make usage of surface dice more general

Author: SarahMuth

run_sbatch_revision.sbatch

@@ -1,15 +1,14 @@
 #! /bin/bash
 #SBATCH -c 4 #4 #8
-#SBATCH --mem 256G #120G #32G #64G #256G
+#SBATCH --mem 120G #120G #32G #64G #256G
 #SBATCH -p grete:shared #grete:shared #grete-h100:shared
 #SBATCH -t 3:00:00 #6:00:00 #48:00:00 
 #SBATCH -G A100:1 #V100:1 #2 #A100:1  #gtx1080:2 #v100:1 #H100:1
 #SBATCH --output=/user/muth9/u12095/synapse-net/slurm_revision/slurm-%j.out 
-#SBATCH -A nim00007 
-#SBATCH --constraint 80gb 
+#SBATCH -A nim00007 #SBATCH --constraint 80gb 
 
 source ~/.bashrc
 conda activate synapse-net
-python /user/muth9/u12095/synapse-net/scripts/cooper/vesicle_segmentation_h5.py \
+python /user/muth9/u12095/synapse-net/scripts/cooper/revision/thin_az_gt.py \
  -i /mnt/ceph-hdd/cold/nim00007/new_AZ_train_data/stem_for_eval/ \
  -o /mnt/ceph-hdd/cold/nim00007/new_AZ_train_data/stem_for_eval/

scripts/cooper/revision/surface_dice.py

@@ -1,7 +1,8 @@
 import sys
 import os
 
-# Add membrain-seg to Python path
+# Add membrain-seg to Python path 
+#Delete before last commit
 MEMBRAIN_SEG_PATH = "/user/muth9/u12095/membrain-seg/src"
 if MEMBRAIN_SEG_PATH not in sys.path:
     sys.path.insert(0, MEMBRAIN_SEG_PATH)
@@ -12,10 +13,14 @@
 from tqdm import tqdm
 import numpy as np
 from scipy.ndimage import label
-from skimage.measure import regionprops
+from skima
 
-from membrain_seg.segmentation.skeletonize import skeletonization
-from membrain_seg.benchmark.metrics import masked_surface_dice
+try:
+    from membrain_seg.segmentation.skeletonize import skeletonization
+    from membrain_seg.benchmark.metrics import masked_surface_dice
+except ImportError:
+    skeletonization=None
+    masked_surface_dice=None
 
 
 def load_segmentation(file_path, key):
@@ -25,6 +30,10 @@ def load_segmentation(file_path, key):
 
 
 def evaluate_surface_dice(pred, gt, raw, check):
+    if skeletonization is None:
+        print("Error! Install membrain_seg. For more information check out https://teamtomo.org/membrain-seg/installation/ ")
+        raise RuntimeError
+    
     gt_skeleton = skeletonization(gt == 1, batch_size=100000)
     pred_skeleton = skeletonization(pred, batch_size=100000)
     mask = gt != 2

scripts/cooper/revision/thin_az_gt.py

@@ -34,7 +34,7 @@ def run_az_thinning(folder=ROOT, out_path=OUTPUT_ROOT):
             az = f_in["labels/az"][:]
 
             az_thin = thin_az(
-                az, boundary_map=boundary_pred, vesicles=vesicles, tomo=tomo, presyn_dist=8, check=True,
+                az, boundary_map=boundary_pred, vesicles=vesicles, tomo=tomo, presyn_dist=8, check=False,
                 min_thinning_size=2500,
             )