idx int64 0 63k | question stringlengths 61 4.03k | target stringlengths 6 1.23k |
|---|---|---|
49,300 | def _extract_local_mean_gauss ( image , mask = slice ( None ) , sigma = 1 , voxelspacing = None ) : if voxelspacing is None : voxelspacing = [ 1. ] * image . ndim sigma = _create_structure_array ( sigma , voxelspacing ) return _extract_intensities ( gaussian_filter ( image , sigma ) , mask ) | Internal single - image version of local_mean_gauss . |
49,301 | def _extract_centerdistance ( image , mask = slice ( None ) , voxelspacing = None ) : image = numpy . array ( image , copy = False ) if None == voxelspacing : voxelspacing = [ 1. ] * image . ndim centers = [ ( x - 1 ) / 2. for x in image . shape ] indices = numpy . indices ( image . shape , dtype = numpy . float ) for ... | Internal single - image version of centerdistance . |
49,302 | def _extract_intensities ( image , mask = slice ( None ) ) : return numpy . array ( image , copy = True ) [ mask ] . ravel ( ) | Internal single - image version of intensities . |
49,303 | def _substract_hemispheres ( active , reference , active_sigma , reference_sigma , voxel_spacing ) : active_kernel = _create_structure_array ( active_sigma , voxel_spacing ) active_smoothed = gaussian_filter ( active , sigma = active_kernel ) reference_kernel = _create_structure_array ( reference_sigma , voxel_spacing ... | Helper function for _extract_hemispheric_difference . Smoothes both images and then substracts the reference from the active image . |
49,304 | def _dispatch ( self , tree ) : "_dispatcher function, _dispatching tree type T to method _T." if isinstance ( tree , list ) : for t in tree : self . _dispatch ( t ) return meth = getattr ( self , "_" + tree . __class__ . __name__ ) if tree . __class__ . __name__ == 'NoneType' and not self . _do_indent : return meth ( ... | _dispatcher function _dispatching tree type T to method _T . |
49,305 | def _AssAttr ( self , t ) : self . _dispatch ( t . expr ) self . _write ( '.' + t . attrname ) | Handle assigning an attribute of an object |
49,306 | def _Assign ( self , t ) : self . _fill ( ) for target in t . nodes : self . _dispatch ( target ) self . _write ( " = " ) self . _dispatch ( t . expr ) if not self . _do_indent : self . _write ( '; ' ) | Expression Assignment such as a = 1 . |
49,307 | def _AssTuple ( self , t ) : for element in t . nodes [ : - 1 ] : self . _dispatch ( element ) self . _write ( ", " ) last_element = t . nodes [ - 1 ] self . _dispatch ( last_element ) | Tuple on left hand side of an expression . |
49,308 | def _CallFunc ( self , t ) : self . _dispatch ( t . node ) self . _write ( "(" ) comma = False for e in t . args : if comma : self . _write ( ", " ) else : comma = True self . _dispatch ( e ) if t . star_args : if comma : self . _write ( ", " ) else : comma = True self . _write ( "*" ) self . _dispatch ( t . star_args ... | Function call . |
49,309 | def _From ( self , t ) : self . _fill ( "from " ) self . _write ( t . modname ) self . _write ( " import " ) for i , ( name , asname ) in enumerate ( t . names ) : if i != 0 : self . _write ( ", " ) self . _write ( name ) if asname is not None : self . _write ( " as " + asname ) | Handle from xyz import foo bar as baz . |
49,310 | def _Function ( self , t ) : if t . decorators is not None : self . _fill ( "@" ) self . _dispatch ( t . decorators ) self . _fill ( "def " + t . name + "(" ) defaults = [ None ] * ( len ( t . argnames ) - len ( t . defaults ) ) + list ( t . defaults ) for i , arg in enumerate ( zip ( t . argnames , defaults ) ) : self... | Handle function definitions |
49,311 | def _Getattr ( self , t ) : if isinstance ( t . expr , ( Div , Mul , Sub , Add ) ) : self . _write ( '(' ) self . _dispatch ( t . expr ) self . _write ( ')' ) else : self . _dispatch ( t . expr ) self . _write ( '.' + t . attrname ) | Handle getting an attribute of an object |
49,312 | def _Import ( self , t ) : self . _fill ( "import " ) for i , ( name , asname ) in enumerate ( t . names ) : if i != 0 : self . _write ( ", " ) self . _write ( name ) if asname is not None : self . _write ( " as " + asname ) | Handle import xyz . foo . |
49,313 | def _Keyword ( self , t ) : self . _write ( t . name ) self . _write ( "=" ) self . _dispatch ( t . expr ) | Keyword value assignment within function calls and definitions . |
49,314 | def __sequenceAscendingStrict ( l ) : "Test a sequences values to be in strictly ascending order." it = iter ( l ) next ( it ) if not all ( b > a for a , b in zip ( l , it ) ) : raise argparse . ArgumentTypeError ( 'All values must be given in strictly ascending order.' ) return l | Test a sequences values to be in strictly ascending order . |
49,315 | def __check_mapping ( self , landmarks ) : sc_udiff = numpy . asarray ( self . __sc_umaxs ) [ 1 : ] - numpy . asarray ( self . __sc_umins ) [ : - 1 ] l_diff = numpy . asarray ( landmarks ) [ 1 : ] - numpy . asarray ( landmarks ) [ : - 1 ] return numpy . all ( sc_udiff > numpy . asarray ( l_diff ) ) | Checks whether the image from which the supplied landmarks were extracted can be transformed to the learned standard intensity space without loss of information . |
49,316 | def is_in_interval ( n , l , r , border = 'included' ) : if 'included' == border : return ( n >= l ) and ( n <= r ) elif 'excluded' == border : return ( n > l ) and ( n < r ) else : raise ValueError ( 'borders must be either \'included\' or \'excluded\'' ) | Checks whether a number is inside the interval l r . |
49,317 | def are_in_interval ( s , l , r , border = 'included' ) : return numpy . all ( [ IntensityRangeStandardization . is_in_interval ( x , l , r , border ) for x in s ] ) | Checks whether all number in the sequence s lie inside the interval formed by l and r . |
49,318 | def template_sphere ( radius , dimensions ) : r if int ( dimensions ) != dimensions : raise TypeError ( 'The supplied dimension parameter must be of type integer.' ) dimensions = int ( dimensions ) return template_ellipsoid ( dimensions * [ radius * 2 ] ) | r Returns a spherical binary structure of a of the supplied radius that can be used as template input to the generalized hough transform . |
49,319 | def looks_like_issubclass ( obj , classname ) : t = obj if t . __name__ == classname : return True for klass in t . __mro__ : if klass . __name__ == classname : return True return False | Return True if the object has a class or superclass with the given class name . |
49,320 | def __make_footprint ( input , size , footprint ) : "Creates a standard footprint element ala scipy.ndimage." if footprint is None : if size is None : raise RuntimeError ( "no footprint or filter size provided" ) sizes = _ni_support . _normalize_sequence ( size , input . ndim ) footprint = numpy . ones ( sizes , dtype ... | Creates a standard footprint element ala scipy . ndimage . |
49,321 | def __check_label_image ( label_image ) : encountered_indices = scipy . unique ( label_image ) expected_indices = scipy . arange ( 1 , label_image . max ( ) + 1 ) if not encountered_indices . size == expected_indices . size or not ( encountered_indices == expected_indices ) . all ( ) : raise AttributeError ( 'The suppl... | Check the label image for consistent labelling starting from 1 . |
49,322 | def __xd_iterator_pass_on ( arr , view , fun ) : iterations = [ [ None ] if dim in view else list ( range ( arr . shape [ dim ] ) ) for dim in range ( arr . ndim ) ] passon = None for indices in itertools . product ( * iterations ) : slicer = [ slice ( None ) if idx is None else slice ( idx , idx + 1 ) for idx in indic... | Like xd_iterator but the fun return values are always passed on to the next and only the last returned . |
49,323 | def set_pixel_spacing ( hdr , spacing ) : r warnings . warn ( 'get_pixel_spacing() is depreciated, use set_voxel_spacing() instead' , category = DeprecationWarning ) set_voxel_spacing ( hdr , spacing ) | r Depreciated synonym of ~medpy . io . header . set_voxel_spacing . |
49,324 | def copy_to ( self , sitkimage ) : if self . sitkimage is not None : for k in self . sitkimage . GetMetaDataKeys ( ) : sitkimage . SetMetaData ( k , self . sitkimage . GetMetaData ( k ) ) ndim = len ( sitkimage . GetSize ( ) ) spacing , offset , direction = self . get_info_consistent ( ndim ) sitkimage . SetSpacing ( s... | Copy all stored meta information info to an sitk Image . |
49,325 | def get_info_consistent ( self , ndim ) : if ndim > len ( self . spacing ) : spacing = self . spacing + ( 1.0 , ) * ( ndim - len ( self . spacing ) ) else : spacing = self . spacing [ : ndim ] if ndim > len ( self . offset ) : offset = self . offset + ( 0.0 , ) * ( ndim - len ( self . offset ) ) else : offset = self . ... | Returns the main meta - data information adapted to the supplied image dimensionality . |
49,326 | def hd95 ( result , reference , voxelspacing = None , connectivity = 1 ) : hd1 = __surface_distances ( result , reference , voxelspacing , connectivity ) hd2 = __surface_distances ( reference , result , voxelspacing , connectivity ) hd95 = numpy . percentile ( numpy . hstack ( ( hd1 , hd2 ) ) , 95 ) return hd95 | 95th percentile of the Hausdorff Distance . |
49,327 | def __surface_distances ( result , reference , voxelspacing = None , connectivity = 1 ) : result = numpy . atleast_1d ( result . astype ( numpy . bool ) ) reference = numpy . atleast_1d ( reference . astype ( numpy . bool ) ) if voxelspacing is not None : voxelspacing = _ni_support . _normalize_sequence ( voxelspacing ... | The distances between the surface voxel of binary objects in result and their nearest partner surface voxel of a binary object in reference . |
49,328 | def __minowski_low_positive_integer_p ( h1 , h2 , p = 2 ) : mult = scipy . absolute ( h1 - h2 ) dif = mult for _ in range ( p - 1 ) : dif = scipy . multiply ( dif , mult ) return math . pow ( scipy . sum ( dif ) , 1. / p ) | A faster implementation of the Minowski distance for positive integer < 25 . |
49,329 | def __kullback_leibler ( h1 , h2 ) : result = h1 . astype ( scipy . float_ ) mask = h1 != 0 result [ mask ] = scipy . multiply ( h1 [ mask ] , scipy . log ( h1 [ mask ] / h2 [ mask ] ) ) return scipy . sum ( result ) | The actual KL implementation . |
49,330 | def __prepare_histogram ( h1 , h2 ) : h1 = h1 if scipy . ndarray == type ( h1 ) else scipy . asarray ( h1 ) h2 = h2 if scipy . ndarray == type ( h2 ) else scipy . asarray ( h2 ) if h1 . shape != h2 . shape or h1 . size != h2 . size : raise ValueError ( 'h1 and h2 must be of same shape and size' ) return h1 , h2 | Convert the histograms to scipy . ndarrays if required . |
49,331 | def find ( ) : spark_home = os . environ . get ( 'SPARK_HOME' , None ) if not spark_home : for path in [ '/usr/local/opt/apache-spark/libexec' , '/usr/lib/spark/' , '/usr/local/spark/' , '/opt/spark/' , ] : if os . path . exists ( path ) : spark_home = path break if not spark_home : raise ValueError ( "Couldn't find Sp... | Find a local spark installation . |
49,332 | def change_rc ( spark_home , spark_python , py4j ) : bashrc_location = os . path . expanduser ( "~/.bashrc" ) if os . path . isfile ( bashrc_location ) : with open ( bashrc_location , 'a' ) as bashrc : bashrc . write ( "\n# Added by findspark\n" ) bashrc . write ( "export SPARK_HOME=" + spark_home + "\n" ) bashrc . wri... | Persists changes to environment by changing shell config . |
49,333 | def edit_ipython_profile ( spark_home , spark_python , py4j ) : from IPython import get_ipython ip = get_ipython ( ) if ip : profile_dir = ip . profile_dir . location else : from IPython . utils . path import locate_profile profile_dir = locate_profile ( ) startup_file_loc = os . path . join ( profile_dir , "startup" ,... | Adds a startup file to the current IPython profile to import pyspark . |
49,334 | def init ( spark_home = None , python_path = None , edit_rc = False , edit_profile = False ) : if not spark_home : spark_home = find ( ) if not python_path : python_path = os . environ . get ( 'PYSPARK_PYTHON' , sys . executable ) os . environ [ 'SPARK_HOME' ] = spark_home os . environ [ 'PYSPARK_PYTHON' ] = python_pat... | Make pyspark importable . |
49,335 | def _add_to_submit_args ( s ) : new_args = os . environ . get ( "PYSPARK_SUBMIT_ARGS" , "" ) + ( " %s" % s ) os . environ [ "PYSPARK_SUBMIT_ARGS" ] = new_args return new_args | Adds string s to the PYSPARK_SUBMIT_ARGS env var |
49,336 | def add_packages ( packages ) : if isinstance ( packages , str ) : packages = [ packages ] _add_to_submit_args ( "--packages " + "," . join ( packages ) + " pyspark-shell" ) | Add external packages to the pyspark interpreter . |
49,337 | def add_jars ( jars ) : if isinstance ( jars , str ) : jars = [ jars ] _add_to_submit_args ( "--jars " + "," . join ( jars ) + " pyspark-shell" ) | Add external jars to the pyspark interpreter . |
49,338 | def parse ( cls , expression ) : parsed = { "name" : None , "arguments" : [ ] , "options" : [ ] } if not expression . strip ( ) : raise ValueError ( "Console command signature is empty." ) expression = expression . replace ( os . linesep , "" ) matches = re . match ( r"[^\s]+" , expression ) if not matches : raise Valu... | Parse the given console command definition into a dict . |
49,339 | def _parameters ( cls , tokens ) : arguments = [ ] options = [ ] for token in tokens : if not token . startswith ( "--" ) : arguments . append ( cls . _parse_argument ( token ) ) else : options . append ( cls . _parse_option ( token ) ) return { "arguments" : arguments , "options" : options } | Extract all of the parameters from the tokens . |
49,340 | def _parse_argument ( cls , token ) : description = "" validator = None if " : " in token : token , description = tuple ( token . split ( " : " , 2 ) ) token = token . strip ( ) description = description . strip ( ) matches = re . match ( r"(.*)\((.*?)\)" , token ) if matches : token = matches . group ( 1 ) . strip ( )... | Parse an argument expression . |
49,341 | def _parse_option ( cls , token ) : description = "" validator = None if " : " in token : token , description = tuple ( token . split ( " : " , 2 ) ) token = token . strip ( ) description = description . strip ( ) matches = re . match ( r"(.*)\((.*?)\)" , token ) if matches : token = matches . group ( 1 ) . strip ( ) v... | Parse an option expression . |
49,342 | def add ( self , command ) : self . add_command ( command . config ) command . set_application ( self ) return self | Adds a command object . |
49,343 | def _configure_using_fluent_definition ( self ) : definition = Parser . parse ( self . signature ) self . _config . set_name ( definition [ "name" ] ) for name , flags , description , default in definition [ "arguments" ] : self . _config . add_argument ( name , flags , description , default ) for long_name , short_nam... | Configure the console command using a fluent definition . |
49,344 | def argument ( self , key = None ) : if key is None : return self . _args . arguments ( ) return self . _args . argument ( key ) | Get the value of a command argument . |
49,345 | def option ( self , key = None ) : if key is None : return self . _args . options ( ) return self . _args . option ( key ) | Get the value of a command option . |
49,346 | def confirm ( self , question , default = False , true_answer_regex = "(?i)^y" ) : return self . _io . confirm ( question , default , true_answer_regex ) | Confirm a question with the user . |
49,347 | def ask ( self , question , default = None ) : if isinstance ( question , Question ) : return self . _io . ask_question ( question ) return self . _io . ask ( question , default ) | Prompt the user for input . |
49,348 | def choice ( self , question , choices , default = None , attempts = None , multiple = False ) : question = ChoiceQuestion ( question , choices , default ) question . set_max_attempts ( attempts ) question . set_multi_select ( multiple ) return self . _io . ask_question ( question ) | Give the user a single choice from an list of answers . |
49,349 | def create_question ( self , question , type = None , ** kwargs ) : if not type : return Question ( question , ** kwargs ) if type == "choice" : return ChoiceQuestion ( question , ** kwargs ) if type == "confirmation" : return ConfirmationQuestion ( question , ** kwargs ) | Returns a Question of specified type . |
49,350 | def table ( self , header = None , rows = None , style = None ) : if style is not None : style = self . TABLE_STYLES [ style ] table = Table ( style ) if header : table . set_header_row ( header ) if rows : table . set_rows ( rows ) return table | Return a Table instance . |
49,351 | def render_table ( self , headers , rows , style = None ) : table = self . table ( headers , rows , style ) table . render ( self . _io ) | Format input to textual table . |
49,352 | def line ( self , text , style = None , verbosity = None ) : if style : styled = "<%s>%s</>" % ( style , text ) else : styled = text self . _io . write_line ( styled , verbosity ) | Write a string as information output . |
49,353 | def line_error ( self , text , style = None , verbosity = None ) : if style : styled = "<%s>%s</>" % ( style , text ) else : styled = text self . _io . error_line ( styled , verbosity ) | Write a string as information output to stderr . |
49,354 | def progress_indicator ( self , fmt = None , interval = 100 , values = None ) : return ProgressIndicator ( self . io , fmt , interval , values ) | Creates a new progress indicator . |
49,355 | def spin ( self , start_message , end_message , fmt = None , interval = 100 , values = None ) : spinner = ProgressIndicator ( self . io , fmt , interval , values ) return spinner . auto ( start_message , end_message ) | Automatically spin a progress indicator . |
49,356 | def add_style ( self , name , fg = None , bg = None , options = None ) : style = Style ( name ) if fg is not None : style . fg ( fg ) if bg is not None : style . bg ( bg ) if options is not None : if "bold" in options : style . bold ( ) if "underline" in options : style . underlined ( ) self . _io . output . formatter ... | Adds a new style |
49,357 | def overwrite ( self , text , size = None ) : self . _io . overwrite ( text , size = size ) | Overwrites the current line . |
49,358 | def get_github_hostname_user_repo_from_url ( url ) : parsed = parse . urlparse ( url ) if parsed . netloc == '' : host , sep , path = parsed . path . partition ( ":" ) if "@" in host : username , sep , host = host . partition ( "@" ) else : path = parsed . path [ 1 : ] . rstrip ( '/' ) host = parsed . netloc user , rep... | Return hostname user and repository to fork from . |
49,359 | def git_get_title_and_message ( begin , end ) : titles = git_get_log_titles ( begin , end ) title = "Pull request for " + end if len ( titles ) == 1 : title = titles [ 0 ] pr_template = find_pull_request_template ( ) if pr_template : message = get_pr_template_message ( pr_template ) else : if len ( titles ) == 1 : mess... | Get title and message summary for patches between 2 commits . |
49,360 | def validate_commit_index ( func ) : @ functools . wraps ( func ) def wrapped ( self , * args , ** kwargs ) : for not_applied in range ( self . log . last_applied + 1 , self . log . commit_index + 1 ) : self . state_machine . apply ( self . log [ not_applied ] [ 'command' ] ) self . log . last_applied += 1 try : self .... | Apply to State Machine everything up to commit index |
49,361 | async def execute_command ( self , command ) : self . apply_future = asyncio . Future ( loop = self . loop ) entry = self . log . write ( self . storage . term , command ) asyncio . ensure_future ( self . append_entries ( ) , loop = self . loop ) await self . apply_future | Write to log & send AppendEntries RPC |
49,362 | def start ( self ) : self . storage . update ( { 'term' : self . storage . term + 1 , 'voted_for' : self . id } ) self . vote_count = 1 self . request_vote ( ) self . election_timer . start ( ) | Increment current term vote for herself & send vote requests |
49,363 | def on_receive_request_vote_response ( self , data ) : if data . get ( 'vote_granted' ) : self . vote_count += 1 if self . state . is_majority ( self . vote_count ) : self . state . to_leader ( ) | Receives response for vote request . If the vote was granted then check if we got majority and may become Leader |
49,364 | def init_storage ( self ) : if not self . storage . exists ( 'term' ) : self . storage . update ( { 'term' : 0 , } ) self . storage . update ( { 'voted_for' : None } ) | Set current term to zero upon initialization & voted_for to None |
49,365 | async def wait_for_election_success ( cls ) : if cls . leader is None : cls . leader_future = asyncio . Future ( loop = cls . loop ) await cls . leader_future | Await this function if your cluster must have a leader |
49,366 | async def wait_until_leader ( cls , node_id ) : if node_id is None : raise ValueError ( 'Node id can not be None!' ) if cls . get_leader ( ) != node_id : cls . wait_until_leader_id = node_id cls . wait_until_leader_future = asyncio . Future ( loop = cls . loop ) await cls . wait_until_leader_future cls . wait_until_lea... | Await this function if you want to do nothing until node_id becomes a leader |
49,367 | def declare ( full_table_name , definition , context ) : table_name = full_table_name . strip ( '`' ) . split ( '.' ) [ 1 ] if len ( table_name ) > MAX_TABLE_NAME_LENGTH : raise DataJointError ( 'Table name `{name}` exceeds the max length of {max_length}' . format ( name = table_name , max_length = MAX_TABLE_NAME_LENGT... | Parse declaration and create new SQL table accordingly . |
49,368 | def create_virtual_module ( module_name , schema_name , create_schema = False , create_tables = False , connection = None ) : module = types . ModuleType ( module_name ) _schema = Schema ( schema_name , create_schema = create_schema , create_tables = create_tables , connection = connection ) _schema . spawn_missing_cla... | Creates a python module with the given name from the name of a schema on the server and automatically adds classes to it corresponding to the tables in the schema . |
49,369 | def drop ( self , force = False ) : if not self . exists : logger . info ( "Schema named `{database}` does not exist. Doing nothing." . format ( database = self . database ) ) elif ( not config [ 'safemode' ] or force or user_choice ( "Proceed to delete entire schema `%s`?" % self . database , default = 'no' ) == 'yes'... | Drop the associated schema if it exists |
49,370 | def process_relation_class ( self , relation_class , context , assert_declared = False ) : relation_class . database = self . database relation_class . _connection = self . connection relation_class . _heading = Heading ( ) instance = relation_class ( ) is_declared = instance . is_declared if not is_declared : if not s... | assign schema properties to the relation class and declare the table |
49,371 | def declare ( self , context = None ) : try : sql , uses_external = declare ( self . full_table_name , self . definition , context ) if uses_external : sql = sql . format ( external_table = self . external_table . full_table_name ) self . connection . query ( sql ) except pymysql . OperationalError as error : if error ... | Use self . definition to declare the table in the schema . |
49,372 | def delete_quick ( self , get_count = False ) : query = 'DELETE FROM ' + self . full_table_name + self . where_clause self . connection . query ( query ) count = self . connection . query ( "SELECT ROW_COUNT()" ) . fetchone ( ) [ 0 ] if get_count else None self . _log ( query [ : 255 ] ) return count | Deletes the table without cascading and without user prompt . If this table has populated dependent tables this will fail . |
49,373 | def _update ( self , attrname , value = None ) : if len ( self ) != 1 : raise DataJointError ( 'Update is only allowed on one tuple at a time' ) if attrname not in self . heading : raise DataJointError ( 'Invalid attribute name' ) if attrname in self . heading . primary_key : raise DataJointError ( 'Cannot update a key... | Updates a field in an existing tuple . This is not a datajoyous operation and should not be used routinely . Relational database maintain referential integrity on the level of a tuple . Therefore the UPDATE operator can violate referential integrity . The datajoyous way to update information is to delete the entire tup... |
49,374 | def where_clause ( self ) : cond = self . _make_condition ( self . restriction ) return '' if cond is True else ' WHERE %s' % cond | convert self . restriction to the SQL WHERE clause |
49,375 | def preview ( self , limit = None , width = None ) : heading = self . heading rel = self . proj ( * heading . non_blobs ) if limit is None : limit = config [ 'display.limit' ] if width is None : width = config [ 'display.width' ] tuples = rel . fetch ( limit = limit + 1 , format = "array" ) has_more = len ( tuples ) > ... | returns a preview of the contents of the query . |
49,376 | def make_argument_subquery ( arg ) : return Subquery . create ( arg ) if isinstance ( arg , ( GroupBy , Projection ) ) or arg . restriction else arg | Decide when a Join argument needs to be wrapped in a subquery |
49,377 | def _need_subquery ( arg , attributes , named_attributes ) : if arg . heading . expressions or arg . distinct : return True restricting_attributes = arg . attributes_in_restriction ( ) return ( not restricting_attributes . issubset ( attributes ) or any ( v . strip ( ) in restricting_attributes for v in named_attribute... | Decide whether the projection argument needs to be wrapped in a subquery |
49,378 | def create ( cls , arg ) : obj = cls ( ) obj . _connection = arg . connection obj . _heading = arg . heading . make_subquery_heading ( ) obj . _arg = arg return obj | construct a subquery from arg |
49,379 | def user_choice ( prompt , choices = ( "yes" , "no" ) , default = None ) : assert default is None or default in choices choice_list = ', ' . join ( ( choice . title ( ) if choice == default else choice for choice in choices ) ) response = None while response not in choices : response = input ( prompt + ' [' + choice_li... | Prompts the user for confirmation . The default value if any is capitalized . |
49,380 | def to_dicts ( recarray ) : for rec in recarray : yield dict ( zip ( recarray . dtype . names , rec . tolist ( ) ) ) | convert record array to a dictionaries |
49,381 | def keys ( self , ** kwargs ) : warnings . warn ( 'Use of `rel.fetch.keys()` notation is deprecated. ' 'Please use `rel.fetch("KEY")` or `rel.fetch(dj.key)` for equivalent result' , stacklevel = 2 ) yield from self . _expression . proj ( ) . fetch ( as_dict = True , ** kwargs ) | DEPRECATED Iterator that returns primary keys as a sequence of dicts . |
49,382 | def key_hash ( key ) : hashed = hashlib . md5 ( ) for k , v in sorted ( key . items ( ) ) : hashed . update ( str ( v ) . encode ( ) ) return hashed . hexdigest ( ) | 32 - byte hash used for lookup of primary keys of jobs |
49,383 | def conn ( host = None , user = None , password = None , init_fun = None , reset = False ) : if not hasattr ( conn , 'connection' ) or reset : host = host if host is not None else config [ 'database.host' ] user = user if user is not None else config [ 'database.user' ] password = password if password is not None else ... | Returns a persistent connection object to be shared by multiple modules . If the connection is not yet established or reset = True a new connection is set up . If connection information is not provided it is taken from config which takes the information from dj_local_conf . json . If the password is not specified in th... |
49,384 | def connect ( self ) : with warnings . catch_warnings ( ) : warnings . filterwarnings ( 'ignore' , '.*deprecated.*' ) self . _conn = client . connect ( init_command = self . init_fun , sql_mode = "NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO," "STRICT_ALL_TABLES,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION" , ... | Connects to the database server . |
49,385 | def start_transaction ( self ) : if self . in_transaction : raise DataJointError ( "Nested connections are not supported." ) self . query ( 'START TRANSACTION WITH CONSISTENT SNAPSHOT' ) self . _in_transaction = True logger . info ( "Transaction started" ) | Starts a transaction error . |
49,386 | def save_global ( self , verbose = False ) : self . save ( os . path . expanduser ( os . path . join ( '~' , GLOBALCONFIG ) ) , verbose ) | saves the settings in the global config file |
49,387 | def todict ( self ) : return OrderedDict ( ( name , self [ i ] ) for i , name in enumerate ( self . _fields ) ) | Convert namedtuple to dict . |
49,388 | def as_dtype ( self ) : return np . dtype ( dict ( names = self . names , formats = [ v . dtype for v in self . attributes . values ( ) ] ) ) | represent the heading as a numpy dtype |
49,389 | def as_sql ( self ) : return ',' . join ( '`%s`' % name if self . attributes [ name ] . sql_expression is None else '%s as `%s`' % ( self . attributes [ name ] . sql_expression , name ) for name in self . names ) | represent heading as SQL field list |
49,390 | def join ( self , other ) : return Heading ( [ self . attributes [ name ] . todict ( ) for name in self . primary_key ] + [ other . attributes [ name ] . todict ( ) for name in other . primary_key if name not in self . primary_key ] + [ self . attributes [ name ] . todict ( ) for name in self . dependent_attributes if ... | Join two headings into a new one . It assumes that self and other are headings that share no common dependent attributes . |
49,391 | def make_subquery_heading ( self ) : return Heading ( dict ( v . todict ( ) , sql_expression = None ) for v in self . attributes . values ( ) ) | Create a new heading with removed attribute sql_expressions . Used by subqueries which resolve the sql_expressions . |
49,392 | def squeeze ( self , array ) : if not self . _squeeze : return array array = array . copy ( ) array = array . squeeze ( ) if array . ndim == 0 : array = array [ ( ) ] return array | Simplify the given array as much as possible - squeeze out all singleton dimensions and also convert a zero dimensional array into array scalar |
49,393 | def read_string ( self , advance = True ) : target = self . _blob . find ( b'\0' , self . pos ) assert target >= self . _pos data = self . _blob [ self . _pos : target ] if advance : self . _pos = target + 1 return data . decode ( 'ascii' ) | Read a string terminated by null byte \ 0 . The returned string object is ASCII decoded and will not include the terminating null byte . |
49,394 | def read_value ( self , dtype = 'uint64' , count = 1 , advance = True ) : data = np . frombuffer ( self . _blob , dtype = dtype , count = count , offset = self . pos ) if advance : self . _pos += data . dtype . itemsize * data . size if count == 1 : data = data [ 0 ] return data | Read one or more scalars of the indicated dtype . Count specifies the number of scalars to be read in . |
49,395 | def put ( self , store , obj ) : spec = self . _get_store_spec ( store ) blob = pack ( obj ) blob_hash = long_hash ( blob ) + store [ len ( 'external-' ) : ] if spec [ 'protocol' ] == 'file' : folder = os . path . join ( spec [ 'location' ] , self . database ) full_path = os . path . join ( folder , blob_hash ) if not ... | put an object in external store |
49,396 | def get ( self , blob_hash ) : if blob_hash is None : return None store = blob_hash [ STORE_HASH_LENGTH : ] store = 'external' + ( '-' if store else '' ) + store cache_folder = config . get ( 'cache' , None ) blob = None if cache_folder : try : with open ( os . path . join ( cache_folder , blob_hash ) , 'rb' ) as f : b... | get an object from external store . Does not need to check whether it s in the table . |
49,397 | def delete_garbage ( self ) : self . connection . query ( "DELETE FROM `{db}`.`{tab}` WHERE " . format ( tab = self . table_name , db = self . database ) + " AND " . join ( 'hash NOT IN (SELECT {column_name} FROM {referencing_table})' . format ( ** ref ) for ref in self . references ) or "TRUE" ) print ( 'Deleted %d it... | Delete items that are no longer referenced . This operation is safe to perform at any time . |
49,398 | def clean_store ( self , store , display_progress = True ) : spec = self . _get_store_spec ( store ) progress = tqdm if display_progress else lambda x : x if spec [ 'protocol' ] == 'file' : folder = os . path . join ( spec [ 'location' ] , self . database ) delete_list = set ( os . listdir ( folder ) ) . difference ( s... | Clean unused data in an external storage repository from unused blobs . This must be performed after delete_garbage during low - usage periods to reduce risks of data loss . |
49,399 | def is_connection_error ( e ) : return ( isinstance ( e , err . InterfaceError ) and e . args [ 0 ] == "(0, '')" ) or ( isinstance ( e , err . OperationalError ) and e . args [ 0 ] in operation_error_codes . values ( ) ) | Checks if error e pertains to a connection issue |
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