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spacetelescope/drizzlepac | drizzlepac/hlautils/astrometric_utils.py | within_footprint | def within_footprint(img, wcs, x, y):
"""Determine whether input x, y fall in the science area of the image.
Parameters
----------
img : ndarray
ndarray of image where non-science areas are marked with value of NaN.
wcs : `stwcs.wcsutil.HSTWCS`
HSTWCS or WCS object with naxis terms... | python | def within_footprint(img, wcs, x, y):
"""Determine whether input x, y fall in the science area of the image.
Parameters
----------
img : ndarray
ndarray of image where non-science areas are marked with value of NaN.
wcs : `stwcs.wcsutil.HSTWCS`
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spacetelescope/drizzlepac | drizzlepac/hlautils/astrometric_utils.py | create_image_footprint | def create_image_footprint(image, refwcs, border=0.):
""" Create the footprint of the image in the reference WCS frame.
Parameters
----------
image : `astropy.io.fits.HDUList` or str
Image to extract sources for matching to
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refwcs : `stwcs.wcsutil.... | python | def create_image_footprint(image, refwcs, border=0.):
""" Create the footprint of the image in the reference WCS frame.
Parameters
----------
image : `astropy.io.fits.HDUList` or str
Image to extract sources for matching to
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spacetelescope/drizzlepac | drizzlepac/hlautils/astrometric_utils.py | find_hist2d_offset | def find_hist2d_offset(filename, reference, refwcs=None, refnames=['ra', 'dec'],
match_tolerance=5., chip_catalog=True, search_radius=15.0,
min_match=10, classify=True):
"""Iteratively look for the best cross-match between the catalog and ref.
Parameters
------... | python | def find_hist2d_offset(filename, reference, refwcs=None, refnames=['ra', 'dec'],
match_tolerance=5., chip_catalog=True, search_radius=15.0,
min_match=10, classify=True):
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spacetelescope/drizzlepac | drizzlepac/hlautils/astrometric_utils.py | build_wcscat | def build_wcscat(image, group_id, source_catalog):
""" Return a list of `~tweakwcs.tpwcs.FITSWCS` objects for all chips in an image.
Parameters
----------
image : str, ~astropy.io.fits.HDUList`
Either filename or HDUList of a single HST observation.
group_id : int
Integer ID for gr... | python | def build_wcscat(image, group_id, source_catalog):
""" Return a list of `~tweakwcs.tpwcs.FITSWCS` objects for all chips in an image.
Parameters
----------
image : str, ~astropy.io.fits.HDUList`
Either filename or HDUList of a single HST observation.
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Integer ID for gr... | [
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spacetelescope/drizzlepac | drizzlepac/updatehdr.py | update_from_shiftfile | def update_from_shiftfile(shiftfile,wcsname=None,force=False):
"""
Update headers of all images specified in shiftfile with shifts
from shiftfile.
Parameters
----------
shiftfile : str
Filename of shiftfile.
wcsname : str
Label to give to new WCS solution being created by t... | python | def update_from_shiftfile(shiftfile,wcsname=None,force=False):
"""
Update headers of all images specified in shiftfile with shifts
from shiftfile.
Parameters
----------
shiftfile : str
Filename of shiftfile.
wcsname : str
Label to give to new WCS solution being created by t... | [
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spacetelescope/drizzlepac | drizzlepac/updatehdr.py | updatewcs_with_shift | def updatewcs_with_shift(image,reference,wcsname=None, reusename=False,
fitgeom='rscale',
rot=0.0,scale=1.0,xsh=0.0,ysh=0.0,fit=None,
xrms=None, yrms = None,
verbose=False,force=False,sciext='SCI'):
"""
Update t... | python | def updatewcs_with_shift(image,reference,wcsname=None, reusename=False,
fitgeom='rscale',
rot=0.0,scale=1.0,xsh=0.0,ysh=0.0,fit=None,
xrms=None, yrms = None,
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spacetelescope/drizzlepac | drizzlepac/updatehdr.py | linearize | def linearize(wcsim, wcsima, wcsref, imcrpix, f, shift, hx=1.0, hy=1.0):
""" linearization using 5-point formula for first order derivative
"""
x0 = imcrpix[0]
y0 = imcrpix[1]
p = np.asarray([[x0, y0],
[x0 - hx, y0],
[x0 - hx * 0.5, y0],
[... | python | def linearize(wcsim, wcsima, wcsref, imcrpix, f, shift, hx=1.0, hy=1.0):
""" linearization using 5-point formula for first order derivative
"""
x0 = imcrpix[0]
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spacetelescope/drizzlepac | drizzlepac/updatehdr.py | update_refchip_with_shift | def update_refchip_with_shift(chip_wcs, wcslin, fitgeom='rscale',
rot=0.0, scale=1.0, xsh=0.0, ysh=0.0,
fit=None, xrms=None, yrms=None):
""" Compute the matrix for the scale and rotation correction
Parameters
----------
chip_wcs: wcs object
... | python | def update_refchip_with_shift(chip_wcs, wcslin, fitgeom='rscale',
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fit=None, xrms=None, yrms=None):
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spacetelescope/drizzlepac | drizzlepac/updatehdr.py | update_wcs | def update_wcs(image,extnum,new_wcs,wcsname="",reusename=False,verbose=False):
"""
Updates the WCS of the specified extension number with the new WCS
after archiving the original WCS.
The value of 'new_wcs' needs to be the full
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----------
image : str
F... | python | def update_wcs(image,extnum,new_wcs,wcsname="",reusename=False,verbose=False):
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Updates the WCS of the specified extension number with the new WCS
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spacetelescope/drizzlepac | drizzlepac/updatehdr.py | create_unique_wcsname | def create_unique_wcsname(fimg, extnum, wcsname):
"""
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already been used in this image. If so, it automatically modifies
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Parameters
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fimg : obj
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"""
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spacetelescope/drizzlepac | drizzlepac/util.py | get_pool_size | def get_pool_size(usr_config_value, num_tasks):
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spacetelescope/drizzlepac | drizzlepac/util.py | init_logging | def init_logging(logfile=DEFAULT_LOGNAME, default=None, level=logging.INFO):
"""
Set up logger for capturing stdout/stderr messages.
Must be called prior to writing any messages that you want to log.
"""
if logfile == "INDEF":
if not is_blank(default):
logname = fileutil.buildN... | python | def init_logging(logfile=DEFAULT_LOGNAME, default=None, level=logging.INFO):
"""
Set up logger for capturing stdout/stderr messages.
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spacetelescope/drizzlepac | drizzlepac/util.py | end_logging | def end_logging(filename=None):
"""
Close log file and restore system defaults.
"""
if logutil.global_logging_started:
if filename:
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else:
# This generally shouldn't happen if logging was started with
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Close log file and restore system defaults.
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spacetelescope/drizzlepac | drizzlepac/util.py | findrootname | def findrootname(filename):
"""
Return the rootname of the given file.
"""
puncloc = [filename.find(char) for char in string.punctuation]
if sys.version_info[0] >= 3:
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... | python | def findrootname(filename):
"""
Return the rootname of the given file.
"""
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if sys.version_info[0] >= 3:
val = sys.maxsize
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spacetelescope/drizzlepac | drizzlepac/util.py | removeFileSafely | def removeFileSafely(filename,clobber=True):
""" Delete the file specified, but only if it exists and clobber is True.
"""
if filename is not None and filename.strip() != '':
if os.path.exists(filename) and clobber: os.remove(filename) | python | def removeFileSafely(filename,clobber=True):
""" Delete the file specified, but only if it exists and clobber is True.
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spacetelescope/drizzlepac | drizzlepac/util.py | displayEmptyInputWarningBox | def displayEmptyInputWarningBox(display=True, parent=None):
""" Displays a warning box for the 'input' parameter.
"""
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else:
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if display:
msg = 'No valid input files fo... | python | def displayEmptyInputWarningBox(display=True, parent=None):
""" Displays a warning box for the 'input' parameter.
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spacetelescope/drizzlepac | drizzlepac/util.py | count_sci_extensions | def count_sci_extensions(filename):
""" Return the number of SCI extensions and the EXTNAME from a input MEF file.
"""
num_sci = 0
extname = 'SCI'
hdu_list = fileutil.openImage(filename, memmap=False)
for extn in hdu_list:
if 'extname' in extn.header and extn.header['extname'] == extna... | python | def count_sci_extensions(filename):
""" Return the number of SCI extensions and the EXTNAME from a input MEF file.
"""
num_sci = 0
extname = 'SCI'
hdu_list = fileutil.openImage(filename, memmap=False)
for extn in hdu_list:
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spacetelescope/drizzlepac | drizzlepac/util.py | verifyUniqueWcsname | def verifyUniqueWcsname(fname,wcsname):
"""
Report whether or not the specified WCSNAME already exists in the file
"""
uniq = True
numsci,extname = count_sci_extensions(fname)
wnames = altwcs.wcsnames(fname,ext=(extname,1))
if wcsname in wnames.values():
uniq = False
return uni... | python | def verifyUniqueWcsname(fname,wcsname):
"""
Report whether or not the specified WCSNAME already exists in the file
"""
uniq = True
numsci,extname = count_sci_extensions(fname)
wnames = altwcs.wcsnames(fname,ext=(extname,1))
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spacetelescope/drizzlepac | drizzlepac/util.py | verifyUpdatewcs | def verifyUpdatewcs(fname):
"""
Verify the existence of WCSNAME in the file. If it is not present,
report this to the user and raise an exception. Returns True if WCSNAME
was found in all SCI extensions.
"""
updated = True
numsci,extname = count_sci_extensions(fname)
for n in range(1,n... | python | def verifyUpdatewcs(fname):
"""
Verify the existence of WCSNAME in the file. If it is not present,
report this to the user and raise an exception. Returns True if WCSNAME
was found in all SCI extensions.
"""
updated = True
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spacetelescope/drizzlepac | drizzlepac/util.py | verifyRefimage | def verifyRefimage(refimage):
"""
Verify that the value of refimage specified by the user points to an
extension with a proper WCS defined. It starts by making sure an extension gets
specified by the user when using a MEF file. The final check comes by looking
for a CD matrix in the WCS object itsel... | python | def verifyRefimage(refimage):
"""
Verify that the value of refimage specified by the user points to an
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spacetelescope/drizzlepac | drizzlepac/util.py | findWCSExtn | def findWCSExtn(filename):
""" Return new filename with extension that points to an extension with a
valid WCS.
Returns
=======
extnum : str, None
Value of extension name as a string either as provided by the user
or based on the extension number for the firs... | python | def findWCSExtn(filename):
""" Return new filename with extension that points to an extension with a
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spacetelescope/drizzlepac | drizzlepac/util.py | verifyFilePermissions | def verifyFilePermissions(filelist, chmod=True):
""" Verify that images specified in 'filelist' can be updated.
A message will be printed reporting the names of any images which
do not have write-permission, then quit.
"""
badfiles = []
archive_dir = False
for img in filelist:
fname... | python | def verifyFilePermissions(filelist, chmod=True):
""" Verify that images specified in 'filelist' can be updated.
A message will be printed reporting the names of any images which
do not have write-permission, then quit.
"""
badfiles = []
archive_dir = False
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spacetelescope/drizzlepac | drizzlepac/util.py | getFullParList | def getFullParList(configObj):
"""
Return a single list of all parameter names included in the configObj
regardless of which section the parameter was stored
"""
plist = []
for par in configObj.keys():
if isinstance(configObj[par],configobj.Section):
plist.extend(getFullParLi... | python | def getFullParList(configObj):
"""
Return a single list of all parameter names included in the configObj
regardless of which section the parameter was stored
"""
plist = []
for par in configObj.keys():
if isinstance(configObj[par],configobj.Section):
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spacetelescope/drizzlepac | drizzlepac/util.py | validateUserPars | def validateUserPars(configObj,input_dict):
""" Compares input parameter names specified by user with those already
recognized by the task.
Any parameters provided by the user that does not match a known
task parameter will be reported and a ValueError exception will be
raised.
... | python | def validateUserPars(configObj,input_dict):
""" Compares input parameter names specified by user with those already
recognized by the task.
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task parameter will be reported and a ValueError exception will be
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spacetelescope/drizzlepac | drizzlepac/util.py | applyUserPars_steps | def applyUserPars_steps(configObj, input_dict, step='3a'):
""" Apply logic to turn on use of user-specified output WCS if user provides
any parameter on command-line regardless of how final_wcs was set.
"""
step_kws = {'7a': 'final_wcs', '3a': 'driz_sep_wcs'}
stepname = getSectionName(configObj,... | python | def applyUserPars_steps(configObj, input_dict, step='3a'):
""" Apply logic to turn on use of user-specified output WCS if user provides
any parameter on command-line regardless of how final_wcs was set.
"""
step_kws = {'7a': 'final_wcs', '3a': 'driz_sep_wcs'}
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spacetelescope/drizzlepac | drizzlepac/util.py | getDefaultConfigObj | def getDefaultConfigObj(taskname,configObj,input_dict={},loadOnly=True):
""" Return default configObj instance for task updated
with user-specified values from input_dict.
Parameters
----------
taskname : string
Name of task to load into TEAL
configObj : string
... | python | def getDefaultConfigObj(taskname,configObj,input_dict={},loadOnly=True):
""" Return default configObj instance for task updated
with user-specified values from input_dict.
Parameters
----------
taskname : string
Name of task to load into TEAL
configObj : string
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spacetelescope/drizzlepac | drizzlepac/util.py | getSectionName | def getSectionName(configObj,stepnum):
""" Return section label based on step number.
"""
for key in configObj.keys():
if key.find('STEP '+str(stepnum)+':') >= 0:
return key | python | def getSectionName(configObj,stepnum):
""" Return section label based on step number.
"""
for key in configObj.keys():
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spacetelescope/drizzlepac | drizzlepac/util.py | displayMakewcsWarningBox | def displayMakewcsWarningBox(display=True, parent=None):
""" Displays a warning box for the 'makewcs' parameter.
"""
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""" Displays a warning box for the 'makewcs' parameter.
"""
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spacetelescope/drizzlepac | drizzlepac/util.py | printParams | def printParams(paramDictionary, all=False, log=None):
"""
Print nicely the parameters from the dictionary.
"""
if log is not None:
def output(msg):
log.info(msg)
else:
def output(msg):
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output('No parameters wer... | python | def printParams(paramDictionary, all=False, log=None):
"""
Print nicely the parameters from the dictionary.
"""
if log is not None:
def output(msg):
log.info(msg)
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def output(msg):
print(msg)
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spacetelescope/drizzlepac | drizzlepac/util.py | isCommaList | def isCommaList(inputFilelist):
"""Return True if the input is a comma separated list of names."""
if isinstance(inputFilelist, int) or isinstance(inputFilelist, np.int32):
ilist = str(inputFilelist)
else:
ilist = inputFilelist
if "," in ilist:
return True
return False | python | def isCommaList(inputFilelist):
"""Return True if the input is a comma separated list of names."""
if isinstance(inputFilelist, int) or isinstance(inputFilelist, np.int32):
ilist = str(inputFilelist)
else:
ilist = inputFilelist
if "," in ilist:
return True
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spacetelescope/drizzlepac | drizzlepac/util.py | loadFileList | def loadFileList(inputFilelist):
"""Open up the '@ file' and read in the science and possible
ivm filenames from the first two columns.
"""
f = open(inputFilelist[1:])
# check the first line in order to determine whether
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lines = f.read... | python | def loadFileList(inputFilelist):
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ivm filenames from the first two columns.
"""
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spacetelescope/drizzlepac | drizzlepac/util.py | readCommaList | def readCommaList(fileList):
""" Return a list of the files with the commas removed. """
names=fileList.split(',')
fileList=[]
for item in names:
fileList.append(item)
return fileList | python | def readCommaList(fileList):
""" Return a list of the files with the commas removed. """
names=fileList.split(',')
fileList=[]
for item in names:
fileList.append(item)
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spacetelescope/drizzlepac | drizzlepac/util.py | update_input | def update_input(filelist, ivmlist=None, removed_files=None):
"""
Removes files flagged to be removed from the input filelist.
Removes the corresponding ivm files if present.
"""
newfilelist = []
if removed_files == []:
return filelist, ivmlist
else:
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"""
Removes files flagged to be removed from the input filelist.
Removes the corresponding ivm files if present.
"""
newfilelist = []
if removed_files == []:
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spacetelescope/drizzlepac | drizzlepac/util.py | get_expstart | def get_expstart(header,primary_hdr):
"""shouldn't this just be defined in the instrument subclass of imageobject?"""
if 'expstart' in primary_hdr:
exphdr = primary_hdr
else:
exphdr = header
if 'EXPSTART' in exphdr:
expstart = float(exphdr['EXPSTART'])
expend = float(ex... | python | def get_expstart(header,primary_hdr):
"""shouldn't this just be defined in the instrument subclass of imageobject?"""
if 'expstart' in primary_hdr:
exphdr = primary_hdr
else:
exphdr = header
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spacetelescope/drizzlepac | drizzlepac/util.py | compute_texptime | def compute_texptime(imageObjectList):
"""
Add up the exposure time for all the members in
the pattern, since 'drizzle' doesn't have the necessary
information to correctly set this itself.
"""
expnames = []
exptimes = []
start = []
end = []
for img in imageObjectList:
exp... | python | def compute_texptime(imageObjectList):
"""
Add up the exposure time for all the members in
the pattern, since 'drizzle' doesn't have the necessary
information to correctly set this itself.
"""
expnames = []
exptimes = []
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spacetelescope/drizzlepac | drizzlepac/util.py | computeRange | def computeRange(corners):
""" Determine the range spanned by an array of pixel positions. """
x = corners[:, 0]
y = corners[:, 1]
_xrange = (np.minimum.reduce(x), np.maximum.reduce(x))
_yrange = (np.minimum.reduce(y), np.maximum.reduce(y))
return _xrange, _yrange | python | def computeRange(corners):
""" Determine the range spanned by an array of pixel positions. """
x = corners[:, 0]
y = corners[:, 1]
_xrange = (np.minimum.reduce(x), np.maximum.reduce(x))
_yrange = (np.minimum.reduce(y), np.maximum.reduce(y))
return _xrange, _yrange | [
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spacetelescope/drizzlepac | drizzlepac/util.py | getRotatedSize | def getRotatedSize(corners, angle):
""" Determine the size of a rotated (meta)image."""
if angle:
_rotm = fileutil.buildRotMatrix(angle)
# Rotate about the center
_corners = np.dot(corners, _rotm)
else:
# If there is no rotation, simply return original values
_corners... | python | def getRotatedSize(corners, angle):
""" Determine the size of a rotated (meta)image."""
if angle:
_rotm = fileutil.buildRotMatrix(angle)
# Rotate about the center
_corners = np.dot(corners, _rotm)
else:
# If there is no rotation, simply return original values
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spacetelescope/drizzlepac | drizzlepac/util.py | readcols | def readcols(infile, cols=[0, 1, 2, 3], hms=False):
"""
Read the columns from an ASCII file as numpy arrays.
Parameters
----------
infile : str
Filename of ASCII file with array data as columns.
cols : list of int
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"""
Read the columns from an ASCII file as numpy arrays.
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infile : str
Filename of ASCII file with array data as columns.
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spacetelescope/drizzlepac | drizzlepac/util.py | parse_colnames | def parse_colnames(colnames,coords=None):
""" Convert colnames input into list of column numbers.
"""
cols = []
if not isinstance(colnames,list):
colnames = colnames.split(',')
# parse column names from coords file and match to input values
if coords is not None and fileutil.isFits(coord... | python | def parse_colnames(colnames,coords=None):
""" Convert colnames input into list of column numbers.
"""
cols = []
if not isinstance(colnames,list):
colnames = colnames.split(',')
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spacetelescope/drizzlepac | drizzlepac/util.py | createFile | def createFile(dataArray=None, outfile=None, header=None):
"""
Create a simple fits file for the given data array and header.
Returns either the FITS object in-membory when outfile==None or
None when the FITS file was written out to a file.
"""
# Insure that at least a data-array has been provid... | python | def createFile(dataArray=None, outfile=None, header=None):
"""
Create a simple fits file for the given data array and header.
Returns either the FITS object in-membory when outfile==None or
None when the FITS file was written out to a file.
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spacetelescope/drizzlepac | drizzlepac/util.py | base_taskname | def base_taskname(taskname, packagename=None):
"""
Extract the base name of the task.
Many tasks in the `drizzlepac` have "compound" names such as
'drizzlepac.sky'. This function will search for the presence of a dot
in the input `taskname` and if found, it will return the string
to the right o... | python | def base_taskname(taskname, packagename=None):
"""
Extract the base name of the task.
Many tasks in the `drizzlepac` have "compound" names such as
'drizzlepac.sky'. This function will search for the presence of a dot
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spacetelescope/drizzlepac | drizzlepac/util.py | ProcSteps.addStep | def addStep(self,key):
"""
Add information about a new step to the dict of steps
The value 'ptime' is the output from '_ptime()' containing
both the formatted and unformatted time for the start of the
step.
"""
ptime = _ptime()
print('==== Processing Step ... | python | def addStep(self,key):
"""
Add information about a new step to the dict of steps
The value 'ptime' is the output from '_ptime()' containing
both the formatted and unformatted time for the start of the
step.
"""
ptime = _ptime()
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spacetelescope/drizzlepac | drizzlepac/util.py | ProcSteps.endStep | def endStep(self,key):
"""
Record the end time for the step.
If key==None, simply record ptime as end time for class to represent
the overall runtime since the initialization of the class.
"""
ptime = _ptime()
if key is not None:
self.steps[key]['end'... | python | def endStep(self,key):
"""
Record the end time for the step.
If key==None, simply record ptime as end time for class to represent
the overall runtime since the initialization of the class.
"""
ptime = _ptime()
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spacetelescope/drizzlepac | drizzlepac/util.py | ProcSteps.reportTimes | def reportTimes(self):
"""
Print out a formatted summary of the elapsed times for all the
performed steps.
"""
self.end = _ptime()
total_time = 0
print(ProcSteps.__report_header)
for step in self.order:
if 'elapsed' in self.steps[step]:
... | python | def reportTimes(self):
"""
Print out a formatted summary of the elapsed times for all the
performed steps.
"""
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# If called from interactive user-interface, configObj will not be
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spacetelescope/drizzlepac | drizzlepac/buildmask.py | buildDQMasks | def buildDQMasks(imageObjectList,configObj):
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"""
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imageObjectList = [imageObjectList]
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spacetelescope/drizzlepac | drizzlepac/buildmask.py | buildMask | def buildMask(dqarr, bitvalue):
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""" Builds a bit-mask from an input DQ array and a bitvalue flag """
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spacetelescope/drizzlepac | drizzlepac/buildmask.py | buildMaskImage | def buildMaskImage(rootname, bitvalue, output, extname='DQ', extver=1):
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spacetelescope/drizzlepac | drizzlepac/buildmask.py | buildShadowMaskImage | def buildShadowMaskImage(dqfile,detnum,extnum,maskname,bitvalue=None,binned=1):
""" Builds mask image from WFPC2 shadow calibrations.
detnum - string value for 'DETECTOR' detector
"""
# insure detnum is a string
if type(detnum) != type(''):
detnum = repr(detnum)
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""" Builds mask image from WFPC2 shadow calibrations.
detnum - string value for 'DETECTOR' detector
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spacetelescope/drizzlepac | drizzlepac/pixtosky.py | xy2rd | def xy2rd(input,x=None,y=None,coords=None, coordfile=None,colnames=None,separator=None,
hms=True, precision=6,output=None,verbose=True):
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spacetelescope/drizzlepac | drizzlepac/adrizzle.py | run | def run(configObj, wcsmap=None):
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spacetelescope/drizzlepac | drizzlepac/adrizzle.py | mergeDQarray | def mergeDQarray(maskname,dqarr):
""" Merge static or CR mask with mask created from DQ array on-the-fly here.
"""
maskarr = None
if maskname is not None:
if isinstance(maskname, str):
# working with file on disk (default case)
if os.path.exists(maskname):
... | python | def mergeDQarray(maskname,dqarr):
""" Merge static or CR mask with mask created from DQ array on-the-fly here.
"""
maskarr = None
if maskname is not None:
if isinstance(maskname, str):
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spacetelescope/drizzlepac | drizzlepac/adrizzle.py | _setDefaults | def _setDefaults(configObj={}):
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spacetelescope/drizzlepac | drizzlepac/adrizzle.py | interpret_maskval | def interpret_maskval(paramDict):
""" Apply logic for interpreting final_maskval value...
"""
# interpret user specified final_maskval value to use for initializing
# output SCI array...
if 'maskval' not in paramDict:
return 0
maskval = paramDict['maskval']
if maskval is None:
... | python | def interpret_maskval(paramDict):
""" Apply logic for interpreting final_maskval value...
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spacetelescope/drizzlepac | drizzlepac/adrizzle.py | run_driz | def run_driz(imageObjectList,output_wcs,paramDict,single,build,wcsmap=None):
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spacetelescope/drizzlepac | drizzlepac/adrizzle.py | run_driz_img | def run_driz_img(img,chiplist,output_wcs,outwcs,template,paramDict,single,
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spacetelescope/drizzlepac | drizzlepac/adrizzle.py | run_driz_chip | def run_driz_chip(img,chip,output_wcs,outwcs,template,paramDict,single,
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spacetelescope/drizzlepac | drizzlepac/adrizzle.py | do_driz | def do_driz(insci, input_wcs, inwht,
output_wcs, outsci, outwht, outcon,
expin, in_units, wt_scl,
wcslin_pscale=1.0,uniqid=1, pixfrac=1.0, kernel='square',
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"""
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output_wcs, outsci, outwht, outcon,
expin, in_units, wt_scl,
wcslin_pscale=1.0,uniqid=1, pixfrac=1.0, kernel='square',
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spacetelescope/drizzlepac | drizzlepac/mapreg.py | _regwrite | def _regwrite(shapelist,outfile):
""" Writes the current shape list out as a region file """
# This function corrects bugs and provides improvements over the pyregion's
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#
# 1. ShapeList.write crashes if regions have no comments;
# 2. ShapeList.write con... | python | def _regwrite(shapelist,outfile):
""" Writes the current shape list out as a region file """
# This function corrects bugs and provides improvements over the pyregion's
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#
# 1. ShapeList.write crashes if regions have no comments;
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spacetelescope/drizzlepac | drizzlepac/mapreg.py | _needs_ref_WCS | def _needs_ref_WCS(reglist):
""" Check if the region list contains shapes in image-like coordinates
"""
from pyregion.wcs_helper import image_like_coordformats
for r in reglist:
if r.coord_format in image_like_coordformats:
return True
return False | python | def _needs_ref_WCS(reglist):
""" Check if the region list contains shapes in image-like coordinates
"""
from pyregion.wcs_helper import image_like_coordformats
for r in reglist:
if r.coord_format in image_like_coordformats:
return True
return False | [
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spacetelescope/drizzlepac | drizzlepac/mapreg.py | extension_from_filename | def extension_from_filename(filename):
"""
Parse out filename from any specified extensions.
Returns rootname and string version of extension name.
"""
# Parse out any extension specified in filename
_indx1 = filename.find('[')
_indx2 = filename.find(']')
if _indx1 > 0:
# check f... | python | def extension_from_filename(filename):
"""
Parse out filename from any specified extensions.
Returns rootname and string version of extension name.
"""
# Parse out any extension specified in filename
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spacetelescope/drizzlepac | drizzlepac/mapreg.py | count_extensions | def count_extensions(img, extname='SCI'):
""" Return the number of 'extname' extensions. 'img' can be either a file
name, an HDU List object (from fits), or None (to get the number of all
HDU headers.
"""
if isinstance(img, str):
img = fits.open(img, memmap=False)
img.close()
eli... | python | def count_extensions(img, extname='SCI'):
""" Return the number of 'extname' extensions. 'img' can be either a file
name, an HDU List object (from fits), or None (to get the number of all
HDU headers.
"""
if isinstance(img, str):
img = fits.open(img, memmap=False)
img.close()
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spacetelescope/drizzlepac | drizzlepac/mapreg.py | get_extver_list | def get_extver_list(img, extname='SCI'):
""" Return a list of all extension versions of 'extname' extensions.
'img' can be either a file name or a HDU List object (from fits).
"""
if isinstance(img, str):
img = fits.open(img, memmap=False)
img.close()
elif not isinstance(img, fits.HD... | python | def get_extver_list(img, extname='SCI'):
""" Return a list of all extension versions of 'extname' extensions.
'img' can be either a file name or a HDU List object (from fits).
"""
if isinstance(img, str):
img = fits.open(img, memmap=False)
img.close()
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spacetelescope/drizzlepac | drizzlepac/mapreg.py | _check_FITS_extvers | def _check_FITS_extvers(img, extname, extvers):
"""Returns True if all (except None) extension versions specified by the
argument 'extvers' and that are of the type specified by the argument
'extname' are present in the 'img' FITS file. Returns False if some of the
extension versions for a given EXTNAME... | python | def _check_FITS_extvers(img, extname, extvers):
"""Returns True if all (except None) extension versions specified by the
argument 'extvers' and that are of the type specified by the argument
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spacetelescope/drizzlepac | drizzlepac/generate_final_product_filenames.py | run_generator | def run_generator(product_category,obs_info):
"""
This is the main calling subroutine. It decides which filename generation subroutine should be run based on the
input product_category, and then passes the information stored in input obs_info to the subroutine so that the
appropriate filenames can be ge... | python | def run_generator(product_category,obs_info):
"""
This is the main calling subroutine. It decides which filename generation subroutine should be run based on the
input product_category, and then passes the information stored in input obs_info to the subroutine so that the
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spacetelescope/drizzlepac | drizzlepac/generate_final_product_filenames.py | single_exposure_product_filename_generator | def single_exposure_product_filename_generator(obs_info,nn):
"""
Generate image and sourcelist filenames for single-exposure products
Parameters
----------
obs_info : list
list of items that will be used to generate the filenames: proposal_id,
visit_id, instrument, detector, filter,... | python | def single_exposure_product_filename_generator(obs_info,nn):
"""
Generate image and sourcelist filenames for single-exposure products
Parameters
----------
obs_info : list
list of items that will be used to generate the filenames: proposal_id,
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spacetelescope/drizzlepac | drizzlepac/generate_final_product_filenames.py | filter_product_filename_generator | def filter_product_filename_generator(obs_info,nn):
"""
Generate image and sourcelist filenames for filter products
Parameters
----------
obs_info : list
list of items that will be used to generate the filenames: proposal_id,
visit_id, instrument, detector, and filter
nn : strin... | python | def filter_product_filename_generator(obs_info,nn):
"""
Generate image and sourcelist filenames for filter products
Parameters
----------
obs_info : list
list of items that will be used to generate the filenames: proposal_id,
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spacetelescope/drizzlepac | drizzlepac/generate_final_product_filenames.py | total_detection_product_filename_generator | def total_detection_product_filename_generator(obs_info,nn):
"""
Generate image and sourcelist filenames for total detection products
Parameters
----------
obs_info : list
list of items that will be used to generate the filenames: proposal_id,
visit_id, instrument, and detector
... | python | def total_detection_product_filename_generator(obs_info,nn):
"""
Generate image and sourcelist filenames for total detection products
Parameters
----------
obs_info : list
list of items that will be used to generate the filenames: proposal_id,
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spacetelescope/drizzlepac | drizzlepac/generate_final_product_filenames.py | multivisit_mosaic_product_filename_generator | def multivisit_mosaic_product_filename_generator(obs_info,nn):
"""
Generate image and sourcelist filenames for multi-visit mosaic products
Parameters
----------
obs_info : list
list of items that will be used to generate the filenames: group_id,
instrument, detector, and filter
... | python | def multivisit_mosaic_product_filename_generator(obs_info,nn):
"""
Generate image and sourcelist filenames for multi-visit mosaic products
Parameters
----------
obs_info : list
list of items that will be used to generate the filenames: group_id,
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | build_referenceWCS | def build_referenceWCS(catalog_list):
""" Compute default reference WCS from list of Catalog objects.
"""
wcslist = []
for catalog in catalog_list:
for scichip in catalog.catalogs:
wcslist.append(catalog.catalogs[scichip]['wcs'])
return utils.output_wcs(wcslist) | python | def build_referenceWCS(catalog_list):
""" Compute default reference WCS from list of Catalog objects.
"""
wcslist = []
for catalog in catalog_list:
for scichip in catalog.catalogs:
wcslist.append(catalog.catalogs[scichip]['wcs'])
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | convex_hull | def convex_hull(points):
"""Computes the convex hull of a set of 2D points.
Implements `Andrew's monotone chain algorithm <http://en.wikibooks.org/wiki/Algorithm_Implementation/Geometry/Convex_hull/Monotone_chain>`_.
The algorithm has O(n log n) complexity.
Credit: `<http://en.wikibooks.org/wiki/Algor... | python | def convex_hull(points):
"""Computes the convex hull of a set of 2D points.
Implements `Andrew's monotone chain algorithm <http://en.wikibooks.org/wiki/Algorithm_Implementation/Geometry/Convex_hull/Monotone_chain>`_.
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | _estimate_2dhist_shift | def _estimate_2dhist_shift(imgxy, refxy, searchrad=3.0):
""" Create a 2D matrix-histogram which contains the delta between each
XY position and each UV position. Then estimate initial offset
between catalogs.
"""
print("Computing initial guess for X and Y shifts...")
# create ZP matrix
... | python | def _estimate_2dhist_shift(imgxy, refxy, searchrad=3.0):
""" Create a 2D matrix-histogram which contains the delta between each
XY position and each UV position. Then estimate initial offset
between catalogs.
"""
print("Computing initial guess for X and Y shifts...")
# create ZP matrix
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | _find_peak | def _find_peak(data, peak_fit_box=5, mask=None):
"""
Find location of the peak in an array. This is done by fitting a second
degree 2D polynomial to the data within a `peak_fit_box` and computing the
location of its maximum. An initial
estimate of the position of the maximum will be performed by sea... | python | def _find_peak(data, peak_fit_box=5, mask=None):
"""
Find location of the peak in an array. This is done by fitting a second
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.openFile | def openFile(self, openDQ=False):
""" Open file and set up filehandle for image file
"""
if self._im.closed:
if not self._dq.closed:
self._dq.release()
assert(self._dq.closed)
fi = FileExtMaskInfo(clobber=False,
... | python | def openFile(self, openDQ=False):
""" Open file and set up filehandle for image file
"""
if self._im.closed:
if not self._dq.closed:
self._dq.release()
assert(self._dq.closed)
fi = FileExtMaskInfo(clobber=False,
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.get_wcs | def get_wcs(self):
""" Helper method to return a list of all the input WCS objects associated
with this image.
"""
wcslist = []
for chip in self.chip_catalogs:
wcslist.append(self.chip_catalogs[chip]['wcs'])
return wcslist | python | def get_wcs(self):
""" Helper method to return a list of all the input WCS objects associated
with this image.
"""
wcslist = []
for chip in self.chip_catalogs:
wcslist.append(self.chip_catalogs[chip]['wcs'])
return wcslist | [
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.buildSkyCatalog | def buildSkyCatalog(self):
""" Convert sky catalog for all chips into a single catalog for
the entire field-of-view of this image.
"""
self.all_radec = None
self.all_radec_orig = None
ralist = []
declist = []
fluxlist = []
idlist = []
f... | python | def buildSkyCatalog(self):
""" Convert sky catalog for all chips into a single catalog for
the entire field-of-view of this image.
"""
self.all_radec = None
self.all_radec_orig = None
ralist = []
declist = []
fluxlist = []
idlist = []
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.buildDefaultRefWCS | def buildDefaultRefWCS(self):
""" Generate a default reference WCS for this image. """
self.default_refWCS = None
if self.use_wcs:
wcslist = []
for scichip in self.chip_catalogs:
wcslist.append(self.chip_catalogs[scichip]['wcs'])
self.default_r... | python | def buildDefaultRefWCS(self):
""" Generate a default reference WCS for this image. """
self.default_refWCS = None
if self.use_wcs:
wcslist = []
for scichip in self.chip_catalogs:
wcslist.append(self.chip_catalogs[scichip]['wcs'])
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.transformToRef | def transformToRef(self,ref_wcs,force=False):
""" Transform sky coords from ALL chips into X,Y coords in reference WCS.
"""
if not isinstance(ref_wcs, pywcs.WCS):
print(textutil.textbox('Reference WCS not a valid HSTWCS object'),
file=sys.stderr)
raise V... | python | def transformToRef(self,ref_wcs,force=False):
""" Transform sky coords from ALL chips into X,Y coords in reference WCS.
"""
if not isinstance(ref_wcs, pywcs.WCS):
print(textutil.textbox('Reference WCS not a valid HSTWCS object'),
file=sys.stderr)
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.sortSkyCatalog | def sortSkyCatalog(self):
""" Sort and clip the source catalog based on the flux range specified
by the user. It keeps a copy of the original full list in order to
support iteration.
"""
if len(self.all_radec_orig[2].nonzero()[0]) == 0:
warn_str = "Source catalog NOT... | python | def sortSkyCatalog(self):
""" Sort and clip the source catalog based on the flux range specified
by the user. It keeps a copy of the original full list in order to
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"""
if len(self.all_radec_orig[2].nonzero()[0]) == 0:
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.match | def match(self,refimage, quiet_identity, **kwargs):
""" Uses xyxymatch to cross-match sources between this catalog and
a reference catalog (refCatalog).
"""
ref_outxy = refimage.outxy
refWCS = refimage.wcs
refname = refimage.name
ref_inxy = refimage.xy_catalog... | python | def match(self,refimage, quiet_identity, **kwargs):
""" Uses xyxymatch to cross-match sources between this catalog and
a reference catalog (refCatalog).
"""
ref_outxy = refimage.outxy
refWCS = refimage.wcs
refname = refimage.name
ref_inxy = refimage.xy_catalog... | [
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.performFit | def performFit(self,**kwargs):
""" Perform a fit between the matched sources.
Parameters
----------
kwargs : dict
Parameter necessary to perform the fit; namely, *fitgeometry*.
Notes
-----
This task still needs to implemen... | python | def performFit(self,**kwargs):
""" Perform a fit between the matched sources.
Parameters
----------
kwargs : dict
Parameter necessary to perform the fit; namely, *fitgeometry*.
Notes
-----
This task still needs to implemen... | [
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.updateHeader | def updateHeader(self, wcsname=None, reusename=False):
""" Update header of image with shifts computed by *perform_fit()*.
"""
# Insure filehandle is open and available...
self.openFile()
verbose_level = 1
if not self.perform_update:
verbose_level = 0
... | python | def updateHeader(self, wcsname=None, reusename=False):
""" Update header of image with shifts computed by *perform_fit()*.
"""
# Insure filehandle is open and available...
self.openFile()
verbose_level = 1
if not self.perform_update:
verbose_level = 0
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.writeHeaderlet | def writeHeaderlet(self,**kwargs):
""" Write and/or attach a headerlet based on update to PRIMARY WCS
"""
# Insure filehandle is open and available...
self.openFile()
pars = kwargs.copy()
rms_pars = self.fit['rms_keys']
str_kw = ['descrip','history','author','hd... | python | def writeHeaderlet(self,**kwargs):
""" Write and/or attach a headerlet based on update to PRIMARY WCS
"""
# Insure filehandle is open and available...
self.openFile()
pars = kwargs.copy()
rms_pars = self.fit['rms_keys']
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.write_skycatalog | def write_skycatalog(self,filename):
""" Write out the all_radec catalog for this image to a file.
"""
if self.all_radec is None:
return
ralist = self.all_radec[0]#.tolist()
declist = self.all_radec[1]#.tolist()
f = open(filename,'w')
f.write("#Sky pos... | python | def write_skycatalog(self,filename):
""" Write out the all_radec catalog for this image to a file.
"""
if self.all_radec is None:
return
ralist = self.all_radec[0]#.tolist()
declist = self.all_radec[1]#.tolist()
f = open(filename,'w')
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.get_xy_catnames | def get_xy_catnames(self):
""" Return a string with the names of input_xy catalog names
"""
catstr = self.name+' '
if 'input_xy' in self.catalog_names:
for xycat in self.catalog_names['input_xy']:
catstr += ' '+xycat
return catstr + '\n' | python | def get_xy_catnames(self):
""" Return a string with the names of input_xy catalog names
"""
catstr = self.name+' '
if 'input_xy' in self.catalog_names:
for xycat in self.catalog_names['input_xy']:
catstr += ' '+xycat
return catstr + '\n' | [
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.write_fit_catalog | def write_fit_catalog(self):
""" Write out the catalog of all sources and resids used in the final fit.
"""
if self.pars['writecat']:
log.info('Creating catalog for the fit: {:s}'.format(self.catalog_names['fitmatch']))
f = open(self.catalog_names['fitmatch'],'w')
... | python | def write_fit_catalog(self):
""" Write out the catalog of all sources and resids used in the final fit.
"""
if self.pars['writecat']:
log.info('Creating catalog for the fit: {:s}'.format(self.catalog_names['fitmatch']))
f = open(self.catalog_names['fitmatch'],'w')
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.write_outxy | def write_outxy(self,filename):
""" Write out the output(transformed) XY catalog for this image to a file.
"""
f = open(filename,'w')
f.write("#Pixel positions for: "+self.name+'\n')
f.write("#X Y\n")
f.write("#(pix) (pix)\n")
for i in range(self.a... | python | def write_outxy(self,filename):
""" Write out the output(transformed) XY catalog for this image to a file.
"""
f = open(filename,'w')
f.write("#Pixel positions for: "+self.name+'\n')
f.write("#X Y\n")
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.get_shiftfile_row | def get_shiftfile_row(self):
""" Return the information for a shiftfile for this image to provide
compatability with the IRAF-based MultiDrizzle.
"""
if self.fit is not None:
rowstr = '%s %0.6f %0.6f %0.6f %0.6f %0.6f %0.6f\n'%(
self.name... | python | def get_shiftfile_row(self):
""" Return the information for a shiftfile for this image to provide
compatability with the IRAF-based MultiDrizzle.
"""
if self.fit is not None:
rowstr = '%s %0.6f %0.6f %0.6f %0.6f %0.6f %0.6f\n'%(
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | Image.clean | def clean(self):
""" Remove intermediate files created.
"""
#TODO: add cleaning of mask files, *if* created ...
for f in self.catalog_names:
if 'match' in f:
if os.path.exists(self.catalog_names[f]):
log.info('Deleting intermediate match fi... | python | def clean(self):
""" Remove intermediate files created.
"""
#TODO: add cleaning of mask files, *if* created ...
for f in self.catalog_names:
if 'match' in f:
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | RefImage.write_skycatalog | def write_skycatalog(self, filename, show_flux=False, show_id=False):
""" Write out the all_radec catalog for this image to a file.
"""
f = open(filename,'w')
f.write("#Sky positions for cumulative reference catalog. Initial catalog from: "+self.name+'\n')
header1 = "#RA D... | python | def write_skycatalog(self, filename, show_flux=False, show_id=False):
""" Write out the all_radec catalog for this image to a file.
"""
f = open(filename,'w')
f.write("#Sky positions for cumulative reference catalog. Initial catalog from: "+self.name+'\n')
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | RefImage.transformToRef | def transformToRef(self):
""" Transform reference catalog sky positions (self.all_radec)
to reference tangent plane (self.wcs) to create output X,Y positions.
"""
if 'refxyunits' in self.pars and self.pars['refxyunits'] == 'pixels':
log.info('Creating RA/Dec positions for ref... | python | def transformToRef(self):
""" Transform reference catalog sky positions (self.all_radec)
to reference tangent plane (self.wcs) to create output X,Y positions.
"""
if 'refxyunits' in self.pars and self.pars['refxyunits'] == 'pixels':
log.info('Creating RA/Dec positions for ref... | [
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spacetelescope/drizzlepac | drizzlepac/imgclasses.py | RefImage.clean | def clean(self):
""" Remove intermediate files created
"""
if not util.is_blank(self.catalog.catname) and os.path.exists(self.catalog.catname):
os.remove(self.catalog.catname) | python | def clean(self):
""" Remove intermediate files created
"""
if not util.is_blank(self.catalog.catname) and os.path.exists(self.catalog.catname):
os.remove(self.catalog.catname) | [
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spacetelescope/drizzlepac | drizzlepac/imageObject.py | baseImageObject.close | def close(self):
""" Close the object nicely and release all the data
arrays from memory YOU CANT GET IT BACK, the pointers
and data are gone so use the getData method to get
the data array returned for future use. You can use
putData to reattach a new data array ... | python | def close(self):
""" Close the object nicely and release all the data
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spacetelescope/drizzlepac | drizzlepac/imageObject.py | baseImageObject.clean | def clean(self):
""" Deletes intermediate products generated for this imageObject.
"""
clean_files = ['blotImage','crmaskImage','finalMask',
'staticMask','singleDrizMask','outSky',
'outSContext','outSWeight','outSingle',
'ou... | python | def clean(self):
""" Deletes intermediate products generated for this imageObject.
"""
clean_files = ['blotImage','crmaskImage','finalMask',
'staticMask','singleDrizMask','outSky',
'outSContext','outSWeight','outSingle',
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spacetelescope/drizzlepac | drizzlepac/imageObject.py | baseImageObject.getData | def getData(self,exten=None):
""" Return just the data array from the specified extension
fileutil is used instead of fits to account for non-
FITS input images. openImage returns a fits object.
"""
if exten.lower().find('sci') > -1:
# For SCI extensions, the ... | python | def getData(self,exten=None):
""" Return just the data array from the specified extension
fileutil is used instead of fits to account for non-
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"""
if exten.lower().find('sci') > -1:
# For SCI extensions, the ... | [
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spacetelescope/drizzlepac | drizzlepac/imageObject.py | baseImageObject.getHeader | def getHeader(self,exten=None):
""" Return just the specified header extension fileutil
is used instead of fits to account for non-FITS
input images. openImage returns a fits object.
"""
_image=fileutil.openImage(self._filename, clobber=False, memmap=False)
_heade... | python | def getHeader(self,exten=None):
""" Return just the specified header extension fileutil
is used instead of fits to account for non-FITS
input images. openImage returns a fits object.
"""
_image=fileutil.openImage(self._filename, clobber=False, memmap=False)
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spacetelescope/drizzlepac | drizzlepac/imageObject.py | baseImageObject.updateData | def updateData(self,exten,data):
""" Write out updated data and header to
the original input file for this object.
"""
_extnum=self._interpretExten(exten)
fimg = fileutil.openImage(self._filename, mode='update', memmap=False)
fimg[_extnum].data = data
fimg[_ex... | python | def updateData(self,exten,data):
""" Write out updated data and header to
the original input file for this object.
"""
_extnum=self._interpretExten(exten)
fimg = fileutil.openImage(self._filename, mode='update', memmap=False)
fimg[_extnum].data = data
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spacetelescope/drizzlepac | drizzlepac/imageObject.py | baseImageObject.putData | def putData(self,data=None,exten=None):
""" Now that we are removing the data from the object to save memory,
we need something that cleanly puts the data array back into
the object so that we can write out everything together using
something like fits.writeto....this method... | python | def putData(self,data=None,exten=None):
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spacetelescope/drizzlepac | drizzlepac/imageObject.py | baseImageObject.getAllData | def getAllData(self,extname=None,exclude=None):
""" This function is meant to make it easier to attach ALL the data
extensions of the image object so that we can write out copies of
the original image nicer.
If no extname is given, the it retrieves all data from the original... | python | def getAllData(self,extname=None,exclude=None):
""" This function is meant to make it easier to attach ALL the data
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the original image nicer.
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spacetelescope/drizzlepac | drizzlepac/imageObject.py | baseImageObject.returnAllChips | def returnAllChips(self,extname=None,exclude=None):
""" Returns a list containing all the chips which match the
extname given minus those specified for exclusion (if any).
"""
extensions = self._findExtnames(extname=extname,exclude=exclude)
chiplist = []
for i in rang... | python | def returnAllChips(self,extname=None,exclude=None):
""" Returns a list containing all the chips which match the
extname given minus those specified for exclusion (if any).
"""
extensions = self._findExtnames(extname=extname,exclude=exclude)
chiplist = []
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