Correct new position of ANDOR camera for data after april 2025

ImageJ/script_mosaic_telemos.py

@@ -15,6 +15,7 @@ and launch it from the script editor by pressing F5. Or using the Run button.
 
 @author: H. Chauvet (synchrotron-soleil)
 Used IJ plugins: Bio-Formats, BaSIC
+VERSION: 02042025
 """
 
 
@@ -126,6 +127,16 @@ def getWidthHeight(metadata):
         
     return width, height
     
+def getAcqDate(metadata):
+    """
+    Get the acquisition date from metadata
+    """
+
+    starttime = metadata['Summary']['StartTime'].split(' ')[0]
+    year, month, day = starttime.split('-')
+
+    return int(year), int(month), int(day)
+
 def load_image_tiles_stack(images_dir):
     """
     Fonction pour charge le stack d'images depuis
@@ -183,7 +194,7 @@ def load_image_tiles_stack(images_dir):
     	regex_cpt_roi = None
     	name_pattern = 'Default'
     	
-    # Save the base directory    
+    #Save the base directory    
     base_dir = os.path.abspath(d)
     
     if regex_cpt_roi is not None:
@@ -870,7 +881,14 @@ def extract_tile_positions(metadata, selected_roi, tilesondisk, tilename='tile_'
     yt = [yt[i] for i in igood]
 
     if ANDOR:
+        # Test the date of acquisition Their as been a rotation of the ANDOR Camera at the beginning of APRIL 2025
+        y, m, d = getAcqDate(metadata)
+        if y <= 2025 and m < 4:
+            IJ.log('Use the old position of the ANDOR camera')
             xt = [-x for x in xt]
+        else:
+            IJ.log('Use the new position of the ANDOR camera after 01/04/2025')
+            yt = [-y for y in yt]
         
     xt = map(lambda x: x/pix2um, xt)
     yt = map(lambda x: x/pix2um, yt)
@@ -878,6 +896,7 @@ def extract_tile_positions(metadata, selected_roi, tilesondisk, tilename='tile_'
     xt = map(lambda x: x-int(roiwidth/2), xt)
     yt = map(lambda x: x-int(roiwidth/2), yt)
 
+    # minus the minimum (before it was minus the first position)
     xt = [x-xt[0] for x in xt]
     yt = [y-yt[0] for y in yt]
 
@@ -912,7 +931,7 @@ if __name__ in ['__builtin__','__main__']:
         fwhite = fwhite.absolutePath
 
     # Start Log
-    IJ.log("------- Start MOSAIC TELEMOS -------")
+    IJ.log("------- Start MOSAIC TELEMOS (version: 02042025)-------")
     IJ.log("Image stack: %s" % fdata)
     IJ.log("Dark stack: %s" % fdark)
     IJ.log("Dark of white stack: %s" % fdarkwhite)