Allow single image processing

ImageJ/script_mosaic_telemos.py

@@ -149,7 +149,9 @@ def load_image_tiles_stack(images_dir):
     # Test if the format is only PosXXX
     directoryPos = os.path.join(os.path.abspath(d), 'Pos*')
     filesPos = glob.glob(directoryPos)
-    regex_cpt_roi = None
+    
+    # Test if the format is from MDAQ with only Default folrder in (when multipos is untick)
+    directoryDefault = os.path.join(os.path.abspath(d), 'Default')
     
     if len(filesSE) > 0:
         format = 'SE'
@@ -172,6 +174,12 @@ def load_image_tiles_stack(images_dir):
         regex_cpt_roi = None
         name_pattern = 'Pos'
        
+    if os.path.isdir(directoryDefault):
+    	format = 'DEFAULT'
+    	files = ['Default']
+    	regex_cpt_roi = None
+    	name_pattern = 'Default'
+    	
     # Save the base directory    
     base_dir = os.path.abspath(d)
     
@@ -217,8 +225,12 @@ def load_image_tiles_stack(images_dir):
     if format == 'POS':
         IJ.log('Load multi-position format from MACQ')
         hstack, good_names = load_mm_images(base_dir, roi=None, tile=False, pos=True, return_filenames=True)
-        metadata = load_metadata(os.path.join(base_dir, good_names[0].split(os.path.sep)[0], 'metadata.txt'))
         
+    if format == 'DEFAULT':
+        IJ.log('Load single position format from MACQ')
+        hstack, good_names = load_mm_images(base_dir, roi=None, tile=False, pos=False, return_filenames=True)  
+        
+    metadata = load_metadata(os.path.join(base_dir, good_names[0].split(os.path.sep)[0], 'metadata.txt'))
     hstack.setTitle("Data")
 
     return hstack, metadata, base_dir, selected_roi, good_names
@@ -287,6 +299,7 @@ def process_white(implus_white, implus_darkofwhite, zofwhite, roi=None):
         xmax = xmin + xmax 
         ymax = ymin + ymax 
     else:
+        print('No crop of white')
         xmin = ymin = 0
         xmax = implus_white.width
         ymax = implus_white.height
@@ -309,6 +322,7 @@ def process_white(implus_white, implus_darkofwhite, zofwhite, roi=None):
         xmax = xmin + xmax 
         ymax = ymin + ymax 
     else:
+        print('No crop of dark of white')
         xmin = ymin = 0
         xmax = implus_darkofwhite.width
         ymax = implus_darkofwhite.height
@@ -400,10 +414,12 @@ def process_tiles(implus_tiles_stack, channel, z, implus_white_corr, implus_dark
         mmversion = getMMversion(metadata)
         roi = getRoi(metadata, mmversion)
         if roi is not None and len(roi) == 4 and implus_dark_stack.width > roi[2] and implus_dark_stack.height > roi[3]:
+            print('I crop the dark')
             xmin, ymin, xmax, ymax = roi
             xmax = xmin + xmax 
             ymax = ymin + ymax 
         else:
+            print('No crop of the dark')
             xmin = ymin = 0
             xmax = implus_dark_stack.width
             ymax = implus_dark_stack.height
@@ -434,17 +450,15 @@ def process_tiles(implus_tiles_stack, channel, z, implus_white_corr, implus_dark
     if data.numDimensions() == 5:
         inter = Intervals.createMinMax(0, 0, channel, z-1, 0,
                                        xLen-1, yLen-1, channel, z-1, Ntiles-1)
-    # Data are x,y,channel, (t or z)
+    # Data are x,y,channel,t
     if data.numDimensions() == 4:
-        if Ntiles > 1:
-    		# x, y, channel, t
         inter = Intervals.createMinMax(0, 0, channel, 0,
                                        xLen-1, yLen-1, channel, Ntiles-1)
-       	else:
-       		# x, y, channel, z
-       		inter = Intervals.createMinMax(0, 0, channel, z-1,
-            	                           xLen-1, yLen-1, channel, z-1)
 
+    # Date are x,y,channel
+    if data.numDimensions() == 3:
+        inter = Intervals.createMinMax(0, 0, channel,
+                                       xLen-1, yLen-1, channel)
     if inter is not None:
         data = ops.transform().crop(data, inter)
 
@@ -519,6 +533,7 @@ def run_processing(channel, zimg, zwhite, run_basic=True, optimizeXY=True, savep
     IJ.run("Image Sequence... ", "format=TIFF name=tile_ start=1 save=["+procfolder+"]")
         
     # Save the tile position file for the stitching
+    if tilesposfile is not None:
         with open(procfolder+'/TileConfiguration.txt', 'w') as f:
             f.write(tilesposfile)
 
@@ -600,6 +615,9 @@ def run_gui(default_values=None):
     if default_values is None:
         default_values = {}
         default_values['optimXY'] = False
+        if tilesposfile is None:
+            default_values['Basic'] = False
+        else:
             default_values['Basic'] = True
         default_values['dir'] = rootdir+'/IJ_roi%s_telemosMosaic' % (selectedroi)
         default_values['zimg'] = 0
@@ -896,7 +914,10 @@ if __name__ in ['__builtin__','__main__']:
     
     # Make a list of tiles names
     tilesondisk = set(os.path.dirname(t) for t in file_names)
+    if len(tilesondisk) > 1:
         tilesposfile = extract_tile_positions(metadata, selectedroi, tilesondisk)
+    else:
+        tilesposfile = None
 
     if fdark is not None:
         darks = load_images(fdark, roi=roi)