Mercurial > repos > iuc > idr_download_by_ids
changeset 3:381f248febba draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
| author | iuc |
|---|---|
| date | Wed, 22 Apr 2020 11:43:18 -0400 |
| parents | 17b1cd0f4812 |
| children | 11036f6197d6 |
| files | idr_download_by_ids.py idr_download_by_ids.xml test-data/test_output.log |
| diffstat | 3 files changed, 116 insertions(+), 44 deletions(-) [+] |
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--- a/idr_download_by_ids.py Tue Apr 14 10:27:25 2020 -0400 +++ b/idr_download_by_ids.py Wed Apr 22 11:43:18 2020 -0400 @@ -7,10 +7,22 @@ from omero.constants.namespaces import NSBULKANNOTATIONS # noqa -def warn(message, image_identifier): +def warn(message, image_identifier, warn_skip=False): + message = message.rstrip() + if warn_skip: + if message[-1] in ['.', '!', '?']: + skip_msg = ' Skipping download!' + else: + skip_msg = '. Skipping download!' + else: + skip_msg = '' print( - 'ImageSpecWarning for {0}: {1}' - .format(image_identifier, message), + 'ImageSpecWarning for {0}: {1}{2}' + .format( + image_identifier, + message, + skip_msg + ), file=sys.stderr ) @@ -93,6 +105,7 @@ if fname[-5:] != '.tiff': fname += '.tiff' try: + fname = fname.replace(' ', '_') tiff = TIFF.open(fname, mode='w') tiff.write_image(selection) finally: @@ -105,6 +118,19 @@ coord=(0, 0), width=0, height=0, region_spec='rectangle', skip_failed=False ): + # basic argument sanity checks and adjustments + prefix = 'image-' + # normalize image ids by stripping off prefix if it exists + image_ids = [ + iid[len(prefix):] if iid[:len(prefix)] == prefix else iid + for iid in image_ids + ] + + if region_spec not in ['rectangle', 'center']: + raise ValueError( + 'Got unknown value "{0}" as region_spec argument' + .format(region_spec) + ) # connect to idr conn = BlitzGateway('public', 'public', @@ -113,20 +139,30 @@ conn.connect() try: - prefix = 'image-' for image_id in image_ids: - if image_id[:len(prefix)] == prefix: - image_id = image_id[len(prefix):] - image_id = int(image_id) - image = conn.getObject("Image", image_id) + image_warning_id = 'Image-ID: {0}'.format(image_id) + try: + image_id = int(image_id) + except ValueError: + image = None + else: + try: + image = conn.getObject("Image", image_id) + except Exception as e: + # respect skip_failed on unexpected errors + if skip_failed: + warn(str(e), image_warning_id, warn_skip=True) + continue + else: + raise if image is None: - image_warning_id = 'Image-ID: {0}'.format(image_id) if skip_failed: warn( 'Unable to find an image with this ID in the ' - 'database. Skipping download!', - image_warning_id + 'database.', + image_warning_id, + warn_skip=True ) continue raise ValueError( @@ -135,23 +171,39 @@ .format(image_warning_id) ) - image_name = os.path.splitext(image.getName())[0] - image_warning_id = '{0} (ID: {1})'.format( - image_name, image_id - ) + try: + # try to extract image properties + # if anything goes wrong here skip the image + # or abort. + image_name = os.path.splitext(image.getName())[0] + image_warning_id = '{0} (ID: {1})'.format( + image_name, image_id + ) + + if region_spec == 'rectangle': + tile = get_clipping_region(image, *coord, width, height) + elif region_spec == 'center': + tile = get_clipping_region( + image, + *_center_to_ul(*coord, width, height) + ) - if region_spec == 'rectangle': - tile = get_clipping_region(image, *coord, width, height) - elif region_spec == 'center': - tile = get_clipping_region( - image, - *_center_to_ul(*coord, width, height) - ) - else: - raise ValueError( - 'Got unknown value "{0}" as region_spec argument' - .format(region_spec) - ) + ori_z, z_stack = z_stack, confine_plane(image, z_stack) + ori_frame, frame = frame, confine_frame(image, frame) + num_channels = image.getSizeC() + if channel is None: + channel_index = 0 + else: + channel_index = find_channel_index(image, channel) + except Exception as e: + # respect skip_failed on unexpected errors + if skip_failed: + warn(str(e), image_warning_id, warn_skip=True) + continue + else: + raise + + # region sanity checks and warnings if tile[2] < width or tile[3] < height: # The downloaded image region will have smaller dimensions # than the specified width x height. @@ -162,7 +214,7 @@ image_warning_id ) - ori_z, z_stack = z_stack, confine_plane(image, z_stack) + # z-stack sanity checks and warnings if z_stack != ori_z: warn( 'Specified image plane ({0}) is out of bounds. Using {1} ' @@ -171,7 +223,7 @@ image_warning_id ) - ori_frame, frame = frame, confine_frame(image, frame) + # frame sanity checks and warnings if frame != ori_frame: warn( 'Specified image frame ({0}) is out of bounds. Using ' @@ -179,10 +231,9 @@ .format(ori_frame, frame), image_warning_id ) - # Get the channel index. If the index is not valid, skip the image + + # channel index sanity checks and warnings if channel is None: - channel_index = 0 - num_channels = image.getSizeC() if num_channels > 1: warn( 'No specific channel selected for multi-channel ' @@ -191,18 +242,35 @@ image_warning_id ) else: - channel_index = find_channel_index(image, channel) - if channel_index == -1 or channel_index >= image.getSizeC(): - raise ValueError( - '"{0}" is not a known channel name for image {1}' - .format(channel, image.getName()) - ) + if channel_index == -1 or channel_index >= num_channels: + if skip_failed: + warn( + str(channel) + + ' is not a known channel name for this image.', + image_warning_id, + warn_skip=True + ) + continue + else: + raise ValueError( + '"{0}" is not a known channel name for image {1}. ' + 'Aborting!' + .format(channel, image_warning_id) + ) # download and save the region as TIFF fname = '__'.join( [image_name, str(image_id)] + [str(x) for x in tile] ) - download_plane_as_tiff(image, tile, z_stack, channel_index, frame, fname) + try: + download_plane_as_tiff(image, tile, z_stack, channel_index, frame, fname) + except Exception as e: + if skip_failed: + # respect skip_failed on unexpected errors + warn(str(e), image_warning_id, warn_skip=True) + continue + else: + raise finally: # Close the connection conn.close()
--- a/idr_download_by_ids.xml Tue Apr 14 10:27:25 2020 -0400 +++ b/idr_download_by_ids.xml Wed Apr 22 11:43:18 2020 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="idr_download_by_ids" name="IDR Download" version="0.20" profile="18.09"> +<tool id="idr_download_by_ids" name="IDR Download" version="0.30" profile="18.09"> <description>- download images from the Image Data Resource using image IDs</description> <macros> <xml name="region_spec" token_pos="upper-left corner"> @@ -218,10 +218,13 @@ A set of image IDs as can be obtained from the IDR webclient_ like this: -1. select the images you want to download -2. click on the 'Link' button on the top right of the page and copy the provided - URL -3. paste the URL into the input field of this tool, for example: :: +1. Select the wells you want to download in the thumbnails. + +2. Select at the bottom the images in those wells that you want to download (one well might contain several images). + +3. Click on the 'Link' button on the top right of the page and copy the provided URL. + +4. Paste the URL into the input field of this tool, for example: https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711