Fix bug for non-mosaic acquisition

ImageJ/script_mosaic_telemos.py

@@ -450,7 +450,11 @@ def process_tiles(implus_tiles_stack, channel, z, implus_white_corr, implus_dark
         for tile in xrange(Ntiles):
             IJ.showProgress(tile+1, Ntiles)
             IJ.log('Compute %i / %i' % (tile+1, Ntiles))
+            if Ntiles > 1:
                 data_views = Views.hyperSlice(data, 2, tile)
+            else:
+                data_views = data
+                
             opsus = sub(data_views, dark)
             # FOR DEGUG: op[cpt] = sub(data_views, dark)
             op[cpt] = IF(GT(opsus, 0.0), THEN(div(opsus, white)), ELSE(0.0))

ImageJ/utils/IJmmlib.py

@@ -28,7 +28,7 @@ def load_mm_images(rootdir, roi=1, tile=True, pos=False,
 
     if not tile and pos:
         stack_order = ['position', 'time', 'z', 'channels']
-    image_files = generate_file_list(metadata, roi, tile, pos, stack_order)
+    image_files = generate_file_list(metadata, rootdir, roi, tile, pos, stack_order)
     
     # Create the virtual stack
     vstack = VirtualStack(dimensions['width'], dimensions['height'], None, rootdir)

ImageJ/utils/mmlib.py

@@ -195,7 +195,7 @@ def get_stage_positions_labels(metadata):
     return stage_label
 
 
-def generate_file_list(metadata, roi=1, tile=True, pos=False, stack_order=None):
+def generate_file_list(metadata, rootdir, roi=1, tile=True, pos=False, stack_order=None):
     """
     Generate a list of all images to load from the metadata
 
@@ -228,6 +228,15 @@ def generate_file_list(metadata, roi=1, tile=True, pos=False, stack_order=None):
     else:
         pre_folder = 'Default' # Is redefined
         
+        # Test if the folder delfault is present 
+        # Test the name of root folder for images
+        if rootdir is not None:
+            if not os.path.isdir(os.path.join(rootdir, 'Default')):
+                if os.path.isdir(os.path.join(rootdir, 'Pos0')):
+                    pre_folder = 'Pos0'
+                else:
+                    print('No folder found !')
+     
     # Get the combination of all conditions of acquisitions
     all_conditions, ordered_keys = groups_dimensions(metadata, roi, stack_order)
 
@@ -247,7 +256,7 @@ def generate_file_list(metadata, roi=1, tile=True, pos=False, stack_order=None):
                 min_pos_index = 0
                 
             if pos:
-                # Define the pre_folder
+                # Define the pre_folder
                 pre_folder = 'Pos{i}'.format(i=group[ordered_keys.index('position')])
                          
             base_fmt = fmtMM2.format(filter=group[ordered_keys.index('channels')],