Add spectial condition to check that file exist. Avoid stitching when only one tile tis processed

ImageJ/README.md

@@ -10,7 +10,7 @@
   
 ## Install as a FiJi Plugins
 
-1. Locate the folder where your ImageJ is installed
+1. Locate the folder where your ImageJ is installed (For mac users it could be locate on the Applications forlder, right click on FiJi and then "Show Package Contents" to access the FiJi folder)
 2. Add a folder **disco_ij** in the **Fiji.app/plugins** folder an copy the **script_mosaic_telemos.py** into the **disco_ij** folder.
 3. Copy the **utils** folder into **Fiji.app/jars/Lib** directory
 4. In Fiji **help>refresh menus** and **restart FiJi*

ImageJ/script_mosaic_telemos.py

@@ -18,7 +18,7 @@ Used IJ plugins: Bio-Formats, BaSIC
 
 
 import glob
-from ij import IJ, ImagePlus, ImageStack
+from ij import IJ, ImagePlus, ImageStack, Macro
 from ij.process import FloatProcessor
 import os
 import json 
@@ -27,6 +27,7 @@ from fiji.util.gui import GenericDialogPlus
 from java.awt.event import WindowAdapter
 from java.lang import Thread
 from ij import WindowManager
+from java.lang import RuntimeException
 import re
 import sys
 
@@ -134,7 +135,7 @@ def load_image_tiles_stack(images_dir):
     - Outils grille (create grid) du multi position
     """
 
-    d = images_dir
+    d = str(images_dir)
 
     # Travail sur le nom du repertoir
 
@@ -153,6 +154,7 @@ def load_image_tiles_stack(images_dir):
     # 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')
     
+    regex_cpt_roi = None
     if len(filesSE) > 0:
         format = 'SE'
         files = filesSE
@@ -579,6 +581,7 @@ def run_processing(channel, zimg, zwhite, run_basic=True, optimizeXY=True, savep
                 imp_tmp = IJ.getImage()
                 imp_tmp.close()
 
+    if tilesposfile is not None:
         IJ.log("Run stitching of tiles")
         # Run the stitching
         # Autre option si on a pas mal de ram sur l'ordinateur 'Save computation time (but use more RAM)'
@@ -908,6 +911,15 @@ if __name__ in ['__builtin__','__main__']:
     IJ.log("Dark of white stack: %s" % fdarkwhite)
     IJ.log("White stack: %s" % fwhite)
     
+    
+    # Sanity checks if files are accessible or not
+    all_good = True
+    for ff in [str(fdata), str(fdark), str(fdarkwhite), str(fwhite)]:
+        if not os.path.exists(str(fdata)):
+            IJ.log("The path "+ff+" does not exist or is not acessible")
+            all_good = False
+            
+    if all_good:
         # LOAD DATA
         hstack, metadata, rootdir, selectedroi, file_names = load_image_tiles_stack(fdata)
         hstack.show()