idx int64 0 63k | question stringlengths 61 4.03k | target stringlengths 6 1.23k |
|---|---|---|
61,600 | 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 . |
61,601 | 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 . |
61,602 | 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 . |
61,603 | 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 ... | Return mime data previously attached to surface using the specified mime type . |
61,604 | 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 . cairo_surface_write_to_png_stream ( self . _pointer , write_func , ffi . NULL ) ) else : _check_status ... | Writes the contents of surface as a PNG image . |
61,605 | def create_from_png ( cls , source ) : 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__ ( cl... | Decode a PNG file into a new image surface . |
61,606 | def add_outline ( self , parent_id , utf8 , link_attribs , flags = None ) : 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 | Add an item to the document outline hierarchy . |
61,607 | def set_metadata ( self , metadata , utf8 ) : cairo . cairo_pdf_surface_set_metadata ( self . _pointer , metadata , _encode_string ( utf8 ) ) self . _check_status ( ) | Sets document metadata . |
61,608 | 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 . |
61,609 | 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 . |
61,610 | 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 . |
61,611 | 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 . |
61,612 | 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 . |
61,613 | 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 . |
61,614 | def _encode_string ( string ) : if not isinstance ( string , bytes ) : string = string . encode ( 'utf8' ) return ffi . new ( 'char[]' , string ) | Return a byte string encoding Unicode with UTF - 8 . |
61,615 | def text_to_glyphs ( self , x , y , text , with_clusters ) : 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_f... | 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 . |
61,616 | def set_variations ( self , variations ) : if variations is None : variations = ffi . NULL else : variations = _encode_string ( variations ) cairo . cairo_font_options_set_variations ( self . _pointer , variations ) self . _check_status ( ) | Sets the OpenType font variations for the font options object . |
61,617 | def get_variations ( self ) : variations = cairo . cairo_font_options_get_variations ( self . _pointer ) if variations != ffi . NULL : return ffi . string ( variations ) . decode ( 'utf8' , 'replace' ) | Gets the OpenType font variations for the font options object . |
61,618 | def decode_to_pixbuf ( image_data , width = None , height = None ) : 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 . g... | Decode an image from memory with GDK - PixBuf . The file format is detected automatically . |
61,619 | def decode_to_image_surface ( image_data , width = None , height = None ) : 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 ) )... | Decode an image from memory into a cairo surface . The file format is detected automatically . |
61,620 | def pixbuf_to_cairo_gdk ( pixbuf ) : 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 ( ) | Convert from PixBuf to ImageSurface using GDK . |
61,621 | def pixbuf_to_cairo_slices ( 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 ... | Convert from PixBuf to ImageSurface using slice - based byte swapping . |
61,622 | def pixbuf_to_cairo_png ( pixbuf ) : 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... | Convert from PixBuf to ImageSurface by going through the PNG format . |
61,623 | def probePlayer ( requested_player = '' ) : 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 ( [... | Probes the multimedia players which are available on the host system . |
61,624 | 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 ( ... | use a multimedia player to play a stream |
61,625 | 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 = "... | send keystroke command to player |
61,626 | 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 |
61,627 | 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 : ret... | format mplayer s title |
61,628 | def _format_volume_string ( self , volume_string ) : return '[' + volume_string [ volume_string . find ( self . volume_string ) : ] . replace ( ' %' , '%' ) . replace ( 'ume' , '' ) + '] ' | format mplayer s volume |
61,629 | 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 |
61,630 | 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 : ret_string = self . icy_title_prefix + sp [ 1 ] return self . _title_string_format_text_tag ( ret_string ) | format vlc s title |
61,631 | def _is_accepted_input ( self , input_string ) : 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 | vlc input filtering |
61,632 | def _no_mute_on_stop_playback ( self ) : 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'... | make sure vlc does not stop muted |
61,633 | def _check_stations_csv ( self , usr , root ) : if path . exists ( path . join ( usr , 'stations.csv' ) ) : return else : 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 |
61,634 | def _is_playlist_in_config_dir ( self ) : 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... | Check if a csv file is in the config dir |
61,635 | def _playlist_format_changed ( self ) : 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 | Check if we have new or old format and report if format has changed |
61,636 | def save_playlist_file ( self , stationFile = '' ) : 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 ) : ... | Save a playlist Create a txt file and write stations in it . Then rename it to final target |
61,637 | def _bytes_to_human ( self , B ) : KB = float ( 1024 ) MB = float ( KB ** 2 ) GB = float ( KB ** 3 ) TB = float ( KB ** 4 ) 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 the given bytes as a human friendly KB MB GB or TB string |
61,638 | def append_station ( self , params , stationFile = '' ) : 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... | Append a station to csv file |
61,639 | def _check_config_file ( self , usr ) : package_config_file = path . join ( path . dirname ( __file__ ) , 'config' ) user_config_file = path . join ( usr , 'config' ) if path . exists ( user_config_file + '.restore' ) : try : copyfile ( user_config_file + '.restore' , user_config_file ) remove ( self . user_config_file... | Make sure a config file exists in the config dir |
61,640 | def save_config ( self ) : if not self . opts [ 'dirty_config' ] [ 1 ] : if logger . isEnabledFor ( logging . INFO ) : logger . info ( 'Config not saved (not modified)' ) return 1 txt = copyfile ( self . config_file , self . config_file + '.restore' ) if self . opts [ 'default_station' ] [ 1 ] is None : self . opts [ '... | Save config file |
61,641 | def ctrl_c_handler ( self , signum , frame ) : self . ctrl_c_pressed = True if self . _cnf . dirty_playlist : self . saveCurrentPlaylist ( ) self . _cnf . save_config ( ) | Try to auto save config on exit Do not check result!!! |
61,642 | def _goto_playing_station ( self , changing_playlist = False ) : 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 ... | make sure playing station is visible |
61,643 | def setStation ( self , number ) : 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 - maxDisplayedItem... | Select the given station number |
61,644 | def _format_playlist_line ( self , lineNum , pad , station ) : 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_d... | format playlist line so that if fills self . maxX |
61,645 | 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 init and row >... | if the selection at the end of the list try to scroll down |
61,646 | 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 : bytes . append ( char ) elif 192 <= char <= 223 : bytes . append ( char ) bytes . append ( get_check_next_byte ( ) ) elif 224 <= char <= 2... | no zero byte allowed |
61,647 | def _get_history_next ( self ) : if self . _has_history : ret = self . _input_history . return_history ( 1 ) self . string = ret self . _curs_pos = len ( ret ) | callback function for key down |
61,648 | def apply_transformations ( collection , transformations , select = None ) : 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 ... | Apply all transformations to the variables in the collection . |
61,649 | def setup ( self , steps = None , drop_na = False , ** kwargs ) : input_nodes = None selectors = self . model . get ( 'input' , { } ) . copy ( ) selectors . update ( kwargs ) for i , b in enumerate ( self . steps ) : if steps is not None and i not in steps and b . name not in steps : continue b . setup ( input_nodes , ... | Set up the sequence of steps for analysis . |
61,650 | def setup ( self , input_nodes = None , drop_na = False , ** kwargs ) : self . output_nodes = [ ] input_nodes = input_nodes or self . input_nodes or [ ] if self . level != 'run' : kwargs = kwargs . copy ( ) kwargs . pop ( 'scan_length' , None ) collections = self . layout . get_collections ( self . level , drop_na = dr... | Set up the Step and construct the design matrix . |
61,651 | def get_slice_info ( slice_times ) : 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_... | Extract slice order from slice timing info . |
61,652 | def get_sizestr ( img ) : 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 ] *... | Extract and reformat voxel size matrix size field of view and number of slices into pretty strings . |
61,653 | def add_config_paths ( ** kwargs ) : 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... | Add to the pool of available configuration files for BIDSLayout . |
61,654 | def add_derivatives ( self , path , ** kwargs ) : paths = listify ( path ) deriv_dirs = [ ] 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_descriptio... | Add BIDS - Derivatives datasets to tracking . |
61,655 | def get_file ( self , filename , scope = 'all' ) : 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 | Returns the BIDSFile object with the specified path . |
61,656 | def get_collections ( self , level , types = None , variables = None , merge = False , sampling_rate = None , skip_empty = False , ** kwargs ) : from bids . variables import load_variables index = load_variables ( self , types = types , levels = level , skip_empty = skip_empty , ** kwargs ) return index . get_collectio... | Return one or more variable Collections in the BIDS project . |
61,657 | def get_metadata ( self , path , include_entities = False , ** kwargs ) : f = self . get_file ( path ) 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 | Return metadata found in JSON sidecars for the specified file . |
61,658 | def get_bval ( self , path , ** kwargs ) : result = self . get_nearest ( path , extensions = 'bval' , suffix = 'dwi' , all_ = True , ** kwargs ) return listify ( result ) [ 0 ] | Get bval file for passed path . |
61,659 | def copy_files ( self , files = None , path_patterns = None , symbolic_links = True , root = None , conflicts = 'fail' , ** kwargs ) : _files = self . get ( return_type = 'objects' , ** kwargs ) if files : _files = list ( set ( files ) . intersection ( _files ) ) for f in _files : f . copy ( path_patterns , symbolic_li... | Copies one or more BIDSFiles to new locations defined by each BIDSFile s entities and the specified path_patterns . |
61,660 | def index_file ( self , f , overwrite = False ) : 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 : return md = self . _get_metadata ( f . path ) for md_key , md_val in md . items ( ) : if md_key no... | Index metadata for the specified file . |
61,661 | def search ( self , files = None , defined_fields = None , ** kwargs ) : 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 files is None : files = set ( self . layout ... | Search files in the layout by metadata fields . |
61,662 | def auto_model ( layout , scan_length = None , one_vs_rest = False ) : base_name = split ( layout . root ) [ - 1 ] tasks = layout . entities [ 'task' ] . unique ( ) task_models = [ ] for task_name in tasks : model = OrderedDict ( ) model [ "Name" ] = "_" . join ( [ base_name , task_name ] ) model [ "Description" ] = ( ... | 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 . |
61,663 | def split ( self , 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... | Split the current SparseRunVariable into multiple columns . |
61,664 | def select_rows ( self , rows ) : 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 ) | Truncate internal arrays to keep only the specified rows . |
61,665 | def split ( self , 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 ... | Split the current DenseRunVariable into multiple columns . |
61,666 | def _build_entity_index ( self , run_info , sampling_rate ) : 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 , c... | Build the entity index from run information . |
61,667 | def resample ( self , sampling_rate , inplace = False , kind = '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... | Resample the Variable to the specified sampling rate . |
61,668 | def to_df ( self , condition = True , entities = True , timing = True , sampling_rate = None ) : 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 [ 'o... | Convert to a DataFrame with columns for name and entities . |
61,669 | def get_collections ( self , unit , names = None , merge = False , sampling_rate = None , ** entities ) : 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 ... | Retrieve variable data for a specified level in the Dataset . |
61,670 | def get_or_create_node ( self , level , entities , * args , ** kwargs ) : 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 res... | Retrieves a child Node based on the specified criteria creating a new Node if necessary . |
61,671 | def merge_collections ( collections , force_dense = False , sampling_rate = 'auto' ) : 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 ... | Merge two or more collections at the same level of analysis . |
61,672 | def merge_variables ( variables , ** kwargs ) : 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 ( ) ) ] | Concatenates Variables along row axis . |
61,673 | def to_df ( self , variables = None , format = 'wide' , fillna = np . nan , ** kwargs ) : if variables is None : variables = list ( self . variables . keys ( ) ) if not isinstance ( variables [ 0 ] , BIDSVariable ) : variables = [ v for v in self . variables . values ( ) if v . name in variables ] dfs = [ v . to_df ( *... | Merge variables into a single pandas DataFrame . |
61,674 | def from_df ( cls , data , entities = None , source = 'contrast' ) : 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 ( SimpleVariabl... | Create a Collection from a pandas DataFrame . |
61,675 | def clone ( self ) : clone = copy ( self ) clone . variables = { k : v . clone ( ) for ( k , v ) in self . variables . items ( ) } return clone | Returns a shallow copy of the current instance except that all variables are deep - cloned . |
61,676 | def _index_entities ( self ) : 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 ] . drop... | Sets current instance s entities based on the existing index . |
61,677 | def match_variables ( self , pattern , return_type = 'name' ) : 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_ ] | Return columns whose names match the provided regex pattern . |
61,678 | def to_df ( self , variables = None , format = 'wide' , sparse = True , sampling_rate = None , include_sparse = True , include_dense = True , ** kwargs ) : 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... | Merge columns into a single pandas DataFrame . |
61,679 | def _transform ( self , var ) : self . collection . variables . pop ( var . name ) return var . values | Rename happens automatically in the base class so all we need to do is unset the original variable in the collection . |
61,680 | def replace_entities ( entities , 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 defa... | Replaces all entity names in a given pattern with the corresponding values provided by entities . |
61,681 | def write_contents_to_file ( path , contents = None , link_to = None , content_mode = 'text' , root = None , conflicts = '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... | Uses provided filename patterns to write contents to a new path given a corresponding entity map . |
61,682 | 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 ( 'Num... | Generate the methods section . |
61,683 | def _report_subject ( self , subject , ** kwargs ) : description_list = [ ] 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 .... | Write a report for a single subject . |
61,684 | def _gamma_difference_hrf ( tr , oversampling = 50 , time_length = 32. , onset = 0. , delay = 6 , undershoot = 16. , dispersion = 1. , u_dispersion = 1. , ratio = 0.167 ) : from scipy . stats import gamma dt = tr / oversampling time_stamps = np . linspace ( 0 , time_length , np . rint ( float ( time_length ) / dt ) . a... | Compute an hrf as the difference of two gamma functions |
61,685 | def spm_hrf ( tr , oversampling = 50 , time_length = 32. , onset = 0. ) : return _gamma_difference_hrf ( tr , oversampling , time_length , onset ) | Implementation of the SPM hrf model |
61,686 | def glover_hrf ( tr , oversampling = 50 , time_length = 32. , onset = 0. ) : return _gamma_difference_hrf ( tr , oversampling , time_length , onset , delay = 6 , undershoot = 12. , dispersion = .9 , u_dispersion = .9 , ratio = .35 ) | Implementation of the Glover hrf model |
61,687 | def spm_dispersion_derivative ( tr , oversampling = 50 , time_length = 32. , onset = 0. ) : 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 | Implementation of the SPM dispersion derivative hrf model |
61,688 | def glover_dispersion_derivative ( tr , oversampling = 50 , time_length = 32. , onset = 0. ) : 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 , o... | Implementation of the Glover dispersion derivative hrf model |
61,689 | def _sample_condition ( exp_condition , frame_times , oversampling = 50 , min_onset = - 24 ) : 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 ) * ove... | Make a possibly oversampled event regressor from condition information . |
61,690 | def _resample_regressor ( hr_regressor , hr_frame_times , frame_times ) : from scipy . interpolate import interp1d f = interp1d ( hr_frame_times , hr_regressor ) return f ( frame_times ) . T | this function sub - samples the regressors at frame times |
61,691 | def _orthogonalize ( X ) : 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 ] ) ) return X | Orthogonalize every column of design X w . r . t preceding columns |
61,692 | def _regressor_names ( con_name , hrf_model , fir_delays = None ) : 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 + derivati... | Returns a list of regressor names computed from con - name and hrf type |
61,693 | def _hrf_kernel ( hrf_model , tr , oversampling = 50 , fir_delays = None ) : acceptable_hrfs = [ 'spm' , 'spm + derivative' , 'spm + derivative + dispersion' , 'fir' , 'glover' , 'glover + derivative' , 'glover + derivative + dispersion' , None ] if hrf_model == 'spm' : hkernel = [ spm_hrf ( tr , oversampling ) ] elif ... | Given the specification of the hemodynamic model and time parameters return the list of matching kernels |
61,694 | def compute_regressor ( exp_condition , hrf_model , frame_times , con_id = 'cond' , oversampling = 50 , fir_delays = None , min_onset = - 24 ) : tr = float ( frame_times . max ( ) ) / ( np . size ( frame_times ) - 1 ) hr_regressor , hr_frame_times = _sample_condition ( exp_condition , frame_times , oversampling , min_o... | This is the main function to convolve regressors with hrf model |
61,695 | def matches_entities ( obj , entities , strict = False ) : if strict and set ( obj . entities . keys ( ) ) != set ( entities . keys ( ) ) : return False comm_ents = list ( set ( obj . entities . keys ( ) ) & set ( entities . keys ( ) ) ) for k in comm_ents : current = obj . entities [ k ] target = entities [ k ] if isi... | Checks whether an object s entities match the input . |
61,696 | def check_path_matches_patterns ( path , patterns ) : path = os . path . abspath ( path ) for patt in patterns : if isinstance ( patt , six . string_types ) : if path == patt : return True elif patt . search ( path ) : return True return False | Check if the path matches at least one of the provided patterns . |
61,697 | def count ( self , files = False ) : return len ( self . files ) if files else len ( self . unique ( ) ) | Returns a count of unique values or files . |
61,698 | def general_acquisition_info ( metadata ) : out_str = ( 'MR data were acquired using a {tesla}-Tesla {manu} {model} ' 'MRI scanner.' ) out_str = out_str . format ( tesla = metadata . get ( 'MagneticFieldStrength' , 'UNKNOWN' ) , manu = metadata . get ( 'Manufacturer' , 'MANUFACTURER' ) , model = metadata . get ( 'Manuf... | General sentence on data acquisition . Should be first sentence in MRI data acquisition section . |
61,699 | def parse_niftis ( layout , niftis , subj , config , ** kwargs ) : kwargs = { k : v for k , v in kwargs . items ( ) if v is not None } description_list = [ ] skip_task = { } for nifti_struct in niftis : nii_file = nifti_struct . path metadata = layout . get_metadata ( nii_file ) if not metadata : LOGGER . warning ( 'No... | Loop through niftis in a BIDSLayout and generate the appropriate description type for each scan . Compile all of the descriptions into a list . |
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