Add fill missing options for input layers

seung-lab · Mar 22, 2024 · 5251308 · 5251308
1 parent 8e87ffc
commit 5251308
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/scripts/cut_chunk_agg.py b/scripts/cut_chunk_agg.py
@@ -30,7 +30,7 @@ def write_metadata(fn, offset, size, ac_offset):
 ac_offset = param["ac_offset"]
 boundary_flags = param["boundary_flags"]
 
-aff = load_data(global_param['AFF_PATH'],mip=global_param['AFF_RESOLUTION'],fill_missing=False)
+aff = load_data(global_param['AFF_PATH'], mip=global_param['AFF_RESOLUTION'], fill_missing=global_param.get('AFF_FILL_MISSING', False))
 aff_cutout = adjust_affinitymap(aff, aff_bbox, boundary_flags, 0, 1)
 
 save_raw_data("aff.raw", aff_cutout)
@@ -39,12 +39,12 @@ def write_metadata(fn, offset, size, ac_offset):
 start_coord = bbox[0:3]
 end_coord = [bbox[i+3]+1-boundary_flags[i+3] for i in range(3)]
 
-seg = load_data(os.environ['WS_PATH'],mip=global_param['AFF_RESOLUTION'],fill_missing=False)
+seg = load_data(os.environ['WS_PATH'], mip=global_param['AFF_RESOLUTION'], fill_missing=global_param.get('WS_FILL_MISSING', False))
 seg_cutout = cut_data(seg, start_coord, end_coord, boundary_flags)
 save_raw_data("seg.raw", seg_cutout)
 
 if "SEM_PATH" in global_param:
-    sem = load_data(global_param['SEM_PATH'],mip=global_param['AFF_RESOLUTION'],fill_missing=False)
+    sem = load_data(global_param['SEM_PATH'], mip=global_param['AFF_RESOLUTION'], fill_missing=global_param.get('SEM_FILL_MISSING', False))
     sem_cutout = cut_data(sem, start_coord, end_coord, boundary_flags)
     save_raw_data("sem.raw", sem_cutout)
 

diff --git a/scripts/cut_chunk_cs.py b/scripts/cut_chunk_cs.py
@@ -32,11 +32,11 @@ def write_metadata(fn, offset, size, ac_offset, low, high):
 end_coord = [bbox[i+3]+1-boundary_flags[i+3] for i in range(3)]
 
 if "AFF_PATH" in global_param:
-    aff = load_data(global_param['AFF_PATH'],mip=global_param['AFF_RESOLUTION'],fill_missing=False)
+    aff = load_data(global_param['AFF_PATH'], mip=global_param['AFF_RESOLUTION'], fill_missing=global_param.get('AFF_FILL_MISSING', False))
     aff_cutout = cut_data(aff, start_coord, end_coord, boundary_flags)
     save_raw_data("aff.raw", aff_cutout)
 
-seg = load_data(os.environ['SEG_PATH'], mip=global_param['AFF_RESOLUTION'], fill_missing=True)
+seg = load_data(os.environ['SEG_PATH'], mip=global_param['AFF_RESOLUTION'], fill_missing=global_param.get('SEG_FILL_MISSING', False))
 seg_cutout = cut_data(seg, start_coord, end_coord, boundary_flags)
 save_raw_data("seg.raw", seg_cutout)
 

diff --git a/scripts/cut_chunk_ws.py b/scripts/cut_chunk_ws.py
@@ -24,11 +24,11 @@ def write_metadata(fn, size, boundaries, offset):
 boundary_flags = param["boundary_flags"]
 offset = param["offset"]
 
-aff = load_data(global_param['AFF_PATH'],mip=global_param['AFF_RESOLUTION'],fill_missing=False)
+aff = load_data(global_param['AFF_PATH'], mip=global_param['AFF_RESOLUTION'], fill_missing=global_param.get('AFF_FILL_MISSING', False))
 aff_cutout = adjust_affinitymap(aff, aff_bbox, boundary_flags, 1, 1)
 
 if "SEM_PATH" in global_param and global_param.get("SEMANTIC_WS", False):
-    sem = load_data(global_param['SEM_PATH'], mip=global_param['AFF_RESOLUTION'], fill_missing=False)
+    sem = load_data(global_param['SEM_PATH'], mip=global_param['AFF_RESOLUTION'], fill_missing=global_param.get('SEM_FILL_MISSING', False))
     aff_cutout = mask_affinity_with_semantic_labels(aff_cutout, sem, bbox, boundary_flags, 1, 1)
 
 if 'ADJUSTED_AFF_PATH' in global_param: