Module Import alias Import alias Import alias Import alias AugAssignAdd AttributeStore NameLoad attr ListLoad Call AttributeLoad AttributeLoad NameLoad attr attr Str Import alias Assign SubscriptStore AttributeLoad NameLoad attr Index Str Str ImportFrom alias Import alias Import alias Import alias Import alias Import alias identifier ImportFrom alias FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index Num Index Num Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index Num Index Num Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index Num Index Num Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index Num Index Num Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index Num Index Num Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list ClassDef bases body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body Expr Str Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore BinOpDiv SubscriptLoad SubscriptLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Index NameLoad Index Num AttributeLoad NameLoad attr Assign NameStore BinOpDiv SubscriptLoad SubscriptLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Index NameLoad Index Num AttributeLoad NameLoad attr Assign NameStore SubscriptLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Index Num Assign NameStore SubscriptLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Index Num Assign NameStore SubscriptLoad SubscriptLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Index NameLoad Index Num Print NameLoad BinOpMult NameLoad NameLoad NameLoad Call AttributeLoad NameLoad attr For NameStore Call NameLoad NameLoad body For NameStore Call NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr ListLoad NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr For NameStore Call NameLoad NameLoad body If CompareGt BinOpAdd BinOpAdd BinOpMult NameLoad NameLoad NameLoad NameLoad NameLoad body Break Assign NameStore Call AttributeLoad Str attr AttributeLoad NameLoad attr NameLoad BinOpAdd BinOpAdd BinOpMult NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad TryExcept body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str Assign SubscriptStore NameLoad ExtSlice Index NameLoad Slice Slice Call AttributeLoad NameLoad attr NameLoad handlers ExceptHandler type NameLoad name NameStore body Print BinOpMod Str NameLoad Assign NameStore Call NameLoad Str Str Expr Call AttributeLoad NameLoad attr BinOpAdd NameLoad Str Expr Call AttributeLoad NameLoad attr Assign NameStore ListLoad BinOpMult NameLoad AttributeLoad NameLoad attr BinOpMult NameLoad AttributeLoad NameLoad attr BinOpMult NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad NameLoad If CompareEq BinOpMod NameLoad Num Num body Expr Call AttributeLoad AttributeLoad NameLoad attr attr decorator_list decorator_list ClassDef bases body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults body Expr Str Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str For NameStore Call NameLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr body If CompareGt NameLoad AttributeLoad NameLoad attr body Continue Print Str NameLoad Str SubscriptLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Index NameLoad Assign NameStore SubscriptLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Index Num Assign NameStore SubscriptLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Index Num Assign NameStore SubscriptLoad SubscriptLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Index NameLoad Index Num Assign NameStore BinOpAdd BinOpDiv BinOpAdd BinOpSub NameLoad NameLoad Num NameLoad Num Assign NameStore BinOpMult ListLoad ListLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Print BinOpSub NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list decorator_list FunctionDef arguments args defaults body Assign NameStore Call AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Str keyword Num Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Str keyword Num Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A argparse N/A sys N/A os N/A pdb N/A N/A sys path N/A N/A N/A N/A os path abspath ../../django N/A OCP.settings N/A N/A N/A os environ N/A DJANGO_SETTINGS_MODULE OCP.settings django.conf settings N/A multiprocessing N/A time N/A ocpcaproj N/A ocpcadb N/A numpy np PIL Image parallel_ingester N/A N/A args N/A N/A N/A Create an object and run parallel ingest for a zslab. N/A token N/A N/A args N/A 0 N/A 0 N/A tilesz N/A N/A args N/A 0 N/A 1 N/A tilepath N/A N/A args N/A 0 N/A 2 N/A reslimit N/A N/A args N/A 0 N/A 3 N/A resolution N/A N/A args N/A 0 N/A 4 N/A zslab N/A args N/A 1 N/A ci N/A CatmaidIngester token tilesz tilepath reslimit N/A N/A N/A ci parallelingest zslab resolution N/A CatmaidIngester N/A N/A __init__ N/A N/A self token tilesz tilepath reslimit N/A N/A N/A Load the CATMAID stack into an OCP database N/A N/A self projdb N/A N/A ocpcaproj OCPCAProjectsDB N/A N/A self proj N/A N/A N/A self projdb loadProject token N/A N/A self db N/A N/A ocpcadb OCPCADB N/A self proj N/A N/A self tilesz tilesz N/A N/A self prefix tilepath N/A N/A self reslimit reslimit N/A parallelingest N/A N/A self zslab resolution N/A N/A N/A numxtiles N/A N/A N/A N/A N/A N/A self proj datasetcfg imagesz N/A resolution N/A 0 N/A self tilesz N/A numytiles N/A N/A N/A N/A N/A N/A self proj datasetcfg imagesz N/A resolution N/A 1 N/A self tilesz N/A zstart N/A N/A N/A N/A self proj datasetcfg slicerange N/A 0 N/A zend N/A N/A N/A N/A self proj datasetcfg slicerange N/A 1 N/A zslices N/A N/A N/A N/A N/A self proj datasetcfg cubedim N/A resolution N/A 2 N/A zslab N/A zslab zslices resolution N/A N/A multiprocessing current_process N/A ytile N/A range numytiles N/A N/A xtile N/A range numxtiles N/A N/A cuboid N/A N/A np zeros N/A zslices N/A self tilesz N/A self tilesz dtype N/A np uint8 N/A zslice N/A range zslices N/A N/A N/A N/A N/A N/A zslab zslices zstart zslice zend N/A N/A N/A filename N/A N/A {}/{}/{}/{}/{}.jpg format N/A self prefix resolution N/A N/A N/A zslab zslices zslice zstart ytile xtile N/A N/A N/A tileimage N/A N/A Image open filename r N/A N/A cuboid N/A N/A zslice N/A N/A N/A N/A np asarray tileimage N/A N/A N/A IOError N/A e N/A N/A N/A Failed to open file %s e N/A f N/A open missing_files a N/A N/A N/A f write N/A filename N/A N/A N/A f close N/A corner N/A N/A xtile N/A self tilesz N/A ytile N/A self tilesz N/A zslab zslices N/A N/A N/A N/A self db writeImageCuboid corner resolution cuboid N/A N/A N/A zslice 64 0 N/A N/A N/A N/A N/A self db commit N/A N/A CatmaidIngest N/A N/A __init__ N/A N/A self token tilesz tilepath reslimit totalprocs N/A N/A N/A Load the CATMAID stack into an OCP database N/A N/A self projdb N/A N/A ocpcaproj OCPCAProjectsDB N/A N/A self proj N/A N/A N/A self projdb loadProject token N/A N/A self db N/A N/A ocpcadb OCPCADB N/A self proj N/A N/A self tilesz tilesz N/A N/A self prefix tilepath N/A N/A self reslimit reslimit N/A N/A self totalprocs totalprocs N/A N/A self token token N/A ingest N/A N/A self N/A N/A N/A Read the stack and ingest N/A resolution N/A reversed N/A N/A N/A self proj datasetcfg resolutions N/A N/A N/A resolution N/A self reslimit N/A N/A N/A Building DB for resolution  resolution  imagesize  N/A N/A N/A N/A self proj datasetcfg imagesz N/A resolution N/A zstart N/A N/A N/A N/A self proj datasetcfg slicerange N/A 0 N/A zend N/A N/A N/A N/A self proj datasetcfg slicerange N/A 1 N/A zslices N/A N/A N/A N/A N/A self proj datasetcfg cubedim N/A resolution N/A 2 N/A numzslabs N/A N/A N/A N/A zend zstart 1 zslices 1 N/A sample_iter N/A N/A N/A N/A self token N/A self tilesz N/A self prefix N/A self reslimit resolution numzslabs N/A ziterable N/A zip sample_iter N/A range numzslabs N/A start N/A N/A time time N/A N/A N/A pdb set_trace N/A end N/A N/A time time N/A N/A end start N/A p N/A N/A multiprocessing Pool N/A self totalprocs N/A N/A N/A p map parallel_ingester ziterable N/A N/A main N/A N/A N/A N/A N/A parser N/A N/A argparse ArgumentParser description Ingest a CATMAID stack N/A N/A N/A parser add_argument token action store help Token for the project N/A N/A N/A parser add_argument tilesz action store type int help Tile size of each jpg image. Mostly 512 N/A N/A N/A parser add_argument tilepath action store help Directory with the image files N/A N/A N/A parser add_argument processes action store type int help Number of processes default 4 N/A N/A N/A parser add_argument --reslimit action store type int help Build upto resolution default 10 N/A result N/A N/A parser parse_args N/A ci N/A CatmaidIngest N/A result token N/A result tilesz N/A result tilepath N/A result reslimit N/A result processes N/A N/A N/A ci ingest N/A N/A N/A __name__ __main__ N/A N/A N/A main