Merge pull request #855 from MouseLand/stitch

updating stitching to improve speed (#845)

cellpose/io.py

@@ -196,6 +196,7 @@ def get_image_files(folder, mask_filter, imf=None, look_one_level_down=False):
             igood &= imfile[-len(imf):]==imf
         if igood:
             imn.append(im)
+
     image_names = imn
 
     # remove duplicates
@@ -240,29 +241,38 @@ def get_label_files(image_names, mask_filter, imf=None):
     #elif os.path.exists(label_names[0] + '_seg.npy'):
     #    io_logger.info('labels found as _seg.npy files, converting to tif')
     else:
-        raise ValueError('labels not provided with correct --mask_filter')
+        if not flow_names:
+            raise ValueError('labels not provided with correct --mask_filter')
+        else:
+            label_names = None
     if not all([os.path.exists(label) for label in label_names]):
-        raise ValueError('labels not provided for all images in train and/or test set')
+        if not flow_names:
+            raise ValueError('labels not provided for all images in train and/or test set')
+        else:
+            label_names = None
 
     return label_names, flow_names
 
 
 def load_images_labels(tdir, mask_filter='_masks', image_filter=None, look_one_level_down=False, unet=False):
     image_names = get_image_files(tdir, mask_filter, image_filter, look_one_level_down)
     nimg = len(image_names)
-
+    
     # training data
     label_names, flow_names = get_label_files(image_names, mask_filter, imf=image_filter)
 
     images = []
     labels = []
     k = 0
     for n in range(nimg):
-        if os.path.isfile(label_names[n]):
+        if os.path.isfile(label_names[n]) or os.path.isfile(flow_names[0]):
+            print(image_names[n])
             image = imread(image_names[n])
-            label = imread(label_names[n])
+            if label_names is not None:
+                label = imread(label_names[n])
             if not unet:
                 if flow_names is not None and not unet:
+                    print(flow_names[n])
                     flow = imread(flow_names[n])
                     if flow.shape[0]<4:
                         label = np.concatenate((label[np.newaxis,:,:], flow), axis=0) 

cellpose/utils.py

@@ -3,7 +3,7 @@
 """
 import logging
 import os, warnings, time, tempfile, datetime, pathlib, shutil, subprocess
-from tqdm import tqdm
+from tqdm import tqdm, trange
 from urllib.request import urlopen
 from urllib.parse import urlparse
 import cv2
@@ -403,7 +403,7 @@ def stitch3D(masks, stitch_threshold=0.25):
     mmax = masks[0].max()
     empty = 0
 
-    for i in range(len(masks)-1):
+    for i in trange(len(masks)-1):
         iou = metrics._intersection_over_union(masks[i+1], masks[i])[1:,1:]
         if not iou.size and empty == 0:
             masks[i+1] = masks[i+1]