thumbnail_size(self, width, height):
"""Set thumbnail image size for the current and all subsequent pages.
Setting a width or height of 0 disables thumbnails for the current and
subsequent pages.
:param width: thumbnail width.
:param height: thumbnail height.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
cairo.cairo_pdf_surface_set_thumbnail_size(
self._pointer, width, height)
|
python
|
def set_thumbnail_size(self, width, height):
"""Set thumbnail image size for the current and all subsequent pages.
Setting a width or height of 0 disables thumbnails for the current and
subsequent pages.
:param width: thumbnail width.
:param height: thumbnail height.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
cairo.cairo_pdf_surface_set_thumbnail_size(
self._pointer, width, height)
|
[
"def",
"set_thumbnail_size",
"(",
"self",
",",
"width",
",",
"height",
")",
":",
"cairo",
".",
"cairo_pdf_surface_set_thumbnail_size",
"(",
"self",
".",
"_pointer",
",",
"width",
",",
"height",
")"
] |
Set thumbnail image size for the current and all subsequent pages.
Setting a width or height of 0 disables thumbnails for the current and
subsequent pages.
:param width: thumbnail width.
:param height: thumbnail height.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
|
[
"Set",
"thumbnail",
"image",
"size",
"for",
"the",
"current",
"and",
"all",
"subsequent",
"pages",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L938-L953
|
17,616
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
PSSurface.dsc_comment
|
def dsc_comment(self, comment):
""" Emit a comment into the PostScript output for the given surface.
The comment is expected to conform to
the PostScript Language Document Structuring Conventions (DSC).
Please see that manual for details on the available comments
and their meanings.
In particular, the ``%%IncludeFeature`` comment allows
a device-independent means of controlling printer device features.
So the PostScript Printer Description Files Specification
will also be a useful reference.
The comment string must begin with a percent character (%)
and the total length of the string
(including any initial percent characters)
must not exceed 255 bytes.
Violating either of these conditions will
place surface into an error state.
But beyond these two conditions,
this method will not enforce conformance of the comment
with any particular specification.
The comment string should not have a trailing newline.
The DSC specifies different sections
in which particular comments can appear.
This method provides for comments to be emitted
within three sections:
the header, the Setup section, and the PageSetup section.
Comments appearing in the first two sections
apply to the entire document
while comments in the BeginPageSetup section
apply only to a single page.
For comments to appear in the header section,
this method should be called after the surface is created,
but before a call to :meth:`dsc_begin_setup`.
For comments to appear in the Setup section,
this method should be called after a call to :meth:`dsc_begin_setup`
but before a call to :meth:`dsc_begin_page_setup`.
For comments to appear in the PageSetup section,
this method should be called after a call to
:meth:`dsc_begin_page_setup`.
Note that it is only necessary to call :meth:`dsc_begin_page_setup`
for the first page of any surface.
After a call to :meth:`~Surface.show_page`
or :meth:`~Surface.copy_page`
comments are unambiguously directed
to the PageSetup section of the current page.
But it doesn't hurt to call this method
at the beginning of every page
as that consistency may make the calling code simpler.
As a final note,
cairo automatically generates several comments on its own.
As such, applications must not manually generate
any of the following comments:
Header section: ``%!PS-Adobe-3.0``, ``%%Creator``, ``%%CreationDate``,
``%%Pages``, ``%%BoundingBox``, ``%%DocumentData``,
``%%LanguageLevel``, ``%%EndComments``.
Setup section: ``%%BeginSetup``, ``%%EndSetup``.
PageSetup section: ``%%BeginPageSetup``, ``%%PageBoundingBox``,
``%%EndPageSetup``.
Other sections: ``%%BeginProlog``, ``%%EndProlog``, ``%%Page``,
``%%Trailer``, ``%%EOF``.
"""
cairo.cairo_ps_surface_dsc_comment(
self._pointer, _encode_string(comment))
self._check_status()
|
python
|
def dsc_comment(self, comment):
""" Emit a comment into the PostScript output for the given surface.
The comment is expected to conform to
the PostScript Language Document Structuring Conventions (DSC).
Please see that manual for details on the available comments
and their meanings.
In particular, the ``%%IncludeFeature`` comment allows
a device-independent means of controlling printer device features.
So the PostScript Printer Description Files Specification
will also be a useful reference.
The comment string must begin with a percent character (%)
and the total length of the string
(including any initial percent characters)
must not exceed 255 bytes.
Violating either of these conditions will
place surface into an error state.
But beyond these two conditions,
this method will not enforce conformance of the comment
with any particular specification.
The comment string should not have a trailing newline.
The DSC specifies different sections
in which particular comments can appear.
This method provides for comments to be emitted
within three sections:
the header, the Setup section, and the PageSetup section.
Comments appearing in the first two sections
apply to the entire document
while comments in the BeginPageSetup section
apply only to a single page.
For comments to appear in the header section,
this method should be called after the surface is created,
but before a call to :meth:`dsc_begin_setup`.
For comments to appear in the Setup section,
this method should be called after a call to :meth:`dsc_begin_setup`
but before a call to :meth:`dsc_begin_page_setup`.
For comments to appear in the PageSetup section,
this method should be called after a call to
:meth:`dsc_begin_page_setup`.
Note that it is only necessary to call :meth:`dsc_begin_page_setup`
for the first page of any surface.
After a call to :meth:`~Surface.show_page`
or :meth:`~Surface.copy_page`
comments are unambiguously directed
to the PageSetup section of the current page.
But it doesn't hurt to call this method
at the beginning of every page
as that consistency may make the calling code simpler.
As a final note,
cairo automatically generates several comments on its own.
As such, applications must not manually generate
any of the following comments:
Header section: ``%!PS-Adobe-3.0``, ``%%Creator``, ``%%CreationDate``,
``%%Pages``, ``%%BoundingBox``, ``%%DocumentData``,
``%%LanguageLevel``, ``%%EndComments``.
Setup section: ``%%BeginSetup``, ``%%EndSetup``.
PageSetup section: ``%%BeginPageSetup``, ``%%PageBoundingBox``,
``%%EndPageSetup``.
Other sections: ``%%BeginProlog``, ``%%EndProlog``, ``%%Page``,
``%%Trailer``, ``%%EOF``.
"""
cairo.cairo_ps_surface_dsc_comment(
self._pointer, _encode_string(comment))
self._check_status()
|
[
"def",
"dsc_comment",
"(",
"self",
",",
"comment",
")",
":",
"cairo",
".",
"cairo_ps_surface_dsc_comment",
"(",
"self",
".",
"_pointer",
",",
"_encode_string",
"(",
"comment",
")",
")",
"self",
".",
"_check_status",
"(",
")"
] |
Emit a comment into the PostScript output for the given surface.
The comment is expected to conform to
the PostScript Language Document Structuring Conventions (DSC).
Please see that manual for details on the available comments
and their meanings.
In particular, the ``%%IncludeFeature`` comment allows
a device-independent means of controlling printer device features.
So the PostScript Printer Description Files Specification
will also be a useful reference.
The comment string must begin with a percent character (%)
and the total length of the string
(including any initial percent characters)
must not exceed 255 bytes.
Violating either of these conditions will
place surface into an error state.
But beyond these two conditions,
this method will not enforce conformance of the comment
with any particular specification.
The comment string should not have a trailing newline.
The DSC specifies different sections
in which particular comments can appear.
This method provides for comments to be emitted
within three sections:
the header, the Setup section, and the PageSetup section.
Comments appearing in the first two sections
apply to the entire document
while comments in the BeginPageSetup section
apply only to a single page.
For comments to appear in the header section,
this method should be called after the surface is created,
but before a call to :meth:`dsc_begin_setup`.
For comments to appear in the Setup section,
this method should be called after a call to :meth:`dsc_begin_setup`
but before a call to :meth:`dsc_begin_page_setup`.
For comments to appear in the PageSetup section,
this method should be called after a call to
:meth:`dsc_begin_page_setup`.
Note that it is only necessary to call :meth:`dsc_begin_page_setup`
for the first page of any surface.
After a call to :meth:`~Surface.show_page`
or :meth:`~Surface.copy_page`
comments are unambiguously directed
to the PageSetup section of the current page.
But it doesn't hurt to call this method
at the beginning of every page
as that consistency may make the calling code simpler.
As a final note,
cairo automatically generates several comments on its own.
As such, applications must not manually generate
any of the following comments:
Header section: ``%!PS-Adobe-3.0``, ``%%Creator``, ``%%CreationDate``,
``%%Pages``, ``%%BoundingBox``, ``%%DocumentData``,
``%%LanguageLevel``, ``%%EndComments``.
Setup section: ``%%BeginSetup``, ``%%EndSetup``.
PageSetup section: ``%%BeginPageSetup``, ``%%PageBoundingBox``,
``%%EndPageSetup``.
Other sections: ``%%BeginProlog``, ``%%EndProlog``, ``%%Page``,
``%%Trailer``, ``%%EOF``.
|
[
"Emit",
"a",
"comment",
"into",
"the",
"PostScript",
"output",
"for",
"the",
"given",
"surface",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L1047-L1123
|
17,617
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
SVGSurface.set_document_unit
|
def set_document_unit(self, unit):
"""Use specified unit for width and height of generated SVG file.
See ``SVG_UNIT_*`` enumerated values for a list of available unit
values that can be used here.
This function can be called at any time before generating the SVG file.
However to minimize the risk of ambiguities it's recommended to call it
before any drawing operations have been performed on the given surface,
to make it clearer what the unit used in the drawing operations is.
The simplest way to do this is to call this function immediately after
creating the SVG surface.
Note if this function is never called, the default unit for SVG
documents generated by cairo will be "pt". This is for historical
reasons.
:param unit: SVG unit.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
cairo.cairo_svg_surface_set_document_unit(self._pointer, unit)
self._check_status()
|
python
|
def set_document_unit(self, unit):
"""Use specified unit for width and height of generated SVG file.
See ``SVG_UNIT_*`` enumerated values for a list of available unit
values that can be used here.
This function can be called at any time before generating the SVG file.
However to minimize the risk of ambiguities it's recommended to call it
before any drawing operations have been performed on the given surface,
to make it clearer what the unit used in the drawing operations is.
The simplest way to do this is to call this function immediately after
creating the SVG surface.
Note if this function is never called, the default unit for SVG
documents generated by cairo will be "pt". This is for historical
reasons.
:param unit: SVG unit.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
cairo.cairo_svg_surface_set_document_unit(self._pointer, unit)
self._check_status()
|
[
"def",
"set_document_unit",
"(",
"self",
",",
"unit",
")",
":",
"cairo",
".",
"cairo_svg_surface_set_document_unit",
"(",
"self",
".",
"_pointer",
",",
"unit",
")",
"self",
".",
"_check_status",
"(",
")"
] |
Use specified unit for width and height of generated SVG file.
See ``SVG_UNIT_*`` enumerated values for a list of available unit
values that can be used here.
This function can be called at any time before generating the SVG file.
However to minimize the risk of ambiguities it's recommended to call it
before any drawing operations have been performed on the given surface,
to make it clearer what the unit used in the drawing operations is.
The simplest way to do this is to call this function immediately after
creating the SVG surface.
Note if this function is never called, the default unit for SVG
documents generated by cairo will be "pt". This is for historical
reasons.
:param unit: SVG unit.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
|
[
"Use",
"specified",
"unit",
"for",
"width",
"and",
"height",
"of",
"generated",
"SVG",
"file",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L1309-L1336
|
17,618
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
SVGSurface.get_document_unit
|
def get_document_unit(self):
"""Get the unit of the SVG surface.
If the surface passed as an argument is not a SVG surface, the function
sets the error status to ``STATUS_SURFACE_TYPE_MISMATCH`` and
returns :ref:`SVG_UNIT_USER`.
:return: The SVG unit of the SVG surface.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
unit = cairo.cairo_svg_surface_get_document_unit(self._pointer)
self._check_status()
return unit
|
python
|
def get_document_unit(self):
"""Get the unit of the SVG surface.
If the surface passed as an argument is not a SVG surface, the function
sets the error status to ``STATUS_SURFACE_TYPE_MISMATCH`` and
returns :ref:`SVG_UNIT_USER`.
:return: The SVG unit of the SVG surface.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
unit = cairo.cairo_svg_surface_get_document_unit(self._pointer)
self._check_status()
return unit
|
[
"def",
"get_document_unit",
"(",
"self",
")",
":",
"unit",
"=",
"cairo",
".",
"cairo_svg_surface_get_document_unit",
"(",
"self",
".",
"_pointer",
")",
"self",
".",
"_check_status",
"(",
")",
"return",
"unit"
] |
Get the unit of the SVG surface.
If the surface passed as an argument is not a SVG surface, the function
sets the error status to ``STATUS_SURFACE_TYPE_MISMATCH`` and
returns :ref:`SVG_UNIT_USER`.
:return: The SVG unit of the SVG surface.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
|
[
"Get",
"the",
"unit",
"of",
"the",
"SVG",
"surface",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L1338-L1354
|
17,619
|
Kozea/cairocffi
|
cairocffi/surfaces.py
|
RecordingSurface.get_extents
|
def get_extents(self):
"""Return the extents of the recording-surface.
:returns:
A ``(x, y, width, height)`` tuple of floats,
or :obj:`None` if the surface is unbounded.
*New in cairo 1.12*
"""
extents = ffi.new('cairo_rectangle_t *')
if cairo.cairo_recording_surface_get_extents(self._pointer, extents):
return (extents.x, extents.y, extents.width, extents.height)
|
python
|
def get_extents(self):
"""Return the extents of the recording-surface.
:returns:
A ``(x, y, width, height)`` tuple of floats,
or :obj:`None` if the surface is unbounded.
*New in cairo 1.12*
"""
extents = ffi.new('cairo_rectangle_t *')
if cairo.cairo_recording_surface_get_extents(self._pointer, extents):
return (extents.x, extents.y, extents.width, extents.height)
|
[
"def",
"get_extents",
"(",
"self",
")",
":",
"extents",
"=",
"ffi",
".",
"new",
"(",
"'cairo_rectangle_t *'",
")",
"if",
"cairo",
".",
"cairo_recording_surface_get_extents",
"(",
"self",
".",
"_pointer",
",",
"extents",
")",
":",
"return",
"(",
"extents",
".",
"x",
",",
"extents",
".",
"y",
",",
"extents",
".",
"width",
",",
"extents",
".",
"height",
")"
] |
Return the extents of the recording-surface.
:returns:
A ``(x, y, width, height)`` tuple of floats,
or :obj:`None` if the surface is unbounded.
*New in cairo 1.12*
|
[
"Return",
"the",
"extents",
"of",
"the",
"recording",
"-",
"surface",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/surfaces.py#L1430-L1442
|
17,620
|
Kozea/cairocffi
|
cairocffi/patterns.py
|
Gradient.add_color_stop_rgba
|
def add_color_stop_rgba(self, offset, red, green, blue, alpha=1):
"""Adds a translucent color stop to a gradient pattern.
The offset specifies the location along the gradient's control vector.
For example,
a linear gradient's control vector is from (x0,y0) to (x1,y1)
while a radial gradient's control vector is
from any point on the start circle
to the corresponding point on the end circle.
If two (or more) stops are specified with identical offset values,
they will be sorted
according to the order in which the stops are added
(stops added earlier before stops added later).
This can be useful for reliably making sharp color transitions
instead of the typical blend.
The color components and offset are in the range 0 to 1.
If the values passed in are outside that range, they will be clamped.
:param offset: Location along the gradient's control vector
:param red: Red component of the color.
:param green: Green component of the color.
:param blue: Blue component of the color.
:param alpha:
Alpha component of the color.
1 (the default) is opaque, 0 fully transparent.
:type offset: float
:type red: float
:type green: float
:type blue: float
:type alpha: float
"""
cairo.cairo_pattern_add_color_stop_rgba(
self._pointer, offset, red, green, blue, alpha)
self._check_status()
|
python
|
def add_color_stop_rgba(self, offset, red, green, blue, alpha=1):
"""Adds a translucent color stop to a gradient pattern.
The offset specifies the location along the gradient's control vector.
For example,
a linear gradient's control vector is from (x0,y0) to (x1,y1)
while a radial gradient's control vector is
from any point on the start circle
to the corresponding point on the end circle.
If two (or more) stops are specified with identical offset values,
they will be sorted
according to the order in which the stops are added
(stops added earlier before stops added later).
This can be useful for reliably making sharp color transitions
instead of the typical blend.
The color components and offset are in the range 0 to 1.
If the values passed in are outside that range, they will be clamped.
:param offset: Location along the gradient's control vector
:param red: Red component of the color.
:param green: Green component of the color.
:param blue: Blue component of the color.
:param alpha:
Alpha component of the color.
1 (the default) is opaque, 0 fully transparent.
:type offset: float
:type red: float
:type green: float
:type blue: float
:type alpha: float
"""
cairo.cairo_pattern_add_color_stop_rgba(
self._pointer, offset, red, green, blue, alpha)
self._check_status()
|
[
"def",
"add_color_stop_rgba",
"(",
"self",
",",
"offset",
",",
"red",
",",
"green",
",",
"blue",
",",
"alpha",
"=",
"1",
")",
":",
"cairo",
".",
"cairo_pattern_add_color_stop_rgba",
"(",
"self",
".",
"_pointer",
",",
"offset",
",",
"red",
",",
"green",
",",
"blue",
",",
"alpha",
")",
"self",
".",
"_check_status",
"(",
")"
] |
Adds a translucent color stop to a gradient pattern.
The offset specifies the location along the gradient's control vector.
For example,
a linear gradient's control vector is from (x0,y0) to (x1,y1)
while a radial gradient's control vector is
from any point on the start circle
to the corresponding point on the end circle.
If two (or more) stops are specified with identical offset values,
they will be sorted
according to the order in which the stops are added
(stops added earlier before stops added later).
This can be useful for reliably making sharp color transitions
instead of the typical blend.
The color components and offset are in the range 0 to 1.
If the values passed in are outside that range, they will be clamped.
:param offset: Location along the gradient's control vector
:param red: Red component of the color.
:param green: Green component of the color.
:param blue: Blue component of the color.
:param alpha:
Alpha component of the color.
1 (the default) is opaque, 0 fully transparent.
:type offset: float
:type red: float
:type green: float
:type blue: float
:type alpha: float
|
[
"Adds",
"a",
"translucent",
"color",
"stop",
"to",
"a",
"gradient",
"pattern",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/patterns.py#L219-L255
|
17,621
|
Kozea/cairocffi
|
cairocffi/fonts.py
|
_encode_string
|
def _encode_string(string):
"""Return a byte string, encoding Unicode with UTF-8."""
if not isinstance(string, bytes):
string = string.encode('utf8')
return ffi.new('char[]', string)
|
python
|
def _encode_string(string):
"""Return a byte string, encoding Unicode with UTF-8."""
if not isinstance(string, bytes):
string = string.encode('utf8')
return ffi.new('char[]', string)
|
[
"def",
"_encode_string",
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"'utf8'",
")",
"return",
"ffi",
".",
"new",
"(",
"'char[]'",
",",
"string",
")"
] |
Return a byte string, encoding Unicode with UTF-8.
|
[
"Return",
"a",
"byte",
"string",
"encoding",
"Unicode",
"with",
"UTF",
"-",
"8",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/fonts.py#L16-L20
|
17,622
|
Kozea/cairocffi
|
cairocffi/fonts.py
|
ScaledFont.text_to_glyphs
|
def text_to_glyphs(self, x, y, text, with_clusters):
"""Converts a string of text to a list of glyphs,
optionally with cluster mapping,
that can be used to render later using this scaled font.
The output values can be readily passed to
:meth:`Context.show_text_glyphs`, :meth:`Context.show_glyphs`
or related methods,
assuming that the exact same :class:`ScaledFont`
is used for the operation.
:type x: float
:type y: float
:type with_clusters: bool
:param x: X position to place first glyph.
:param y: Y position to place first glyph.
:param text: The text to convert, as an Unicode or UTF-8 string.
:param with_clusters: Whether to compute the cluster mapping.
:returns:
A ``(glyphs, clusters, clusters_flags)`` tuple
if :obj:`with_clusters` is true, otherwise just :obj:`glyphs`.
See :meth:`Context.show_text_glyphs` for the data structure.
.. note::
This method is part of
what the cairo designers call the "toy" text API.
It is convenient for short demos and simple programs,
but it is not expected to be adequate
for serious text-using applications.
See :ref:`fonts` for details
and :meth:`Context.show_glyphs`
for the "real" text display API in cairo.
"""
glyphs = ffi.new('cairo_glyph_t **', ffi.NULL)
num_glyphs = ffi.new('int *')
if with_clusters:
clusters = ffi.new('cairo_text_cluster_t **', ffi.NULL)
num_clusters = ffi.new('int *')
cluster_flags = ffi.new('cairo_text_cluster_flags_t *')
else:
clusters = ffi.NULL
num_clusters = ffi.NULL
cluster_flags = ffi.NULL
# TODO: Pass len_utf8 explicitly to support NULL bytes?
status = cairo.cairo_scaled_font_text_to_glyphs(
self._pointer, x, y, _encode_string(text), -1,
glyphs, num_glyphs, clusters, num_clusters, cluster_flags)
glyphs = ffi.gc(glyphs[0], _keepref(cairo, cairo.cairo_glyph_free))
if with_clusters:
clusters = ffi.gc(
clusters[0], _keepref(cairo, cairo.cairo_text_cluster_free))
_check_status(status)
glyphs = [
(glyph.index, glyph.x, glyph.y)
for i in range(num_glyphs[0])
for glyph in [glyphs[i]]]
if with_clusters:
clusters = [
(cluster.num_bytes, cluster.num_glyphs)
for i in range(num_clusters[0])
for cluster in [clusters[i]]]
return glyphs, clusters, cluster_flags[0]
else:
return glyphs
|
python
|
def text_to_glyphs(self, x, y, text, with_clusters):
"""Converts a string of text to a list of glyphs,
optionally with cluster mapping,
that can be used to render later using this scaled font.
The output values can be readily passed to
:meth:`Context.show_text_glyphs`, :meth:`Context.show_glyphs`
or related methods,
assuming that the exact same :class:`ScaledFont`
is used for the operation.
:type x: float
:type y: float
:type with_clusters: bool
:param x: X position to place first glyph.
:param y: Y position to place first glyph.
:param text: The text to convert, as an Unicode or UTF-8 string.
:param with_clusters: Whether to compute the cluster mapping.
:returns:
A ``(glyphs, clusters, clusters_flags)`` tuple
if :obj:`with_clusters` is true, otherwise just :obj:`glyphs`.
See :meth:`Context.show_text_glyphs` for the data structure.
.. note::
This method is part of
what the cairo designers call the "toy" text API.
It is convenient for short demos and simple programs,
but it is not expected to be adequate
for serious text-using applications.
See :ref:`fonts` for details
and :meth:`Context.show_glyphs`
for the "real" text display API in cairo.
"""
glyphs = ffi.new('cairo_glyph_t **', ffi.NULL)
num_glyphs = ffi.new('int *')
if with_clusters:
clusters = ffi.new('cairo_text_cluster_t **', ffi.NULL)
num_clusters = ffi.new('int *')
cluster_flags = ffi.new('cairo_text_cluster_flags_t *')
else:
clusters = ffi.NULL
num_clusters = ffi.NULL
cluster_flags = ffi.NULL
# TODO: Pass len_utf8 explicitly to support NULL bytes?
status = cairo.cairo_scaled_font_text_to_glyphs(
self._pointer, x, y, _encode_string(text), -1,
glyphs, num_glyphs, clusters, num_clusters, cluster_flags)
glyphs = ffi.gc(glyphs[0], _keepref(cairo, cairo.cairo_glyph_free))
if with_clusters:
clusters = ffi.gc(
clusters[0], _keepref(cairo, cairo.cairo_text_cluster_free))
_check_status(status)
glyphs = [
(glyph.index, glyph.x, glyph.y)
for i in range(num_glyphs[0])
for glyph in [glyphs[i]]]
if with_clusters:
clusters = [
(cluster.num_bytes, cluster.num_glyphs)
for i in range(num_clusters[0])
for cluster in [clusters[i]]]
return glyphs, clusters, cluster_flags[0]
else:
return glyphs
|
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"[",
"0",
"]",
"else",
":",
"return",
"glyphs"
] |
Converts a string of text to a list of glyphs,
optionally with cluster mapping,
that can be used to render later using this scaled font.
The output values can be readily passed to
:meth:`Context.show_text_glyphs`, :meth:`Context.show_glyphs`
or related methods,
assuming that the exact same :class:`ScaledFont`
is used for the operation.
:type x: float
:type y: float
:type with_clusters: bool
:param x: X position to place first glyph.
:param y: Y position to place first glyph.
:param text: The text to convert, as an Unicode or UTF-8 string.
:param with_clusters: Whether to compute the cluster mapping.
:returns:
A ``(glyphs, clusters, clusters_flags)`` tuple
if :obj:`with_clusters` is true, otherwise just :obj:`glyphs`.
See :meth:`Context.show_text_glyphs` for the data structure.
.. note::
This method is part of
what the cairo designers call the "toy" text API.
It is convenient for short demos and simple programs,
but it is not expected to be adequate
for serious text-using applications.
See :ref:`fonts` for details
and :meth:`Context.show_glyphs`
for the "real" text display API in cairo.
|
[
"Converts",
"a",
"string",
"of",
"text",
"to",
"a",
"list",
"of",
"glyphs",
"optionally",
"with",
"cluster",
"mapping",
"that",
"can",
"be",
"used",
"to",
"render",
"later",
"using",
"this",
"scaled",
"font",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/fonts.py#L301-L366
|
17,623
|
Kozea/cairocffi
|
cairocffi/fonts.py
|
FontOptions.set_variations
|
def set_variations(self, variations):
"""Sets the OpenType font variations for the font options object.
Font variations are specified as a string with a format that is similar
to the CSS font-variation-settings. The string contains a
comma-separated list of axis assignments, which each assignment
consists of a 4-character axis name and a value, separated by
whitespace and optional equals sign.
:param variations: the new font variations, or ``None``.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
if variations is None:
variations = ffi.NULL
else:
variations = _encode_string(variations)
cairo.cairo_font_options_set_variations(self._pointer, variations)
self._check_status()
|
python
|
def set_variations(self, variations):
"""Sets the OpenType font variations for the font options object.
Font variations are specified as a string with a format that is similar
to the CSS font-variation-settings. The string contains a
comma-separated list of axis assignments, which each assignment
consists of a 4-character axis name and a value, separated by
whitespace and optional equals sign.
:param variations: the new font variations, or ``None``.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
if variations is None:
variations = ffi.NULL
else:
variations = _encode_string(variations)
cairo.cairo_font_options_set_variations(self._pointer, variations)
self._check_status()
|
[
"def",
"set_variations",
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"self",
",",
"variations",
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":",
"if",
"variations",
"is",
"None",
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"NULL",
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"(",
"self",
".",
"_pointer",
",",
"variations",
")",
"self",
".",
"_check_status",
"(",
")"
] |
Sets the OpenType font variations for the font options object.
Font variations are specified as a string with a format that is similar
to the CSS font-variation-settings. The string contains a
comma-separated list of axis assignments, which each assignment
consists of a 4-character axis name and a value, separated by
whitespace and optional equals sign.
:param variations: the new font variations, or ``None``.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
|
[
"Sets",
"the",
"OpenType",
"font",
"variations",
"for",
"the",
"font",
"options",
"object",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/fonts.py#L494-L515
|
17,624
|
Kozea/cairocffi
|
cairocffi/fonts.py
|
FontOptions.get_variations
|
def get_variations(self):
"""Gets the OpenType font variations for the font options object.
See :meth:`set_variations` for details about the
string format.
:return: the font variations for the font options object. The
returned string belongs to the ``options`` and must not be modified.
It is valid until either the font options object is destroyed or the
font variations in this object is modified with :meth:`set_variations`.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
variations = cairo.cairo_font_options_get_variations(self._pointer)
if variations != ffi.NULL:
return ffi.string(variations).decode('utf8', 'replace')
|
python
|
def get_variations(self):
"""Gets the OpenType font variations for the font options object.
See :meth:`set_variations` for details about the
string format.
:return: the font variations for the font options object. The
returned string belongs to the ``options`` and must not be modified.
It is valid until either the font options object is destroyed or the
font variations in this object is modified with :meth:`set_variations`.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
"""
variations = cairo.cairo_font_options_get_variations(self._pointer)
if variations != ffi.NULL:
return ffi.string(variations).decode('utf8', 'replace')
|
[
"def",
"get_variations",
"(",
"self",
")",
":",
"variations",
"=",
"cairo",
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"cairo_font_options_get_variations",
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"string",
"(",
"variations",
")",
".",
"decode",
"(",
"'utf8'",
",",
"'replace'",
")"
] |
Gets the OpenType font variations for the font options object.
See :meth:`set_variations` for details about the
string format.
:return: the font variations for the font options object. The
returned string belongs to the ``options`` and must not be modified.
It is valid until either the font options object is destroyed or the
font variations in this object is modified with :meth:`set_variations`.
*New in cairo 1.16.*
*New in cairocffi 0.9.*
|
[
"Gets",
"the",
"OpenType",
"font",
"variations",
"for",
"the",
"font",
"options",
"object",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/fonts.py#L517-L535
|
17,625
|
Kozea/cairocffi
|
cairocffi/pixbuf.py
|
decode_to_pixbuf
|
def decode_to_pixbuf(image_data, width=None, height=None):
"""Decode an image from memory with GDK-PixBuf.
The file format is detected automatically.
:param image_data: A byte string
:param width: Integer width in pixels or None
:param height: Integer height in pixels or None
:returns:
A tuple of a new :class:`PixBuf` object
and the name of the detected image format.
:raises:
:exc:`ImageLoadingError` if the image data is invalid
or in an unsupported format.
"""
loader = ffi.gc(
gdk_pixbuf.gdk_pixbuf_loader_new(), gobject.g_object_unref)
error = ffi.new('GError **')
if width and height:
gdk_pixbuf.gdk_pixbuf_loader_set_size(loader, width, height)
handle_g_error(error, gdk_pixbuf.gdk_pixbuf_loader_write(
loader, ffi.new('guchar[]', image_data), len(image_data), error))
handle_g_error(error, gdk_pixbuf.gdk_pixbuf_loader_close(loader, error))
format_ = gdk_pixbuf.gdk_pixbuf_loader_get_format(loader)
format_name = (
ffi.string(gdk_pixbuf.gdk_pixbuf_format_get_name(format_))
.decode('ascii')
if format_ != ffi.NULL else None)
pixbuf = gdk_pixbuf.gdk_pixbuf_loader_get_pixbuf(loader)
if pixbuf == ffi.NULL: # pragma: no cover
raise ImageLoadingError('Not enough image data (got a NULL pixbuf.)')
return Pixbuf(pixbuf), format_name
|
python
|
def decode_to_pixbuf(image_data, width=None, height=None):
"""Decode an image from memory with GDK-PixBuf.
The file format is detected automatically.
:param image_data: A byte string
:param width: Integer width in pixels or None
:param height: Integer height in pixels or None
:returns:
A tuple of a new :class:`PixBuf` object
and the name of the detected image format.
:raises:
:exc:`ImageLoadingError` if the image data is invalid
or in an unsupported format.
"""
loader = ffi.gc(
gdk_pixbuf.gdk_pixbuf_loader_new(), gobject.g_object_unref)
error = ffi.new('GError **')
if width and height:
gdk_pixbuf.gdk_pixbuf_loader_set_size(loader, width, height)
handle_g_error(error, gdk_pixbuf.gdk_pixbuf_loader_write(
loader, ffi.new('guchar[]', image_data), len(image_data), error))
handle_g_error(error, gdk_pixbuf.gdk_pixbuf_loader_close(loader, error))
format_ = gdk_pixbuf.gdk_pixbuf_loader_get_format(loader)
format_name = (
ffi.string(gdk_pixbuf.gdk_pixbuf_format_get_name(format_))
.decode('ascii')
if format_ != ffi.NULL else None)
pixbuf = gdk_pixbuf.gdk_pixbuf_loader_get_pixbuf(loader)
if pixbuf == ffi.NULL: # pragma: no cover
raise ImageLoadingError('Not enough image data (got a NULL pixbuf.)')
return Pixbuf(pixbuf), format_name
|
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"'Not enough image data (got a NULL pixbuf.)'",
")",
"return",
"Pixbuf",
"(",
"pixbuf",
")",
",",
"format_name"
] |
Decode an image from memory with GDK-PixBuf.
The file format is detected automatically.
:param image_data: A byte string
:param width: Integer width in pixels or None
:param height: Integer height in pixels or None
:returns:
A tuple of a new :class:`PixBuf` object
and the name of the detected image format.
:raises:
:exc:`ImageLoadingError` if the image data is invalid
or in an unsupported format.
|
[
"Decode",
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"with",
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"-",
"PixBuf",
".",
"The",
"file",
"format",
"is",
"detected",
"automatically",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/pixbuf.py#L69-L102
|
17,626
|
Kozea/cairocffi
|
cairocffi/pixbuf.py
|
decode_to_image_surface
|
def decode_to_image_surface(image_data, width=None, height=None):
"""Decode an image from memory into a cairo surface.
The file format is detected automatically.
:param image_data: A byte string
:param width: Integer width in pixels or None
:param height: Integer height in pixels or None
:returns:
A tuple of a new :class:`~cairocffi.ImageSurface` object
and the name of the detected image format.
:raises:
:exc:`ImageLoadingError` if the image data is invalid
or in an unsupported format.
"""
pixbuf, format_name = decode_to_pixbuf(image_data, width, height)
surface = (
pixbuf_to_cairo_gdk(pixbuf) if gdk is not None
else pixbuf_to_cairo_slices(pixbuf) if not pixbuf.get_has_alpha()
else pixbuf_to_cairo_png(pixbuf))
return surface, format_name
|
python
|
def decode_to_image_surface(image_data, width=None, height=None):
"""Decode an image from memory into a cairo surface.
The file format is detected automatically.
:param image_data: A byte string
:param width: Integer width in pixels or None
:param height: Integer height in pixels or None
:returns:
A tuple of a new :class:`~cairocffi.ImageSurface` object
and the name of the detected image format.
:raises:
:exc:`ImageLoadingError` if the image data is invalid
or in an unsupported format.
"""
pixbuf, format_name = decode_to_pixbuf(image_data, width, height)
surface = (
pixbuf_to_cairo_gdk(pixbuf) if gdk is not None
else pixbuf_to_cairo_slices(pixbuf) if not pixbuf.get_has_alpha()
else pixbuf_to_cairo_png(pixbuf))
return surface, format_name
|
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"pixbuf_to_cairo_png",
"(",
"pixbuf",
")",
")",
"return",
"surface",
",",
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Decode an image from memory into a cairo surface.
The file format is detected automatically.
:param image_data: A byte string
:param width: Integer width in pixels or None
:param height: Integer height in pixels or None
:returns:
A tuple of a new :class:`~cairocffi.ImageSurface` object
and the name of the detected image format.
:raises:
:exc:`ImageLoadingError` if the image data is invalid
or in an unsupported format.
|
[
"Decode",
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"image",
"from",
"memory",
"into",
"a",
"cairo",
"surface",
".",
"The",
"file",
"format",
"is",
"detected",
"automatically",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/pixbuf.py#L105-L125
|
17,627
|
Kozea/cairocffi
|
cairocffi/pixbuf.py
|
pixbuf_to_cairo_gdk
|
def pixbuf_to_cairo_gdk(pixbuf):
"""Convert from PixBuf to ImageSurface, using GDK.
This method is fastest but GDK is not always available.
"""
dummy_context = Context(ImageSurface(constants.FORMAT_ARGB32, 1, 1))
gdk.gdk_cairo_set_source_pixbuf(
dummy_context._pointer, pixbuf._pointer, 0, 0)
return dummy_context.get_source().get_surface()
|
python
|
def pixbuf_to_cairo_gdk(pixbuf):
"""Convert from PixBuf to ImageSurface, using GDK.
This method is fastest but GDK is not always available.
"""
dummy_context = Context(ImageSurface(constants.FORMAT_ARGB32, 1, 1))
gdk.gdk_cairo_set_source_pixbuf(
dummy_context._pointer, pixbuf._pointer, 0, 0)
return dummy_context.get_source().get_surface()
|
[
"def",
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"get_source",
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Convert from PixBuf to ImageSurface, using GDK.
This method is fastest but GDK is not always available.
|
[
"Convert",
"from",
"PixBuf",
"to",
"ImageSurface",
"using",
"GDK",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/pixbuf.py#L128-L137
|
17,628
|
Kozea/cairocffi
|
cairocffi/pixbuf.py
|
pixbuf_to_cairo_slices
|
def pixbuf_to_cairo_slices(pixbuf):
"""Convert from PixBuf to ImageSurface, using slice-based byte swapping.
This method is 2~5x slower than GDK but does not support an alpha channel.
(cairo uses pre-multiplied alpha, but not Pixbuf.)
"""
assert pixbuf.get_colorspace() == gdk_pixbuf.GDK_COLORSPACE_RGB
assert pixbuf.get_n_channels() == 3
assert pixbuf.get_bits_per_sample() == 8
width = pixbuf.get_width()
height = pixbuf.get_height()
rowstride = pixbuf.get_rowstride()
pixels = ffi.buffer(pixbuf.get_pixels(), pixbuf.get_byte_length())
# TODO: remove this when cffi buffers support slicing with a stride.
pixels = pixels[:]
# Convert GdkPixbuf’s big-endian RGBA to cairo’s native-endian ARGB
cairo_stride = ImageSurface.format_stride_for_width(
constants.FORMAT_RGB24, width)
data = bytearray(cairo_stride * height)
big_endian = sys.byteorder == 'big'
pixbuf_row_length = width * 3 # stride == row_length + padding
cairo_row_length = width * 4 # stride == row_length + padding
alpha = b'\xff' * width # opaque
for y in range(height):
offset = rowstride * y
end = offset + pixbuf_row_length
red = pixels[offset:end:3]
green = pixels[offset + 1:end:3]
blue = pixels[offset + 2:end:3]
offset = cairo_stride * y
end = offset + cairo_row_length
if big_endian: # pragma: no cover
data[offset:end:4] = alpha
data[offset + 1:end:4] = red
data[offset + 2:end:4] = green
data[offset + 3:end:4] = blue
else:
data[offset + 3:end:4] = alpha
data[offset + 2:end:4] = red
data[offset + 1:end:4] = green
data[offset:end:4] = blue
data = array('B', data)
return ImageSurface(constants.FORMAT_RGB24,
width, height, data, cairo_stride)
|
python
|
def pixbuf_to_cairo_slices(pixbuf):
"""Convert from PixBuf to ImageSurface, using slice-based byte swapping.
This method is 2~5x slower than GDK but does not support an alpha channel.
(cairo uses pre-multiplied alpha, but not Pixbuf.)
"""
assert pixbuf.get_colorspace() == gdk_pixbuf.GDK_COLORSPACE_RGB
assert pixbuf.get_n_channels() == 3
assert pixbuf.get_bits_per_sample() == 8
width = pixbuf.get_width()
height = pixbuf.get_height()
rowstride = pixbuf.get_rowstride()
pixels = ffi.buffer(pixbuf.get_pixels(), pixbuf.get_byte_length())
# TODO: remove this when cffi buffers support slicing with a stride.
pixels = pixels[:]
# Convert GdkPixbuf’s big-endian RGBA to cairo’s native-endian ARGB
cairo_stride = ImageSurface.format_stride_for_width(
constants.FORMAT_RGB24, width)
data = bytearray(cairo_stride * height)
big_endian = sys.byteorder == 'big'
pixbuf_row_length = width * 3 # stride == row_length + padding
cairo_row_length = width * 4 # stride == row_length + padding
alpha = b'\xff' * width # opaque
for y in range(height):
offset = rowstride * y
end = offset + pixbuf_row_length
red = pixels[offset:end:3]
green = pixels[offset + 1:end:3]
blue = pixels[offset + 2:end:3]
offset = cairo_stride * y
end = offset + cairo_row_length
if big_endian: # pragma: no cover
data[offset:end:4] = alpha
data[offset + 1:end:4] = red
data[offset + 2:end:4] = green
data[offset + 3:end:4] = blue
else:
data[offset + 3:end:4] = alpha
data[offset + 2:end:4] = red
data[offset + 1:end:4] = green
data[offset:end:4] = blue
data = array('B', data)
return ImageSurface(constants.FORMAT_RGB24,
width, height, data, cairo_stride)
|
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",",
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",",
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] |
Convert from PixBuf to ImageSurface, using slice-based byte swapping.
This method is 2~5x slower than GDK but does not support an alpha channel.
(cairo uses pre-multiplied alpha, but not Pixbuf.)
|
[
"Convert",
"from",
"PixBuf",
"to",
"ImageSurface",
"using",
"slice",
"-",
"based",
"byte",
"swapping",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/pixbuf.py#L140-L187
|
17,629
|
Kozea/cairocffi
|
cairocffi/pixbuf.py
|
pixbuf_to_cairo_png
|
def pixbuf_to_cairo_png(pixbuf):
"""Convert from PixBuf to ImageSurface, by going through the PNG format.
This method is 10~30x slower than GDK but always works.
"""
buffer_pointer = ffi.new('gchar **')
buffer_size = ffi.new('gsize *')
error = ffi.new('GError **')
handle_g_error(error, pixbuf.save_to_buffer(
buffer_pointer, buffer_size, ffi.new('char[]', b'png'), error,
ffi.new('char[]', b'compression'), ffi.new('char[]', b'0'),
ffi.NULL))
png_bytes = ffi.buffer(buffer_pointer[0], buffer_size[0])
return ImageSurface.create_from_png(BytesIO(png_bytes))
|
python
|
def pixbuf_to_cairo_png(pixbuf):
"""Convert from PixBuf to ImageSurface, by going through the PNG format.
This method is 10~30x slower than GDK but always works.
"""
buffer_pointer = ffi.new('gchar **')
buffer_size = ffi.new('gsize *')
error = ffi.new('GError **')
handle_g_error(error, pixbuf.save_to_buffer(
buffer_pointer, buffer_size, ffi.new('char[]', b'png'), error,
ffi.new('char[]', b'compression'), ffi.new('char[]', b'0'),
ffi.NULL))
png_bytes = ffi.buffer(buffer_pointer[0], buffer_size[0])
return ImageSurface.create_from_png(BytesIO(png_bytes))
|
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"ImageSurface",
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"create_from_png",
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"BytesIO",
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")",
")"
] |
Convert from PixBuf to ImageSurface, by going through the PNG format.
This method is 10~30x slower than GDK but always works.
|
[
"Convert",
"from",
"PixBuf",
"to",
"ImageSurface",
"by",
"going",
"through",
"the",
"PNG",
"format",
"."
] |
450853add7e32eea20985b6aa5f54d9cb3cd04fe
|
https://github.com/Kozea/cairocffi/blob/450853add7e32eea20985b6aa5f54d9cb3cd04fe/cairocffi/pixbuf.py#L190-L204
|
17,630
|
coderholic/pyradio
|
pyradio/player.py
|
probePlayer
|
def probePlayer(requested_player=''):
""" Probes the multimedia players which are available on the host
system."""
ret_player = None
if logger.isEnabledFor(logging.INFO):
logger.info("Probing available multimedia players...")
implementedPlayers = Player.__subclasses__()
if logger.isEnabledFor(logging.INFO):
logger.info("Implemented players: " +
", ".join([player.PLAYER_CMD
for player in implementedPlayers]))
if requested_player:
req = requested_player.split(',')
for r_player in req:
if r_player == 'vlc':
r_player = 'cvlc'
for player in implementedPlayers:
if player.PLAYER_CMD == r_player:
ret_player = check_player(player)
if ret_player is not None:
return ret_player
if ret_player is None:
if logger.isEnabledFor(logging.INFO):
logger.info('Requested player "{}" not supported'.format(r_player))
else:
for player in implementedPlayers:
ret_player = check_player(player)
if ret_player is not None:
break
return ret_player
|
python
|
def probePlayer(requested_player=''):
""" Probes the multimedia players which are available on the host
system."""
ret_player = None
if logger.isEnabledFor(logging.INFO):
logger.info("Probing available multimedia players...")
implementedPlayers = Player.__subclasses__()
if logger.isEnabledFor(logging.INFO):
logger.info("Implemented players: " +
", ".join([player.PLAYER_CMD
for player in implementedPlayers]))
if requested_player:
req = requested_player.split(',')
for r_player in req:
if r_player == 'vlc':
r_player = 'cvlc'
for player in implementedPlayers:
if player.PLAYER_CMD == r_player:
ret_player = check_player(player)
if ret_player is not None:
return ret_player
if ret_player is None:
if logger.isEnabledFor(logging.INFO):
logger.info('Requested player "{}" not supported'.format(r_player))
else:
for player in implementedPlayers:
ret_player = check_player(player)
if ret_player is not None:
break
return ret_player
|
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"=",
"check_player",
"(",
"player",
")",
"if",
"ret_player",
"is",
"not",
"None",
":",
"break",
"return",
"ret_player"
] |
Probes the multimedia players which are available on the host
system.
|
[
"Probes",
"the",
"multimedia",
"players",
"which",
"are",
"available",
"on",
"the",
"host",
"system",
"."
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/player.py#L763-L793
|
17,631
|
coderholic/pyradio
|
pyradio/player.py
|
Player.play
|
def play(self, name, streamUrl, encoding = ''):
""" use a multimedia player to play a stream """
self.close()
self.name = name
self.oldUserInput = {'Input': '', 'Volume': '', 'Title': ''}
self.muted = False
self.show_volume = True
self.title_prefix = ''
self.playback_is_on = False
self.outputStream.write('Station: "{}"'.format(name), self.status_update_lock)
if logger.isEnabledFor(logging.INFO):
logger.info('Selected Station: "{}"'.format(name))
if encoding:
self._station_encoding = encoding
else:
self._station_encoding = 'utf-8'
opts = []
isPlayList = streamUrl.split("?")[0][-3:] in ['m3u', 'pls']
opts = self._buildStartOpts(streamUrl, isPlayList)
self.process = subprocess.Popen(opts, shell=False,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.STDOUT)
t = threading.Thread(target=self.updateStatus, args=(self.status_update_lock, ))
t.start()
# start playback check timer thread
try:
self.connection_timeout_thread = threading.Timer(self.playback_timeout, self.playback_timeout_handler)
self.connection_timeout_thread.start()
except:
self.connection_timeout_thread = None
if (logger.isEnabledFor(logging.ERROR)):
logger.error("playback detection thread start failed")
if logger.isEnabledFor(logging.INFO):
logger.info("Player started")
|
python
|
def play(self, name, streamUrl, encoding = ''):
""" use a multimedia player to play a stream """
self.close()
self.name = name
self.oldUserInput = {'Input': '', 'Volume': '', 'Title': ''}
self.muted = False
self.show_volume = True
self.title_prefix = ''
self.playback_is_on = False
self.outputStream.write('Station: "{}"'.format(name), self.status_update_lock)
if logger.isEnabledFor(logging.INFO):
logger.info('Selected Station: "{}"'.format(name))
if encoding:
self._station_encoding = encoding
else:
self._station_encoding = 'utf-8'
opts = []
isPlayList = streamUrl.split("?")[0][-3:] in ['m3u', 'pls']
opts = self._buildStartOpts(streamUrl, isPlayList)
self.process = subprocess.Popen(opts, shell=False,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.STDOUT)
t = threading.Thread(target=self.updateStatus, args=(self.status_update_lock, ))
t.start()
# start playback check timer thread
try:
self.connection_timeout_thread = threading.Timer(self.playback_timeout, self.playback_timeout_handler)
self.connection_timeout_thread.start()
except:
self.connection_timeout_thread = None
if (logger.isEnabledFor(logging.ERROR)):
logger.error("playback detection thread start failed")
if logger.isEnabledFor(logging.INFO):
logger.info("Player started")
|
[
"def",
"play",
"(",
"self",
",",
"name",
",",
"streamUrl",
",",
"encoding",
"=",
"''",
")",
":",
"self",
".",
"close",
"(",
")",
"self",
".",
"name",
"=",
"name",
"self",
".",
"oldUserInput",
"=",
"{",
"'Input'",
":",
"''",
",",
"'Volume'",
":",
"''",
",",
"'Title'",
":",
"''",
"}",
"self",
".",
"muted",
"=",
"False",
"self",
".",
"show_volume",
"=",
"True",
"self",
".",
"title_prefix",
"=",
"''",
"self",
".",
"playback_is_on",
"=",
"False",
"self",
".",
"outputStream",
".",
"write",
"(",
"'Station: \"{}\"'",
".",
"format",
"(",
"name",
")",
",",
"self",
".",
"status_update_lock",
")",
"if",
"logger",
".",
"isEnabledFor",
"(",
"logging",
".",
"INFO",
")",
":",
"logger",
".",
"info",
"(",
"'Selected Station: \"{}\"'",
".",
"format",
"(",
"name",
")",
")",
"if",
"encoding",
":",
"self",
".",
"_station_encoding",
"=",
"encoding",
"else",
":",
"self",
".",
"_station_encoding",
"=",
"'utf-8'",
"opts",
"=",
"[",
"]",
"isPlayList",
"=",
"streamUrl",
".",
"split",
"(",
"\"?\"",
")",
"[",
"0",
"]",
"[",
"-",
"3",
":",
"]",
"in",
"[",
"'m3u'",
",",
"'pls'",
"]",
"opts",
"=",
"self",
".",
"_buildStartOpts",
"(",
"streamUrl",
",",
"isPlayList",
")",
"self",
".",
"process",
"=",
"subprocess",
".",
"Popen",
"(",
"opts",
",",
"shell",
"=",
"False",
",",
"stdout",
"=",
"subprocess",
".",
"PIPE",
",",
"stdin",
"=",
"subprocess",
".",
"PIPE",
",",
"stderr",
"=",
"subprocess",
".",
"STDOUT",
")",
"t",
"=",
"threading",
".",
"Thread",
"(",
"target",
"=",
"self",
".",
"updateStatus",
",",
"args",
"=",
"(",
"self",
".",
"status_update_lock",
",",
")",
")",
"t",
".",
"start",
"(",
")",
"# start playback check timer thread",
"try",
":",
"self",
".",
"connection_timeout_thread",
"=",
"threading",
".",
"Timer",
"(",
"self",
".",
"playback_timeout",
",",
"self",
".",
"playback_timeout_handler",
")",
"self",
".",
"connection_timeout_thread",
".",
"start",
"(",
")",
"except",
":",
"self",
".",
"connection_timeout_thread",
"=",
"None",
"if",
"(",
"logger",
".",
"isEnabledFor",
"(",
"logging",
".",
"ERROR",
")",
")",
":",
"logger",
".",
"error",
"(",
"\"playback detection thread start failed\"",
")",
"if",
"logger",
".",
"isEnabledFor",
"(",
"logging",
".",
"INFO",
")",
":",
"logger",
".",
"info",
"(",
"\"Player started\"",
")"
] |
use a multimedia player to play a stream
|
[
"use",
"a",
"multimedia",
"player",
"to",
"play",
"a",
"stream"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/player.py#L285-L319
|
17,632
|
coderholic/pyradio
|
pyradio/player.py
|
Player._sendCommand
|
def _sendCommand(self, command):
""" send keystroke command to player """
if(self.process is not None):
try:
if logger.isEnabledFor(logging.DEBUG):
logger.debug("Command: {}".format(command).strip())
self.process.stdin.write(command.encode('utf-8', 'replace'))
self.process.stdin.flush()
except:
msg = "Error when sending: {}"
if logger.isEnabledFor(logging.ERROR):
logger.error(msg.format(command).strip(), exc_info=True)
|
python
|
def _sendCommand(self, command):
""" send keystroke command to player """
if(self.process is not None):
try:
if logger.isEnabledFor(logging.DEBUG):
logger.debug("Command: {}".format(command).strip())
self.process.stdin.write(command.encode('utf-8', 'replace'))
self.process.stdin.flush()
except:
msg = "Error when sending: {}"
if logger.isEnabledFor(logging.ERROR):
logger.error(msg.format(command).strip(), exc_info=True)
|
[
"def",
"_sendCommand",
"(",
"self",
",",
"command",
")",
":",
"if",
"(",
"self",
".",
"process",
"is",
"not",
"None",
")",
":",
"try",
":",
"if",
"logger",
".",
"isEnabledFor",
"(",
"logging",
".",
"DEBUG",
")",
":",
"logger",
".",
"debug",
"(",
"\"Command: {}\"",
".",
"format",
"(",
"command",
")",
".",
"strip",
"(",
")",
")",
"self",
".",
"process",
".",
"stdin",
".",
"write",
"(",
"command",
".",
"encode",
"(",
"'utf-8'",
",",
"'replace'",
")",
")",
"self",
".",
"process",
".",
"stdin",
".",
"flush",
"(",
")",
"except",
":",
"msg",
"=",
"\"Error when sending: {}\"",
"if",
"logger",
".",
"isEnabledFor",
"(",
"logging",
".",
"ERROR",
")",
":",
"logger",
".",
"error",
"(",
"msg",
".",
"format",
"(",
"command",
")",
".",
"strip",
"(",
")",
",",
"exc_info",
"=",
"True",
")"
] |
send keystroke command to player
|
[
"send",
"keystroke",
"command",
"to",
"player"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/player.py#L321-L333
|
17,633
|
coderholic/pyradio
|
pyradio/player.py
|
MpvPlayer._format_title_string
|
def _format_title_string(self, title_string):
""" format mpv's title """
return self._title_string_format_text_tag(title_string.replace(self.icy_tokkens[0], self.icy_title_prefix))
|
python
|
def _format_title_string(self, title_string):
""" format mpv's title """
return self._title_string_format_text_tag(title_string.replace(self.icy_tokkens[0], self.icy_title_prefix))
|
[
"def",
"_format_title_string",
"(",
"self",
",",
"title_string",
")",
":",
"return",
"self",
".",
"_title_string_format_text_tag",
"(",
"title_string",
".",
"replace",
"(",
"self",
".",
"icy_tokkens",
"[",
"0",
"]",
",",
"self",
".",
"icy_title_prefix",
")",
")"
] |
format mpv's title
|
[
"format",
"mpv",
"s",
"title"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/player.py#L529-L531
|
17,634
|
coderholic/pyradio
|
pyradio/player.py
|
MpPlayer._format_title_string
|
def _format_title_string(self, title_string):
""" format mplayer's title """
if "StreamTitle='" in title_string:
tmp = title_string[title_string.find("StreamTitle='"):].replace("StreamTitle='", self.icy_title_prefix)
ret_string = tmp[:tmp.find("';")]
else:
ret_string = title_string
if '"artist":"' in ret_string:
""" work on format:
ICY Info: START_SONG='{"artist":"Clelia Cafiero","title":"M. Mussorgsky-Quadri di un'esposizione"}';
Fund on "ClassicaViva Web Radio: Classical"
"""
ret_string = self.icy_title_prefix + ret_string[ret_string.find('"artist":')+10:].replace('","title":"', ' - ').replace('"}\';', '')
return self._title_string_format_text_tag(ret_string)
|
python
|
def _format_title_string(self, title_string):
""" format mplayer's title """
if "StreamTitle='" in title_string:
tmp = title_string[title_string.find("StreamTitle='"):].replace("StreamTitle='", self.icy_title_prefix)
ret_string = tmp[:tmp.find("';")]
else:
ret_string = title_string
if '"artist":"' in ret_string:
""" work on format:
ICY Info: START_SONG='{"artist":"Clelia Cafiero","title":"M. Mussorgsky-Quadri di un'esposizione"}';
Fund on "ClassicaViva Web Radio: Classical"
"""
ret_string = self.icy_title_prefix + ret_string[ret_string.find('"artist":')+10:].replace('","title":"', ' - ').replace('"}\';', '')
return self._title_string_format_text_tag(ret_string)
|
[
"def",
"_format_title_string",
"(",
"self",
",",
"title_string",
")",
":",
"if",
"\"StreamTitle='\"",
"in",
"title_string",
":",
"tmp",
"=",
"title_string",
"[",
"title_string",
".",
"find",
"(",
"\"StreamTitle='\"",
")",
":",
"]",
".",
"replace",
"(",
"\"StreamTitle='\"",
",",
"self",
".",
"icy_title_prefix",
")",
"ret_string",
"=",
"tmp",
"[",
":",
"tmp",
".",
"find",
"(",
"\"';\"",
")",
"]",
"else",
":",
"ret_string",
"=",
"title_string",
"if",
"'\"artist\":\"'",
"in",
"ret_string",
":",
"\"\"\" work on format:\n ICY Info: START_SONG='{\"artist\":\"Clelia Cafiero\",\"title\":\"M. Mussorgsky-Quadri di un'esposizione\"}';\n Fund on \"ClassicaViva Web Radio: Classical\"\n \"\"\"",
"ret_string",
"=",
"self",
".",
"icy_title_prefix",
"+",
"ret_string",
"[",
"ret_string",
".",
"find",
"(",
"'\"artist\":'",
")",
"+",
"10",
":",
"]",
".",
"replace",
"(",
"'\",\"title\":\"'",
",",
"' - '",
")",
".",
"replace",
"(",
"'\"}\\';'",
",",
"''",
")",
"return",
"self",
".",
"_title_string_format_text_tag",
"(",
"ret_string",
")"
] |
format mplayer's title
|
[
"format",
"mplayer",
"s",
"title"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/player.py#L625-L638
|
17,635
|
coderholic/pyradio
|
pyradio/player.py
|
MpPlayer._format_volume_string
|
def _format_volume_string(self, volume_string):
""" format mplayer's volume """
return '[' + volume_string[volume_string.find(self.volume_string):].replace(' %','%').replace('ume', '')+'] '
|
python
|
def _format_volume_string(self, volume_string):
""" format mplayer's volume """
return '[' + volume_string[volume_string.find(self.volume_string):].replace(' %','%').replace('ume', '')+'] '
|
[
"def",
"_format_volume_string",
"(",
"self",
",",
"volume_string",
")",
":",
"return",
"'['",
"+",
"volume_string",
"[",
"volume_string",
".",
"find",
"(",
"self",
".",
"volume_string",
")",
":",
"]",
".",
"replace",
"(",
"' %'",
",",
"'%'",
")",
".",
"replace",
"(",
"'ume'",
",",
"''",
")",
"+",
"'] '"
] |
format mplayer's volume
|
[
"format",
"mplayer",
"s",
"volume"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/player.py#L640-L642
|
17,636
|
coderholic/pyradio
|
pyradio/player.py
|
VlcPlayer._format_volume_string
|
def _format_volume_string(self, volume_string):
""" format vlc's volume """
self.actual_volume = int(volume_string.split(self.volume_string)[1].split(',')[0].split()[0])
return '[Vol: {}%] '.format(int(100 * self.actual_volume / self.max_volume))
|
python
|
def _format_volume_string(self, volume_string):
""" format vlc's volume """
self.actual_volume = int(volume_string.split(self.volume_string)[1].split(',')[0].split()[0])
return '[Vol: {}%] '.format(int(100 * self.actual_volume / self.max_volume))
|
[
"def",
"_format_volume_string",
"(",
"self",
",",
"volume_string",
")",
":",
"self",
".",
"actual_volume",
"=",
"int",
"(",
"volume_string",
".",
"split",
"(",
"self",
".",
"volume_string",
")",
"[",
"1",
"]",
".",
"split",
"(",
"','",
")",
"[",
"0",
"]",
".",
"split",
"(",
")",
"[",
"0",
"]",
")",
"return",
"'[Vol: {}%] '",
".",
"format",
"(",
"int",
"(",
"100",
"*",
"self",
".",
"actual_volume",
"/",
"self",
".",
"max_volume",
")",
")"
] |
format vlc's volume
|
[
"format",
"vlc",
"s",
"volume"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/player.py#L706-L709
|
17,637
|
coderholic/pyradio
|
pyradio/player.py
|
VlcPlayer._format_title_string
|
def _format_title_string(self, title_string):
""" format vlc's title """
sp = title_string.split(self.icy_tokkens[0])
if sp[0] == title_string:
ret_string = title_string
else:
ret_string = self.icy_title_prefix + sp[1]
return self._title_string_format_text_tag(ret_string)
|
python
|
def _format_title_string(self, title_string):
""" format vlc's title """
sp = title_string.split(self.icy_tokkens[0])
if sp[0] == title_string:
ret_string = title_string
else:
ret_string = self.icy_title_prefix + sp[1]
return self._title_string_format_text_tag(ret_string)
|
[
"def",
"_format_title_string",
"(",
"self",
",",
"title_string",
")",
":",
"sp",
"=",
"title_string",
".",
"split",
"(",
"self",
".",
"icy_tokkens",
"[",
"0",
"]",
")",
"if",
"sp",
"[",
"0",
"]",
"==",
"title_string",
":",
"ret_string",
"=",
"title_string",
"else",
":",
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"=",
"self",
".",
"icy_title_prefix",
"+",
"sp",
"[",
"1",
"]",
"return",
"self",
".",
"_title_string_format_text_tag",
"(",
"ret_string",
")"
] |
format vlc's title
|
[
"format",
"vlc",
"s",
"title"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/player.py#L711-L718
|
17,638
|
coderholic/pyradio
|
pyradio/player.py
|
VlcPlayer._is_accepted_input
|
def _is_accepted_input(self, input_string):
""" vlc input filtering """
ret = False
accept_filter = (self.volume_string, "http stream debug: ")
reject_filter = ()
for n in accept_filter:
if n in input_string:
ret = True
break
if ret:
for n in reject_filter:
if n in input_string:
ret = False
break
return ret
|
python
|
def _is_accepted_input(self, input_string):
""" vlc input filtering """
ret = False
accept_filter = (self.volume_string, "http stream debug: ")
reject_filter = ()
for n in accept_filter:
if n in input_string:
ret = True
break
if ret:
for n in reject_filter:
if n in input_string:
ret = False
break
return ret
|
[
"def",
"_is_accepted_input",
"(",
"self",
",",
"input_string",
")",
":",
"ret",
"=",
"False",
"accept_filter",
"=",
"(",
"self",
".",
"volume_string",
",",
"\"http stream debug: \"",
")",
"reject_filter",
"=",
"(",
")",
"for",
"n",
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"accept_filter",
":",
"if",
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"input_string",
":",
"ret",
"=",
"True",
"break",
"if",
"ret",
":",
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"reject_filter",
":",
"if",
"n",
"in",
"input_string",
":",
"ret",
"=",
"False",
"break",
"return",
"ret"
] |
vlc input filtering
|
[
"vlc",
"input",
"filtering"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/player.py#L720-L734
|
17,639
|
coderholic/pyradio
|
pyradio/player.py
|
VlcPlayer._no_mute_on_stop_playback
|
def _no_mute_on_stop_playback(self):
""" make sure vlc does not stop muted """
if self.ctrl_c_pressed:
return
if self.isPlaying():
if self.actual_volume == -1:
self._get_volume()
while self.actual_volume == -1:
pass
if self.actual_volume == 0:
self.actual_volume = int(self.max_volume*0.25)
self._sendCommand('volume {}\n'.format(self.actual_volume))
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Unmuting VLC on exit: {} (25%)'.format(self.actual_volume))
elif self.muted:
if self.actual_volume > 0:
self._sendCommand('volume {}\n'.format(self.actual_volume))
if logger.isEnabledFor(logging.DEBUG):
logger.debug('VLC volume restored on exit: {0} ({1}%)'.format(self.actual_volume, int(100 * self.actual_volume / self.max_volume)))
self.show_volume = True
|
python
|
def _no_mute_on_stop_playback(self):
""" make sure vlc does not stop muted """
if self.ctrl_c_pressed:
return
if self.isPlaying():
if self.actual_volume == -1:
self._get_volume()
while self.actual_volume == -1:
pass
if self.actual_volume == 0:
self.actual_volume = int(self.max_volume*0.25)
self._sendCommand('volume {}\n'.format(self.actual_volume))
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Unmuting VLC on exit: {} (25%)'.format(self.actual_volume))
elif self.muted:
if self.actual_volume > 0:
self._sendCommand('volume {}\n'.format(self.actual_volume))
if logger.isEnabledFor(logging.DEBUG):
logger.debug('VLC volume restored on exit: {0} ({1}%)'.format(self.actual_volume, int(100 * self.actual_volume / self.max_volume)))
self.show_volume = True
|
[
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"max_volume",
")",
")",
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"show_volume",
"=",
"True"
] |
make sure vlc does not stop muted
|
[
"make",
"sure",
"vlc",
"does",
"not",
"stop",
"muted"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/player.py#L741-L761
|
17,640
|
coderholic/pyradio
|
pyradio/config.py
|
PyRadioStations._check_stations_csv
|
def _check_stations_csv(self, usr, root):
''' Reclocate a stations.csv copy in user home for easy manage.
E.g. not need sudo when you add new station, etc '''
if path.exists(path.join(usr, 'stations.csv')):
return
else:
copyfile(root, path.join(usr, 'stations.csv'))
|
python
|
def _check_stations_csv(self, usr, root):
''' Reclocate a stations.csv copy in user home for easy manage.
E.g. not need sudo when you add new station, etc '''
if path.exists(path.join(usr, 'stations.csv')):
return
else:
copyfile(root, path.join(usr, 'stations.csv'))
|
[
"def",
"_check_stations_csv",
"(",
"self",
",",
"usr",
",",
"root",
")",
":",
"if",
"path",
".",
"exists",
"(",
"path",
".",
"join",
"(",
"usr",
",",
"'stations.csv'",
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")",
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"return",
"else",
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"copyfile",
"(",
"root",
",",
"path",
".",
"join",
"(",
"usr",
",",
"'stations.csv'",
")",
")"
] |
Reclocate a stations.csv copy in user home for easy manage.
E.g. not need sudo when you add new station, etc
|
[
"Reclocate",
"a",
"stations",
".",
"csv",
"copy",
"in",
"user",
"home",
"for",
"easy",
"manage",
".",
"E",
".",
"g",
".",
"not",
"need",
"sudo",
"when",
"you",
"add",
"new",
"station",
"etc"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/config.py#L89-L96
|
17,641
|
coderholic/pyradio
|
pyradio/config.py
|
PyRadioStations._is_playlist_in_config_dir
|
def _is_playlist_in_config_dir(self):
""" Check if a csv file is in the config dir """
if path.dirname(self.stations_file) == self.stations_dir:
self.foreign_file = False
self.foreign_filename_only_no_extension = ''
else:
self.foreign_file = True
self.foreign_filename_only_no_extension = self.stations_filename_only_no_extension
self.foreign_copy_asked = False
|
python
|
def _is_playlist_in_config_dir(self):
""" Check if a csv file is in the config dir """
if path.dirname(self.stations_file) == self.stations_dir:
self.foreign_file = False
self.foreign_filename_only_no_extension = ''
else:
self.foreign_file = True
self.foreign_filename_only_no_extension = self.stations_filename_only_no_extension
self.foreign_copy_asked = False
|
[
"def",
"_is_playlist_in_config_dir",
"(",
"self",
")",
":",
"if",
"path",
".",
"dirname",
"(",
"self",
".",
"stations_file",
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"self",
".",
"stations_dir",
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"foreign_file",
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"foreign_filename_only_no_extension",
"=",
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"True",
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"foreign_filename_only_no_extension",
"=",
"self",
".",
"stations_filename_only_no_extension",
"self",
".",
"foreign_copy_asked",
"=",
"False"
] |
Check if a csv file is in the config dir
|
[
"Check",
"if",
"a",
"csv",
"file",
"is",
"in",
"the",
"config",
"dir"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/config.py#L134-L142
|
17,642
|
coderholic/pyradio
|
pyradio/config.py
|
PyRadioStations._playlist_format_changed
|
def _playlist_format_changed(self):
""" Check if we have new or old format
and report if format has changed
Format type can change by editing encoding,
deleting a non-utf-8 station etc.
"""
new_format = False
for n in self.stations:
if n[2] != '':
new_format = True
break
if self.new_format == new_format:
return False
else:
return True
|
python
|
def _playlist_format_changed(self):
""" Check if we have new or old format
and report if format has changed
Format type can change by editing encoding,
deleting a non-utf-8 station etc.
"""
new_format = False
for n in self.stations:
if n[2] != '':
new_format = True
break
if self.new_format == new_format:
return False
else:
return True
|
[
"def",
"_playlist_format_changed",
"(",
"self",
")",
":",
"new_format",
"=",
"False",
"for",
"n",
"in",
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"stations",
":",
"if",
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"[",
"2",
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"!=",
"''",
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".",
"new_format",
"==",
"new_format",
":",
"return",
"False",
"else",
":",
"return",
"True"
] |
Check if we have new or old format
and report if format has changed
Format type can change by editing encoding,
deleting a non-utf-8 station etc.
|
[
"Check",
"if",
"we",
"have",
"new",
"or",
"old",
"format",
"and",
"report",
"if",
"format",
"has",
"changed"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/config.py#L241-L256
|
17,643
|
coderholic/pyradio
|
pyradio/config.py
|
PyRadioStations.save_playlist_file
|
def save_playlist_file(self, stationFile=''):
""" Save a playlist
Create a txt file and write stations in it.
Then rename it to final target
return 0: All ok
-1: Error writing file
-2: Error renaming file
"""
if self._playlist_format_changed():
self.dirty_playlist = True
self.new_format = not self.new_format
if stationFile:
st_file = stationFile
else:
st_file = self.stations_file
if not self.dirty_playlist:
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Playlist not modified...')
return 0
st_new_file = st_file.replace('.csv', '.txt')
tmp_stations = self.stations[:]
tmp_stations.reverse()
if self.new_format:
tmp_stations.append([ '# Find lots more stations at http://www.iheart.com' , '', '' ])
else:
tmp_stations.append([ '# Find lots more stations at http://www.iheart.com' , '' ])
tmp_stations.reverse()
try:
with open(st_new_file, 'w') as cfgfile:
writter = csv.writer(cfgfile)
for a_station in tmp_stations:
writter.writerow(self._format_playlist_row(a_station))
except:
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Cannot open playlist file for writing,,,')
return -1
try:
move(st_new_file, st_file)
except:
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Cannot rename playlist file...')
return -2
self.dirty_playlist = False
return 0
|
python
|
def save_playlist_file(self, stationFile=''):
""" Save a playlist
Create a txt file and write stations in it.
Then rename it to final target
return 0: All ok
-1: Error writing file
-2: Error renaming file
"""
if self._playlist_format_changed():
self.dirty_playlist = True
self.new_format = not self.new_format
if stationFile:
st_file = stationFile
else:
st_file = self.stations_file
if not self.dirty_playlist:
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Playlist not modified...')
return 0
st_new_file = st_file.replace('.csv', '.txt')
tmp_stations = self.stations[:]
tmp_stations.reverse()
if self.new_format:
tmp_stations.append([ '# Find lots more stations at http://www.iheart.com' , '', '' ])
else:
tmp_stations.append([ '# Find lots more stations at http://www.iheart.com' , '' ])
tmp_stations.reverse()
try:
with open(st_new_file, 'w') as cfgfile:
writter = csv.writer(cfgfile)
for a_station in tmp_stations:
writter.writerow(self._format_playlist_row(a_station))
except:
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Cannot open playlist file for writing,,,')
return -1
try:
move(st_new_file, st_file)
except:
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Cannot rename playlist file...')
return -2
self.dirty_playlist = False
return 0
|
[
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"-",
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"dirty_playlist",
"=",
"False",
"return",
"0"
] |
Save a playlist
Create a txt file and write stations in it.
Then rename it to final target
return 0: All ok
-1: Error writing file
-2: Error renaming file
|
[
"Save",
"a",
"playlist",
"Create",
"a",
"txt",
"file",
"and",
"write",
"stations",
"in",
"it",
".",
"Then",
"rename",
"it",
"to",
"final",
"target"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/config.py#L258-L306
|
17,644
|
coderholic/pyradio
|
pyradio/config.py
|
PyRadioStations._bytes_to_human
|
def _bytes_to_human(self, B):
''' Return the given bytes as a human friendly KB, MB, GB, or TB string '''
KB = float(1024)
MB = float(KB ** 2) # 1,048,576
GB = float(KB ** 3) # 1,073,741,824
TB = float(KB ** 4) # 1,099,511,627,776
if B < KB:
return '{0} B'.format(B)
B = float(B)
if KB <= B < MB:
return '{0:.2f} KB'.format(B/KB)
elif MB <= B < GB:
return '{0:.2f} MB'.format(B/MB)
elif GB <= B < TB:
return '{0:.2f} GB'.format(B/GB)
elif TB <= B:
return '{0:.2f} TB'.format(B/TB)
|
python
|
def _bytes_to_human(self, B):
''' Return the given bytes as a human friendly KB, MB, GB, or TB string '''
KB = float(1024)
MB = float(KB ** 2) # 1,048,576
GB = float(KB ** 3) # 1,073,741,824
TB = float(KB ** 4) # 1,099,511,627,776
if B < KB:
return '{0} B'.format(B)
B = float(B)
if KB <= B < MB:
return '{0:.2f} KB'.format(B/KB)
elif MB <= B < GB:
return '{0:.2f} MB'.format(B/MB)
elif GB <= B < TB:
return '{0:.2f} GB'.format(B/GB)
elif TB <= B:
return '{0:.2f} TB'.format(B/TB)
|
[
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"(",
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"/",
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")"
] |
Return the given bytes as a human friendly KB, MB, GB, or TB string
|
[
"Return",
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"given",
"bytes",
"as",
"a",
"human",
"friendly",
"KB",
"MB",
"GB",
"or",
"TB",
"string"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/config.py#L321-L338
|
17,645
|
coderholic/pyradio
|
pyradio/config.py
|
PyRadioStations.append_station
|
def append_station(self, params, stationFile=''):
""" Append a station to csv file
return 0: All ok
-2 - playlist not found
-3 - negative number specified
-4 - number not found
-5: Error writing file
-6: Error renaming file
"""
if self.new_format:
if stationFile:
st_file = stationFile
else:
st_file = self.stations_file
st_file, ret = self._get_playlist_abspath_from_data(st_file)
if ret < -1:
return ret
try:
with open(st_file, 'a') as cfgfile:
writter = csv.writer(cfgfile)
writter.writerow(params)
return 0
except:
return -5
else:
self.stations.append([ params[0], params[1], params[2] ])
self.dirty_playlist = True
st_file, ret = self._get_playlist_abspath_from_data(stationFile)
if ret < -1:
return ret
ret = self.save_playlist_file(st_file)
if ret < 0:
ret -= 4
return ret
|
python
|
def append_station(self, params, stationFile=''):
""" Append a station to csv file
return 0: All ok
-2 - playlist not found
-3 - negative number specified
-4 - number not found
-5: Error writing file
-6: Error renaming file
"""
if self.new_format:
if stationFile:
st_file = stationFile
else:
st_file = self.stations_file
st_file, ret = self._get_playlist_abspath_from_data(st_file)
if ret < -1:
return ret
try:
with open(st_file, 'a') as cfgfile:
writter = csv.writer(cfgfile)
writter.writerow(params)
return 0
except:
return -5
else:
self.stations.append([ params[0], params[1], params[2] ])
self.dirty_playlist = True
st_file, ret = self._get_playlist_abspath_from_data(stationFile)
if ret < -1:
return ret
ret = self.save_playlist_file(st_file)
if ret < 0:
ret -= 4
return ret
|
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"-=",
"4",
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] |
Append a station to csv file
return 0: All ok
-2 - playlist not found
-3 - negative number specified
-4 - number not found
-5: Error writing file
-6: Error renaming file
|
[
"Append",
"a",
"station",
"to",
"csv",
"file"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/config.py#L340-L375
|
17,646
|
coderholic/pyradio
|
pyradio/config.py
|
PyRadioConfig._check_config_file
|
def _check_config_file(self, usr):
''' Make sure a config file exists in the config dir '''
package_config_file = path.join(path.dirname(__file__), 'config')
user_config_file = path.join(usr, 'config')
''' restore config from bck file '''
if path.exists(user_config_file + '.restore'):
try:
copyfile(user_config_file + '.restore', user_config_file)
remove(self.user_config_file + '.restore')
except:
pass
''' Copy package config into user dir '''
if not path.exists(user_config_file):
copyfile(package_config_file, user_config_file)
|
python
|
def _check_config_file(self, usr):
''' Make sure a config file exists in the config dir '''
package_config_file = path.join(path.dirname(__file__), 'config')
user_config_file = path.join(usr, 'config')
''' restore config from bck file '''
if path.exists(user_config_file + '.restore'):
try:
copyfile(user_config_file + '.restore', user_config_file)
remove(self.user_config_file + '.restore')
except:
pass
''' Copy package config into user dir '''
if not path.exists(user_config_file):
copyfile(package_config_file, user_config_file)
|
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Make sure a config file exists in the config dir
|
[
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c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/config.py#L566-L581
|
17,647
|
coderholic/pyradio
|
pyradio/config.py
|
PyRadioConfig.save_config
|
def save_config(self):
""" Save config file
Creates config.restore (back up file)
Returns:
-1: Error saving config
0: Config saved successfully
1: Config not saved (not modified"""
if not self.opts['dirty_config'][1]:
if logger.isEnabledFor(logging.INFO):
logger.info('Config not saved (not modified)')
return 1
txt ='''# PyRadio Configuration File
# Player selection
# This is the equivalent to the -u , --use-player command line parameter
# Specify the player to use with PyRadio, or the player detection order
# Example:
# player = vlc
# or
# player = vlc,mpv, mplayer
# Default value: mpv,mplayer,vlc
player = {0}
# Default playlist
# This is the playlist to open if none is specified
# You can scecify full path to CSV file, or if the playlist is in the
# config directory, playlist name (filename without extension) or
# playlist number (as reported by -ls command line option)
# Default value: stations
default_playlist = {1}
# Default station
# This is the equivalent to the -p , --play command line parameter
# The station number within the default playlist to play
# Value is 1..number of stations, "-1" or "False" means no auto play
# "0" or "Random" means play a random station
# Default value: False
default_station = {2}
# Default encoding
# This is the encoding used by default when reading data provided by
# a station (such as song title, etc.) If reading said data ends up
# in an error, 'utf-8' will be used instead.
#
# A valid encoding list can be found at:
# https://docs.python.org/2.7/library/codecs.html#standard-encodings
# replacing 2.7 with specific version:
# 3.0 up to current python version.
#
# Default value: utf-8
default_encoding = {3}
# Connection timeout
# PyRadio will wait for this number of seconds to get a station/server
# message indicating that playback has actually started.
# If this does not happen (within this number of seconds after the
# connection is initiated), PyRadio will consider the station
# unreachable, and display the "Failed to connect to: [station]"
# message.
#
# Valid values: 5 - 60
# Default value: 10
connection_timeout = {4}
# Default theme
# Hardcooded themes:
# dark (default) (8 colors)
# light (8 colors)
# dark_16_colors (16 colors dark theme alternative)
# light_16_colors (16 colors light theme alternative)
# black_on_white (bow) (256 colors)
# white_on_black (wob) (256 colors)
# Default value = 'dark'
theme = {5}
# Transparency setting
# If False, theme colors will be used.
# If True and a compositor is running, the stations' window
# background will be transparent. If True and a compositor is
# not running, the terminal's background color will be used.
# Valid values: True, true, False, false
# Default value: False
use_transparency = {6}
# Playlist management
#
# Specify whether you will be asked to confirm
# every station deletion action
# Valid values: True, true, False, false
# Default value: True
confirm_station_deletion = {7}
# Specify whether you will be asked to confirm
# playlist reloading, when the playlist has not
# been modified within Pyradio
# Valid values: True, true, False, false
# Default value: True
confirm_playlist_reload = {8}
# Specify whether you will be asked to save a
# modified playlist whenever it needs saving
# Valid values: True, true, False, false
# Default value: False
auto_save_playlist = {9}
'''
copyfile(self.config_file, self.config_file + '.restore')
if self.opts['default_station'][1] is None:
self.opts['default_station'][1] = '-1'
try:
with open(self.config_file, 'w') as cfgfile:
cfgfile.write(txt.format(self.opts['player'][1],
self.opts['default_playlist'][1],
self.opts['default_station'][1],
self.opts['default_encoding'][1],
self.opts['connection_timeout'][1],
self.opts['theme'][1],
self.opts['use_transparency'][1],
self.opts['confirm_station_deletion'][1],
self.opts['confirm_playlist_reload'][1],
self.opts['auto_save_playlist'][1]))
except:
if logger.isEnabledFor(logging.ERROR):
logger.error('Error saving config')
return -1
try:
remove(self.config_file + '.restore')
except:
pass
if logger.isEnabledFor(logging.INFO):
logger.info('Config saved')
self.opts['dirty_config'][1] = False
return 0
|
python
|
def save_config(self):
""" Save config file
Creates config.restore (back up file)
Returns:
-1: Error saving config
0: Config saved successfully
1: Config not saved (not modified"""
if not self.opts['dirty_config'][1]:
if logger.isEnabledFor(logging.INFO):
logger.info('Config not saved (not modified)')
return 1
txt ='''# PyRadio Configuration File
# Player selection
# This is the equivalent to the -u , --use-player command line parameter
# Specify the player to use with PyRadio, or the player detection order
# Example:
# player = vlc
# or
# player = vlc,mpv, mplayer
# Default value: mpv,mplayer,vlc
player = {0}
# Default playlist
# This is the playlist to open if none is specified
# You can scecify full path to CSV file, or if the playlist is in the
# config directory, playlist name (filename without extension) or
# playlist number (as reported by -ls command line option)
# Default value: stations
default_playlist = {1}
# Default station
# This is the equivalent to the -p , --play command line parameter
# The station number within the default playlist to play
# Value is 1..number of stations, "-1" or "False" means no auto play
# "0" or "Random" means play a random station
# Default value: False
default_station = {2}
# Default encoding
# This is the encoding used by default when reading data provided by
# a station (such as song title, etc.) If reading said data ends up
# in an error, 'utf-8' will be used instead.
#
# A valid encoding list can be found at:
# https://docs.python.org/2.7/library/codecs.html#standard-encodings
# replacing 2.7 with specific version:
# 3.0 up to current python version.
#
# Default value: utf-8
default_encoding = {3}
# Connection timeout
# PyRadio will wait for this number of seconds to get a station/server
# message indicating that playback has actually started.
# If this does not happen (within this number of seconds after the
# connection is initiated), PyRadio will consider the station
# unreachable, and display the "Failed to connect to: [station]"
# message.
#
# Valid values: 5 - 60
# Default value: 10
connection_timeout = {4}
# Default theme
# Hardcooded themes:
# dark (default) (8 colors)
# light (8 colors)
# dark_16_colors (16 colors dark theme alternative)
# light_16_colors (16 colors light theme alternative)
# black_on_white (bow) (256 colors)
# white_on_black (wob) (256 colors)
# Default value = 'dark'
theme = {5}
# Transparency setting
# If False, theme colors will be used.
# If True and a compositor is running, the stations' window
# background will be transparent. If True and a compositor is
# not running, the terminal's background color will be used.
# Valid values: True, true, False, false
# Default value: False
use_transparency = {6}
# Playlist management
#
# Specify whether you will be asked to confirm
# every station deletion action
# Valid values: True, true, False, false
# Default value: True
confirm_station_deletion = {7}
# Specify whether you will be asked to confirm
# playlist reloading, when the playlist has not
# been modified within Pyradio
# Valid values: True, true, False, false
# Default value: True
confirm_playlist_reload = {8}
# Specify whether you will be asked to save a
# modified playlist whenever it needs saving
# Valid values: True, true, False, false
# Default value: False
auto_save_playlist = {9}
'''
copyfile(self.config_file, self.config_file + '.restore')
if self.opts['default_station'][1] is None:
self.opts['default_station'][1] = '-1'
try:
with open(self.config_file, 'w') as cfgfile:
cfgfile.write(txt.format(self.opts['player'][1],
self.opts['default_playlist'][1],
self.opts['default_station'][1],
self.opts['default_encoding'][1],
self.opts['connection_timeout'][1],
self.opts['theme'][1],
self.opts['use_transparency'][1],
self.opts['confirm_station_deletion'][1],
self.opts['confirm_playlist_reload'][1],
self.opts['auto_save_playlist'][1]))
except:
if logger.isEnabledFor(logging.ERROR):
logger.error('Error saving config')
return -1
try:
remove(self.config_file + '.restore')
except:
pass
if logger.isEnabledFor(logging.INFO):
logger.info('Config saved')
self.opts['dirty_config'][1] = False
return 0
|
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] |
Save config file
Creates config.restore (back up file)
Returns:
-1: Error saving config
0: Config saved successfully
1: Config not saved (not modified
|
[
"Save",
"config",
"file"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/config.py#L639-L773
|
17,648
|
coderholic/pyradio
|
pyradio/radio.py
|
PyRadio.ctrl_c_handler
|
def ctrl_c_handler(self, signum, frame):
self.ctrl_c_pressed = True
if self._cnf.dirty_playlist:
""" Try to auto save playlist on exit
Do not check result!!! """
self.saveCurrentPlaylist()
""" Try to auto save config on exit
Do not check result!!! """
self._cnf.save_config()
|
python
|
def ctrl_c_handler(self, signum, frame):
self.ctrl_c_pressed = True
if self._cnf.dirty_playlist:
""" Try to auto save playlist on exit
Do not check result!!! """
self.saveCurrentPlaylist()
""" Try to auto save config on exit
Do not check result!!! """
self._cnf.save_config()
|
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Try to auto save config on exit
Do not check result!!!
|
[
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c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/radio.py#L432-L440
|
17,649
|
coderholic/pyradio
|
pyradio/radio.py
|
PyRadio._goto_playing_station
|
def _goto_playing_station(self, changing_playlist=False):
""" make sure playing station is visible """
if (self.player.isPlaying() or self.operation_mode == PLAYLIST_MODE) and \
(self.selection != self.playing or changing_playlist):
if changing_playlist:
self.startPos = 0
max_lines = self.bodyMaxY - 2
if logger.isEnabledFor(logging.INFO):
logger.info('max_lines = {0}, self.playing = {1}'.format(max_lines, self.playing))
if self.number_of_items < max_lines:
self.startPos = 0
elif self.playing < self.startPos or \
self.playing >= self.startPos + max_lines:
if logger.isEnabledFor(logging.INFO):
logger.info('=== _goto:adjusting startPos')
if self.playing < max_lines:
self.startPos = 0
if self.playing - int(max_lines/2) > 0:
self.startPos = self.playing - int(max_lines/2)
elif self.playing > self.number_of_items - max_lines:
self.startPos = self.number_of_items - max_lines
else:
self.startPos = int(self.playing+1/max_lines) - int(max_lines/2)
if logger.isEnabledFor(logging.INFO):
logger.info('===== _goto:startPos = {0}, changing_playlist = {1}'.format(self.startPos, changing_playlist))
self.selection = self.playing
self.refreshBody()
|
python
|
def _goto_playing_station(self, changing_playlist=False):
""" make sure playing station is visible """
if (self.player.isPlaying() or self.operation_mode == PLAYLIST_MODE) and \
(self.selection != self.playing or changing_playlist):
if changing_playlist:
self.startPos = 0
max_lines = self.bodyMaxY - 2
if logger.isEnabledFor(logging.INFO):
logger.info('max_lines = {0}, self.playing = {1}'.format(max_lines, self.playing))
if self.number_of_items < max_lines:
self.startPos = 0
elif self.playing < self.startPos or \
self.playing >= self.startPos + max_lines:
if logger.isEnabledFor(logging.INFO):
logger.info('=== _goto:adjusting startPos')
if self.playing < max_lines:
self.startPos = 0
if self.playing - int(max_lines/2) > 0:
self.startPos = self.playing - int(max_lines/2)
elif self.playing > self.number_of_items - max_lines:
self.startPos = self.number_of_items - max_lines
else:
self.startPos = int(self.playing+1/max_lines) - int(max_lines/2)
if logger.isEnabledFor(logging.INFO):
logger.info('===== _goto:startPos = {0}, changing_playlist = {1}'.format(self.startPos, changing_playlist))
self.selection = self.playing
self.refreshBody()
|
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")",
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"selection",
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"self",
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"playing",
"self",
".",
"refreshBody",
"(",
")"
] |
make sure playing station is visible
|
[
"make",
"sure",
"playing",
"station",
"is",
"visible"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/radio.py#L442-L468
|
17,650
|
coderholic/pyradio
|
pyradio/radio.py
|
PyRadio.setStation
|
def setStation(self, number):
""" Select the given station number """
# If we press up at the first station, we go to the last one
# and if we press down on the last one we go back to the first one.
if number < 0:
number = len(self.stations) - 1
elif number >= len(self.stations):
number = 0
self.selection = number
maxDisplayedItems = self.bodyMaxY - 2
if self.selection - self.startPos >= maxDisplayedItems:
self.startPos = self.selection - maxDisplayedItems + 1
elif self.selection < self.startPos:
self.startPos = self.selection
|
python
|
def setStation(self, number):
""" Select the given station number """
# If we press up at the first station, we go to the last one
# and if we press down on the last one we go back to the first one.
if number < 0:
number = len(self.stations) - 1
elif number >= len(self.stations):
number = 0
self.selection = number
maxDisplayedItems = self.bodyMaxY - 2
if self.selection - self.startPos >= maxDisplayedItems:
self.startPos = self.selection - maxDisplayedItems + 1
elif self.selection < self.startPos:
self.startPos = self.selection
|
[
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",",
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"# If we press up at the first station, we go to the last one",
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"startPos",
":",
"self",
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"startPos",
"=",
"self",
".",
"selection"
] |
Select the given station number
|
[
"Select",
"the",
"given",
"station",
"number"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/radio.py#L489-L504
|
17,651
|
coderholic/pyradio
|
pyradio/radio.py
|
PyRadio._format_playlist_line
|
def _format_playlist_line(self, lineNum, pad, station):
""" format playlist line so that if fills self.maxX """
line = "{0}. {1}".format(str(lineNum + self.startPos + 1).rjust(pad), station[0])
f_data = ' [{0}, {1}]'.format(station[2], station[1])
if version_info < (3, 0):
if len(line.decode('utf-8', 'replace')) + len(f_data.decode('utf-8', 'replace')) > self.bodyMaxX -2:
""" this is too long, try to shorten it
by removing file size """
f_data = ' [{0}]'.format(station[1])
if len(line.decode('utf-8', 'replace')) + len(f_data.decode('utf-8', 'replace')) > self.bodyMaxX - 2:
""" still too long. start removing chars """
while len(line.decode('utf-8', 'replace')) + len(f_data.decode('utf-8', 'replace')) > self.bodyMaxX - 3:
f_data = f_data[:-1]
f_data += ']'
""" if too short, pad f_data to the right """
if len(line.decode('utf-8', 'replace')) + len(f_data.decode('utf-8', 'replace')) < self.maxX - 2:
while len(line.decode('utf-8', 'replace')) + len(f_data.decode('utf-8', 'replace')) < self.maxX - 2:
line += ' '
else:
if len(line) + len(f_data) > self.bodyMaxX -2:
""" this is too long, try to shorten it
by removing file size """
f_data = ' [{0}]'.format(station[1])
if len(line) + len(f_data) > self.bodyMaxX - 2:
""" still too long. start removing chars """
while len(line) + len(f_data) > self.bodyMaxX - 3:
f_data = f_data[:-1]
f_data += ']'
""" if too short, pad f_data to the right """
if len(line) + len(f_data) < self.maxX - 2:
while len(line) + len(f_data) < self.maxX - 2:
line += ' '
line += f_data
return line
|
python
|
def _format_playlist_line(self, lineNum, pad, station):
""" format playlist line so that if fills self.maxX """
line = "{0}. {1}".format(str(lineNum + self.startPos + 1).rjust(pad), station[0])
f_data = ' [{0}, {1}]'.format(station[2], station[1])
if version_info < (3, 0):
if len(line.decode('utf-8', 'replace')) + len(f_data.decode('utf-8', 'replace')) > self.bodyMaxX -2:
""" this is too long, try to shorten it
by removing file size """
f_data = ' [{0}]'.format(station[1])
if len(line.decode('utf-8', 'replace')) + len(f_data.decode('utf-8', 'replace')) > self.bodyMaxX - 2:
""" still too long. start removing chars """
while len(line.decode('utf-8', 'replace')) + len(f_data.decode('utf-8', 'replace')) > self.bodyMaxX - 3:
f_data = f_data[:-1]
f_data += ']'
""" if too short, pad f_data to the right """
if len(line.decode('utf-8', 'replace')) + len(f_data.decode('utf-8', 'replace')) < self.maxX - 2:
while len(line.decode('utf-8', 'replace')) + len(f_data.decode('utf-8', 'replace')) < self.maxX - 2:
line += ' '
else:
if len(line) + len(f_data) > self.bodyMaxX -2:
""" this is too long, try to shorten it
by removing file size """
f_data = ' [{0}]'.format(station[1])
if len(line) + len(f_data) > self.bodyMaxX - 2:
""" still too long. start removing chars """
while len(line) + len(f_data) > self.bodyMaxX - 3:
f_data = f_data[:-1]
f_data += ']'
""" if too short, pad f_data to the right """
if len(line) + len(f_data) < self.maxX - 2:
while len(line) + len(f_data) < self.maxX - 2:
line += ' '
line += f_data
return line
|
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"-",
"2",
":",
"line",
"+=",
"' '",
"line",
"+=",
"f_data",
"return",
"line"
] |
format playlist line so that if fills self.maxX
|
[
"format",
"playlist",
"line",
"so",
"that",
"if",
"fills",
"self",
".",
"maxX"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/radio.py#L772-L805
|
17,652
|
coderholic/pyradio
|
pyradio/config_window.py
|
PyRadioSelectEncodings._resize
|
def _resize(self, init=False):
col, row = self._selection_to_col_row(self.selection)
if not (self.startPos <= row <= self.startPos + self.list_maxY - 1):
while row > self.startPos:
self.startPos += 1
while row < self.startPos + self.list_maxY - 1:
self.startPos -= 1
''' if the selection at the end of the list,
try to scroll down '''
if init and row > self.list_maxY:
new_startPos = self._num_of_rows - self.list_maxY + 1
if row > new_startPos:
if logger.isEnabledFor(logging.DEBUG):
logger.debug('setting startPos at {}'.format(new_startPos))
self.startPos = new_startPos
self.refresh_selection()
|
python
|
def _resize(self, init=False):
col, row = self._selection_to_col_row(self.selection)
if not (self.startPos <= row <= self.startPos + self.list_maxY - 1):
while row > self.startPos:
self.startPos += 1
while row < self.startPos + self.list_maxY - 1:
self.startPos -= 1
''' if the selection at the end of the list,
try to scroll down '''
if init and row > self.list_maxY:
new_startPos = self._num_of_rows - self.list_maxY + 1
if row > new_startPos:
if logger.isEnabledFor(logging.DEBUG):
logger.debug('setting startPos at {}'.format(new_startPos))
self.startPos = new_startPos
self.refresh_selection()
|
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"self",
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"startPos",
"=",
"new_startPos",
"self",
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"refresh_selection",
"(",
")"
] |
if the selection at the end of the list,
try to scroll down
|
[
"if",
"the",
"selection",
"at",
"the",
"end",
"of",
"the",
"list",
"try",
"to",
"scroll",
"down"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/config_window.py#L745-L760
|
17,653
|
coderholic/pyradio
|
pyradio/simple_curses_widgets.py
|
SimpleCursesLineEdit._get_char
|
def _get_char(self, win, char):
def get_check_next_byte():
char = win.getch()
if 128 <= char <= 191:
return char
else:
raise UnicodeError
bytes = []
if char <= 127:
# 1 bytes
bytes.append(char)
#elif 194 <= char <= 223:
elif 192 <= char <= 223:
# 2 bytes
bytes.append(char)
bytes.append(get_check_next_byte())
elif 224 <= char <= 239:
# 3 bytes
bytes.append(char)
bytes.append(get_check_next_byte())
bytes.append(get_check_next_byte())
elif 240 <= char <= 244:
# 4 bytes
bytes.append(char)
bytes.append(get_check_next_byte())
bytes.append(get_check_next_byte())
bytes.append(get_check_next_byte())
#print('bytes = {}'.format(bytes))
""" no zero byte allowed """
while 0 in bytes:
bytes.remove(0)
if version_info < (3, 0):
out = ''.join([chr(b) for b in bytes])
else:
buf = bytearray(bytes)
out = self._decode_string(buf)
#out = buf.decode('utf-8')
return out
|
python
|
def _get_char(self, win, char):
def get_check_next_byte():
char = win.getch()
if 128 <= char <= 191:
return char
else:
raise UnicodeError
bytes = []
if char <= 127:
# 1 bytes
bytes.append(char)
#elif 194 <= char <= 223:
elif 192 <= char <= 223:
# 2 bytes
bytes.append(char)
bytes.append(get_check_next_byte())
elif 224 <= char <= 239:
# 3 bytes
bytes.append(char)
bytes.append(get_check_next_byte())
bytes.append(get_check_next_byte())
elif 240 <= char <= 244:
# 4 bytes
bytes.append(char)
bytes.append(get_check_next_byte())
bytes.append(get_check_next_byte())
bytes.append(get_check_next_byte())
#print('bytes = {}'.format(bytes))
""" no zero byte allowed """
while 0 in bytes:
bytes.remove(0)
if version_info < (3, 0):
out = ''.join([chr(b) for b in bytes])
else:
buf = bytearray(bytes)
out = self._decode_string(buf)
#out = buf.decode('utf-8')
return out
|
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"return",
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] |
no zero byte allowed
|
[
"no",
"zero",
"byte",
"allowed"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/simple_curses_widgets.py#L342-L380
|
17,654
|
coderholic/pyradio
|
pyradio/edit.py
|
PyRadioSearch._get_history_next
|
def _get_history_next(self):
""" callback function for key down """
if self._has_history:
ret = self._input_history.return_history(1)
self.string = ret
self._curs_pos = len(ret)
|
python
|
def _get_history_next(self):
""" callback function for key down """
if self._has_history:
ret = self._input_history.return_history(1)
self.string = ret
self._curs_pos = len(ret)
|
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] |
callback function for key down
|
[
"callback",
"function",
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"key",
"down"
] |
c5219d350bccbccd49dbd627c1f886a952ea1963
|
https://github.com/coderholic/pyradio/blob/c5219d350bccbccd49dbd627c1f886a952ea1963/pyradio/edit.py#L49-L54
|
17,655
|
bids-standard/pybids
|
bids/analysis/analysis.py
|
apply_transformations
|
def apply_transformations(collection, transformations, select=None):
''' Apply all transformations to the variables in the collection.
Args:
transformations (list): List of transformations to apply.
select (list): Optional list of names of variables to retain after all
transformations are applied.
'''
for t in transformations:
kwargs = dict(t)
func = kwargs.pop('name')
cols = kwargs.pop('input', None)
if isinstance(func, string_types):
if func in ('and', 'or'):
func += '_'
if not hasattr(transform, func):
raise ValueError("No transformation '%s' found!" % func)
func = getattr(transform, func)
func(collection, cols, **kwargs)
if select is not None:
transform.Select(collection, select)
return collection
|
python
|
def apply_transformations(collection, transformations, select=None):
''' Apply all transformations to the variables in the collection.
Args:
transformations (list): List of transformations to apply.
select (list): Optional list of names of variables to retain after all
transformations are applied.
'''
for t in transformations:
kwargs = dict(t)
func = kwargs.pop('name')
cols = kwargs.pop('input', None)
if isinstance(func, string_types):
if func in ('and', 'or'):
func += '_'
if not hasattr(transform, func):
raise ValueError("No transformation '%s' found!" % func)
func = getattr(transform, func)
func(collection, cols, **kwargs)
if select is not None:
transform.Select(collection, select)
return collection
|
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Apply all transformations to the variables in the collection.
Args:
transformations (list): List of transformations to apply.
select (list): Optional list of names of variables to retain after all
transformations are applied.
|
[
"Apply",
"all",
"transformations",
"to",
"the",
"variables",
"in",
"the",
"collection",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/analysis.py#L489-L513
|
17,656
|
bids-standard/pybids
|
bids/analysis/analysis.py
|
Analysis.setup
|
def setup(self, steps=None, drop_na=False, **kwargs):
''' Set up the sequence of steps for analysis.
Args:
steps (list): Optional list of steps to set up. Each element
must be either an int giving the index of the step in the
JSON config block list, or a str giving the (unique) name of
the step, as specified in the JSON config. Steps that do not
match either index or name will be skipped.
drop_na (bool): Boolean indicating whether or not to automatically
drop events that have a n/a amplitude when reading in data
from event files.
'''
# In the beginning, there was nothing
input_nodes = None
# Use inputs from model, and update with kwargs
selectors = self.model.get('input', {}).copy()
selectors.update(kwargs)
for i, b in enumerate(self.steps):
# Skip any steps whose names or indexes don't match block list
if steps is not None and i not in steps and b.name not in steps:
continue
b.setup(input_nodes, drop_na=drop_na, **selectors)
input_nodes = b.output_nodes
|
python
|
def setup(self, steps=None, drop_na=False, **kwargs):
''' Set up the sequence of steps for analysis.
Args:
steps (list): Optional list of steps to set up. Each element
must be either an int giving the index of the step in the
JSON config block list, or a str giving the (unique) name of
the step, as specified in the JSON config. Steps that do not
match either index or name will be skipped.
drop_na (bool): Boolean indicating whether or not to automatically
drop events that have a n/a amplitude when reading in data
from event files.
'''
# In the beginning, there was nothing
input_nodes = None
# Use inputs from model, and update with kwargs
selectors = self.model.get('input', {}).copy()
selectors.update(kwargs)
for i, b in enumerate(self.steps):
# Skip any steps whose names or indexes don't match block list
if steps is not None and i not in steps and b.name not in steps:
continue
b.setup(input_nodes, drop_na=drop_na, **selectors)
input_nodes = b.output_nodes
|
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",",
"*",
"*",
"selectors",
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"input_nodes",
"=",
"b",
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"output_nodes"
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Set up the sequence of steps for analysis.
Args:
steps (list): Optional list of steps to set up. Each element
must be either an int giving the index of the step in the
JSON config block list, or a str giving the (unique) name of
the step, as specified in the JSON config. Steps that do not
match either index or name will be skipped.
drop_na (bool): Boolean indicating whether or not to automatically
drop events that have a n/a amplitude when reading in data
from event files.
|
[
"Set",
"up",
"the",
"sequence",
"of",
"steps",
"for",
"analysis",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/analysis.py#L62-L90
|
17,657
|
bids-standard/pybids
|
bids/analysis/analysis.py
|
Step.setup
|
def setup(self, input_nodes=None, drop_na=False, **kwargs):
''' Set up the Step and construct the design matrix.
Args:
input_nodes (list): Optional list of Node objects produced by
the preceding Step in the analysis. If None, uses any inputs
passed in at Step initialization.
drop_na (bool): Boolean indicating whether or not to automatically
drop events that have a n/a amplitude when reading in data
from event files.
kwargs: Optional keyword arguments to pass onto load_variables.
'''
self.output_nodes = []
input_nodes = input_nodes or self.input_nodes or []
# TODO: remove the scan_length argument entirely once we switch tests
# to use the synthetic dataset with image headers.
if self.level != 'run':
kwargs = kwargs.copy()
kwargs.pop('scan_length', None)
collections = self.layout.get_collections(self.level, drop_na=drop_na,
**kwargs)
objects = collections + input_nodes
objects, kwargs = self._filter_objects(objects, kwargs)
groups = self._group_objects(objects)
# Set up and validate variable lists
model = self.model or {}
X = model.get('x', [])
for grp in groups:
# Split into separate lists of Collections and Nodes
input_nodes = [o for o in grp if isinstance(o, AnalysisNode)]
colls = list(set(grp) - set(input_nodes))
if input_nodes:
node_coll = self._concatenate_input_nodes(input_nodes)
colls.append(node_coll)
coll = merge_collections(colls) if len(colls) > 1 else colls[0]
coll = apply_transformations(coll, self.transformations)
if X:
transform.Select(coll, X)
node = AnalysisNode(self.level, coll, self.contrasts, input_nodes,
self.auto_contrasts)
self.output_nodes.append(node)
|
python
|
def setup(self, input_nodes=None, drop_na=False, **kwargs):
''' Set up the Step and construct the design matrix.
Args:
input_nodes (list): Optional list of Node objects produced by
the preceding Step in the analysis. If None, uses any inputs
passed in at Step initialization.
drop_na (bool): Boolean indicating whether or not to automatically
drop events that have a n/a amplitude when reading in data
from event files.
kwargs: Optional keyword arguments to pass onto load_variables.
'''
self.output_nodes = []
input_nodes = input_nodes or self.input_nodes or []
# TODO: remove the scan_length argument entirely once we switch tests
# to use the synthetic dataset with image headers.
if self.level != 'run':
kwargs = kwargs.copy()
kwargs.pop('scan_length', None)
collections = self.layout.get_collections(self.level, drop_na=drop_na,
**kwargs)
objects = collections + input_nodes
objects, kwargs = self._filter_objects(objects, kwargs)
groups = self._group_objects(objects)
# Set up and validate variable lists
model = self.model or {}
X = model.get('x', [])
for grp in groups:
# Split into separate lists of Collections and Nodes
input_nodes = [o for o in grp if isinstance(o, AnalysisNode)]
colls = list(set(grp) - set(input_nodes))
if input_nodes:
node_coll = self._concatenate_input_nodes(input_nodes)
colls.append(node_coll)
coll = merge_collections(colls) if len(colls) > 1 else colls[0]
coll = apply_transformations(coll, self.transformations)
if X:
transform.Select(coll, X)
node = AnalysisNode(self.level, coll, self.contrasts, input_nodes,
self.auto_contrasts)
self.output_nodes.append(node)
|
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Set up the Step and construct the design matrix.
Args:
input_nodes (list): Optional list of Node objects produced by
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passed in at Step initialization.
drop_na (bool): Boolean indicating whether or not to automatically
drop events that have a n/a amplitude when reading in data
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kwargs: Optional keyword arguments to pass onto load_variables.
|
[
"Set",
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"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/analysis.py#L168-L218
|
17,658
|
bids-standard/pybids
|
bids/reports/utils.py
|
get_slice_info
|
def get_slice_info(slice_times):
"""
Extract slice order from slice timing info.
TODO: Be more specific with slice orders.
Currently anything where there's some kind of skipping is interpreted as
interleaved of some kind.
Parameters
----------
slice_times : array-like
A list of slice times in seconds or milliseconds or whatever.
Returns
-------
slice_order_name : :obj:`str`
The name of the slice order sequence.
"""
# Slice order
slice_times = remove_duplicates(slice_times)
slice_order = sorted(range(len(slice_times)), key=lambda k: slice_times[k])
if slice_order == range(len(slice_order)):
slice_order_name = 'sequential ascending'
elif slice_order == reversed(range(len(slice_order))):
slice_order_name = 'sequential descending'
elif slice_order[0] < slice_order[1]:
# We're allowing some wiggle room on interleaved.
slice_order_name = 'interleaved ascending'
elif slice_order[0] > slice_order[1]:
slice_order_name = 'interleaved descending'
else:
slice_order = [str(s) for s in slice_order]
raise Exception('Unknown slice order: [{0}]'.format(', '.join(slice_order)))
return slice_order_name
|
python
|
def get_slice_info(slice_times):
"""
Extract slice order from slice timing info.
TODO: Be more specific with slice orders.
Currently anything where there's some kind of skipping is interpreted as
interleaved of some kind.
Parameters
----------
slice_times : array-like
A list of slice times in seconds or milliseconds or whatever.
Returns
-------
slice_order_name : :obj:`str`
The name of the slice order sequence.
"""
# Slice order
slice_times = remove_duplicates(slice_times)
slice_order = sorted(range(len(slice_times)), key=lambda k: slice_times[k])
if slice_order == range(len(slice_order)):
slice_order_name = 'sequential ascending'
elif slice_order == reversed(range(len(slice_order))):
slice_order_name = 'sequential descending'
elif slice_order[0] < slice_order[1]:
# We're allowing some wiggle room on interleaved.
slice_order_name = 'interleaved ascending'
elif slice_order[0] > slice_order[1]:
slice_order_name = 'interleaved descending'
else:
slice_order = [str(s) for s in slice_order]
raise Exception('Unknown slice order: [{0}]'.format(', '.join(slice_order)))
return slice_order_name
|
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TODO: Be more specific with slice orders.
Currently anything where there's some kind of skipping is interpreted as
interleaved of some kind.
Parameters
----------
slice_times : array-like
A list of slice times in seconds or milliseconds or whatever.
Returns
-------
slice_order_name : :obj:`str`
The name of the slice order sequence.
|
[
"Extract",
"slice",
"order",
"from",
"slice",
"timing",
"info",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/reports/utils.py#L70-L104
|
17,659
|
bids-standard/pybids
|
bids/reports/utils.py
|
get_sizestr
|
def get_sizestr(img):
"""
Extract and reformat voxel size, matrix size, field of view, and number of
slices into pretty strings.
Parameters
----------
img : :obj:`nibabel.Nifti1Image`
Image from scan from which to derive parameters.
Returns
-------
n_slices : :obj:`int`
Number of slices.
voxel_size : :obj:`str`
Voxel size string (e.g., '2x2x2')
matrix_size : :obj:`str`
Matrix size string (e.g., '128x128')
fov : :obj:`str`
Field of view string (e.g., '256x256')
"""
n_x, n_y, n_slices = img.shape[:3]
import numpy as np
voxel_dims = np.array(img.header.get_zooms()[:3])
matrix_size = '{0}x{1}'.format(num_to_str(n_x), num_to_str(n_y))
voxel_size = 'x'.join([num_to_str(s) for s in voxel_dims])
fov = [n_x, n_y] * voxel_dims[:2]
fov = 'x'.join([num_to_str(s) for s in fov])
return n_slices, voxel_size, matrix_size, fov
|
python
|
def get_sizestr(img):
"""
Extract and reformat voxel size, matrix size, field of view, and number of
slices into pretty strings.
Parameters
----------
img : :obj:`nibabel.Nifti1Image`
Image from scan from which to derive parameters.
Returns
-------
n_slices : :obj:`int`
Number of slices.
voxel_size : :obj:`str`
Voxel size string (e.g., '2x2x2')
matrix_size : :obj:`str`
Matrix size string (e.g., '128x128')
fov : :obj:`str`
Field of view string (e.g., '256x256')
"""
n_x, n_y, n_slices = img.shape[:3]
import numpy as np
voxel_dims = np.array(img.header.get_zooms()[:3])
matrix_size = '{0}x{1}'.format(num_to_str(n_x), num_to_str(n_y))
voxel_size = 'x'.join([num_to_str(s) for s in voxel_dims])
fov = [n_x, n_y] * voxel_dims[:2]
fov = 'x'.join([num_to_str(s) for s in fov])
return n_slices, voxel_size, matrix_size, fov
|
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Extract and reformat voxel size, matrix size, field of view, and number of
slices into pretty strings.
Parameters
----------
img : :obj:`nibabel.Nifti1Image`
Image from scan from which to derive parameters.
Returns
-------
n_slices : :obj:`int`
Number of slices.
voxel_size : :obj:`str`
Voxel size string (e.g., '2x2x2')
matrix_size : :obj:`str`
Matrix size string (e.g., '128x128')
fov : :obj:`str`
Field of view string (e.g., '256x256')
|
[
"Extract",
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"view",
"and",
"number",
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"slices",
"into",
"pretty",
"strings",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/reports/utils.py#L138-L166
|
17,660
|
bids-standard/pybids
|
bids/layout/layout.py
|
add_config_paths
|
def add_config_paths(**kwargs):
""" Add to the pool of available configuration files for BIDSLayout.
Args:
kwargs: dictionary specifying where to find additional config files.
Keys are names, values are paths to the corresponding .json file.
Example:
> add_config_paths(my_config='/path/to/config')
> layout = BIDSLayout('/path/to/bids', config=['bids', 'my_config'])
"""
for k, path in kwargs.items():
if not os.path.exists(path):
raise ValueError(
'Configuration file "{}" does not exist'.format(k))
if k in cf.get_option('config_paths'):
raise ValueError('Configuration {!r} already exists'.format(k))
kwargs.update(**cf.get_option('config_paths'))
cf.set_option('config_paths', kwargs)
|
python
|
def add_config_paths(**kwargs):
""" Add to the pool of available configuration files for BIDSLayout.
Args:
kwargs: dictionary specifying where to find additional config files.
Keys are names, values are paths to the corresponding .json file.
Example:
> add_config_paths(my_config='/path/to/config')
> layout = BIDSLayout('/path/to/bids', config=['bids', 'my_config'])
"""
for k, path in kwargs.items():
if not os.path.exists(path):
raise ValueError(
'Configuration file "{}" does not exist'.format(k))
if k in cf.get_option('config_paths'):
raise ValueError('Configuration {!r} already exists'.format(k))
kwargs.update(**cf.get_option('config_paths'))
cf.set_option('config_paths', kwargs)
|
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",",
"kwargs",
")"
] |
Add to the pool of available configuration files for BIDSLayout.
Args:
kwargs: dictionary specifying where to find additional config files.
Keys are names, values are paths to the corresponding .json file.
Example:
> add_config_paths(my_config='/path/to/config')
> layout = BIDSLayout('/path/to/bids', config=['bids', 'my_config'])
|
[
"Add",
"to",
"the",
"pool",
"of",
"available",
"configuration",
"files",
"for",
"BIDSLayout",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/layout.py#L77-L97
|
17,661
|
bids-standard/pybids
|
bids/layout/layout.py
|
BIDSLayout.add_derivatives
|
def add_derivatives(self, path, **kwargs):
''' Add BIDS-Derivatives datasets to tracking.
Args:
path (str, list): One or more paths to BIDS-Derivatives datasets.
Each path can point to either a derivatives/ directory
containing one more more pipeline directories, or to a single
pipeline directory (e.g., derivatives/fmriprep).
kwargs (dict): Optional keyword arguments to pass on to
BIDSLayout() when initializing each of the derivative datasets.
Note: Every derivatives directory intended for indexing MUST contain a
valid dataset_description.json file. See the BIDS-Derivatives
specification for details.
'''
paths = listify(path)
deriv_dirs = []
# Collect all paths that contain a dataset_description.json
def check_for_description(dir):
dd = os.path.join(dir, 'dataset_description.json')
return os.path.exists(dd)
for p in paths:
p = os.path.abspath(p)
if os.path.exists(p):
if check_for_description(p):
deriv_dirs.append(p)
else:
subdirs = [d for d in os.listdir(p)
if os.path.isdir(os.path.join(p, d))]
for sd in subdirs:
sd = os.path.join(p, sd)
if check_for_description(sd):
deriv_dirs.append(sd)
if not deriv_dirs:
warnings.warn("Derivative indexing was enabled, but no valid "
"derivatives datasets were found in any of the "
"provided or default locations. Please make sure "
"all derivatives datasets you intend to index "
"contain a 'dataset_description.json' file, as "
"described in the BIDS-derivatives specification.")
for deriv in deriv_dirs:
dd = os.path.join(deriv, 'dataset_description.json')
with open(dd, 'r', encoding='utf-8') as ddfd:
description = json.load(ddfd)
pipeline_name = description.get(
'PipelineDescription', {}).get('Name')
if pipeline_name is None:
raise ValueError("Every valid BIDS-derivatives dataset must "
"have a PipelineDescription.Name field set "
"inside dataset_description.json.")
if pipeline_name in self.derivatives:
raise ValueError("Pipeline name '%s' has already been added "
"to this BIDSLayout. Every added pipeline "
"must have a unique name!")
# Default config and sources values
kwargs['config'] = kwargs.get('config') or ['bids', 'derivatives']
kwargs['sources'] = kwargs.get('sources') or self
self.derivatives[pipeline_name] = BIDSLayout(deriv, **kwargs)
# Consolidate all entities post-indexing. Note: no conflicts occur b/c
# multiple entries with the same name all point to the same instance.
for deriv in self.derivatives.values():
self.entities.update(deriv.entities)
|
python
|
def add_derivatives(self, path, **kwargs):
''' Add BIDS-Derivatives datasets to tracking.
Args:
path (str, list): One or more paths to BIDS-Derivatives datasets.
Each path can point to either a derivatives/ directory
containing one more more pipeline directories, or to a single
pipeline directory (e.g., derivatives/fmriprep).
kwargs (dict): Optional keyword arguments to pass on to
BIDSLayout() when initializing each of the derivative datasets.
Note: Every derivatives directory intended for indexing MUST contain a
valid dataset_description.json file. See the BIDS-Derivatives
specification for details.
'''
paths = listify(path)
deriv_dirs = []
# Collect all paths that contain a dataset_description.json
def check_for_description(dir):
dd = os.path.join(dir, 'dataset_description.json')
return os.path.exists(dd)
for p in paths:
p = os.path.abspath(p)
if os.path.exists(p):
if check_for_description(p):
deriv_dirs.append(p)
else:
subdirs = [d for d in os.listdir(p)
if os.path.isdir(os.path.join(p, d))]
for sd in subdirs:
sd = os.path.join(p, sd)
if check_for_description(sd):
deriv_dirs.append(sd)
if not deriv_dirs:
warnings.warn("Derivative indexing was enabled, but no valid "
"derivatives datasets were found in any of the "
"provided or default locations. Please make sure "
"all derivatives datasets you intend to index "
"contain a 'dataset_description.json' file, as "
"described in the BIDS-derivatives specification.")
for deriv in deriv_dirs:
dd = os.path.join(deriv, 'dataset_description.json')
with open(dd, 'r', encoding='utf-8') as ddfd:
description = json.load(ddfd)
pipeline_name = description.get(
'PipelineDescription', {}).get('Name')
if pipeline_name is None:
raise ValueError("Every valid BIDS-derivatives dataset must "
"have a PipelineDescription.Name field set "
"inside dataset_description.json.")
if pipeline_name in self.derivatives:
raise ValueError("Pipeline name '%s' has already been added "
"to this BIDSLayout. Every added pipeline "
"must have a unique name!")
# Default config and sources values
kwargs['config'] = kwargs.get('config') or ['bids', 'derivatives']
kwargs['sources'] = kwargs.get('sources') or self
self.derivatives[pipeline_name] = BIDSLayout(deriv, **kwargs)
# Consolidate all entities post-indexing. Note: no conflicts occur b/c
# multiple entries with the same name all point to the same instance.
for deriv in self.derivatives.values():
self.entities.update(deriv.entities)
|
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":",
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"(",
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Add BIDS-Derivatives datasets to tracking.
Args:
path (str, list): One or more paths to BIDS-Derivatives datasets.
Each path can point to either a derivatives/ directory
containing one more more pipeline directories, or to a single
pipeline directory (e.g., derivatives/fmriprep).
kwargs (dict): Optional keyword arguments to pass on to
BIDSLayout() when initializing each of the derivative datasets.
Note: Every derivatives directory intended for indexing MUST contain a
valid dataset_description.json file. See the BIDS-Derivatives
specification for details.
|
[
"Add",
"BIDS",
"-",
"Derivatives",
"datasets",
"to",
"tracking",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/layout.py#L352-L418
|
17,662
|
bids-standard/pybids
|
bids/layout/layout.py
|
BIDSLayout.get_file
|
def get_file(self, filename, scope='all'):
''' Returns the BIDSFile object with the specified path.
Args:
filename (str): The path of the file to retrieve. Must be either
an absolute path, or relative to the root of this BIDSLayout.
scope (str, list): Scope of the search space. If passed, only
BIDSLayouts that match the specified scope will be
searched. See BIDSLayout docstring for valid values.
Returns: A BIDSFile, or None if no match was found.
'''
filename = os.path.abspath(os.path.join(self.root, filename))
layouts = self._get_layouts_in_scope(scope)
for ly in layouts:
if filename in ly.files:
return ly.files[filename]
return None
|
python
|
def get_file(self, filename, scope='all'):
''' Returns the BIDSFile object with the specified path.
Args:
filename (str): The path of the file to retrieve. Must be either
an absolute path, or relative to the root of this BIDSLayout.
scope (str, list): Scope of the search space. If passed, only
BIDSLayouts that match the specified scope will be
searched. See BIDSLayout docstring for valid values.
Returns: A BIDSFile, or None if no match was found.
'''
filename = os.path.abspath(os.path.join(self.root, filename))
layouts = self._get_layouts_in_scope(scope)
for ly in layouts:
if filename in ly.files:
return ly.files[filename]
return None
|
[
"def",
"get_file",
"(",
"self",
",",
"filename",
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"scope",
"=",
"'all'",
")",
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":",
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Returns the BIDSFile object with the specified path.
Args:
filename (str): The path of the file to retrieve. Must be either
an absolute path, or relative to the root of this BIDSLayout.
scope (str, list): Scope of the search space. If passed, only
BIDSLayouts that match the specified scope will be
searched. See BIDSLayout docstring for valid values.
Returns: A BIDSFile, or None if no match was found.
|
[
"Returns",
"the",
"BIDSFile",
"object",
"with",
"the",
"specified",
"path",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/layout.py#L600-L617
|
17,663
|
bids-standard/pybids
|
bids/layout/layout.py
|
BIDSLayout.get_collections
|
def get_collections(self, level, types=None, variables=None, merge=False,
sampling_rate=None, skip_empty=False, **kwargs):
"""Return one or more variable Collections in the BIDS project.
Args:
level (str): The level of analysis to return variables for. Must be
one of 'run', 'session', 'subject', or 'dataset'.
types (str, list): Types of variables to retrieve. All valid values
reflect the filename stipulated in the BIDS spec for each kind of
variable. Valid values include: 'events', 'physio', 'stim',
'scans', 'participants', 'sessions', and 'regressors'.
variables (list): Optional list of variables names to return. If
None, all available variables are returned.
merge (bool): If True, variables are merged across all observations
of the current level. E.g., if level='subject', variables from
all subjects will be merged into a single collection. If False,
each observation is handled separately, and the result is
returned as a list.
sampling_rate (int, str): If level='run', the sampling rate to
pass onto the returned BIDSRunVariableCollection.
skip_empty (bool): Whether or not to skip empty Variables (i.e.,
where there are no rows/records in a file after applying any
filtering operations like dropping NaNs).
kwargs: Optional additional arguments to pass onto load_variables.
"""
from bids.variables import load_variables
index = load_variables(self, types=types, levels=level,
skip_empty=skip_empty, **kwargs)
return index.get_collections(level, variables, merge,
sampling_rate=sampling_rate)
|
python
|
def get_collections(self, level, types=None, variables=None, merge=False,
sampling_rate=None, skip_empty=False, **kwargs):
"""Return one or more variable Collections in the BIDS project.
Args:
level (str): The level of analysis to return variables for. Must be
one of 'run', 'session', 'subject', or 'dataset'.
types (str, list): Types of variables to retrieve. All valid values
reflect the filename stipulated in the BIDS spec for each kind of
variable. Valid values include: 'events', 'physio', 'stim',
'scans', 'participants', 'sessions', and 'regressors'.
variables (list): Optional list of variables names to return. If
None, all available variables are returned.
merge (bool): If True, variables are merged across all observations
of the current level. E.g., if level='subject', variables from
all subjects will be merged into a single collection. If False,
each observation is handled separately, and the result is
returned as a list.
sampling_rate (int, str): If level='run', the sampling rate to
pass onto the returned BIDSRunVariableCollection.
skip_empty (bool): Whether or not to skip empty Variables (i.e.,
where there are no rows/records in a file after applying any
filtering operations like dropping NaNs).
kwargs: Optional additional arguments to pass onto load_variables.
"""
from bids.variables import load_variables
index = load_variables(self, types=types, levels=level,
skip_empty=skip_empty, **kwargs)
return index.get_collections(level, variables, merge,
sampling_rate=sampling_rate)
|
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"sampling_rate",
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Return one or more variable Collections in the BIDS project.
Args:
level (str): The level of analysis to return variables for. Must be
one of 'run', 'session', 'subject', or 'dataset'.
types (str, list): Types of variables to retrieve. All valid values
reflect the filename stipulated in the BIDS spec for each kind of
variable. Valid values include: 'events', 'physio', 'stim',
'scans', 'participants', 'sessions', and 'regressors'.
variables (list): Optional list of variables names to return. If
None, all available variables are returned.
merge (bool): If True, variables are merged across all observations
of the current level. E.g., if level='subject', variables from
all subjects will be merged into a single collection. If False,
each observation is handled separately, and the result is
returned as a list.
sampling_rate (int, str): If level='run', the sampling rate to
pass onto the returned BIDSRunVariableCollection.
skip_empty (bool): Whether or not to skip empty Variables (i.e.,
where there are no rows/records in a file after applying any
filtering operations like dropping NaNs).
kwargs: Optional additional arguments to pass onto load_variables.
|
[
"Return",
"one",
"or",
"more",
"variable",
"Collections",
"in",
"the",
"BIDS",
"project",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/layout.py#L619-L648
|
17,664
|
bids-standard/pybids
|
bids/layout/layout.py
|
BIDSLayout.get_metadata
|
def get_metadata(self, path, include_entities=False, **kwargs):
"""Return metadata found in JSON sidecars for the specified file.
Args:
path (str): Path to the file to get metadata for.
include_entities (bool): If True, all available entities extracted
from the filename (rather than JSON sidecars) are included in
the returned metadata dictionary.
kwargs (dict): Optional keyword arguments to pass onto
get_nearest().
Returns: A dictionary of key/value pairs extracted from all of the
target file's associated JSON sidecars.
Notes:
A dictionary containing metadata extracted from all matching .json
files is returned. In cases where the same key is found in multiple
files, the values in files closer to the input filename will take
precedence, per the inheritance rules in the BIDS specification.
"""
f = self.get_file(path)
# For querying efficiency, store metadata in the MetadataIndex cache
self.metadata_index.index_file(f.path)
if include_entities:
entities = f.entities
results = entities
else:
results = {}
results.update(self.metadata_index.file_index[path])
return results
|
python
|
def get_metadata(self, path, include_entities=False, **kwargs):
"""Return metadata found in JSON sidecars for the specified file.
Args:
path (str): Path to the file to get metadata for.
include_entities (bool): If True, all available entities extracted
from the filename (rather than JSON sidecars) are included in
the returned metadata dictionary.
kwargs (dict): Optional keyword arguments to pass onto
get_nearest().
Returns: A dictionary of key/value pairs extracted from all of the
target file's associated JSON sidecars.
Notes:
A dictionary containing metadata extracted from all matching .json
files is returned. In cases where the same key is found in multiple
files, the values in files closer to the input filename will take
precedence, per the inheritance rules in the BIDS specification.
"""
f = self.get_file(path)
# For querying efficiency, store metadata in the MetadataIndex cache
self.metadata_index.index_file(f.path)
if include_entities:
entities = f.entities
results = entities
else:
results = {}
results.update(self.metadata_index.file_index[path])
return results
|
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"file_index",
"[",
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"results"
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Return metadata found in JSON sidecars for the specified file.
Args:
path (str): Path to the file to get metadata for.
include_entities (bool): If True, all available entities extracted
from the filename (rather than JSON sidecars) are included in
the returned metadata dictionary.
kwargs (dict): Optional keyword arguments to pass onto
get_nearest().
Returns: A dictionary of key/value pairs extracted from all of the
target file's associated JSON sidecars.
Notes:
A dictionary containing metadata extracted from all matching .json
files is returned. In cases where the same key is found in multiple
files, the values in files closer to the input filename will take
precedence, per the inheritance rules in the BIDS specification.
|
[
"Return",
"metadata",
"found",
"in",
"JSON",
"sidecars",
"for",
"the",
"specified",
"file",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/layout.py#L650-L684
|
17,665
|
bids-standard/pybids
|
bids/layout/layout.py
|
BIDSLayout.get_bval
|
def get_bval(self, path, **kwargs):
""" Get bval file for passed path. """
result = self.get_nearest(path, extensions='bval', suffix='dwi',
all_=True, **kwargs)
return listify(result)[0]
|
python
|
def get_bval(self, path, **kwargs):
""" Get bval file for passed path. """
result = self.get_nearest(path, extensions='bval', suffix='dwi',
all_=True, **kwargs)
return listify(result)[0]
|
[
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Get bval file for passed path.
|
[
"Get",
"bval",
"file",
"for",
"passed",
"path",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/layout.py#L794-L798
|
17,666
|
bids-standard/pybids
|
bids/layout/layout.py
|
BIDSLayout.copy_files
|
def copy_files(self, files=None, path_patterns=None, symbolic_links=True,
root=None, conflicts='fail', **kwargs):
"""
Copies one or more BIDSFiles to new locations defined by each
BIDSFile's entities and the specified path_patterns.
Args:
files (list): Optional list of BIDSFile objects to write out. If
none provided, use files from running a get() query using
remaining **kwargs.
path_patterns (str, list): Write patterns to pass to each file's
write_file method.
symbolic_links (bool): Whether to copy each file as a symbolic link
or a deep copy.
root (str): Optional root directory that all patterns are relative
to. Defaults to current working directory.
conflicts (str): Defines the desired action when the output path
already exists. Must be one of:
'fail': raises an exception
'skip' does nothing
'overwrite': overwrites the existing file
'append': adds a suffix to each file copy, starting with 1
kwargs (kwargs): Optional key word arguments to pass into a get()
query.
"""
_files = self.get(return_type='objects', **kwargs)
if files:
_files = list(set(files).intersection(_files))
for f in _files:
f.copy(path_patterns, symbolic_link=symbolic_links,
root=self.root, conflicts=conflicts)
|
python
|
def copy_files(self, files=None, path_patterns=None, symbolic_links=True,
root=None, conflicts='fail', **kwargs):
"""
Copies one or more BIDSFiles to new locations defined by each
BIDSFile's entities and the specified path_patterns.
Args:
files (list): Optional list of BIDSFile objects to write out. If
none provided, use files from running a get() query using
remaining **kwargs.
path_patterns (str, list): Write patterns to pass to each file's
write_file method.
symbolic_links (bool): Whether to copy each file as a symbolic link
or a deep copy.
root (str): Optional root directory that all patterns are relative
to. Defaults to current working directory.
conflicts (str): Defines the desired action when the output path
already exists. Must be one of:
'fail': raises an exception
'skip' does nothing
'overwrite': overwrites the existing file
'append': adds a suffix to each file copy, starting with 1
kwargs (kwargs): Optional key word arguments to pass into a get()
query.
"""
_files = self.get(return_type='objects', **kwargs)
if files:
_files = list(set(files).intersection(_files))
for f in _files:
f.copy(path_patterns, symbolic_link=symbolic_links,
root=self.root, conflicts=conflicts)
|
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Copies one or more BIDSFiles to new locations defined by each
BIDSFile's entities and the specified path_patterns.
Args:
files (list): Optional list of BIDSFile objects to write out. If
none provided, use files from running a get() query using
remaining **kwargs.
path_patterns (str, list): Write patterns to pass to each file's
write_file method.
symbolic_links (bool): Whether to copy each file as a symbolic link
or a deep copy.
root (str): Optional root directory that all patterns are relative
to. Defaults to current working directory.
conflicts (str): Defines the desired action when the output path
already exists. Must be one of:
'fail': raises an exception
'skip' does nothing
'overwrite': overwrites the existing file
'append': adds a suffix to each file copy, starting with 1
kwargs (kwargs): Optional key word arguments to pass into a get()
query.
|
[
"Copies",
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"and",
"the",
"specified",
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"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/layout.py#L950-L981
|
17,667
|
bids-standard/pybids
|
bids/layout/layout.py
|
MetadataIndex.index_file
|
def index_file(self, f, overwrite=False):
"""Index metadata for the specified file.
Args:
f (BIDSFile, str): A BIDSFile or path to an indexed file.
overwrite (bool): If True, forces reindexing of the file even if
an entry already exists.
"""
if isinstance(f, six.string_types):
f = self.layout.get_file(f)
if f.path in self.file_index and not overwrite:
return
if 'suffix' not in f.entities: # Skip files without suffixes
return
md = self._get_metadata(f.path)
for md_key, md_val in md.items():
if md_key not in self.key_index:
self.key_index[md_key] = {}
self.key_index[md_key][f.path] = md_val
self.file_index[f.path][md_key] = md_val
|
python
|
def index_file(self, f, overwrite=False):
"""Index metadata for the specified file.
Args:
f (BIDSFile, str): A BIDSFile or path to an indexed file.
overwrite (bool): If True, forces reindexing of the file even if
an entry already exists.
"""
if isinstance(f, six.string_types):
f = self.layout.get_file(f)
if f.path in self.file_index and not overwrite:
return
if 'suffix' not in f.entities: # Skip files without suffixes
return
md = self._get_metadata(f.path)
for md_key, md_val in md.items():
if md_key not in self.key_index:
self.key_index[md_key] = {}
self.key_index[md_key][f.path] = md_val
self.file_index[f.path][md_key] = md_val
|
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Index metadata for the specified file.
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f (BIDSFile, str): A BIDSFile or path to an indexed file.
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|
[
"Index",
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"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/layout.py#L1036-L1059
|
17,668
|
bids-standard/pybids
|
bids/layout/layout.py
|
MetadataIndex.search
|
def search(self, files=None, defined_fields=None, **kwargs):
"""Search files in the layout by metadata fields.
Args:
files (list): Optional list of names of files to search. If None,
all files in the layout are scanned.
defined_fields (list): Optional list of names of fields that must
be defined in the JSON sidecar in order to consider the file a
match, but which don't need to match any particular value.
kwargs: Optional keyword arguments defining search constraints;
keys are names of metadata fields, and values are the values
to match those fields against (e.g., SliceTiming=0.017) would
return all files that have a SliceTiming value of 0.071 in
metadata.
Returns: A list of filenames that match all constraints.
"""
if defined_fields is None:
defined_fields = []
all_keys = set(defined_fields) | set(kwargs.keys())
if not all_keys:
raise ValueError("At least one field to search on must be passed.")
# If no list of files is passed, use all files in layout
if files is None:
files = set(self.layout.files.keys())
# Index metadata for any previously unseen files
for f in files:
self.index_file(f)
# Get file intersection of all kwargs keys--this is fast
filesets = [set(self.key_index.get(k, [])) for k in all_keys]
matches = reduce(lambda x, y: x & y, filesets)
if files is not None:
matches &= set(files)
if not matches:
return []
def check_matches(f, key, val):
if isinstance(val, six.string_types) and '*' in val:
val = ('^%s$' % val).replace('*', ".*")
return re.search(str(self.file_index[f][key]), val) is not None
else:
return val == self.file_index[f][key]
# Serially check matches against each pattern, with early termination
for k, val in kwargs.items():
matches = list(filter(lambda x: check_matches(x, k, val), matches))
if not matches:
return []
return matches
|
python
|
def search(self, files=None, defined_fields=None, **kwargs):
"""Search files in the layout by metadata fields.
Args:
files (list): Optional list of names of files to search. If None,
all files in the layout are scanned.
defined_fields (list): Optional list of names of fields that must
be defined in the JSON sidecar in order to consider the file a
match, but which don't need to match any particular value.
kwargs: Optional keyword arguments defining search constraints;
keys are names of metadata fields, and values are the values
to match those fields against (e.g., SliceTiming=0.017) would
return all files that have a SliceTiming value of 0.071 in
metadata.
Returns: A list of filenames that match all constraints.
"""
if defined_fields is None:
defined_fields = []
all_keys = set(defined_fields) | set(kwargs.keys())
if not all_keys:
raise ValueError("At least one field to search on must be passed.")
# If no list of files is passed, use all files in layout
if files is None:
files = set(self.layout.files.keys())
# Index metadata for any previously unseen files
for f in files:
self.index_file(f)
# Get file intersection of all kwargs keys--this is fast
filesets = [set(self.key_index.get(k, [])) for k in all_keys]
matches = reduce(lambda x, y: x & y, filesets)
if files is not None:
matches &= set(files)
if not matches:
return []
def check_matches(f, key, val):
if isinstance(val, six.string_types) and '*' in val:
val = ('^%s$' % val).replace('*', ".*")
return re.search(str(self.file_index[f][key]), val) is not None
else:
return val == self.file_index[f][key]
# Serially check matches against each pattern, with early termination
for k, val in kwargs.items():
matches = list(filter(lambda x: check_matches(x, k, val), matches))
if not matches:
return []
return matches
|
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] |
Search files in the layout by metadata fields.
Args:
files (list): Optional list of names of files to search. If None,
all files in the layout are scanned.
defined_fields (list): Optional list of names of fields that must
be defined in the JSON sidecar in order to consider the file a
match, but which don't need to match any particular value.
kwargs: Optional keyword arguments defining search constraints;
keys are names of metadata fields, and values are the values
to match those fields against (e.g., SliceTiming=0.017) would
return all files that have a SliceTiming value of 0.071 in
metadata.
Returns: A list of filenames that match all constraints.
|
[
"Search",
"files",
"in",
"the",
"layout",
"by",
"metadata",
"fields",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/layout.py#L1080-L1136
|
17,669
|
bids-standard/pybids
|
bids/analysis/auto_model.py
|
auto_model
|
def auto_model(layout, scan_length=None, one_vs_rest=False):
'''Create a simple default model for each of the tasks in a BIDSLayout.
Contrasts each trial type against all other trial types and trial types
at the run level and then uses t-tests at each other level present to
aggregate these results up.
Args:
layout (BIDSLayout) A BIDSLayout instance
scan_length (Int) Scan length for loading event varibles in cases
where the scan length can not be read from the nifti.
Primarily for testing.
one_vs_rest (Bool) Set to True if you would like to autogenerate
contrasts of each trial type against everyother trialtype.
Returns:
models (list) list of model dictionaries for each task
'''
base_name = split(layout.root)[-1]
tasks = layout.entities['task'].unique()
task_models = []
for task_name in tasks:
# Populate model meta-data
model = OrderedDict()
model["Name"] = "_".join([base_name, task_name])
model["Description"] = ("Autogenerated model for the %s task from %s" %
(task_name, base_name))
model["Input"] = {"Task": task_name}
steps = []
# Make run level block
transformations = OrderedDict(Name='Factor', Input=['trial_type'])
run = OrderedDict(Level='Run', Name='Run',
Transformations=[transformations])
# Get trial types
run_nodes = load_variables(layout, task=task_name, levels=['run'],
scan_length=scan_length)
evs = []
for n in run_nodes.nodes:
evs.extend(n.variables['trial_type'].values.values)
trial_types = np.unique(evs)
trial_type_factors = ["trial_type." + tt for tt in trial_types]
# Add HRF
run['Transformations'].append(
OrderedDict(Name='Convolve', Input=trial_type_factors))
run_model = OrderedDict(X=trial_type_factors)
run["Model"] = run_model
if one_vs_rest:
# if there are multiple trial types, build contrasts
contrasts = []
for i, tt in enumerate(trial_types):
cdict = OrderedDict()
if len(trial_types) > 1:
cdict["Name"] = "run_" + tt + "_vs_others"
else:
cdict["Name"] = "run_" + tt
cdict["ConditionList"] = trial_type_factors
# Calculate weights for contrast
weights = np.ones(len(trial_types))
try:
weights[trial_types != tt] = -1.0 / (len(trial_types) - 1)
except ZeroDivisionError:
pass
cdict["Weights"] = list(weights)
cdict["Type"] = "t"
contrasts.append(cdict)
run["Contrasts"] = contrasts
steps.append(run)
if one_vs_rest:
# if there are multiple sessions, t-test run level contrasts at
# session level
sessions = layout.get_sessions()
if len(sessions) > 1:
# get contrasts names from previous block
contrast_names = [cc["Name"] for cc in steps[-1]["Contrasts"]]
steps.append(_make_passthrough_contrast("Session",
contrast_names))
subjects = layout.get_subjects()
if len(subjects) > 1:
# get contrasts names from previous block
contrast_names = [cc["Name"] for cc in steps[-1]["Contrasts"]]
steps.append(_make_passthrough_contrast("Subject",
contrast_names))
# get contrasts names from previous block
contrast_names = [cc["Name"] for cc in steps[-1]["Contrasts"]]
steps.append(_make_passthrough_contrast("Dataset",
contrast_names))
model["Steps"] = steps
task_models.append(model)
return task_models
|
python
|
def auto_model(layout, scan_length=None, one_vs_rest=False):
'''Create a simple default model for each of the tasks in a BIDSLayout.
Contrasts each trial type against all other trial types and trial types
at the run level and then uses t-tests at each other level present to
aggregate these results up.
Args:
layout (BIDSLayout) A BIDSLayout instance
scan_length (Int) Scan length for loading event varibles in cases
where the scan length can not be read from the nifti.
Primarily for testing.
one_vs_rest (Bool) Set to True if you would like to autogenerate
contrasts of each trial type against everyother trialtype.
Returns:
models (list) list of model dictionaries for each task
'''
base_name = split(layout.root)[-1]
tasks = layout.entities['task'].unique()
task_models = []
for task_name in tasks:
# Populate model meta-data
model = OrderedDict()
model["Name"] = "_".join([base_name, task_name])
model["Description"] = ("Autogenerated model for the %s task from %s" %
(task_name, base_name))
model["Input"] = {"Task": task_name}
steps = []
# Make run level block
transformations = OrderedDict(Name='Factor', Input=['trial_type'])
run = OrderedDict(Level='Run', Name='Run',
Transformations=[transformations])
# Get trial types
run_nodes = load_variables(layout, task=task_name, levels=['run'],
scan_length=scan_length)
evs = []
for n in run_nodes.nodes:
evs.extend(n.variables['trial_type'].values.values)
trial_types = np.unique(evs)
trial_type_factors = ["trial_type." + tt for tt in trial_types]
# Add HRF
run['Transformations'].append(
OrderedDict(Name='Convolve', Input=trial_type_factors))
run_model = OrderedDict(X=trial_type_factors)
run["Model"] = run_model
if one_vs_rest:
# if there are multiple trial types, build contrasts
contrasts = []
for i, tt in enumerate(trial_types):
cdict = OrderedDict()
if len(trial_types) > 1:
cdict["Name"] = "run_" + tt + "_vs_others"
else:
cdict["Name"] = "run_" + tt
cdict["ConditionList"] = trial_type_factors
# Calculate weights for contrast
weights = np.ones(len(trial_types))
try:
weights[trial_types != tt] = -1.0 / (len(trial_types) - 1)
except ZeroDivisionError:
pass
cdict["Weights"] = list(weights)
cdict["Type"] = "t"
contrasts.append(cdict)
run["Contrasts"] = contrasts
steps.append(run)
if one_vs_rest:
# if there are multiple sessions, t-test run level contrasts at
# session level
sessions = layout.get_sessions()
if len(sessions) > 1:
# get contrasts names from previous block
contrast_names = [cc["Name"] for cc in steps[-1]["Contrasts"]]
steps.append(_make_passthrough_contrast("Session",
contrast_names))
subjects = layout.get_subjects()
if len(subjects) > 1:
# get contrasts names from previous block
contrast_names = [cc["Name"] for cc in steps[-1]["Contrasts"]]
steps.append(_make_passthrough_contrast("Subject",
contrast_names))
# get contrasts names from previous block
contrast_names = [cc["Name"] for cc in steps[-1]["Contrasts"]]
steps.append(_make_passthrough_contrast("Dataset",
contrast_names))
model["Steps"] = steps
task_models.append(model)
return task_models
|
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] |
Create a simple default model for each of the tasks in a BIDSLayout.
Contrasts each trial type against all other trial types and trial types
at the run level and then uses t-tests at each other level present to
aggregate these results up.
Args:
layout (BIDSLayout) A BIDSLayout instance
scan_length (Int) Scan length for loading event varibles in cases
where the scan length can not be read from the nifti.
Primarily for testing.
one_vs_rest (Bool) Set to True if you would like to autogenerate
contrasts of each trial type against everyother trialtype.
Returns:
models (list) list of model dictionaries for each task
|
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"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/auto_model.py#L19-L122
|
17,670
|
bids-standard/pybids
|
bids/variables/variables.py
|
SimpleVariable.split
|
def split(self, grouper):
''' Split the current SparseRunVariable into multiple columns.
Args:
grouper (iterable): list to groupby, where each unique value will
be taken as the name of the resulting column.
Returns:
A list of SparseRunVariables, one per unique value in the
grouper.
'''
data = self.to_df(condition=True, entities=True)
data = data.drop('condition', axis=1)
subsets = []
for i, (name, g) in enumerate(data.groupby(grouper)):
name = '%s.%s' % (self.name, name)
col = self.__class__(name=name, data=g, source=self.source,
run_info=getattr(self, 'run_info', None))
subsets.append(col)
return subsets
|
python
|
def split(self, grouper):
''' Split the current SparseRunVariable into multiple columns.
Args:
grouper (iterable): list to groupby, where each unique value will
be taken as the name of the resulting column.
Returns:
A list of SparseRunVariables, one per unique value in the
grouper.
'''
data = self.to_df(condition=True, entities=True)
data = data.drop('condition', axis=1)
subsets = []
for i, (name, g) in enumerate(data.groupby(grouper)):
name = '%s.%s' % (self.name, name)
col = self.__class__(name=name, data=g, source=self.source,
run_info=getattr(self, 'run_info', None))
subsets.append(col)
return subsets
|
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Split the current SparseRunVariable into multiple columns.
Args:
grouper (iterable): list to groupby, where each unique value will
be taken as the name of the resulting column.
Returns:
A list of SparseRunVariables, one per unique value in the
grouper.
|
[
"Split",
"the",
"current",
"SparseRunVariable",
"into",
"multiple",
"columns",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/variables.py#L240-L260
|
17,671
|
bids-standard/pybids
|
bids/variables/variables.py
|
SimpleVariable.select_rows
|
def select_rows(self, rows):
''' Truncate internal arrays to keep only the specified rows.
Args:
rows (array): An integer or boolean array identifying the indices
of rows to keep.
'''
self.values = self.values.iloc[rows]
self.index = self.index.iloc[rows, :]
for prop in self._property_columns:
vals = getattr(self, prop)[rows]
setattr(self, prop, vals)
|
python
|
def select_rows(self, rows):
''' Truncate internal arrays to keep only the specified rows.
Args:
rows (array): An integer or boolean array identifying the indices
of rows to keep.
'''
self.values = self.values.iloc[rows]
self.index = self.index.iloc[rows, :]
for prop in self._property_columns:
vals = getattr(self, prop)[rows]
setattr(self, prop, vals)
|
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Truncate internal arrays to keep only the specified rows.
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|
[
"Truncate",
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"to",
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"only",
"the",
"specified",
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"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/variables.py#L269-L280
|
17,672
|
bids-standard/pybids
|
bids/variables/variables.py
|
DenseRunVariable.split
|
def split(self, grouper):
'''Split the current DenseRunVariable into multiple columns.
Parameters
----------
grouper : :obj:`pandas.DataFrame`
Binary DF specifying the design matrix to use for splitting. Number
of rows must match current ``DenseRunVariable``; a new ``DenseRunVariable``
will be generated for each column in the grouper.
Returns
-------
A list of DenseRunVariables, one per unique value in the grouper.
'''
values = grouper.values * self.values.values
df = pd.DataFrame(values, columns=grouper.columns)
return [DenseRunVariable(name='%s.%s' % (self.name, name),
values=df[name].values,
run_info=self.run_info,
source=self.source,
sampling_rate=self.sampling_rate)
for i, name in enumerate(df.columns)]
|
python
|
def split(self, grouper):
'''Split the current DenseRunVariable into multiple columns.
Parameters
----------
grouper : :obj:`pandas.DataFrame`
Binary DF specifying the design matrix to use for splitting. Number
of rows must match current ``DenseRunVariable``; a new ``DenseRunVariable``
will be generated for each column in the grouper.
Returns
-------
A list of DenseRunVariables, one per unique value in the grouper.
'''
values = grouper.values * self.values.values
df = pd.DataFrame(values, columns=grouper.columns)
return [DenseRunVariable(name='%s.%s' % (self.name, name),
values=df[name].values,
run_info=self.run_info,
source=self.source,
sampling_rate=self.sampling_rate)
for i, name in enumerate(df.columns)]
|
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"i",
",",
"name",
"in",
"enumerate",
"(",
"df",
".",
"columns",
")",
"]"
] |
Split the current DenseRunVariable into multiple columns.
Parameters
----------
grouper : :obj:`pandas.DataFrame`
Binary DF specifying the design matrix to use for splitting. Number
of rows must match current ``DenseRunVariable``; a new ``DenseRunVariable``
will be generated for each column in the grouper.
Returns
-------
A list of DenseRunVariables, one per unique value in the grouper.
|
[
"Split",
"the",
"current",
"DenseRunVariable",
"into",
"multiple",
"columns",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/variables.py#L393-L414
|
17,673
|
bids-standard/pybids
|
bids/variables/variables.py
|
DenseRunVariable._build_entity_index
|
def _build_entity_index(self, run_info, sampling_rate):
''' Build the entity index from run information. '''
index = []
interval = int(round(1000. / sampling_rate))
_timestamps = []
for run in run_info:
reps = int(math.ceil(run.duration * sampling_rate))
ent_vals = list(run.entities.values())
df = pd.DataFrame([ent_vals] * reps, columns=list(run.entities.keys()))
ts = pd.date_range(0, periods=len(df), freq='%sms' % interval)
_timestamps.append(ts.to_series())
index.append(df)
self.timestamps = pd.concat(_timestamps, axis=0, sort=True)
return pd.concat(index, axis=0, sort=True).reset_index(drop=True)
|
python
|
def _build_entity_index(self, run_info, sampling_rate):
''' Build the entity index from run information. '''
index = []
interval = int(round(1000. / sampling_rate))
_timestamps = []
for run in run_info:
reps = int(math.ceil(run.duration * sampling_rate))
ent_vals = list(run.entities.values())
df = pd.DataFrame([ent_vals] * reps, columns=list(run.entities.keys()))
ts = pd.date_range(0, periods=len(df), freq='%sms' % interval)
_timestamps.append(ts.to_series())
index.append(df)
self.timestamps = pd.concat(_timestamps, axis=0, sort=True)
return pd.concat(index, axis=0, sort=True).reset_index(drop=True)
|
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Build the entity index from run information.
|
[
"Build",
"the",
"entity",
"index",
"from",
"run",
"information",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/variables.py#L416-L430
|
17,674
|
bids-standard/pybids
|
bids/variables/variables.py
|
DenseRunVariable.resample
|
def resample(self, sampling_rate, inplace=False, kind='linear'):
'''Resample the Variable to the specified sampling rate.
Parameters
----------
sampling_rate : :obj:`int`, :obj:`float`
Target sampling rate (in Hz).
inplace : :obj:`bool`, optional
If True, performs resampling in-place. If False, returns a resampled
copy of the current Variable. Default is False.
kind : {'linear', 'nearest', 'zero', 'slinear', 'quadratic', 'cubic'}
Argument to pass to :obj:`scipy.interpolate.interp1d`; indicates
the kind of interpolation approach to use. See interp1d docs for
valid values. Default is 'linear'.
'''
if not inplace:
var = self.clone()
var.resample(sampling_rate, True, kind)
return var
if sampling_rate == self.sampling_rate:
return
old_sr = self.sampling_rate
n = len(self.index)
self.index = self._build_entity_index(self.run_info, sampling_rate)
x = np.arange(n)
num = len(self.index)
from scipy.interpolate import interp1d
f = interp1d(x, self.values.values.ravel(), kind=kind)
x_new = np.linspace(0, n - 1, num=num)
self.values = pd.DataFrame(f(x_new))
assert len(self.values) == len(self.index)
self.sampling_rate = sampling_rate
|
python
|
def resample(self, sampling_rate, inplace=False, kind='linear'):
'''Resample the Variable to the specified sampling rate.
Parameters
----------
sampling_rate : :obj:`int`, :obj:`float`
Target sampling rate (in Hz).
inplace : :obj:`bool`, optional
If True, performs resampling in-place. If False, returns a resampled
copy of the current Variable. Default is False.
kind : {'linear', 'nearest', 'zero', 'slinear', 'quadratic', 'cubic'}
Argument to pass to :obj:`scipy.interpolate.interp1d`; indicates
the kind of interpolation approach to use. See interp1d docs for
valid values. Default is 'linear'.
'''
if not inplace:
var = self.clone()
var.resample(sampling_rate, True, kind)
return var
if sampling_rate == self.sampling_rate:
return
old_sr = self.sampling_rate
n = len(self.index)
self.index = self._build_entity_index(self.run_info, sampling_rate)
x = np.arange(n)
num = len(self.index)
from scipy.interpolate import interp1d
f = interp1d(x, self.values.values.ravel(), kind=kind)
x_new = np.linspace(0, n - 1, num=num)
self.values = pd.DataFrame(f(x_new))
assert len(self.values) == len(self.index)
self.sampling_rate = sampling_rate
|
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"(",
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")",
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"sampling_rate",
"=",
"sampling_rate"
] |
Resample the Variable to the specified sampling rate.
Parameters
----------
sampling_rate : :obj:`int`, :obj:`float`
Target sampling rate (in Hz).
inplace : :obj:`bool`, optional
If True, performs resampling in-place. If False, returns a resampled
copy of the current Variable. Default is False.
kind : {'linear', 'nearest', 'zero', 'slinear', 'quadratic', 'cubic'}
Argument to pass to :obj:`scipy.interpolate.interp1d`; indicates
the kind of interpolation approach to use. See interp1d docs for
valid values. Default is 'linear'.
|
[
"Resample",
"the",
"Variable",
"to",
"the",
"specified",
"sampling",
"rate",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/variables.py#L432-L469
|
17,675
|
bids-standard/pybids
|
bids/variables/variables.py
|
DenseRunVariable.to_df
|
def to_df(self, condition=True, entities=True, timing=True, sampling_rate=None):
'''Convert to a DataFrame, with columns for name and entities.
Parameters
----------
condition : :obj:`bool`
If True, adds a column for condition name, and names the amplitude
column 'amplitude'. If False, returns just onset, duration, and
amplitude, and gives the amplitude column the current column name.
entities : :obj:`bool`
If True, adds extra columns for all entities.
timing : :obj:`bool`
If True, includes onset and duration columns (even though events are
sampled uniformly). If False, omits them.
'''
if sampling_rate not in (None, self.sampling_rate):
return self.resample(sampling_rate).to_df(condition, entities)
df = super(DenseRunVariable, self).to_df(condition, entities)
if timing:
df['onset'] = self.timestamps.values.astype(float) / 1e+9
df['duration'] = 1. / self.sampling_rate
return df
|
python
|
def to_df(self, condition=True, entities=True, timing=True, sampling_rate=None):
'''Convert to a DataFrame, with columns for name and entities.
Parameters
----------
condition : :obj:`bool`
If True, adds a column for condition name, and names the amplitude
column 'amplitude'. If False, returns just onset, duration, and
amplitude, and gives the amplitude column the current column name.
entities : :obj:`bool`
If True, adds extra columns for all entities.
timing : :obj:`bool`
If True, includes onset and duration columns (even though events are
sampled uniformly). If False, omits them.
'''
if sampling_rate not in (None, self.sampling_rate):
return self.resample(sampling_rate).to_df(condition, entities)
df = super(DenseRunVariable, self).to_df(condition, entities)
if timing:
df['onset'] = self.timestamps.values.astype(float) / 1e+9
df['duration'] = 1. / self.sampling_rate
return df
|
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"]",
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"/",
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] |
Convert to a DataFrame, with columns for name and entities.
Parameters
----------
condition : :obj:`bool`
If True, adds a column for condition name, and names the amplitude
column 'amplitude'. If False, returns just onset, duration, and
amplitude, and gives the amplitude column the current column name.
entities : :obj:`bool`
If True, adds extra columns for all entities.
timing : :obj:`bool`
If True, includes onset and duration columns (even though events are
sampled uniformly). If False, omits them.
|
[
"Convert",
"to",
"a",
"DataFrame",
"with",
"columns",
"for",
"name",
"and",
"entities",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/variables.py#L471-L495
|
17,676
|
bids-standard/pybids
|
bids/variables/entities.py
|
NodeIndex.get_collections
|
def get_collections(self, unit, names=None, merge=False,
sampling_rate=None, **entities):
''' Retrieve variable data for a specified level in the Dataset.
Args:
unit (str): The unit of analysis to return variables for. Must be
one of 'run', 'session', 'subject', or 'dataset'.
names (list): Optional list of variables names to return. If
None, all available variables are returned.
merge (bool): If True, variables are merged across all observations
of the current unit. E.g., if unit='subject' and return_type=
'collection', variablesfrom all subjects will be merged into a
single collection. If False, each observation is handled
separately, and the result is returned as a list.
sampling_rate (int, str): If unit='run', the sampling rate to
pass onto the returned BIDSRunVariableCollection.
entities: Optional constraints used to limit what gets returned.
Returns:
'''
nodes = self.get_nodes(unit, entities)
var_sets = []
for n in nodes:
var_set = list(n.variables.values())
var_set = [v for v in var_set if v.matches_entities(entities)]
if names is not None:
var_set = [v for v in var_set if v.name in names]
# Additional filtering on Variables past run level, because their
# contents are extracted from TSV files containing rows from
# multiple observations
if unit != 'run':
var_set = [v.filter(entities) for v in var_set]
var_sets.append(var_set)
if merge:
var_sets = [list(chain(*var_sets))]
results = []
for vs in var_sets:
if not vs:
continue
if unit == 'run':
vs = clc.BIDSRunVariableCollection(vs, sampling_rate)
else:
vs = clc.BIDSVariableCollection(vs)
results.append(vs)
if merge:
return results[0] if results else None
return results
|
python
|
def get_collections(self, unit, names=None, merge=False,
sampling_rate=None, **entities):
''' Retrieve variable data for a specified level in the Dataset.
Args:
unit (str): The unit of analysis to return variables for. Must be
one of 'run', 'session', 'subject', or 'dataset'.
names (list): Optional list of variables names to return. If
None, all available variables are returned.
merge (bool): If True, variables are merged across all observations
of the current unit. E.g., if unit='subject' and return_type=
'collection', variablesfrom all subjects will be merged into a
single collection. If False, each observation is handled
separately, and the result is returned as a list.
sampling_rate (int, str): If unit='run', the sampling rate to
pass onto the returned BIDSRunVariableCollection.
entities: Optional constraints used to limit what gets returned.
Returns:
'''
nodes = self.get_nodes(unit, entities)
var_sets = []
for n in nodes:
var_set = list(n.variables.values())
var_set = [v for v in var_set if v.matches_entities(entities)]
if names is not None:
var_set = [v for v in var_set if v.name in names]
# Additional filtering on Variables past run level, because their
# contents are extracted from TSV files containing rows from
# multiple observations
if unit != 'run':
var_set = [v.filter(entities) for v in var_set]
var_sets.append(var_set)
if merge:
var_sets = [list(chain(*var_sets))]
results = []
for vs in var_sets:
if not vs:
continue
if unit == 'run':
vs = clc.BIDSRunVariableCollection(vs, sampling_rate)
else:
vs = clc.BIDSVariableCollection(vs)
results.append(vs)
if merge:
return results[0] if results else None
return results
|
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"[",
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Retrieve variable data for a specified level in the Dataset.
Args:
unit (str): The unit of analysis to return variables for. Must be
one of 'run', 'session', 'subject', or 'dataset'.
names (list): Optional list of variables names to return. If
None, all available variables are returned.
merge (bool): If True, variables are merged across all observations
of the current unit. E.g., if unit='subject' and return_type=
'collection', variablesfrom all subjects will be merged into a
single collection. If False, each observation is handled
separately, and the result is returned as a list.
sampling_rate (int, str): If unit='run', the sampling rate to
pass onto the returned BIDSRunVariableCollection.
entities: Optional constraints used to limit what gets returned.
Returns:
|
[
"Retrieve",
"variable",
"data",
"for",
"a",
"specified",
"level",
"in",
"the",
"Dataset",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/entities.py#L65-L118
|
17,677
|
bids-standard/pybids
|
bids/variables/entities.py
|
NodeIndex.get_or_create_node
|
def get_or_create_node(self, level, entities, *args, **kwargs):
''' Retrieves a child Node based on the specified criteria, creating a
new Node if necessary.
Args:
entities (dict): Dictionary of entities specifying which Node to
return.
args, kwargs: Optional positional or named arguments to pass onto
class-specific initializers. These arguments are only used if
a Node that matches the passed entities doesn't already exist,
and a new one must be created.
Returns:
A Node instance.
'''
result = self.get_nodes(level, entities)
if result:
if len(result) > 1:
raise ValueError("More than one matching Node found! If you're"
" expecting more than one Node, use "
"get_nodes() instead of get_or_create_node()."
)
return result[0]
# Create Node
if level == 'run':
node = RunNode(entities, *args, **kwargs)
else:
node = Node(level, entities)
entities = dict(entities, node_index=len(self.nodes), level=level)
self.nodes.append(node)
node_row = pd.Series(entities)
self.index = self.index.append(node_row, ignore_index=True)
return node
|
python
|
def get_or_create_node(self, level, entities, *args, **kwargs):
''' Retrieves a child Node based on the specified criteria, creating a
new Node if necessary.
Args:
entities (dict): Dictionary of entities specifying which Node to
return.
args, kwargs: Optional positional or named arguments to pass onto
class-specific initializers. These arguments are only used if
a Node that matches the passed entities doesn't already exist,
and a new one must be created.
Returns:
A Node instance.
'''
result = self.get_nodes(level, entities)
if result:
if len(result) > 1:
raise ValueError("More than one matching Node found! If you're"
" expecting more than one Node, use "
"get_nodes() instead of get_or_create_node()."
)
return result[0]
# Create Node
if level == 'run':
node = RunNode(entities, *args, **kwargs)
else:
node = Node(level, entities)
entities = dict(entities, node_index=len(self.nodes), level=level)
self.nodes.append(node)
node_row = pd.Series(entities)
self.index = self.index.append(node_row, ignore_index=True)
return node
|
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entities (dict): Dictionary of entities specifying which Node to
return.
args, kwargs: Optional positional or named arguments to pass onto
class-specific initializers. These arguments are only used if
a Node that matches the passed entities doesn't already exist,
and a new one must be created.
Returns:
A Node instance.
|
[
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"Node",
"if",
"necessary",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/entities.py#L160-L198
|
17,678
|
bids-standard/pybids
|
bids/variables/kollekshuns.py
|
merge_collections
|
def merge_collections(collections, force_dense=False, sampling_rate='auto'):
''' Merge two or more collections at the same level of analysis.
Args:
collections (list): List of Collections to merge.
sampling_rate (int, str): Sampling rate to use if it becomes necessary
to resample DenseRunVariables. Either an integer or 'auto' (see
merge_variables docstring for further explanation).
Returns:
A BIDSVariableCollection or BIDSRunVariableCollection, depending
on the type of the input collections.
'''
if len(listify(collections)) == 1:
return collections
levels = set([c.level for c in collections])
if len(levels) > 1:
raise ValueError("At the moment, it's only possible to merge "
"Collections at the same level of analysis. You "
"passed collections at levels: %s." % levels)
variables = list(chain(*[c.variables.values() for c in collections]))
cls = collections[0].__class__
variables = cls.merge_variables(variables, sampling_rate=sampling_rate)
if isinstance(collections[0], BIDSRunVariableCollection):
if sampling_rate == 'auto':
rates = [var.sampling_rate for var in variables
if isinstance(var, DenseRunVariable)]
sampling_rate = rates[0] if rates else None
return cls(variables, sampling_rate)
return cls(variables)
|
python
|
def merge_collections(collections, force_dense=False, sampling_rate='auto'):
''' Merge two or more collections at the same level of analysis.
Args:
collections (list): List of Collections to merge.
sampling_rate (int, str): Sampling rate to use if it becomes necessary
to resample DenseRunVariables. Either an integer or 'auto' (see
merge_variables docstring for further explanation).
Returns:
A BIDSVariableCollection or BIDSRunVariableCollection, depending
on the type of the input collections.
'''
if len(listify(collections)) == 1:
return collections
levels = set([c.level for c in collections])
if len(levels) > 1:
raise ValueError("At the moment, it's only possible to merge "
"Collections at the same level of analysis. You "
"passed collections at levels: %s." % levels)
variables = list(chain(*[c.variables.values() for c in collections]))
cls = collections[0].__class__
variables = cls.merge_variables(variables, sampling_rate=sampling_rate)
if isinstance(collections[0], BIDSRunVariableCollection):
if sampling_rate == 'auto':
rates = [var.sampling_rate for var in variables
if isinstance(var, DenseRunVariable)]
sampling_rate = rates[0] if rates else None
return cls(variables, sampling_rate)
return cls(variables)
|
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Merge two or more collections at the same level of analysis.
Args:
collections (list): List of Collections to merge.
sampling_rate (int, str): Sampling rate to use if it becomes necessary
to resample DenseRunVariables. Either an integer or 'auto' (see
merge_variables docstring for further explanation).
Returns:
A BIDSVariableCollection or BIDSRunVariableCollection, depending
on the type of the input collections.
|
[
"Merge",
"two",
"or",
"more",
"collections",
"at",
"the",
"same",
"level",
"of",
"analysis",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/kollekshuns.py#L354-L390
|
17,679
|
bids-standard/pybids
|
bids/variables/kollekshuns.py
|
BIDSVariableCollection.merge_variables
|
def merge_variables(variables, **kwargs):
''' Concatenates Variables along row axis.
Args:
variables (list): List of Variables to merge. Variables can have
different names (and all Variables that share a name will be
concatenated together).
Returns:
A list of Variables.
'''
var_dict = OrderedDict()
for v in variables:
if v.name not in var_dict:
var_dict[v.name] = []
var_dict[v.name].append(v)
return [merge_variables(vars_, **kwargs)
for vars_ in list(var_dict.values())]
|
python
|
def merge_variables(variables, **kwargs):
''' Concatenates Variables along row axis.
Args:
variables (list): List of Variables to merge. Variables can have
different names (and all Variables that share a name will be
concatenated together).
Returns:
A list of Variables.
'''
var_dict = OrderedDict()
for v in variables:
if v.name not in var_dict:
var_dict[v.name] = []
var_dict[v.name].append(v)
return [merge_variables(vars_, **kwargs)
for vars_ in list(var_dict.values())]
|
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"in",
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"(",
"var_dict",
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] |
Concatenates Variables along row axis.
Args:
variables (list): List of Variables to merge. Variables can have
different names (and all Variables that share a name will be
concatenated together).
Returns:
A list of Variables.
|
[
"Concatenates",
"Variables",
"along",
"row",
"axis",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/kollekshuns.py#L69-L86
|
17,680
|
bids-standard/pybids
|
bids/variables/kollekshuns.py
|
BIDSVariableCollection.to_df
|
def to_df(self, variables=None, format='wide', fillna=np.nan, **kwargs):
''' Merge variables into a single pandas DataFrame.
Args:
variables (list): Optional list of column names to retain; if None,
all variables are returned.
format (str): Whether to return a DataFrame in 'wide' or 'long'
format. In 'wide' format, each row is defined by a unique
onset/duration, and each variable is in a separate column. In
'long' format, each row is a unique combination of onset,
duration, and variable name, and a single 'amplitude' column
provides the value.
fillna: Replace missing values with the specified value.
kwargs: Optional keyword arguments to pass onto each Variable's
to_df() call (e.g., condition, entities, and timing).
Returns: A pandas DataFrame.
'''
if variables is None:
variables = list(self.variables.keys())
# Can receive already-selected Variables from sub-classes
if not isinstance(variables[0], BIDSVariable):
variables = [v for v in self.variables.values()
if v.name in variables]
dfs = [v.to_df(**kwargs) for v in variables]
df = pd.concat(dfs, axis=0, sort=True)
if format == 'long':
return df.reset_index(drop=True).fillna(fillna)
ind_cols = list(set(df.columns) - {'condition', 'amplitude'})
df['amplitude'] = df['amplitude'].fillna('n/a')
df = df.pivot_table(index=ind_cols, columns='condition',
values='amplitude', aggfunc='first')
df = df.reset_index().replace('n/a', fillna)
df.columns.name = None
return df
|
python
|
def to_df(self, variables=None, format='wide', fillna=np.nan, **kwargs):
''' Merge variables into a single pandas DataFrame.
Args:
variables (list): Optional list of column names to retain; if None,
all variables are returned.
format (str): Whether to return a DataFrame in 'wide' or 'long'
format. In 'wide' format, each row is defined by a unique
onset/duration, and each variable is in a separate column. In
'long' format, each row is a unique combination of onset,
duration, and variable name, and a single 'amplitude' column
provides the value.
fillna: Replace missing values with the specified value.
kwargs: Optional keyword arguments to pass onto each Variable's
to_df() call (e.g., condition, entities, and timing).
Returns: A pandas DataFrame.
'''
if variables is None:
variables = list(self.variables.keys())
# Can receive already-selected Variables from sub-classes
if not isinstance(variables[0], BIDSVariable):
variables = [v for v in self.variables.values()
if v.name in variables]
dfs = [v.to_df(**kwargs) for v in variables]
df = pd.concat(dfs, axis=0, sort=True)
if format == 'long':
return df.reset_index(drop=True).fillna(fillna)
ind_cols = list(set(df.columns) - {'condition', 'amplitude'})
df['amplitude'] = df['amplitude'].fillna('n/a')
df = df.pivot_table(index=ind_cols, columns='condition',
values='amplitude', aggfunc='first')
df = df.reset_index().replace('n/a', fillna)
df.columns.name = None
return df
|
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format (str): Whether to return a DataFrame in 'wide' or 'long'
format. In 'wide' format, each row is defined by a unique
onset/duration, and each variable is in a separate column. In
'long' format, each row is a unique combination of onset,
duration, and variable name, and a single 'amplitude' column
provides the value.
fillna: Replace missing values with the specified value.
kwargs: Optional keyword arguments to pass onto each Variable's
to_df() call (e.g., condition, entities, and timing).
Returns: A pandas DataFrame.
|
[
"Merge",
"variables",
"into",
"a",
"single",
"pandas",
"DataFrame",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/kollekshuns.py#L88-L128
|
17,681
|
bids-standard/pybids
|
bids/variables/kollekshuns.py
|
BIDSVariableCollection.from_df
|
def from_df(cls, data, entities=None, source='contrast'):
''' Create a Collection from a pandas DataFrame.
Args:
df (DataFrame): The DataFrame to convert to a Collection. Each
column will be converted to a SimpleVariable.
entities (DataFrame): An optional second DataFrame containing
entity information.
source (str): The value to set as the source for all Variables.
Returns:
A BIDSVariableCollection.
'''
variables = []
for col in data.columns:
_data = pd.DataFrame(data[col].values, columns=['amplitude'])
if entities is not None:
_data = pd.concat([_data, entities], axis=1, sort=True)
variables.append(SimpleVariable(name=col, data=_data, source=source))
return BIDSVariableCollection(variables)
|
python
|
def from_df(cls, data, entities=None, source='contrast'):
''' Create a Collection from a pandas DataFrame.
Args:
df (DataFrame): The DataFrame to convert to a Collection. Each
column will be converted to a SimpleVariable.
entities (DataFrame): An optional second DataFrame containing
entity information.
source (str): The value to set as the source for all Variables.
Returns:
A BIDSVariableCollection.
'''
variables = []
for col in data.columns:
_data = pd.DataFrame(data[col].values, columns=['amplitude'])
if entities is not None:
_data = pd.concat([_data, entities], axis=1, sort=True)
variables.append(SimpleVariable(name=col, data=_data, source=source))
return BIDSVariableCollection(variables)
|
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Create a Collection from a pandas DataFrame.
Args:
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column will be converted to a SimpleVariable.
entities (DataFrame): An optional second DataFrame containing
entity information.
source (str): The value to set as the source for all Variables.
Returns:
A BIDSVariableCollection.
|
[
"Create",
"a",
"Collection",
"from",
"a",
"pandas",
"DataFrame",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/kollekshuns.py#L131-L150
|
17,682
|
bids-standard/pybids
|
bids/variables/kollekshuns.py
|
BIDSVariableCollection.clone
|
def clone(self):
''' Returns a shallow copy of the current instance, except that all
variables are deep-cloned.
'''
clone = copy(self)
clone.variables = {k: v.clone() for (k, v) in self.variables.items()}
return clone
|
python
|
def clone(self):
''' Returns a shallow copy of the current instance, except that all
variables are deep-cloned.
'''
clone = copy(self)
clone.variables = {k: v.clone() for (k, v) in self.variables.items()}
return clone
|
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"def",
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"copy",
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"in",
"self",
".",
"variables",
".",
"items",
"(",
")",
"}",
"return",
"clone"
] |
Returns a shallow copy of the current instance, except that all
variables are deep-cloned.
|
[
"Returns",
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"of",
"the",
"current",
"instance",
"except",
"that",
"all",
"variables",
"are",
"deep",
"-",
"cloned",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/kollekshuns.py#L152-L158
|
17,683
|
bids-standard/pybids
|
bids/variables/kollekshuns.py
|
BIDSVariableCollection._index_entities
|
def _index_entities(self):
''' Sets current instance's entities based on the existing index.
Note: Only entity key/value pairs common to all rows in all contained
Variables are returned. E.g., if a Collection contains Variables
extracted from runs 1, 2 and 3 from subject '01', the returned dict
will be {'subject': '01'}; the runs will be excluded as they vary
across the Collection contents.
'''
all_ents = pd.DataFrame.from_records(
[v.entities for v in self.variables.values()])
constant = all_ents.apply(lambda x: x.nunique() == 1)
if constant.empty:
self.entities = {}
else:
keep = all_ents.columns[constant]
ents = {k: all_ents[k].dropna().iloc[0] for k in keep}
self.entities = {k: v for k, v in ents.items() if pd.notnull(v)}
|
python
|
def _index_entities(self):
''' Sets current instance's entities based on the existing index.
Note: Only entity key/value pairs common to all rows in all contained
Variables are returned. E.g., if a Collection contains Variables
extracted from runs 1, 2 and 3 from subject '01', the returned dict
will be {'subject': '01'}; the runs will be excluded as they vary
across the Collection contents.
'''
all_ents = pd.DataFrame.from_records(
[v.entities for v in self.variables.values()])
constant = all_ents.apply(lambda x: x.nunique() == 1)
if constant.empty:
self.entities = {}
else:
keep = all_ents.columns[constant]
ents = {k: all_ents[k].dropna().iloc[0] for k in keep}
self.entities = {k: v for k, v in ents.items() if pd.notnull(v)}
|
[
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"(",
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"(",
"v",
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"}"
] |
Sets current instance's entities based on the existing index.
Note: Only entity key/value pairs common to all rows in all contained
Variables are returned. E.g., if a Collection contains Variables
extracted from runs 1, 2 and 3 from subject '01', the returned dict
will be {'subject': '01'}; the runs will be excluded as they vary
across the Collection contents.
|
[
"Sets",
"current",
"instance",
"s",
"entities",
"based",
"on",
"the",
"existing",
"index",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/kollekshuns.py#L164-L181
|
17,684
|
bids-standard/pybids
|
bids/variables/kollekshuns.py
|
BIDSVariableCollection.match_variables
|
def match_variables(self, pattern, return_type='name'):
''' Return columns whose names match the provided regex pattern.
Args:
pattern (str): A regex pattern to match all variable names against.
return_type (str): What to return. Must be one of:
'name': Returns a list of names of matching variables.
'variable': Returns a list of Variable objects whose names
match.
'''
pattern = re.compile(pattern)
vars_ = [v for v in self.variables.values() if pattern.search(v.name)]
return vars_ if return_type.startswith('var') \
else [v.name for v in vars_]
|
python
|
def match_variables(self, pattern, return_type='name'):
''' Return columns whose names match the provided regex pattern.
Args:
pattern (str): A regex pattern to match all variable names against.
return_type (str): What to return. Must be one of:
'name': Returns a list of names of matching variables.
'variable': Returns a list of Variable objects whose names
match.
'''
pattern = re.compile(pattern)
vars_ = [v for v in self.variables.values() if pattern.search(v.name)]
return vars_ if return_type.startswith('var') \
else [v.name for v in vars_]
|
[
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"'var'",
")",
"else",
"[",
"v",
".",
"name",
"for",
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"vars_",
"]"
] |
Return columns whose names match the provided regex pattern.
Args:
pattern (str): A regex pattern to match all variable names against.
return_type (str): What to return. Must be one of:
'name': Returns a list of names of matching variables.
'variable': Returns a list of Variable objects whose names
match.
|
[
"Return",
"columns",
"whose",
"names",
"match",
"the",
"provided",
"regex",
"pattern",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/kollekshuns.py#L196-L209
|
17,685
|
bids-standard/pybids
|
bids/variables/kollekshuns.py
|
BIDSRunVariableCollection.to_df
|
def to_df(self, variables=None, format='wide', sparse=True,
sampling_rate=None, include_sparse=True, include_dense=True,
**kwargs):
''' Merge columns into a single pandas DataFrame.
Args:
variables (list): Optional list of variable names to retain;
if None, all variables are written out.
format (str): Whether to return a DataFrame in 'wide' or 'long'
format. In 'wide' format, each row is defined by a unique
onset/duration, and each variable is in a separate column. In
'long' format, each row is a unique combination of onset,
duration, and variable name, and a single 'amplitude' column
provides the value.
sparse (bool): If True, variables will be kept in a sparse
format provided they are all internally represented as such.
If False, a dense matrix (i.e., uniform sampling rate for all
events) will be exported. Will be ignored if at least one
variable is dense.
sampling_rate (float): If a dense matrix is written out, the
sampling rate (in Hz) to use for downsampling. Defaults to the
value currently set in the instance.
kwargs: Optional keyword arguments to pass onto each Variable's
to_df() call (e.g., condition, entities, and timing).
include_sparse (bool): Whether or not to include sparse Variables.
include_dense (bool): Whether or not to include dense Variables.
Returns: A pandas DataFrame.
'''
if not include_sparse and not include_dense:
raise ValueError("You can't exclude both dense and sparse "
"variables! That leaves nothing!")
if variables is None:
variables = list(self.variables.keys())
if not include_sparse:
variables = [v for v in variables if
isinstance(self.variables[v], DenseRunVariable)]
if not include_dense:
variables = [v for v in variables if not
isinstance(self.variables[v], DenseRunVariable)]
if not variables:
return None
_vars = [self.variables[v] for v in variables]
if sparse and all(isinstance(v, SimpleVariable) for v in _vars):
variables = _vars
else:
sampling_rate = sampling_rate or self.sampling_rate
# Make sure all variables have the same sampling rate
variables = list(self.resample(sampling_rate, variables,
force_dense=True,
in_place=False).values())
return super(BIDSRunVariableCollection, self).to_df(variables, format,
**kwargs)
|
python
|
def to_df(self, variables=None, format='wide', sparse=True,
sampling_rate=None, include_sparse=True, include_dense=True,
**kwargs):
''' Merge columns into a single pandas DataFrame.
Args:
variables (list): Optional list of variable names to retain;
if None, all variables are written out.
format (str): Whether to return a DataFrame in 'wide' or 'long'
format. In 'wide' format, each row is defined by a unique
onset/duration, and each variable is in a separate column. In
'long' format, each row is a unique combination of onset,
duration, and variable name, and a single 'amplitude' column
provides the value.
sparse (bool): If True, variables will be kept in a sparse
format provided they are all internally represented as such.
If False, a dense matrix (i.e., uniform sampling rate for all
events) will be exported. Will be ignored if at least one
variable is dense.
sampling_rate (float): If a dense matrix is written out, the
sampling rate (in Hz) to use for downsampling. Defaults to the
value currently set in the instance.
kwargs: Optional keyword arguments to pass onto each Variable's
to_df() call (e.g., condition, entities, and timing).
include_sparse (bool): Whether or not to include sparse Variables.
include_dense (bool): Whether or not to include dense Variables.
Returns: A pandas DataFrame.
'''
if not include_sparse and not include_dense:
raise ValueError("You can't exclude both dense and sparse "
"variables! That leaves nothing!")
if variables is None:
variables = list(self.variables.keys())
if not include_sparse:
variables = [v for v in variables if
isinstance(self.variables[v], DenseRunVariable)]
if not include_dense:
variables = [v for v in variables if not
isinstance(self.variables[v], DenseRunVariable)]
if not variables:
return None
_vars = [self.variables[v] for v in variables]
if sparse and all(isinstance(v, SimpleVariable) for v in _vars):
variables = _vars
else:
sampling_rate = sampling_rate or self.sampling_rate
# Make sure all variables have the same sampling rate
variables = list(self.resample(sampling_rate, variables,
force_dense=True,
in_place=False).values())
return super(BIDSRunVariableCollection, self).to_df(variables, format,
**kwargs)
|
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Merge columns into a single pandas DataFrame.
Args:
variables (list): Optional list of variable names to retain;
if None, all variables are written out.
format (str): Whether to return a DataFrame in 'wide' or 'long'
format. In 'wide' format, each row is defined by a unique
onset/duration, and each variable is in a separate column. In
'long' format, each row is a unique combination of onset,
duration, and variable name, and a single 'amplitude' column
provides the value.
sparse (bool): If True, variables will be kept in a sparse
format provided they are all internally represented as such.
If False, a dense matrix (i.e., uniform sampling rate for all
events) will be exported. Will be ignored if at least one
variable is dense.
sampling_rate (float): If a dense matrix is written out, the
sampling rate (in Hz) to use for downsampling. Defaults to the
value currently set in the instance.
kwargs: Optional keyword arguments to pass onto each Variable's
to_df() call (e.g., condition, entities, and timing).
include_sparse (bool): Whether or not to include sparse Variables.
include_dense (bool): Whether or not to include dense Variables.
Returns: A pandas DataFrame.
|
[
"Merge",
"columns",
"into",
"a",
"single",
"pandas",
"DataFrame",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/variables/kollekshuns.py#L290-L351
|
17,686
|
bids-standard/pybids
|
bids/analysis/transformations/munge.py
|
Rename._transform
|
def _transform(self, var):
''' Rename happens automatically in the base class, so all we need to
do is unset the original variable in the collection. '''
self.collection.variables.pop(var.name)
return var.values
|
python
|
def _transform(self, var):
''' Rename happens automatically in the base class, so all we need to
do is unset the original variable in the collection. '''
self.collection.variables.pop(var.name)
return var.values
|
[
"def",
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] |
Rename happens automatically in the base class, so all we need to
do is unset the original variable in the collection.
|
[
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"in",
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"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/transformations/munge.py#L215-L219
|
17,687
|
bids-standard/pybids
|
bids/layout/writing.py
|
replace_entities
|
def replace_entities(entities, pattern):
"""
Replaces all entity names in a given pattern with the corresponding
values provided by entities.
Args:
entities (dict): A dictionary mapping entity names to entity values.
pattern (str): A path pattern that contains entity names denoted
by curly braces. Optional portions denoted by square braces.
For example: 'sub-{subject}/[var-{name}/]{id}.csv'
Accepted entity values, using regex matching, denoted within angle
brackets.
For example: 'sub-{subject<01|02>}/{task}.csv'
Returns:
A new string with the entity values inserted where entity names
were denoted in the provided pattern.
"""
ents = re.findall(r'\{(.*?)\}', pattern)
new_path = pattern
for ent in ents:
match = re.search(r'([^|<]+)(<.*?>)?(\|.*)?', ent)
if match is None:
return None
name, valid, default = match.groups()
default = default[1:] if default is not None else default
if name in entities and valid is not None:
ent_val = str(entities[name])
if not re.match(valid[1:-1], ent_val):
if default is None:
return None
entities[name] = default
ent_val = entities.get(name, default)
if ent_val is None:
return None
new_path = new_path.replace('{%s}' % ent, str(ent_val))
return new_path
|
python
|
def replace_entities(entities, pattern):
"""
Replaces all entity names in a given pattern with the corresponding
values provided by entities.
Args:
entities (dict): A dictionary mapping entity names to entity values.
pattern (str): A path pattern that contains entity names denoted
by curly braces. Optional portions denoted by square braces.
For example: 'sub-{subject}/[var-{name}/]{id}.csv'
Accepted entity values, using regex matching, denoted within angle
brackets.
For example: 'sub-{subject<01|02>}/{task}.csv'
Returns:
A new string with the entity values inserted where entity names
were denoted in the provided pattern.
"""
ents = re.findall(r'\{(.*?)\}', pattern)
new_path = pattern
for ent in ents:
match = re.search(r'([^|<]+)(<.*?>)?(\|.*)?', ent)
if match is None:
return None
name, valid, default = match.groups()
default = default[1:] if default is not None else default
if name in entities and valid is not None:
ent_val = str(entities[name])
if not re.match(valid[1:-1], ent_val):
if default is None:
return None
entities[name] = default
ent_val = entities.get(name, default)
if ent_val is None:
return None
new_path = new_path.replace('{%s}' % ent, str(ent_val))
return new_path
|
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Replaces all entity names in a given pattern with the corresponding
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Args:
entities (dict): A dictionary mapping entity names to entity values.
pattern (str): A path pattern that contains entity names denoted
by curly braces. Optional portions denoted by square braces.
For example: 'sub-{subject}/[var-{name}/]{id}.csv'
Accepted entity values, using regex matching, denoted within angle
brackets.
For example: 'sub-{subject<01|02>}/{task}.csv'
Returns:
A new string with the entity values inserted where entity names
were denoted in the provided pattern.
|
[
"Replaces",
"all",
"entity",
"names",
"in",
"a",
"given",
"pattern",
"with",
"the",
"corresponding",
"values",
"provided",
"by",
"entities",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/writing.py#L16-L55
|
17,688
|
bids-standard/pybids
|
bids/layout/writing.py
|
write_contents_to_file
|
def write_contents_to_file(path, contents=None, link_to=None,
content_mode='text', root=None, conflicts='fail'):
"""
Uses provided filename patterns to write contents to a new path, given
a corresponding entity map.
Args:
path (str): Destination path of the desired contents.
contents (str): Raw text or binary encoded string of contents to write
to the new path.
link_to (str): Optional path with which to create a symbolic link to.
Used as an alternative to and takes priority over the contents
argument.
content_mode (str): Either 'text' or 'binary' to indicate the writing
mode for the new file. Only relevant if contents is provided.
root (str): Optional root directory that all patterns are relative
to. Defaults to current working directory.
conflicts (str): One of 'fail', 'skip', 'overwrite', or 'append'
that defines the desired action when the output path already
exists. 'fail' raises an exception; 'skip' does nothing;
'overwrite' overwrites the existing file; 'append' adds a suffix
to each file copy, starting with 1. Default is 'fail'.
"""
if root is None and not isabs(path):
root = os.getcwd()
if root:
path = join(root, path)
if exists(path) or islink(path):
if conflicts == 'fail':
msg = 'A file at path {} already exists.'
raise ValueError(msg.format(path))
elif conflicts == 'skip':
msg = 'A file at path {} already exists, skipping writing file.'
logging.warn(msg.format(path))
return
elif conflicts == 'overwrite':
if isdir(path):
logging.warn('New path is a directory, not going to '
'overwrite it, skipping instead.')
return
os.remove(path)
elif conflicts == 'append':
i = 1
while i < sys.maxsize:
path_splits = splitext(path)
path_splits[0] = path_splits[0] + '_%d' % i
appended_filename = os.extsep.join(path_splits)
if not exists(appended_filename) and \
not islink(appended_filename):
path = appended_filename
break
i += 1
else:
raise ValueError('Did not provide a valid conflicts parameter')
if not exists(dirname(path)):
os.makedirs(dirname(path))
if link_to:
os.symlink(link_to, path)
elif contents:
mode = 'wb' if content_mode == 'binary' else 'w'
with open(path, mode) as f:
f.write(contents)
else:
raise ValueError('One of contents or link_to must be provided.')
|
python
|
def write_contents_to_file(path, contents=None, link_to=None,
content_mode='text', root=None, conflicts='fail'):
"""
Uses provided filename patterns to write contents to a new path, given
a corresponding entity map.
Args:
path (str): Destination path of the desired contents.
contents (str): Raw text or binary encoded string of contents to write
to the new path.
link_to (str): Optional path with which to create a symbolic link to.
Used as an alternative to and takes priority over the contents
argument.
content_mode (str): Either 'text' or 'binary' to indicate the writing
mode for the new file. Only relevant if contents is provided.
root (str): Optional root directory that all patterns are relative
to. Defaults to current working directory.
conflicts (str): One of 'fail', 'skip', 'overwrite', or 'append'
that defines the desired action when the output path already
exists. 'fail' raises an exception; 'skip' does nothing;
'overwrite' overwrites the existing file; 'append' adds a suffix
to each file copy, starting with 1. Default is 'fail'.
"""
if root is None and not isabs(path):
root = os.getcwd()
if root:
path = join(root, path)
if exists(path) or islink(path):
if conflicts == 'fail':
msg = 'A file at path {} already exists.'
raise ValueError(msg.format(path))
elif conflicts == 'skip':
msg = 'A file at path {} already exists, skipping writing file.'
logging.warn(msg.format(path))
return
elif conflicts == 'overwrite':
if isdir(path):
logging.warn('New path is a directory, not going to '
'overwrite it, skipping instead.')
return
os.remove(path)
elif conflicts == 'append':
i = 1
while i < sys.maxsize:
path_splits = splitext(path)
path_splits[0] = path_splits[0] + '_%d' % i
appended_filename = os.extsep.join(path_splits)
if not exists(appended_filename) and \
not islink(appended_filename):
path = appended_filename
break
i += 1
else:
raise ValueError('Did not provide a valid conflicts parameter')
if not exists(dirname(path)):
os.makedirs(dirname(path))
if link_to:
os.symlink(link_to, path)
elif contents:
mode = 'wb' if content_mode == 'binary' else 'w'
with open(path, mode) as f:
f.write(contents)
else:
raise ValueError('One of contents or link_to must be provided.')
|
[
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",",
"path",
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"'w'",
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"(",
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",",
"mode",
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"f",
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"write",
"(",
"contents",
")",
"else",
":",
"raise",
"ValueError",
"(",
"'One of contents or link_to must be provided.'",
")"
] |
Uses provided filename patterns to write contents to a new path, given
a corresponding entity map.
Args:
path (str): Destination path of the desired contents.
contents (str): Raw text or binary encoded string of contents to write
to the new path.
link_to (str): Optional path with which to create a symbolic link to.
Used as an alternative to and takes priority over the contents
argument.
content_mode (str): Either 'text' or 'binary' to indicate the writing
mode for the new file. Only relevant if contents is provided.
root (str): Optional root directory that all patterns are relative
to. Defaults to current working directory.
conflicts (str): One of 'fail', 'skip', 'overwrite', or 'append'
that defines the desired action when the output path already
exists. 'fail' raises an exception; 'skip' does nothing;
'overwrite' overwrites the existing file; 'append' adds a suffix
to each file copy, starting with 1. Default is 'fail'.
|
[
"Uses",
"provided",
"filename",
"patterns",
"to",
"write",
"contents",
"to",
"a",
"new",
"path",
"given",
"a",
"corresponding",
"entity",
"map",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/layout/writing.py#L109-L177
|
17,689
|
bids-standard/pybids
|
bids/reports/report.py
|
BIDSReport.generate
|
def generate(self, **kwargs):
"""Generate the methods section.
Parameters
----------
task_converter : :obj:`dict`, optional
A dictionary with information for converting task names from BIDS
filename format to human-readable strings.
Returns
-------
counter : :obj:`collections.Counter`
A dictionary of unique descriptions across subjects in the dataset,
along with the number of times each pattern occurred. In cases
where all subjects underwent the same protocol, the most common
pattern is most likely the most complete. In cases where the
dataset contains multiple protocols, each pattern will need to be
inspected manually.
Examples
--------
>>> from os.path import join
>>> from bids.layout import BIDSLayout
>>> from bids.reports import BIDSReport
>>> from bids.tests import get_test_data_path
>>> layout = BIDSLayout(join(get_test_data_path(), 'synthetic'))
>>> report = BIDSReport(layout)
>>> counter = report.generate(session='01')
>>> counter.most_common()[0][0]
"""
descriptions = []
subjs = self.layout.get_subjects(**kwargs)
kwargs = {k: v for k, v in kwargs.items() if k != 'subject'}
for sid in subjs:
descriptions.append(self._report_subject(subject=sid, **kwargs))
counter = Counter(descriptions)
print('Number of patterns detected: {0}'.format(len(counter.keys())))
print(utils.reminder())
return counter
|
python
|
def generate(self, **kwargs):
"""Generate the methods section.
Parameters
----------
task_converter : :obj:`dict`, optional
A dictionary with information for converting task names from BIDS
filename format to human-readable strings.
Returns
-------
counter : :obj:`collections.Counter`
A dictionary of unique descriptions across subjects in the dataset,
along with the number of times each pattern occurred. In cases
where all subjects underwent the same protocol, the most common
pattern is most likely the most complete. In cases where the
dataset contains multiple protocols, each pattern will need to be
inspected manually.
Examples
--------
>>> from os.path import join
>>> from bids.layout import BIDSLayout
>>> from bids.reports import BIDSReport
>>> from bids.tests import get_test_data_path
>>> layout = BIDSLayout(join(get_test_data_path(), 'synthetic'))
>>> report = BIDSReport(layout)
>>> counter = report.generate(session='01')
>>> counter.most_common()[0][0]
"""
descriptions = []
subjs = self.layout.get_subjects(**kwargs)
kwargs = {k: v for k, v in kwargs.items() if k != 'subject'}
for sid in subjs:
descriptions.append(self._report_subject(subject=sid, **kwargs))
counter = Counter(descriptions)
print('Number of patterns detected: {0}'.format(len(counter.keys())))
print(utils.reminder())
return counter
|
[
"def",
"generate",
"(",
"self",
",",
"*",
"*",
"kwargs",
")",
":",
"descriptions",
"=",
"[",
"]",
"subjs",
"=",
"self",
".",
"layout",
".",
"get_subjects",
"(",
"*",
"*",
"kwargs",
")",
"kwargs",
"=",
"{",
"k",
":",
"v",
"for",
"k",
",",
"v",
"in",
"kwargs",
".",
"items",
"(",
")",
"if",
"k",
"!=",
"'subject'",
"}",
"for",
"sid",
"in",
"subjs",
":",
"descriptions",
".",
"append",
"(",
"self",
".",
"_report_subject",
"(",
"subject",
"=",
"sid",
",",
"*",
"*",
"kwargs",
")",
")",
"counter",
"=",
"Counter",
"(",
"descriptions",
")",
"print",
"(",
"'Number of patterns detected: {0}'",
".",
"format",
"(",
"len",
"(",
"counter",
".",
"keys",
"(",
")",
")",
")",
")",
"print",
"(",
"utils",
".",
"reminder",
"(",
")",
")",
"return",
"counter"
] |
Generate the methods section.
Parameters
----------
task_converter : :obj:`dict`, optional
A dictionary with information for converting task names from BIDS
filename format to human-readable strings.
Returns
-------
counter : :obj:`collections.Counter`
A dictionary of unique descriptions across subjects in the dataset,
along with the number of times each pattern occurred. In cases
where all subjects underwent the same protocol, the most common
pattern is most likely the most complete. In cases where the
dataset contains multiple protocols, each pattern will need to be
inspected manually.
Examples
--------
>>> from os.path import join
>>> from bids.layout import BIDSLayout
>>> from bids.reports import BIDSReport
>>> from bids.tests import get_test_data_path
>>> layout = BIDSLayout(join(get_test_data_path(), 'synthetic'))
>>> report = BIDSReport(layout)
>>> counter = report.generate(session='01')
>>> counter.most_common()[0][0]
|
[
"Generate",
"the",
"methods",
"section",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/reports/report.py#L53-L92
|
17,690
|
bids-standard/pybids
|
bids/reports/report.py
|
BIDSReport._report_subject
|
def _report_subject(self, subject, **kwargs):
"""Write a report for a single subject.
Parameters
----------
subject : :obj:`str`
Subject ID.
Attributes
----------
layout : :obj:`bids.layout.BIDSLayout`
Layout object for a BIDS dataset.
config : :obj:`dict`
Configuration info for methods generation.
Returns
-------
description : :obj:`str`
A publication-ready report of the dataset's data acquisition
information. Each scan type is given its own paragraph.
"""
description_list = []
# Remove sess from kwargs if provided, else set sess as all available
sessions = kwargs.pop('session',
self.layout.get_sessions(subject=subject,
**kwargs))
if not sessions:
sessions = [None]
elif not isinstance(sessions, list):
sessions = [sessions]
for ses in sessions:
niftis = self.layout.get(subject=subject, extensions='nii.gz',
**kwargs)
if niftis:
description_list.append('For session {0}:'.format(ses))
description_list += parsing.parse_niftis(self.layout, niftis,
subject, self.config,
session=ses)
metadata = self.layout.get_metadata(niftis[0].path)
else:
raise Exception('No niftis for subject {0}'.format(subject))
# Assume all data were converted the same way and use the last nifti
# file's json for conversion information.
if 'metadata' not in vars():
raise Exception('No valid jsons found. Cannot generate final '
'paragraph.')
description = '\n\t'.join(description_list)
description = description.replace('\tFor session', '\nFor session')
description += '\n\n{0}'.format(parsing.final_paragraph(metadata))
return description
|
python
|
def _report_subject(self, subject, **kwargs):
"""Write a report for a single subject.
Parameters
----------
subject : :obj:`str`
Subject ID.
Attributes
----------
layout : :obj:`bids.layout.BIDSLayout`
Layout object for a BIDS dataset.
config : :obj:`dict`
Configuration info for methods generation.
Returns
-------
description : :obj:`str`
A publication-ready report of the dataset's data acquisition
information. Each scan type is given its own paragraph.
"""
description_list = []
# Remove sess from kwargs if provided, else set sess as all available
sessions = kwargs.pop('session',
self.layout.get_sessions(subject=subject,
**kwargs))
if not sessions:
sessions = [None]
elif not isinstance(sessions, list):
sessions = [sessions]
for ses in sessions:
niftis = self.layout.get(subject=subject, extensions='nii.gz',
**kwargs)
if niftis:
description_list.append('For session {0}:'.format(ses))
description_list += parsing.parse_niftis(self.layout, niftis,
subject, self.config,
session=ses)
metadata = self.layout.get_metadata(niftis[0].path)
else:
raise Exception('No niftis for subject {0}'.format(subject))
# Assume all data were converted the same way and use the last nifti
# file's json for conversion information.
if 'metadata' not in vars():
raise Exception('No valid jsons found. Cannot generate final '
'paragraph.')
description = '\n\t'.join(description_list)
description = description.replace('\tFor session', '\nFor session')
description += '\n\n{0}'.format(parsing.final_paragraph(metadata))
return description
|
[
"def",
"_report_subject",
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"self",
",",
"subject",
",",
"*",
"*",
"kwargs",
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":",
"description_list",
"=",
"[",
"]",
"# Remove sess from kwargs if provided, else set sess as all available",
"sessions",
"=",
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",",
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":",
"raise",
"Exception",
"(",
"'No valid jsons found. Cannot generate final '",
"'paragraph.'",
")",
"description",
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".",
"join",
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"description_list",
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"description",
"=",
"description",
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"replace",
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"'\\tFor session'",
",",
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".",
"format",
"(",
"parsing",
".",
"final_paragraph",
"(",
"metadata",
")",
")",
"return",
"description"
] |
Write a report for a single subject.
Parameters
----------
subject : :obj:`str`
Subject ID.
Attributes
----------
layout : :obj:`bids.layout.BIDSLayout`
Layout object for a BIDS dataset.
config : :obj:`dict`
Configuration info for methods generation.
Returns
-------
description : :obj:`str`
A publication-ready report of the dataset's data acquisition
information. Each scan type is given its own paragraph.
|
[
"Write",
"a",
"report",
"for",
"a",
"single",
"subject",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/reports/report.py#L94-L147
|
17,691
|
bids-standard/pybids
|
bids/analysis/hrf.py
|
_gamma_difference_hrf
|
def _gamma_difference_hrf(tr, oversampling=50, time_length=32., onset=0.,
delay=6, undershoot=16., dispersion=1.,
u_dispersion=1., ratio=0.167):
""" Compute an hrf as the difference of two gamma functions
Parameters
----------
tr : float
scan repeat time, in seconds
oversampling : int, optional (default=16)
temporal oversampling factor
time_length : float, optional (default=32)
hrf kernel length, in seconds
onset: float
onset time of the hrf
delay: float, optional
delay parameter of the hrf (in s.)
undershoot: float, optional
undershoot parameter of the hrf (in s.)
dispersion : float, optional
dispersion parameter for the first gamma function
u_dispersion : float, optional
dispersion parameter for the second gamma function
ratio : float, optional
ratio of the two gamma components
Returns
-------
hrf : array of shape(length / tr * oversampling, dtype=float)
hrf sampling on the oversampled time grid
"""
from scipy.stats import gamma
dt = tr / oversampling
time_stamps = np.linspace(0, time_length, np.rint(float(time_length) / dt).astype(np.int))
time_stamps -= onset
hrf = gamma.pdf(time_stamps, delay / dispersion, dt / dispersion) -\
ratio * gamma.pdf(
time_stamps, undershoot / u_dispersion, dt / u_dispersion)
hrf /= hrf.sum()
return hrf
|
python
|
def _gamma_difference_hrf(tr, oversampling=50, time_length=32., onset=0.,
delay=6, undershoot=16., dispersion=1.,
u_dispersion=1., ratio=0.167):
""" Compute an hrf as the difference of two gamma functions
Parameters
----------
tr : float
scan repeat time, in seconds
oversampling : int, optional (default=16)
temporal oversampling factor
time_length : float, optional (default=32)
hrf kernel length, in seconds
onset: float
onset time of the hrf
delay: float, optional
delay parameter of the hrf (in s.)
undershoot: float, optional
undershoot parameter of the hrf (in s.)
dispersion : float, optional
dispersion parameter for the first gamma function
u_dispersion : float, optional
dispersion parameter for the second gamma function
ratio : float, optional
ratio of the two gamma components
Returns
-------
hrf : array of shape(length / tr * oversampling, dtype=float)
hrf sampling on the oversampled time grid
"""
from scipy.stats import gamma
dt = tr / oversampling
time_stamps = np.linspace(0, time_length, np.rint(float(time_length) / dt).astype(np.int))
time_stamps -= onset
hrf = gamma.pdf(time_stamps, delay / dispersion, dt / dispersion) -\
ratio * gamma.pdf(
time_stamps, undershoot / u_dispersion, dt / u_dispersion)
hrf /= hrf.sum()
return hrf
|
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Compute an hrf as the difference of two gamma functions
Parameters
----------
tr : float
scan repeat time, in seconds
oversampling : int, optional (default=16)
temporal oversampling factor
time_length : float, optional (default=32)
hrf kernel length, in seconds
onset: float
onset time of the hrf
delay: float, optional
delay parameter of the hrf (in s.)
undershoot: float, optional
undershoot parameter of the hrf (in s.)
dispersion : float, optional
dispersion parameter for the first gamma function
u_dispersion : float, optional
dispersion parameter for the second gamma function
ratio : float, optional
ratio of the two gamma components
Returns
-------
hrf : array of shape(length / tr * oversampling, dtype=float)
hrf sampling on the oversampled time grid
|
[
"Compute",
"an",
"hrf",
"as",
"the",
"difference",
"of",
"two",
"gamma",
"functions"
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/hrf.py#L13-L61
|
17,692
|
bids-standard/pybids
|
bids/analysis/hrf.py
|
spm_hrf
|
def spm_hrf(tr, oversampling=50, time_length=32., onset=0.):
""" Implementation of the SPM hrf model
Parameters
----------
tr : float
scan repeat time, in seconds
oversampling : int, optional
temporal oversampling factor
time_length : float, optional
hrf kernel length, in seconds
onset : float, optional
hrf onset time, in seconds
Returns
-------
hrf: array of shape(length / tr * oversampling, dtype=float)
hrf sampling on the oversampled time grid
"""
return _gamma_difference_hrf(tr, oversampling, time_length, onset)
|
python
|
def spm_hrf(tr, oversampling=50, time_length=32., onset=0.):
""" Implementation of the SPM hrf model
Parameters
----------
tr : float
scan repeat time, in seconds
oversampling : int, optional
temporal oversampling factor
time_length : float, optional
hrf kernel length, in seconds
onset : float, optional
hrf onset time, in seconds
Returns
-------
hrf: array of shape(length / tr * oversampling, dtype=float)
hrf sampling on the oversampled time grid
"""
return _gamma_difference_hrf(tr, oversampling, time_length, onset)
|
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Implementation of the SPM hrf model
Parameters
----------
tr : float
scan repeat time, in seconds
oversampling : int, optional
temporal oversampling factor
time_length : float, optional
hrf kernel length, in seconds
onset : float, optional
hrf onset time, in seconds
Returns
-------
hrf: array of shape(length / tr * oversampling, dtype=float)
hrf sampling on the oversampled time grid
|
[
"Implementation",
"of",
"the",
"SPM",
"hrf",
"model"
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/hrf.py#L64-L86
|
17,693
|
bids-standard/pybids
|
bids/analysis/hrf.py
|
glover_hrf
|
def glover_hrf(tr, oversampling=50, time_length=32., onset=0.):
""" Implementation of the Glover hrf model
Parameters
----------
tr : float
scan repeat time, in seconds
oversampling : int, optional
temporal oversampling factor
time_length : float, optional
hrf kernel length, in seconds
onset : float, optional
onset of the response
Returns
-------
hrf: array of shape(length / tr * oversampling, dtype=float)
hrf sampling on the oversampled time grid
"""
return _gamma_difference_hrf(tr, oversampling, time_length, onset,
delay=6, undershoot=12., dispersion=.9,
u_dispersion=.9, ratio=.35)
|
python
|
def glover_hrf(tr, oversampling=50, time_length=32., onset=0.):
""" Implementation of the Glover hrf model
Parameters
----------
tr : float
scan repeat time, in seconds
oversampling : int, optional
temporal oversampling factor
time_length : float, optional
hrf kernel length, in seconds
onset : float, optional
onset of the response
Returns
-------
hrf: array of shape(length / tr * oversampling, dtype=float)
hrf sampling on the oversampled time grid
"""
return _gamma_difference_hrf(tr, oversampling, time_length, onset,
delay=6, undershoot=12., dispersion=.9,
u_dispersion=.9, ratio=.35)
|
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Implementation of the Glover hrf model
Parameters
----------
tr : float
scan repeat time, in seconds
oversampling : int, optional
temporal oversampling factor
time_length : float, optional
hrf kernel length, in seconds
onset : float, optional
onset of the response
Returns
-------
hrf: array of shape(length / tr * oversampling, dtype=float)
hrf sampling on the oversampled time grid
|
[
"Implementation",
"of",
"the",
"Glover",
"hrf",
"model"
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/hrf.py#L89-L113
|
17,694
|
bids-standard/pybids
|
bids/analysis/hrf.py
|
spm_dispersion_derivative
|
def spm_dispersion_derivative(tr, oversampling=50, time_length=32., onset=0.):
"""Implementation of the SPM dispersion derivative hrf model
Parameters
----------
tr: float
scan repeat time, in seconds
oversampling: int, optional
temporal oversampling factor in seconds
time_length: float, optional
hrf kernel length, in seconds
onset : float, optional
onset of the response in seconds
Returns
-------
dhrf: array of shape(length / tr * oversampling), dtype=float
dhrf sampling on the oversampled time grid
"""
dd = .01
dhrf = 1. / dd * (
- _gamma_difference_hrf(tr, oversampling, time_length,
onset, dispersion=1. + dd)
+ _gamma_difference_hrf(tr, oversampling, time_length, onset))
return dhrf
|
python
|
def spm_dispersion_derivative(tr, oversampling=50, time_length=32., onset=0.):
"""Implementation of the SPM dispersion derivative hrf model
Parameters
----------
tr: float
scan repeat time, in seconds
oversampling: int, optional
temporal oversampling factor in seconds
time_length: float, optional
hrf kernel length, in seconds
onset : float, optional
onset of the response in seconds
Returns
-------
dhrf: array of shape(length / tr * oversampling), dtype=float
dhrf sampling on the oversampled time grid
"""
dd = .01
dhrf = 1. / dd * (
- _gamma_difference_hrf(tr, oversampling, time_length,
onset, dispersion=1. + dd)
+ _gamma_difference_hrf(tr, oversampling, time_length, onset))
return dhrf
|
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Implementation of the SPM dispersion derivative hrf model
Parameters
----------
tr: float
scan repeat time, in seconds
oversampling: int, optional
temporal oversampling factor in seconds
time_length: float, optional
hrf kernel length, in seconds
onset : float, optional
onset of the response in seconds
Returns
-------
dhrf: array of shape(length / tr * oversampling), dtype=float
dhrf sampling on the oversampled time grid
|
[
"Implementation",
"of",
"the",
"SPM",
"dispersion",
"derivative",
"hrf",
"model"
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/hrf.py#L169-L196
|
17,695
|
bids-standard/pybids
|
bids/analysis/hrf.py
|
glover_dispersion_derivative
|
def glover_dispersion_derivative(tr, oversampling=50, time_length=32.,
onset=0.):
"""Implementation of the Glover dispersion derivative hrf model
Parameters
----------
tr: float
scan repeat time, in seconds
oversampling: int, optional
temporal oversampling factor in seconds
time_length: float, optional
hrf kernel length, in seconds
onset : float, optional
onset of the response in seconds
Returns
-------
dhrf: array of shape(length / tr * oversampling), dtype=float
dhrf sampling on the oversampled time grid
"""
dd = .01
dhrf = 1. / dd * (
- _gamma_difference_hrf(
tr, oversampling, time_length, onset,
delay=6, undershoot=12., dispersion=.9 + dd, ratio=.35)
+ _gamma_difference_hrf(
tr, oversampling, time_length, onset, delay=6, undershoot=12.,
dispersion=.9, ratio=.35))
return dhrf
|
python
|
def glover_dispersion_derivative(tr, oversampling=50, time_length=32.,
onset=0.):
"""Implementation of the Glover dispersion derivative hrf model
Parameters
----------
tr: float
scan repeat time, in seconds
oversampling: int, optional
temporal oversampling factor in seconds
time_length: float, optional
hrf kernel length, in seconds
onset : float, optional
onset of the response in seconds
Returns
-------
dhrf: array of shape(length / tr * oversampling), dtype=float
dhrf sampling on the oversampled time grid
"""
dd = .01
dhrf = 1. / dd * (
- _gamma_difference_hrf(
tr, oversampling, time_length, onset,
delay=6, undershoot=12., dispersion=.9 + dd, ratio=.35)
+ _gamma_difference_hrf(
tr, oversampling, time_length, onset, delay=6, undershoot=12.,
dispersion=.9, ratio=.35))
return dhrf
|
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Implementation of the Glover dispersion derivative hrf model
Parameters
----------
tr: float
scan repeat time, in seconds
oversampling: int, optional
temporal oversampling factor in seconds
time_length: float, optional
hrf kernel length, in seconds
onset : float, optional
onset of the response in seconds
Returns
-------
dhrf: array of shape(length / tr * oversampling), dtype=float
dhrf sampling on the oversampled time grid
|
[
"Implementation",
"of",
"the",
"Glover",
"dispersion",
"derivative",
"hrf",
"model"
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/hrf.py#L199-L230
|
17,696
|
bids-standard/pybids
|
bids/analysis/hrf.py
|
_sample_condition
|
def _sample_condition(exp_condition, frame_times, oversampling=50,
min_onset=-24):
"""Make a possibly oversampled event regressor from condition information.
Parameters
----------
exp_condition : arraylike of shape (3, n_events)
yields description of events for this condition as a
(onsets, durations, amplitudes) triplet
frame_times : array of shape(n_scans)
sample time points
over_sampling : int, optional
factor for oversampling event regressor
min_onset : float, optional
minimal onset relative to frame_times[0] (in seconds)
events that start before frame_times[0] + min_onset are not considered
Returns
-------
regressor: array of shape(over_sampling * n_scans)
possibly oversampled event regressor
hr_frame_times : array of shape(over_sampling * n_scans)
time points used for regressor sampling
"""
# Find the high-resolution frame_times
n = frame_times.size
min_onset = float(min_onset)
n_hr = ((n - 1) * 1. / (frame_times.max() - frame_times.min()) *
(frame_times.max() * (1 + 1. / (n - 1)) - frame_times.min() -
min_onset) * oversampling) + 1
hr_frame_times = np.linspace(frame_times.min() + min_onset,
frame_times.max() * (1 + 1. / (n - 1)),
np.rint(n_hr).astype(np.int))
# Get the condition information
onsets, durations, values = tuple(map(np.asanyarray, exp_condition))
if (onsets < frame_times[0] + min_onset).any():
warnings.warn(('Some stimulus onsets are earlier than %s in the'
' experiment and are thus not considered in the model'
% (frame_times[0] + min_onset)), UserWarning)
# Set up the regressor timecourse
tmax = len(hr_frame_times)
regressor = np.zeros_like(hr_frame_times).astype(np.float)
t_onset = np.minimum(np.searchsorted(hr_frame_times, onsets), tmax - 1)
regressor[t_onset] += values
t_offset = np.minimum(
np.searchsorted(hr_frame_times, onsets + durations),
tmax - 1)
# Handle the case where duration is 0 by offsetting at t + 1
for i, t in enumerate(t_offset):
if t < (tmax - 1) and t == t_onset[i]:
t_offset[i] += 1
regressor[t_offset] -= values
regressor = np.cumsum(regressor)
return regressor, hr_frame_times
|
python
|
def _sample_condition(exp_condition, frame_times, oversampling=50,
min_onset=-24):
"""Make a possibly oversampled event regressor from condition information.
Parameters
----------
exp_condition : arraylike of shape (3, n_events)
yields description of events for this condition as a
(onsets, durations, amplitudes) triplet
frame_times : array of shape(n_scans)
sample time points
over_sampling : int, optional
factor for oversampling event regressor
min_onset : float, optional
minimal onset relative to frame_times[0] (in seconds)
events that start before frame_times[0] + min_onset are not considered
Returns
-------
regressor: array of shape(over_sampling * n_scans)
possibly oversampled event regressor
hr_frame_times : array of shape(over_sampling * n_scans)
time points used for regressor sampling
"""
# Find the high-resolution frame_times
n = frame_times.size
min_onset = float(min_onset)
n_hr = ((n - 1) * 1. / (frame_times.max() - frame_times.min()) *
(frame_times.max() * (1 + 1. / (n - 1)) - frame_times.min() -
min_onset) * oversampling) + 1
hr_frame_times = np.linspace(frame_times.min() + min_onset,
frame_times.max() * (1 + 1. / (n - 1)),
np.rint(n_hr).astype(np.int))
# Get the condition information
onsets, durations, values = tuple(map(np.asanyarray, exp_condition))
if (onsets < frame_times[0] + min_onset).any():
warnings.warn(('Some stimulus onsets are earlier than %s in the'
' experiment and are thus not considered in the model'
% (frame_times[0] + min_onset)), UserWarning)
# Set up the regressor timecourse
tmax = len(hr_frame_times)
regressor = np.zeros_like(hr_frame_times).astype(np.float)
t_onset = np.minimum(np.searchsorted(hr_frame_times, onsets), tmax - 1)
regressor[t_onset] += values
t_offset = np.minimum(
np.searchsorted(hr_frame_times, onsets + durations),
tmax - 1)
# Handle the case where duration is 0 by offsetting at t + 1
for i, t in enumerate(t_offset):
if t < (tmax - 1) and t == t_onset[i]:
t_offset[i] += 1
regressor[t_offset] -= values
regressor = np.cumsum(regressor)
return regressor, hr_frame_times
|
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",",
"tmax",
"-",
"1",
")",
"regressor",
"[",
"t_onset",
"]",
"+=",
"values",
"t_offset",
"=",
"np",
".",
"minimum",
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"np",
".",
"searchsorted",
"(",
"hr_frame_times",
",",
"onsets",
"+",
"durations",
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",",
"tmax",
"-",
"1",
")",
"# Handle the case where duration is 0 by offsetting at t + 1",
"for",
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"=",
"np",
".",
"cumsum",
"(",
"regressor",
")",
"return",
"regressor",
",",
"hr_frame_times"
] |
Make a possibly oversampled event regressor from condition information.
Parameters
----------
exp_condition : arraylike of shape (3, n_events)
yields description of events for this condition as a
(onsets, durations, amplitudes) triplet
frame_times : array of shape(n_scans)
sample time points
over_sampling : int, optional
factor for oversampling event regressor
min_onset : float, optional
minimal onset relative to frame_times[0] (in seconds)
events that start before frame_times[0] + min_onset are not considered
Returns
-------
regressor: array of shape(over_sampling * n_scans)
possibly oversampled event regressor
hr_frame_times : array of shape(over_sampling * n_scans)
time points used for regressor sampling
|
[
"Make",
"a",
"possibly",
"oversampled",
"event",
"regressor",
"from",
"condition",
"information",
"."
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/hrf.py#L233-L295
|
17,697
|
bids-standard/pybids
|
bids/analysis/hrf.py
|
_resample_regressor
|
def _resample_regressor(hr_regressor, hr_frame_times, frame_times):
""" this function sub-samples the regressors at frame times
Parameters
----------
hr_regressor : array of shape(n_samples),
the regressor time course sampled at high temporal resolution
hr_frame_times : array of shape(n_samples),
the corresponding time stamps
frame_times: array of shape(n_scans),
the desired time stamps
Returns
-------
regressor: array of shape(n_scans)
the resampled regressor
"""
from scipy.interpolate import interp1d
f = interp1d(hr_frame_times, hr_regressor)
return f(frame_times).T
|
python
|
def _resample_regressor(hr_regressor, hr_frame_times, frame_times):
""" this function sub-samples the regressors at frame times
Parameters
----------
hr_regressor : array of shape(n_samples),
the regressor time course sampled at high temporal resolution
hr_frame_times : array of shape(n_samples),
the corresponding time stamps
frame_times: array of shape(n_scans),
the desired time stamps
Returns
-------
regressor: array of shape(n_scans)
the resampled regressor
"""
from scipy.interpolate import interp1d
f = interp1d(hr_frame_times, hr_regressor)
return f(frame_times).T
|
[
"def",
"_resample_regressor",
"(",
"hr_regressor",
",",
"hr_frame_times",
",",
"frame_times",
")",
":",
"from",
"scipy",
".",
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"hr_frame_times",
",",
"hr_regressor",
")",
"return",
"f",
"(",
"frame_times",
")",
".",
"T"
] |
this function sub-samples the regressors at frame times
Parameters
----------
hr_regressor : array of shape(n_samples),
the regressor time course sampled at high temporal resolution
hr_frame_times : array of shape(n_samples),
the corresponding time stamps
frame_times: array of shape(n_scans),
the desired time stamps
Returns
-------
regressor: array of shape(n_scans)
the resampled regressor
|
[
"this",
"function",
"sub",
"-",
"samples",
"the",
"regressors",
"at",
"frame",
"times"
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/hrf.py#L298-L319
|
17,698
|
bids-standard/pybids
|
bids/analysis/hrf.py
|
_orthogonalize
|
def _orthogonalize(X):
""" Orthogonalize every column of design `X` w.r.t preceding columns
Parameters
----------
X: array of shape(n, p)
the data to be orthogonalized
Returns
-------
X: array of shape(n, p)
the data after orthogonalization
Notes
-----
X is changed in place. The columns are not normalized
"""
if X.size == X.shape[0]:
return X
from scipy.linalg import pinv, norm
for i in range(1, X.shape[1]):
X[:, i] -= np.dot(np.dot(X[:, i], X[:, :i]), pinv(X[:, :i]))
# X[:, i] /= norm(X[:, i])
return X
|
python
|
def _orthogonalize(X):
""" Orthogonalize every column of design `X` w.r.t preceding columns
Parameters
----------
X: array of shape(n, p)
the data to be orthogonalized
Returns
-------
X: array of shape(n, p)
the data after orthogonalization
Notes
-----
X is changed in place. The columns are not normalized
"""
if X.size == X.shape[0]:
return X
from scipy.linalg import pinv, norm
for i in range(1, X.shape[1]):
X[:, i] -= np.dot(np.dot(X[:, i], X[:, :i]), pinv(X[:, :i]))
# X[:, i] /= norm(X[:, i])
return X
|
[
"def",
"_orthogonalize",
"(",
"X",
")",
":",
"if",
"X",
".",
"size",
"==",
"X",
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"0",
"]",
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"return",
"X",
"from",
"scipy",
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",",
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"[",
":",
",",
":",
"i",
"]",
")",
")",
"# X[:, i] /= norm(X[:, i])",
"return",
"X"
] |
Orthogonalize every column of design `X` w.r.t preceding columns
Parameters
----------
X: array of shape(n, p)
the data to be orthogonalized
Returns
-------
X: array of shape(n, p)
the data after orthogonalization
Notes
-----
X is changed in place. The columns are not normalized
|
[
"Orthogonalize",
"every",
"column",
"of",
"design",
"X",
"w",
".",
"r",
".",
"t",
"preceding",
"columns"
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/hrf.py#L322-L345
|
17,699
|
bids-standard/pybids
|
bids/analysis/hrf.py
|
_regressor_names
|
def _regressor_names(con_name, hrf_model, fir_delays=None):
""" Returns a list of regressor names, computed from con-name and hrf type
Parameters
----------
con_name: string
identifier of the condition
hrf_model: string or None,
hrf model chosen
fir_delays: 1D array_like, optional,
Delays used in case of an FIR model
Returns
-------
names: list of strings,
regressor names
"""
if hrf_model in ['glover', 'spm', None]:
return [con_name]
elif hrf_model in ["glover + derivative", 'spm + derivative']:
return [con_name, con_name + "_derivative"]
elif hrf_model in ['spm + derivative + dispersion',
'glover + derivative + dispersion']:
return [con_name, con_name + "_derivative", con_name + "_dispersion"]
elif hrf_model == 'fir':
return [con_name + "_delay_%d" % i for i in fir_delays]
|
python
|
def _regressor_names(con_name, hrf_model, fir_delays=None):
""" Returns a list of regressor names, computed from con-name and hrf type
Parameters
----------
con_name: string
identifier of the condition
hrf_model: string or None,
hrf model chosen
fir_delays: 1D array_like, optional,
Delays used in case of an FIR model
Returns
-------
names: list of strings,
regressor names
"""
if hrf_model in ['glover', 'spm', None]:
return [con_name]
elif hrf_model in ["glover + derivative", 'spm + derivative']:
return [con_name, con_name + "_derivative"]
elif hrf_model in ['spm + derivative + dispersion',
'glover + derivative + dispersion']:
return [con_name, con_name + "_derivative", con_name + "_dispersion"]
elif hrf_model == 'fir':
return [con_name + "_delay_%d" % i for i in fir_delays]
|
[
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",",
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"hrf_model",
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"'glover'",
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"'spm'",
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"'spm + derivative + dispersion'",
",",
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":",
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"\"_derivative\"",
",",
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"+",
"\"_dispersion\"",
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"'fir'",
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"return",
"[",
"con_name",
"+",
"\"_delay_%d\"",
"%",
"i",
"for",
"i",
"in",
"fir_delays",
"]"
] |
Returns a list of regressor names, computed from con-name and hrf type
Parameters
----------
con_name: string
identifier of the condition
hrf_model: string or None,
hrf model chosen
fir_delays: 1D array_like, optional,
Delays used in case of an FIR model
Returns
-------
names: list of strings,
regressor names
|
[
"Returns",
"a",
"list",
"of",
"regressor",
"names",
"computed",
"from",
"con",
"-",
"name",
"and",
"hrf",
"type"
] |
30d924ce770622bda0e390d613a8da42a2a20c32
|
https://github.com/bids-standard/pybids/blob/30d924ce770622bda0e390d613a8da42a2a20c32/bids/analysis/hrf.py#L348-L375
|
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