9999
100100def _load_meshdict_from_bmfmesh (bmfmesh , pos_multipliers , translation ):
101101
102- vertices = np .array (bmfmesh .positions ).reshape (- 1 , 3 )[:,::- 1 ]
102+ vertices = np .array (bmfmesh .positions ).reshape (- 1 , 3 )[:, ::- 1 ]
103103 faces = np .array (bmfmesh .triangles ).reshape (- 1 , 3 )
104104
105105 pos_multipliers = np .array (pos_multipliers , dtype = float )
106106 translation = np .array (translation , dtype = float )
107107 vertices = vertices * pos_multipliers + translation
108108
109- return { # could be a class
110- 'vertices' : vertices ,
111- 'faces' : faces
112- }
109+ return {"vertices" : vertices , "faces" : faces } # could be a class
113110
114111
115112def read_from_bmf (
@@ -149,12 +146,14 @@ def read_from_bmf(
149146 for track in tracks :
150147 pred = None
151148 for t , mesh in track .meshes .items ():
152- mesh = _load_meshdict_from_bmfmesh (mesh , pos_multipliers , translation )
149+ mesh = _load_meshdict_from_bmfmesh (
150+ mesh , pos_multipliers , translation
151+ )
153152 pos [cell_id ] = mesh .center_mass
154-
153+
155154 if store_meshes :
156155 lT_mesh [cell_id ] = mesh
157-
156+
158157 predecessor [cell_id ] = (pred ,)
159158 pred = cell_id
160159 times [cell_id ] = t
@@ -1059,31 +1058,31 @@ def read_from_mamut_xml(
10591058 )
10601059
10611060
1062- LOADERS = { # put all formats in smaller case
1061+ LOADERS = { # put all formats in smaller case
10631062 "bmf" : {
1064- "BMF loader" : read_from_bmf
1063+ "BMF loader" : read_from_bmf ,
10651064 },
10661065 "csv" : {
10671066 "Standard CSV loader" : read_from_csv ,
1068- "Mastodon CSV loader" : read_from_mastodon_csv
1067+ "Mastodon CSV loader" : read_from_mastodon_csv ,
10691068 },
10701069 "binary" : {
1071- "Binary loader" : read_from_binary
1070+ "Binary loader" : read_from_binary ,
10721071 },
10731072 "xml" : {
10741073 # "TGMM XML loader": read_from_tgmm_xml, # commented out because it requires a specific file format
10751074 "MaMuT XML loader" : read_from_mamut_xml ,
10761075 "ASTEC XML loader" : read_from_ASTEC ,
10771076 },
10781077 "mastodon" : {
1079- "Mastodon loader" : read_from_mastodon
1078+ "Mastodon loader" : read_from_mastodon ,
10801079 },
10811080 "pkl" : {
1082- "ASTEC PKL loader" : read_from_ASTEC
1081+ "ASTEC PKL loader" : read_from_ASTEC ,
10831082 },
10841083 "txt" : {
10851084 "C. elegans loader" : read_from_txt_for_celegans ,
10861085 "C. elegans CAO loader" : read_from_txt_for_celegans_CAO ,
10871086 "C. elegans BAO loader" : read_from_txt_for_celegans_BAO ,
10881087 },
1089- }
1088+ }
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