display sequence will now allow the loading of sequences with missing frames

Sequences with missing frames are not uncommon in the raw images that were collected at soleil. I beleive that these missing frames are caused by the sequence captures that are stopped, resting in missing frames at the end compared to what was planned....

fixes #10

Makefile

@@ -7,7 +7,7 @@ TEMP_PATH:=$(shell echo ~/work/lipase/tmp)
 TESTS_OUTPUT_DATA_PATH:=$(TEMP_PATH)
 LIB_SRC_FILES=$(shell find ./src/lipase -name "*.py")
 PLUGINS_SRC_FILES=$(shell find ./src/ij-plugins -name "*.py")
-LIPASE_VERSION=1.10
+LIPASE_VERSION=1.11
 
 BUILD_ROOT_PATH:=$(TEMP_PATH)/build
 PACKAGE_FILE_PATH=$(BUILD_ROOT_PATH)/lipase-$(LIPASE_VERSION).zip

src/lipase/catalog.py

@@ -28,6 +28,19 @@ class DacMetadata(object):
         return channels[channel_index]["Name"]
 
 
+class MissingImageFile(Exception):
+    
+    def __init__(self, sequence_id, frame_index, slice_index, channel_index):
+        self.sequence_id = sequence_id
+        self.frame_index= frame_index
+        self.slice_index = slice_index
+        self.channel_index = channel_index
+        super(MissingImageFile, self).__init__(self, 'missing image file')
+
+    def __str__(self):
+        return 'the image file for sequence "%s" frame %d, slice %d and channel %d is missing' % (self.sequence_id, self.frame_index, self.slice_index, self.channel_index)
+
+
 class Sequence(object):
     """A sequence of images stored in micro manager format
     """
@@ -121,7 +134,10 @@ class Sequence(object):
         '''
         assert frame_index < self.num_frames
         assert channel_index < self.num_channels
-        frame_info = self.mmm['FrameKey-%d-%d-%d' % (frame_index, channel_index, slice_index)]
+        try:
+            frame_info = self.mmm['FrameKey-%d-%d-%d' % (frame_index, channel_index, slice_index)]
+        except KeyError as e:
+            raise MissingImageFile(sequence_id=self.id, frame_index=frame_index, slice_index=slice_index, channel_index=channel_index)
         rel_file_path = frame_info['FileName']
         return os.path.join(self.get_root_path(), rel_file_path)
 
@@ -192,8 +208,13 @@ class Sequence(object):
         for frame_index in selected_frames:
             for slice_index in selected_slices:
                 for channel_index in selected_channel_indices:
-                    image = IImageEngine.get_instance().load_image(self.get_image_file_path(channel_index=channel_index, frame_index=frame_index, slice_index=slice_index))
+                    try:
-                    stack.set_image(image=image, channel_index=channel_index, frame_index=frame_index, slice_index=slice_index)
+                        image_file_path = self.get_image_file_path(channel_index=channel_index, frame_index=frame_index, slice_index=slice_index)
+                        image = IImageEngine.get_instance().load_image(image_file_path)
+                        stack.set_image(image=image, channel_index=channel_index, frame_index=frame_index, slice_index=slice_index)
+                    except MissingImageFile as e:
+                        logger.warn('%s. As a result, the hyperstack will be black at this frame' % str(e))
+                        # logger.warn('the image file for sequence "%s" frame %d, slice %d and channel %d is missing. As a result, the hyperstack will be black at this frame' % (self.id, frame_index, slice_index, channel_index))
         return stack
 
 def find_dirs_containing_file(file_name, root_dir):

src/lipase/imagej/__init__.py

@@ -1,15 +1,20 @@
+import os
 from ij import IJ, ImagePlus  # pylint: disable=import-error
 import re
-
+from .. import logger
+from ..catalog import MissingImageFile
 
 def open_sequence_as_hyperstack(sequence):
     hyperstack = IJ.createHyperStack(sequence.id, sequence.width, sequence.height, sequence.num_channels, sequence.num_slices, sequence.num_frames, sequence.num_bits_per_pixels)
     for channel_index in range(sequence.num_channels):
         for frame_index in range(sequence.num_frames):
             slice_index = 0
-            src_image_file_path = sequence.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
+            try:
-            # print(src_image_file_path)
+                src_image_file_path = sequence.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
-            src_image = IJ.openImage(src_image_file_path)
+                src_image = IJ.openImage(src_image_file_path)
+            except MissingImageFile as e:
+                logger.warn('%s. As a result, the hyperstack will be black at this frame' % str(e))
+                #logger.warn('the image file for frame %d and channel %d is missing. As a result, the hyperstack will be black at this frame' % (frame_index, channel_index))
             # print(src_image.getProperties())
             hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
             hyperstack.setProcessor(src_image.getProcessor())
@@ -23,9 +28,13 @@ def open_sequence_as_stack(sequence, channel_id):
     hyperstack = IJ.createHyperStack(sequence.id, sequence.width, sequence.height, 1, sequence.num_slices, sequence.num_frames, sequence.num_bits_per_pixels)
     for frame_index in range(sequence.num_frames):
         slice_index = 0
-        src_image_file_path = sequence.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
+        try:
-        # print(src_image_file_path)
+            src_image_file_path = sequence.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
-        src_image = IJ.openImage(src_image_file_path)
+            # print(src_image_file_path)
+            src_image = IJ.openImage(src_image_file_path)
+        except MissingImageFile as e:
+            logger.warn('%s. As a result, the hyperstack will be black at this frame' % str(e))
+            # logger.warn('the image file for frame %d and channel %d is missing. As a result, the hyperstack will be black at this frame' % (frame_index, channel_index))
         # print(src_image.getProperties())
         hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
         hyperstack.setProcessor(src_image.getProcessor())