fix MM1 version bugs in image order

ImageJ/script_mosaic_telemos.py

@@ -45,7 +45,7 @@ except:
     
 finally:
     from utils.IJmmlib import load_mm_images
-    from utils.mmlib import load_metadata, get_mm2_first_image_metadata, get_dimensions
+    from utils.mmlib import load_metadata, get_mm2_first_image_metadata, get_mm1_first_image_metadata, get_dimensions, get_micromanager_version
 
 # Import to do operation with ImageJ2 and ImgMath
 from net.imglib2.util import Intervals
@@ -68,8 +68,8 @@ def getMMversion(metadata):
     """
     Get MM version from metadata 
     """
-
-    if int(metadata['Summary']["MicroManagerVersion"].split('.')[0]) >= 2:
+    mmversion = get_micromanager_version(metadata)
+    if mmversion[0] == '2':
         version = 2
     else:
         version = 1
@@ -345,7 +345,8 @@ def process_tiles(implus_tiles_stack, channel, z, implus_white_corr, implus_dark
             dark = Views.hyperSlice(dark, 2, channel)
 
         # Need to apply crop on dark
-        roi = getRoi(metadata)
+        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]:
             xmin, ymin, xmax, ymax = roi
             xmax = xmin + xmax 
@@ -734,11 +735,18 @@ def extract_tile_positions(metadata, selected_roi, tilesondisk, tilename='tile_'
     xt, yt = getMMtiles(metadata, selected_roi, tilesondisk)
     
     # Is the microscope use Andor camera ? (tilted at 90)
+    ANDOR = False
+    mmversion = getMMversion(metadata)
+    if mmversion == 2:
         fmeta = get_mm2_first_image_metadata(metadata)
         if fmeta['Camera'] == 'Andor':
             ANDOR = True
     else:
-        ANDOR = False    
+        fmeta = get_mm1_first_image_metadata(metadata)
+        if fmeta['Core-Camera'] == 'Andor':
+            ANDOR = True
+            
+   
     
     if ANDOR:
         xtmp = yt

ImageJ/utils/IJmmlib.py

@@ -4,7 +4,7 @@ Usefull jython functions for micro manager and imagej
 """
 import os
 from ij import ImagePlus, VirtualStack, IJ
-from mmlib import generate_file_list, load_metadata, get_dimensions, get_resolution
+from mmlib import generate_file_list, load_metadata, get_dimensions, get_resolution, get_micromanager_version
 
 
 def load_mm_images(rootdir, roi=1, tile=True, pos=False, 
@@ -15,8 +15,14 @@ def load_mm_images(rootdir, roi=1, tile=True, pos=False,
     """
     
     metadata = load_metadata(rootdir)
+    mmversion = int(get_micromanager_version(metadata)[0])
     dimensions = get_dimensions(metadata)
-    image_files = generate_file_list(metadata, roi, tile, pos)
+    if mmversion == 1:
+        stack_order = ['position', 'z', 'time', 'channels']
+    else:
+        stack_order = ['position', 'time', 'channels', 'z']
+        
+    image_files = generate_file_list(metadata, roi, tile, pos, stack_order)
     
     # Create the virtual stack
     vstack = VirtualStack(dimensions['width'], dimensions['height'], None, rootdir)

ImageJ/utils/mmlib.py

@@ -63,6 +63,30 @@ def get_mm2_first_image_metadata(metadata):
 
     return None
 
+
+def get_mm1_first_image_metadata(metadata):
+    """
+    Return the first metadata in the list of images starting with Metadata
+    """
+
+    for k in metadata.keys():
+        if k.startswith('FrameKey-'):
+            return metadata[k]
+
+    return None
+    
+def get_mm_first_image_metadata(metadata):
+    """
+    Return the first metadata in the list of images starting with Metadata
+    """
+    
+    v = get_micromanager_version(metadata)
+    
+    if v[0] == '1':
+        return get_mm1_first_image_metadata(metadata)
+        
+    return get_mm2_first_image_metadata(metadata)
+    
 def get_dimensions(metadata):
     """
     Extract from metadata the dimensions of data and export a consistent
@@ -145,7 +169,7 @@ def get_stage_positions_labels(metadata):
     return stage_label
 
 
-def generate_file_list(metadata, roi=1, tile=True, pos=False):
+def generate_file_list(metadata, roi=1, tile=True, pos=False, stack_order=None):
     """
     Generate a list of all images to load from the metadata
 
@@ -178,7 +202,7 @@ def generate_file_list(metadata, roi=1, tile=True, pos=False):
         pre_folder = 'Default'
         
     # Get the combination of all conditions of acquisitions
-    all_conditions, ordered_keys = groups_dimensions(metadata)
+    all_conditions, ordered_keys = groups_dimensions(metadata, stack_order)
 
     # Loop over conditions to create the correct file name
     image_files = []