idx int64 0 251k | question stringlengths 53 3.53k | target stringlengths 5 1.23k | len_question int64 20 893 | len_target int64 3 238 |
|---|---|---|---|---|
243,900 | def list_attributes ( self , namespace = None , network = None , verbose = False ) : network = check_network ( self , network , verbose = verbose ) PARAMS = set_param ( [ "namespace" , "network" ] , [ namespace , network ] ) response = api ( url = self . __url + "/list attributes" , PARAMS = PARAMS , method = "POST" , ... | Returns a list of column names assocated with a network . | 98 | 12 |
243,901 | def rename ( self , name = None , sourceNetwork = None , verbose = False ) : sourceNetwork = check_network ( self , sourceNetwork , verbose = verbose ) PARAMS = set_param ( [ "name" , "sourceNetwork" ] , [ name , sourceNetwork ] ) response = api ( url = self . __url + "/rename" , PARAMS = PARAMS , method = "POST" , ver... | Rename an existing network . The SUID of the network is returned | 99 | 14 |
243,902 | def new ( self , verbose = False ) : response = api ( url = self . __url + "/new" , verbose = verbose ) return response | Destroys the current session and creates a new empty one . | 34 | 13 |
243,903 | def open ( self , session_file = None , session_url = None , verbose = False ) : PARAMS = set_param ( [ "file" , "url" ] , [ session_file , session_url ] ) response = api ( url = self . __url + "/open" , PARAMS = PARAMS , verbose = verbose ) return response | Opens a session from a local file or URL . | 79 | 11 |
243,904 | def save ( self , session_file , verbose = False ) : PARAMS = { "file" : session_file } response = api ( url = self . __url + "/save" , PARAMS = PARAMS , verbose = verbose ) return response | Saves the current session to an existing file which will be replaced . If this is a new session that has not been saved yet use save as instead . | 56 | 31 |
243,905 | def apply ( self , styles = None , verbose = False ) : PARAMS = set_param ( [ "styles" ] , [ styles ] ) response = api ( url = self . __url + "/apply" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Applies the specified style to the selected views and returns the SUIDs of the affected views . | 67 | 19 |
243,906 | def create_style ( self , title = None , defaults = None , mappings = None , verbose = VERBOSE ) : u = self . __url host = u . split ( "//" ) [ 1 ] . split ( ":" ) [ 0 ] port = u . split ( ":" ) [ 2 ] . split ( "/" ) [ 0 ] version = u . split ( ":" ) [ 2 ] . split ( "/" ) [ 1 ] if defaults : defaults_ = [ ] for d in de... | Creates a new visual style | 293 | 6 |
243,907 | def update_style ( self , title = None , defaults = None , mappings = None , verbose = False ) : u = self . __url host = u . split ( "//" ) [ 1 ] . split ( ":" ) [ 0 ] port = u . split ( ":" ) [ 2 ] . split ( "/" ) [ 0 ] version = u . split ( ":" ) [ 2 ] . split ( "/" ) [ 1 ] if defaults : defaults_ = [ ] for d in defa... | Updates a visual style | 473 | 5 |
243,908 | def simple_defaults ( self , defaults_dic ) : defaults = [ ] for d in defaults_dic . keys ( ) : dic = { } dic [ "visualProperty" ] = d dic [ "value" ] = defaults_dic [ d ] defaults . append ( dic ) return defaults | Simplifies defaults . | 69 | 5 |
243,909 | def attribute_circle ( self , EdgeAttribute = None , network = None , NodeAttribute = None , nodeList = None , singlePartition = None , spacing = None , verbose = False ) : network = check_network ( self , network , verbose = verbose ) PARAMS = set_param ( [ "EdgeAttribute" , "network" , "NodeAttribute" , "nodeList" , ... | Execute the Attribute Circle Layout on a network . | 153 | 11 |
243,910 | def attributes_layout ( self , EdgeAttribute = None , maxwidth = None , minrad = None , network = None , NodeAttribute = None , nodeList = None , radmult = None , spacingx = None , spacingy = None , verbose = False ) : network = check_network ( self , network , verbose = verbose ) PARAMS = set_param ( [ "EdgeAttribute"... | Execute the Group Attributes Layout on a network | 178 | 9 |
243,911 | def circular ( self , EdgeAttribute = None , leftEdge = None , network = None , NodeAttribute = None , nodeHorizontalSpacing = None , nodeList = None , nodeVerticalSpacing = None , rightMargin = None , singlePartition = None , topEdge = None , verbose = None ) : network = check_network ( self , network , verbose = verb... | Execute the Circular Layout on a network | 225 | 9 |
243,912 | def copycat ( self , gridUnmapped = None , selectUnmapped = None , sourceColumn = None , sourceNetwork = None , targetColumn = None , targetNetwork = None , verbose = None ) : PARAMS = set_param ( [ 'gridUnmapped' , 'selectUnmapped' , 'sourceColumn' , 'sourceNetwork' , 'targetColumn' , 'targetNetwork' ] , [ gridUnmappe... | Sets the coordinates for each node in the target network to the coordinates of a matching node in the source network . Optional parameters such as gridUnmapped and selectUnmapped determine the behavior of target network nodes that could not be matched . | 149 | 49 |
243,913 | def degree_circle ( self , EdgeAttribute = None , network = None , NodeAttribute = None , nodeList = None , singlePartition = None , verbose = None ) : network = check_network ( self , network , verbose = verbose ) PARAMS = set_param ( [ 'EdgeAttribute' , 'network' , 'NodeAttribute' , 'nodeList' , 'singlePartition' ] ,... | Execute the Degree Sorted Circle Layout on a network . | 142 | 12 |
243,914 | def force_directed ( self , defaultEdgeWeight = None , defaultNodeMass = None , defaultSpringCoefficient = None , defaultSpringLength = None , EdgeAttribute = None , isDeterministic = None , maxWeightCutoff = None , minWeightCutoff = None , network = None , NodeAttribute = None , nodeList = None , numIterations = None ... | Execute the Prefuse Force Directed Layout on a network | 295 | 12 |
243,915 | def genemania_force_directed ( self , curveSteepness = None , defaultEdgeWeight = None , defaultSpringCoefficient = None , defaultSpringLength = None , EdgeAttribute = None , ignoreHiddenElements = None , isDeterministic = None , maxNodeMass = None , maxWeightCutoff = None , midpointEdges = None , minNodeMass = None , ... | Execute the GeneMANIA Force Directed Layout on a network . | 377 | 14 |
243,916 | def get_preferred ( self , network = None , verbose = None ) : network = check_network ( self , network , verbose = verbose ) PARAMS = set_param ( [ 'network' ] , [ network ] ) response = api ( url = self . __url + "/get preferred" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Returns the name of the current preferred layout or empty string if not set . Default is grid . | 87 | 19 |
243,917 | def grid ( self , EdgeAttribute = None , network = None , NodeAttribute = None , nodeHorizontalSpacing = None , nodeList = None , nodeVerticalSpacing = None , verbose = None ) : network = check_network ( self , network , verbose = verbose ) PARAMS = set_param ( [ 'EdgeAttribute' , 'network' , 'NodeAttribute' , 'nodeHor... | Execute the Grid Layout on a network . | 166 | 9 |
243,918 | def hierarchical ( self , bandGap = None , componentSpacing = None , EdgeAttribute = None , leftEdge = None , network = None , NodeAttribute = None , nodeHorizontalSpacing = None , nodeList = None , nodeVerticalSpacing = None , rightMargin = None , topEdge = None , verbose = None ) : network = check_network ( self , ne... | Execute the Hierarchical Layout on a network . | 243 | 11 |
243,919 | def isom ( self , coolingFactor = None , EdgeAttribute = None , initialAdaptation = None , maxEpoch = None , minAdaptation = None , minRadius = None , network = None , NodeAttribute = None , nodeList = None , radius = None , radiusConstantTime = None , singlePartition = None , sizeFactor = None , verbose = None ) : net... | Execute the Inverted Self - Organizing Map Layout on a network . | 260 | 15 |
243,920 | def kamada_kawai ( self , defaultEdgeWeight = None , EdgeAttribute = None , m_anticollisionSpringStrength = None , m_averageIterationsPerNode = None , m_disconnectedNodeDistanceSpringRestLength = None , m_disconnectedNodeDistanceSpringStrength = None , m_layoutPass = None , m_nodeDistanceRestLengthConstant = None , m_n... | Execute the Edge - weighted Spring Embedded Layout on a network . | 442 | 14 |
243,921 | def set_preferred ( self , preferredLayout = None , verbose = None ) : PARAMS = set_param ( [ 'preferredLayout' ] , [ preferredLayout ] ) response = api ( url = self . __url + "/set preferred" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Sets the preferred layout . Takes a specific name as defined in the API Default is grid . | 75 | 19 |
243,922 | def stacked_node_layout ( self , EdgeAttribute = None , network = None , NodeAttribute = None , nodeList = None , x_position = None , y_start_position = None , verbose = None ) : network = check_network ( self , network , verbose = verbose ) PARAMS = set_param ( [ 'EdgeAttribute' , 'network' , 'NodeAttribute' , 'nodeLi... | Execute the Stacked Node Layout on a network . | 169 | 11 |
243,923 | def create_column ( self , columnName = None , listType = None , table = None , ntype = None , verbose = None ) : PARAMS = set_param ( [ 'columnName' , 'listType' , 'table' , 'type' ] , [ columnName , listType , table , ntype ] ) response = api ( url = self . __url + "/create column" , PARAMS = PARAMS , method = "POST"... | Appends an additional column of attribute values to the current table . | 108 | 13 |
243,924 | def create_table ( self , keyColumn = None , keyColumnType = None , title = None , verbose = None ) : PARAMS = set_param ( [ 'keyColumn' , 'keyColumnType' , 'title' ] , [ keyColumn , keyColumnType , title ] ) response = api ( url = self . __url + "/create table" , PARAMS = PARAMS , method = "POST" , verbose = verbose )... | Adds a new table to the network . | 99 | 8 |
243,925 | def delete_column ( self , column = None , table = None , verbose = None ) : PARAMS = set_param ( [ 'column' , 'table' ] , [ column , table ] ) response = api ( url = self . __url + "/delete column" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Remove a column from a table specified by its name . Returns the name of the column removed . | 80 | 19 |
243,926 | def delete_row ( self , keyValue = None , table = None , verbose = None ) : PARAMS = set_param ( [ 'keyValue' , 'table' ] , [ keyValue , table ] ) response = api ( url = self . __url + "/delete row" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Deletes a row from a table . Requires the table name or SUID and the row key . | 83 | 20 |
243,927 | def get_value ( self , column = None , keyValue = None , table = None , verbose = None ) : PARAMS = set_param ( [ 'column' , 'keyValue' , 'table' ] , [ column , keyValue , table ] ) response = api ( url = self . __url + "/get value" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Returns the value from a cell as specified by row and column ids . | 93 | 15 |
243,928 | def import_url ( self , caseSensitiveNetworkCollectionKeys = None , caseSensitiveNetworkKeys = None , dataTypeList = None , DataTypeTargetForNetworkCollection = None , DataTypeTargetForNetworkList = None , delimiters = None , delimitersForDataList = None , firstRowAsColumnNames = None , KeyColumnForMapping = None , Key... | Similar to Import Table this uses a long list of input parameters to specify the attributes of the table the mapping keys and the destination table for the input . | 394 | 30 |
243,929 | def list_tables ( self , includePrivate = None , namespace = None , atype = None , verbose = None ) : PARAMS = set_param ( [ 'includePrivate' , 'namespace' , 'type' ] , [ includePrivate , namespace , atype ] ) response = api ( url = self . __url + "/list" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return... | Returns a list of the table SUIDs associated with the passed network parameter . | 96 | 15 |
243,930 | def list_columns ( self , table = None , verbose = None ) : PARAMS = set_param ( [ 'table' ] , [ table ] ) response = api ( url = self . __url + "/list columns" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Returns the list of columns in the table . | 71 | 9 |
243,931 | def list_rows ( self , rowList = None , table = None , verbose = None ) : PARAMS = set_param ( [ 'rowList' , 'table' ] , [ rowList , table ] ) response = api ( url = self . __url + "/list rows" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Returns the list of primary keys for each of the rows in the specified table . | 83 | 16 |
243,932 | def merge ( self , DataTypeTargetForNetworkCollection = None , dataTypeTargetForNetworkList = None , mergeType = None , SourceMergeColumns = None , SourceMergeKey = None , SourceTable = None , TargetKeyNetworkCollection = None , TargetMergeKey = None , TargetNetworkCollection = None , TargetNetworkList = None , Unassig... | Merge tables together joining around a designated key column . Depending on the arguments might merge into multiple local tables . | 284 | 22 |
243,933 | def rename_column ( self , columnName = None , newColumnName = None , table = None , verbose = None ) : PARAMS = set_param ( [ 'columnName' , 'newColumnName' , 'table' ] , [ columnName , newColumnName , table ] ) response = api ( url = self . __url + "/rename column" , PARAMS = PARAMS , method = "POST" , verbose = verb... | Changes the name of a specified column in the table . | 100 | 11 |
243,934 | def set_title ( self , table = None , title = None , verbose = None ) : PARAMS = set_param ( [ 'table' , 'title' ] , [ table , title ] ) response = api ( url = self . __url + "/set title" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Changes the visible identifier of a single table . | 80 | 9 |
243,935 | def set_values ( self , columnName = None , rowList = None , table = None , value = None , verbose = None ) : PARAMS = set_param ( [ 'columnName' , 'rowList' , 'table' , 'value' ] , [ columnName , rowList , table , value ] ) response = api ( url = self . __url + "/set values" , PARAMS = PARAMS , method = "POST" , verbo... | Set all the values in the specified list of rows with a single value . | 106 | 15 |
243,936 | def getTable ( self , columns = None , table = None , network = "current" , namespace = 'default' , verbose = VERBOSE ) : u = self . __url host = u . split ( "//" ) [ 1 ] . split ( ":" ) [ 0 ] port = u . split ( ":" ) [ 2 ] . split ( "/" ) [ 0 ] version = u . split ( ":" ) [ 2 ] . split ( "/" ) [ 1 ] if type ( network ... | Gets tables from cytoscape . | 482 | 8 |
243,937 | def loadTableData ( self , df , df_key = 'index' , table = "node" , table_key_column = "name" , network = "current" , namespace = "default" , verbose = False ) : u = self . __url host = u . split ( "//" ) [ 1 ] . split ( ":" ) [ 0 ] port = u . split ( ":" ) [ 2 ] . split ( "/" ) [ 0 ] version = u . split ( ":" ) [ 2 ] ... | Loads tables into cytoscape . | 612 | 8 |
243,938 | def getTableCount ( verbose = None ) : response = api ( url = self . url + 'tables/count' , method = "GET" , verbose = verbose , parse_params = False ) return response | Returns the number of global tables . | 48 | 7 |
243,939 | def set_value ( self , visual_property , value ) : if visual_property is None or value is None : raise ValueError ( 'Both VP and value are required.' ) new_value = [ { 'visualProperty' : visual_property , "value" : value } ] requests . put ( self . url , data = json . dumps ( new_value ) , headers = HEADERS ) | Set a single Visual Property Value | 84 | 6 |
243,940 | def set_values ( self , values ) : if values is None : raise ValueError ( 'Values are required.' ) new_values = [ ] for vp in values . keys ( ) : new_val = { 'visualProperty' : vp , 'value' : values [ vp ] } new_values . append ( new_val ) requests . put ( self . url , data = json . dumps ( new_values ) , headers = HEA... | Set multiple Visual properties at once . | 98 | 7 |
243,941 | def get_value ( self , visual_property ) : res = requests . get ( self . url + '/' + visual_property ) return res . json ( ) [ 'value' ] | Get a value for the Visual Property | 40 | 7 |
243,942 | def get_values ( self ) : results = requests . get ( self . url ) . json ( ) values = { } for entry in results : values [ entry [ 'visualProperty' ] ] = entry [ 'value' ] return values | Get all visual property values for the object | 50 | 8 |
243,943 | def update_network_view ( self , visual_property = None , value = None ) : new_value = [ { "visualProperty" : visual_property , "value" : value } ] res = requests . put ( self . __url + '/network' , data = json . dumps ( new_value ) , headers = HEADERS ) check_response ( res ) | Updates single value for Network - related VP . | 79 | 10 |
243,944 | def export ( self , Height = None , options = None , outputFile = None , Resolution = None , Units = None , Width = None , Zoom = None , view = "current" , verbose = False ) : PARAMS = set_param ( [ "Height" , "options" , "outputFile" , "Resolution" , "Units" , "Width" , "Zoom" , "view" ] , [ Height , options , outputF... | Exports the current view to a graphics file and returns the path to the saved file . PNG and JPEG formats have options for scaling while other formats only have the option exportTextAsFont . For the PDF format exporting text as font does not work for two - byte characters such as Chinese or Japanese . To avoid corrupte... | 145 | 86 |
243,945 | def fit_content ( self , verbose = False ) : PARAMS = { } response = api ( url = self . __url + "/fit content" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Zooms out the current view in order to display all of its elements . | 54 | 16 |
243,946 | def get_current ( self , layout = None , network = None , verbose = False ) : PARAMS = { } response = api ( url = self . __url + "/get_current" , PARAMS = PARAMS , method = "POST" , verbose = verbose ) return response | Returns the current view or null if there is none . | 63 | 11 |
243,947 | def update_defaults ( self , prop_value_dict ) : body = [ ] for key in prop_value_dict : entry = { 'visualProperty' : key , 'value' : prop_value_dict [ key ] } body . append ( entry ) url = self . __url + 'defaults' requests . put ( url , data = json . dumps ( body ) , headers = HEADERS ) | Updates the value of one or more visual properties . | 88 | 11 |
243,948 | def status ( self , verbose = False ) : try : response = api ( url = self . __url , method = "GET" , verbose = verbose ) except Exception as e : print ( 'Could not get status from CyREST:\n\n' + str ( e ) ) else : print ( 'CyREST online!' ) | Checks the status of your CyREST server . | 74 | 11 |
243,949 | def version ( self , verbose = False ) : response = api ( url = self . __url + "version" , method = "H" , verbose = verbose ) response = json . loads ( response ) for k in response . keys ( ) : print ( k , response [ k ] ) | Checks Cytoscape version | 64 | 7 |
243,950 | def map_column ( self , only_use_one = None , source_column = None , species = None , target_selection = None , verbose = False ) : PARAMS = set_param ( [ "only_use_one" , "source_column" , "species" , "target_selection" ] , [ only_use_one , source_column , species , target_selection ] ) response = api ( url = self . _... | Uses the BridgeDB service to look up analogous identifiers from a wide selection of other databases | 124 | 18 |
243,951 | def echo ( self , variableName , verbose = False ) : PARAMS = { "variableName" : variableName } response = api ( url = self . __url + "/echo" , PARAMS = PARAMS , verbose = verbose ) return response | The echo command will display the value of the variable specified by the variableName argument or all variables if variableName is not provided . | 55 | 26 |
243,952 | def open_dialog ( self , verbose = False ) : response = api ( url = self . __url + "/open dialog" , verbose = verbose ) return response | The command line dialog provides a field to enter commands and view results . It also provides the help command to display namespaces commands and arguments . | 38 | 28 |
243,953 | def pause ( self , message = None , verbose = False ) : PARAMS = set_param ( [ "message" ] , [ message ] ) response = api ( url = self . __url + "/pause" , PARAMS = PARAMS , verbose = verbose ) return response | The pause command displays a dialog with the text provided in the message argument and waits for the user to click OK | 61 | 22 |
243,954 | def quit ( self , verbose = False ) : response = api ( url = self . __url + "/quit" , verbose = verbose ) return response | This command causes Cytoscape to exit . It is typically used at the end of a script file . | 34 | 22 |
243,955 | def run ( self , script_file , args = None , verbose = False ) : PARAMS = set_param ( [ "file" , "args" ] , [ script_file , args ] ) response = api ( url = self . __url + "/run" , PARAMS = PARAMS , verbose = verbose ) return response | The run command will execute a command script from the file pointed to by the file argument which should contain Cytoscape commands one per line . Arguments to the script are provided by the args argument . | 73 | 41 |
243,956 | def sleep ( self , duration , verbose = False ) : PARAMS = { "duration" : str ( duration ) } response = api ( url = self . __url + "/sleep" , PARAMS = PARAMS , verbose = verbose ) return response | The sleep command will pause processing for a period of time as specified by duration seconds . It is typically used as part of a command script . | 55 | 28 |
243,957 | def to_curl ( request , compressed = False , verify = True ) : parts = [ ( 'curl' , None ) , ( '-X' , request . method ) , ] for k , v in sorted ( request . headers . items ( ) ) : parts += [ ( '-H' , '{0}: {1}' . format ( k , v ) ) ] if request . body : body = request . body if isinstance ( body , bytes ) : body = bod... | Returns string with curl command by provided request object | 224 | 9 |
243,958 | def shared_options ( rq ) : return { 'url' : rq . redis_url , 'config' : None , 'worker_class' : rq . worker_class , 'job_class' : rq . job_class , 'queue_class' : rq . queue_class , 'connection_class' : rq . connection_class , } | Default class options to pass to the CLI commands . | 82 | 10 |
243,959 | def empty ( rq , ctx , all , queues ) : return ctx . invoke ( rq_cli . empty , all = all , queues = queues or rq . queues , * * shared_options ( rq ) ) | Empty given queues . | 50 | 4 |
243,960 | def requeue ( rq , ctx , all , job_ids ) : return ctx . invoke ( rq_cli . requeue , all = all , job_ids = job_ids , * * shared_options ( rq ) ) | Requeue failed jobs . | 55 | 5 |
243,961 | def info ( rq , ctx , path , interval , raw , only_queues , only_workers , by_queue , queues ) : return ctx . invoke ( rq_cli . info , path = path , interval = interval , raw = raw , only_queues = only_queues , only_workers = only_workers , by_queue = by_queue , queues = queues or rq . queues , * * shared_options ( rq ... | RQ command - line monitor . | 101 | 7 |
243,962 | def worker ( rq , ctx , burst , logging_level , name , path , results_ttl , worker_ttl , verbose , quiet , sentry_dsn , exception_handler , pid , queues ) : ctx . invoke ( rq_cli . worker , burst = burst , logging_level = logging_level , name = name , path = path , results_ttl = results_ttl , worker_ttl = worker_ttl , ... | Starts an RQ worker . | 164 | 7 |
243,963 | def suspend ( rq , ctx , duration ) : ctx . invoke ( rq_cli . suspend , duration = duration , * * shared_options ( rq ) ) | Suspends all workers . | 38 | 6 |
243,964 | def scheduler ( rq , ctx , verbose , burst , queue , interval , pid ) : scheduler = rq . get_scheduler ( interval = interval , queue = queue ) if pid : with open ( os . path . expanduser ( pid ) , 'w' ) as fp : fp . write ( str ( os . getpid ( ) ) ) if verbose : level = 'DEBUG' else : level = 'INFO' setup_loghandlers (... | Periodically checks for scheduled jobs . | 115 | 8 |
243,965 | def init_cli ( self , app ) : # in case click isn't installed after all if click is None : raise RuntimeError ( 'Cannot import click. Is it installed?' ) # only add commands if we have a click context available from . cli import add_commands add_commands ( app . cli , self ) | Initialize the Flask CLI support in case it was enabled for the app . | 71 | 15 |
243,966 | def set_trace ( host = None , port = None , patch_stdstreams = False ) : if host is None : host = os . environ . get ( 'REMOTE_PDB_HOST' , '127.0.0.1' ) if port is None : port = int ( os . environ . get ( 'REMOTE_PDB_PORT' , '0' ) ) rdb = RemotePdb ( host = host , port = port , patch_stdstreams = patch_stdstreams ) rdb... | Opens a remote PDB on first available port . | 136 | 11 |
243,967 | def quasi_newton_uniform_lloyd ( points , cells , * args , omega = 1.0 , * * kwargs ) : def get_new_points ( mesh ) : x = ( mesh . node_coords - omega / 2 * jac_uniform ( mesh ) / mesh . control_volumes [ : , None ] ) # update boundary and ghosts idx = mesh . is_boundary_node & ~ ghosted_mesh . is_ghost_point x [ idx ]... | Relaxed Lloyd s algorithm . omega = 1 leads to Lloyd s algorithm overrelaxation omega = 2 gives good results . Check out | 280 | 28 |
243,968 | def _energy_uniform_per_node ( X , cells ) : dim = 2 mesh = MeshTri ( X , cells ) star_integrals = numpy . zeros ( mesh . node_coords . shape [ 0 ] ) # Python loop over the cells... slow! for cell , cell_volume in zip ( mesh . cells [ "nodes" ] , mesh . cell_volumes ) : for idx in cell : xi = mesh . node_coords [ idx ]... | The CPT mesh energy is defined as | 202 | 8 |
243,969 | def jac_uniform ( X , cells ) : dim = 2 mesh = MeshTri ( X , cells ) jac = numpy . zeros ( X . shape ) for k in range ( mesh . cells [ "nodes" ] . shape [ 1 ] ) : i = mesh . cells [ "nodes" ] [ : , k ] fastfunc . add . at ( jac , i , ( ( mesh . node_coords [ i ] - mesh . cell_barycenters ) . T * mesh . cell_volumes ) .... | The approximated Jacobian is | 132 | 6 |
243,970 | def solve_hessian_approx_uniform ( X , cells , rhs ) : dim = 2 mesh = MeshTri ( X , cells ) # Create matrix in IJV format row_idx = [ ] col_idx = [ ] val = [ ] cells = mesh . cells [ "nodes" ] . T n = X . shape [ 0 ] # Main diagonal, 2/(d+1) |omega_i| x_i a = mesh . cell_volumes * ( 2 / ( dim + 1 ) ) for i in [ 0 , 1 ,... | As discussed above the approximated Jacobian is | 710 | 9 |
243,971 | def quasi_newton_uniform ( points , cells , * args , * * kwargs ) : def get_new_points ( mesh ) : # do one Newton step # TODO need copy? x = mesh . node_coords . copy ( ) cells = mesh . cells [ "nodes" ] jac_x = jac_uniform ( x , cells ) x -= solve_hessian_approx_uniform ( x , cells , jac_x ) return x mesh = MeshTri ( ... | Like linear_solve above but assuming rho == 1 . Note that the energy gradient | 151 | 18 |
243,972 | def fixed_point ( points , cells , * args , * * kwargs ) : def get_new_points ( mesh ) : # move interior points into average of their neighbors num_neighbors = numpy . zeros ( len ( mesh . node_coords ) , dtype = int ) idx = mesh . edges [ "nodes" ] fastfunc . add . at ( num_neighbors , idx , numpy . ones ( idx . shape... | Perform k steps of Laplacian smoothing to the mesh i . e . moving each interior vertex to the arithmetic average of its neighboring points . | 291 | 31 |
243,973 | def energy ( mesh , uniform_density = False ) : # E = 1/(d+1) sum_i ||x_i||^2 |omega_i| - int_Omega_i ||x||^2 dim = mesh . cells [ "nodes" ] . shape [ 1 ] - 1 star_volume = numpy . zeros ( mesh . node_coords . shape [ 0 ] ) for i in range ( 3 ) : idx = mesh . cells [ "nodes" ] [ : , i ] if uniform_density : # rho = 1, ... | The mesh energy is defined as | 442 | 6 |
243,974 | def quasi_newton_uniform_blocks ( points , cells , * args , * * kwargs ) : def get_new_points ( mesh ) : # TODO need copy? x = mesh . node_coords . copy ( ) x += update ( mesh ) # update ghosts x [ ghosted_mesh . is_ghost_point ] = ghosted_mesh . reflect_ghost ( x [ ghosted_mesh . mirrors ] ) return x ghosted_mesh = Gh... | Lloyd s algorithm can be though of a diagonal - only Hessian ; this method incorporates the diagonal blocks too . | 220 | 24 |
243,975 | def new ( filename : str , * , file_attrs : Optional [ Dict [ str , str ] ] = None ) -> LoomConnection : if filename . startswith ( "~/" ) : filename = os . path . expanduser ( filename ) if file_attrs is None : file_attrs = { } # Create the file (empty). # Yes, this might cause an exception, which we prefer to send to... | Create an empty Loom file and return it as a context manager . | 286 | 14 |
243,976 | def create ( filename : str , layers : Union [ np . ndarray , Dict [ str , np . ndarray ] , loompy . LayerManager ] , row_attrs : Union [ loompy . AttributeManager , Dict [ str , np . ndarray ] ] , col_attrs : Union [ loompy . AttributeManager , Dict [ str , np . ndarray ] ] , * , file_attrs : Dict [ str , str ] = None... | Create a new Loom file from the given data . | 648 | 11 |
243,977 | def connect ( filename : str , mode : str = 'r+' , * , validate : bool = True , spec_version : str = "2.0.1" ) -> LoomConnection : return LoomConnection ( filename , mode , validate = validate , spec_version = spec_version ) | Establish a connection to a . loom file . | 64 | 11 |
243,978 | def last_modified ( self ) -> str : if "last_modified" in self . attrs : return self . attrs [ "last_modified" ] elif self . mode == "r+" : # Make sure the file has modification timestamps self . attrs [ "last_modified" ] = timestamp ( ) return self . attrs [ "last_modified" ] return timestamp ( ) | Return an ISO8601 timestamp indicating when the file was last modified | 86 | 13 |
243,979 | def get_changes_since ( self , timestamp : str ) -> Dict [ str , List ] : rg = [ ] cg = [ ] ra = [ ] ca = [ ] layers = [ ] if self . last_modified ( ) > timestamp : if self . row_graphs . last_modified ( ) > timestamp : for name in self . row_graphs . keys ( ) : if self . row_graphs . last_modified ( name ) > timestamp... | Get a summary of the parts of the file that changed since the given time | 339 | 15 |
243,980 | def sparse ( self , rows : np . ndarray = None , cols : np . ndarray = None , layer : str = None ) -> scipy . sparse . coo_matrix : if layer is None : return self . layers [ "" ] . sparse ( rows = rows , cols = cols ) else : return self . layers [ layer ] . sparse ( rows = rows , cols = cols ) | Return the main matrix or specified layer as a scipy . sparse . coo_matrix without loading dense matrix in RAM | 92 | 26 |
243,981 | def close ( self , suppress_warning : bool = False ) -> None : if self . _file is None : if not suppress_warning : # Warn user that they're being paranoid # and should clean up their code logging . warn ( "Connection to %s is already closed" , self . filename ) else : self . _file . close ( ) self . _file = None self .... | Close the connection . After this the connection object becomes invalid . Warns user if called after closing . | 169 | 20 |
243,982 | def permute ( self , ordering : np . ndarray , axis : int ) -> None : if self . _file . __contains__ ( "tiles" ) : del self . _file [ 'tiles' ] ordering = list ( np . array ( ordering ) . flatten ( ) ) # Flatten the ordering, in case we got a column vector self . layers . _permute ( ordering , axis = axis ) if axis == ... | Permute the dataset along the indicated axis . | 154 | 10 |
243,983 | def aggregate ( self , out_file : str = None , select : np . ndarray = None , group_by : Union [ str , np . ndarray ] = "Clusters" , aggr_by : str = "mean" , aggr_ca_by : Dict [ str , str ] = None ) -> np . ndarray : ca = { } # type: Dict[str, np.ndarray] if select is not None : raise ValueError ( "The 'select' argumen... | Aggregate the Loom file by applying aggregation functions to the main matrix as well as to the column attributes | 714 | 21 |
243,984 | def get ( self , name : str , default : Any = None ) -> np . ndarray : if name in self : return self [ name ] else : return default | Return the value for a named attribute if it exists else default . If default is not given it defaults to None so that this method never raises a KeyError . | 36 | 32 |
243,985 | def cat_colors ( N : int = 1 , * , hue : str = None , luminosity : str = None , bgvalue : int = None , loop : bool = False , seed : str = "cat" ) -> Union [ List [ Any ] , colors . LinearSegmentedColormap ] : c : List [ str ] = [ ] if N <= 25 and hue is None and luminosity is None : c = _color_alphabet [ : N ] elif not... | Return a colormap suitable for N categorical values optimized to be both aesthetically pleasing and perceptually distinct . | 202 | 23 |
243,986 | def _renumber ( a : np . ndarray , keys : np . ndarray , values : np . ndarray ) -> np . ndarray : ordering = np . argsort ( keys ) keys = keys [ ordering ] values = keys [ ordering ] index = np . digitize ( a . ravel ( ) , keys , right = True ) return ( values [ index ] . reshape ( a . shape ) ) | Renumber a by replacing any occurrence of keys by the corresponding values | 92 | 13 |
243,987 | def validate ( self , path : str , strictness : str = "speconly" ) -> bool : valid1 = True with h5py . File ( path , mode = "r" ) as f : valid1 = self . validate_spec ( f ) if not valid1 : self . errors . append ( "For help, see http://linnarssonlab.org/loompy/format/" ) valid2 = True if strictness == "conventions" : w... | Validate a file for conformance to the Loom specification | 172 | 12 |
243,988 | def _permute ( self , ordering : np . ndarray ) -> None : for key in self . keys ( ) : self [ key ] = self [ key ] [ ordering ] | Permute all the attributes in the collection | 39 | 9 |
243,989 | def get ( self , name : str , default : np . ndarray ) -> np . ndarray : if name in self : return self [ name ] else : if not isinstance ( default , np . ndarray ) : raise ValueError ( f"Default must be an np.ndarray with exactly {self.ds.shape[self.axis]} values" ) if default . shape [ 0 ] != self . ds . shape [ self ... | Return the value for a named attribute if it exists else default . Default has to be a numpy array of correct size . | 140 | 25 |
243,990 | def normalize_attr_array ( a : Any ) -> np . ndarray : if type ( a ) is np . ndarray : return a elif type ( a ) is np . matrix : if a . shape [ 0 ] == 1 : return np . array ( a ) [ 0 , : ] elif a . shape [ 1 ] == 1 : return np . array ( a ) [ : , 0 ] else : raise ValueError ( "Attribute values must be 1-dimensional." )... | Take all kinds of array - like inputs and normalize to a one - dimensional np . ndarray | 184 | 21 |
243,991 | def to_html ( ds : Any ) -> str : rm = min ( 10 , ds . shape [ 0 ] ) cm = min ( 10 , ds . shape [ 1 ] ) html = "<p>" if ds . attrs . __contains__ ( "title" ) : html += "<strong>" + ds . attrs [ "title" ] + "</strong> " html += f"{ds.shape[0]} rows, {ds.shape[1]} columns, {len(ds.layers)} layer{'s' if len(ds.layers) > 1... | Return an HTML representation of the loom file or view showing the upper - left 10x10 corner . | 675 | 21 |
243,992 | def permute ( self , ordering : np . ndarray , * , axis : int ) -> None : if axis not in ( 0 , 1 ) : raise ValueError ( "Axis must be 0 (rows) or 1 (columns)" ) for layer in self . layers . values ( ) : layer . _permute ( ordering , axis = axis ) if axis == 0 : if self . row_graphs is not None : for g in self . row_gra... | Permute the view by permuting its layers attributes and graphs | 197 | 13 |
243,993 | def permute ( self , ordering : np . ndarray , * , axis : int ) -> None : if axis == 0 : self . values = self . values [ ordering , : ] elif axis == 1 : self . values = self . values [ : , ordering ] else : raise ValueError ( "axis must be 0 or 1" ) | Permute the layer along an axis | 73 | 8 |
243,994 | def _resize ( self , size : Tuple [ int , int ] , axis : int = None ) -> None : if self . name == "" : self . ds . _file [ '/matrix' ] . resize ( size , axis ) else : self . ds . _file [ '/layers/' + self . name ] . resize ( size , axis ) | Resize the dataset or the specified axis . | 80 | 9 |
243,995 | def is_datafile_valid ( datafile ) : try : datafile_json = json . loads ( datafile ) except : return False try : jsonschema . Draft4Validator ( constants . JSON_SCHEMA ) . validate ( datafile_json ) except : return False return True | Given a datafile determine if it is valid or not . | 64 | 12 |
243,996 | def is_user_profile_valid ( user_profile ) : if not user_profile : return False if not type ( user_profile ) is dict : return False if UserProfile . USER_ID_KEY not in user_profile : return False if UserProfile . EXPERIMENT_BUCKET_MAP_KEY not in user_profile : return False experiment_bucket_map = user_profile . get ( U... | Determine if provided user profile is valid or not . | 163 | 12 |
243,997 | def is_attribute_valid ( attribute_key , attribute_value ) : if not isinstance ( attribute_key , string_types ) : return False if isinstance ( attribute_value , ( string_types , bool ) ) : return True if isinstance ( attribute_value , ( numbers . Integral , float ) ) : return is_finite_number ( attribute_value ) return... | Determine if given attribute is valid . | 83 | 9 |
243,998 | def is_finite_number ( value ) : if not isinstance ( value , ( numbers . Integral , float ) ) : # numbers.Integral instead of int to accomodate long integer in python 2 return False if isinstance ( value , bool ) : # bool is a subclass of int return False if isinstance ( value , float ) : if math . isnan ( value ) or m... | Validates if the given value is a number enforces absolute limit of 2^53 and restricts NAN INF - INF . | 110 | 25 |
243,999 | def are_values_same_type ( first_val , second_val ) : first_val_type = type ( first_val ) second_val_type = type ( second_val ) # use isinstance to accomodate Python 2 unicode and str types. if isinstance ( first_val , string_types ) and isinstance ( second_val , string_types ) : return True # Compare types if one of t... | Method to verify that both values belong to same type . Float and integer are considered as same type . | 186 | 20 |
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