vv_temp change + skip_lists for fafb and minnie

inference/align_blocks.py

@@ -49,7 +49,9 @@ def ranges_overlap(a_pair, b_pair):
   parser = get_argparser()
   parser.add_argument('--param_lookup', type=str,
     help='relative path to CSV file identifying params to use per z range')
-  # parser.add_argument('--z_range_path', type=str, 
+  parser.add_argument('--skip_list_lookup', type=str,
+    help='relative path to file identifying list of skip sections')
+  # parser.add_argument('--z_range_path', type=str,
   #   help='path to csv file with list of z indices to use')
   parser.add_argument('--src_path', type=str)
   parser.add_argument('--src_mask_path', type=str, default='',
@@ -142,6 +144,14 @@ def ranges_overlap(a_pair, b_pair):
            tgt_radius_lookup[z] = tgt_radius
            vvote_lookup[z] = [-i for i in range(1, tgt_radius+1)]
 
+  if args.skip_list_lookup is not None:
+    with open(args.skip_list_lookup, 'r') as f:
+      line = f.readline()
+      while line:
+        skip_ind = int(line)
+        skip_list.append(skip_ind)
+        line = f.readline()
+
   # Filter out skipped sections from vvote_offsets
   min_offset = 0
   for z, tgt_radius in vvote_lookup.items():
@@ -246,6 +256,8 @@ def ranges_overlap(a_pair, b_pair):
     print(b)
     assert(len(v) % 2 == 1)
 
+  default_vv_temp = (2**mip)/6
+
   # Create field CloudVolumes
   print('Creating field & overlap CloudVolumes')
   block_pair_fields = {}
@@ -400,8 +412,9 @@ def __iter__(self):
         bbox = bbox_lookup[z]
         tgt_offsets = vvote_lookup[z]
         fields = {i: block_pair_fields[i] for i in tgt_offsets}
-        t = a.vector_vote(cm, fields, block_vvote_field, z, bbox, mip, 
-                          inverse=False, serial=True, softmin_temp=2**mip, blur_sigma=1)
+        t = a.vector_vote(cm, fields, block_vvote_field, z, bbox, mip,
+                          inverse=False, serial=True,
+                          softmin_temp=default_vv_temp, blur_sigma=1)
         yield from t
 
   class BlockAlignRender(object):
@@ -462,8 +475,8 @@ def __iter__(self):
         bbox = bbox_lookup[z]
         tgt_offsets = vvote_lookup[z]
         fields = {i: stitch_pair_fields[i] for i in tgt_offsets}
-        t = a.vector_vote(cm, fields, overlap_vvote_field, z, bbox, mip, 
-                          inverse=False, serial=True, softmin_temp=2**mip, blur_sigma=1)
+        t = a.vector_vote(cm, fields, overlap_vvote_field, z, bbox, mip,
+                          inverse=False, serial=True, softmin_temp=default_vv_temp, blur_sigma=1)
         yield from t
 
   class StitchAlignRender(object):
@@ -502,8 +515,8 @@ def __iter__(self):
         bbox = bbox_lookup[z]
         offsets = block_start_to_stitch_offsets[z]
         fields = {i: stitch_fields[i] for i in offsets}
-        t = a.vector_vote(cm, fields, broadcasting_field, z, bbox, mip, 
-                          inverse=False, serial=True, softmin_temp=2**mip, blur_sigma=1)
+        t = a.vector_vote(cm, fields, broadcasting_field, z, bbox, mip,
+                          inverse=False, serial=True, softmin_temp=default_vv_temp, blur_sigma=1)
         yield from t
 
   # Serial alignment with block stitching 

inference/aligner.py

@@ -641,7 +641,7 @@ def vector_vote_chunk(self, pairwise_cvs, vvote_cv, z, bbox, mip,
       d = 2**mip
       n = len(fields)
       m = int(binom(n, (n+1)//2)) - 1
-      softmin_temp = 2**mip
+      softmin_temp = (2**mip)/6
     return vector_vote(fields, softmin_temp=softmin_temp, blur_sigma=blur_sigma)
 
   def invert_field(self, z, src_cv, dst_cv, bbox, mip, pad, model_path):

inference/params/191213_FAFB_skip_list.csv

@@ -0,0 +1,12 @@
+3595
+3596
+3597
+3715
+4192
+4353
+4474
+4951
+6462
+6883
+6884
+6885

inference/params/191213_minnie_march_skip_list.csv

@@ -0,0 +1,17 @@
+15171
+17491
+17891
+18332
+18733
+19186
+21357
+21559
+21660
+21671
+21937
+22052
+22168
+23329
+23447
+24737
+25345