Mercurial > repos > iuc > idr_download_by_ids
changeset 11:cbd605a24336 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
| author | iuc |
|---|---|
| date | Sat, 15 Jan 2022 12:25:29 +0000 |
| parents | 4aed70472589 |
| children | 4b794652dcdc |
| files | idr_download_by_ids.py idr_download_by_ids.xml |
| diffstat | 2 files changed, 293 insertions(+), 195 deletions(-) [+] |
line wrap: on
line diff
--- a/idr_download_by_ids.py Wed Nov 24 21:01:02 2021 +0000 +++ b/idr_download_by_ids.py Sat Jan 15 12:25:29 2022 +0000 @@ -7,6 +7,7 @@ from tempfile import TemporaryDirectory from libtiff import TIFF +from omero.cli import cli_login from omero.gateway import BlitzGateway # noqa from omero.constants.namespaces import NSBULKANNOTATIONS # noqa @@ -111,6 +112,7 @@ def download_image_data( image_ids_or_dataset_id, dataset=False, + download_original=False, channel=None, z_stack=0, frame=0, coord=(0, 0), width=0, height=0, region_spec='rectangle', skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None @@ -129,7 +131,7 @@ omero_username = 'public' omero_password = 'public' - if region_spec not in ['rectangle', 'center']: + if not download_original and region_spec not in ['rectangle', 'center']: raise ValueError( 'Got unknown value "{0}" as region_spec argument' .format(region_spec) @@ -224,124 +226,159 @@ 'database. Aborting!' .format(image_warning_id) ) + if not download_original: + 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 + ) - 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) + ) + + 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 - 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) + # 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. + warn( + 'Downloaded image dimensions ({0} x {1}) will be smaller ' + 'than the specified width and height ({2} x {3}).' + .format(tile[2], tile[3], width, height), + image_warning_id + ) + + # z-stack sanity checks and warnings + if z_stack != ori_z: + warn( + 'Specified image plane ({0}) is out of bounds. Using {1} ' + 'instead.' + .format(ori_z, z_stack), + image_warning_id + ) + + # frame sanity checks and warnings + if frame != ori_frame: + warn( + 'Specified image frame ({0}) is out of bounds. Using ' + 'frame {1} instead.' + .format(ori_frame, frame), + image_warning_id ) - ori_z, z_stack = z_stack, confine_plane(image, z_stack) - ori_frame, frame = frame, confine_frame(image, frame) - num_channels = image.getSizeC() + # channel index sanity checks and warnings 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 + if num_channels > 1: + warn( + 'No specific channel selected for multi-channel ' + 'image. Using first of {0} channels.' + .format(num_channels), + image_warning_id + ) 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. - warn( - 'Downloaded image dimensions ({0} x {1}) will be smaller ' - 'than the specified width and height ({2} x {3}).' - .format(tile[2], tile[3], width, height), - image_warning_id - ) + 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) + ) - # z-stack sanity checks and warnings - if z_stack != ori_z: - warn( - 'Specified image plane ({0}) is out of bounds. Using {1} ' - 'instead.' - .format(ori_z, z_stack), - image_warning_id + # download and save the region as TIFF + fname = '__'.join( + [image_name, str(image_id)] + [str(x) for x in tile] ) + try: + if fname[-5:] != '.tiff': + fname += '.tiff' - # frame sanity checks and warnings - if frame != ori_frame: - warn( - 'Specified image frame ({0}) is out of bounds. Using ' - 'frame {1} instead.' - .format(ori_frame, frame), - image_warning_id - ) + fname = fname.replace(' ', '_') + + im_array = get_image_array(image, tile, z_stack, channel_index, frame) - # channel index sanity checks and warnings - if channel is None: - if num_channels > 1: - warn( - 'No specific channel selected for multi-channel ' - 'image. Using first of {0} channels.' - .format(num_channels), - image_warning_id - ) - else: - if channel_index == -1 or channel_index >= num_channels: + if download_tar: + fname = os.path.join(tempdir, fname) + try: + tiff = TIFF.open(fname, mode='w') + tiff.write_image(im_array) + finally: + tiff.close() + # move image into tarball + if download_tar: + archive.add(fname, os.path.basename(fname)) + os.remove(fname) + except Exception as e: if skip_failed: - warn( - str(channel) - + ' is not a known channel name for this image.', - image_warning_id, - warn_skip=True - ) + # respect skip_failed on unexpected errors + warn(str(e), 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] - ) - try: - if fname[-5:] != '.tiff': - fname += '.tiff' - - fname = fname.replace(' ', '_') - - im_array = get_image_array(image, tile, z_stack, channel_index, frame) - - if download_tar: - fname = os.path.join(tempdir, fname) + raise + else: try: - tiff = TIFF.open(fname, mode='w') - tiff.write_image(im_array) - finally: - tiff.close() - # move image into tarball - if download_tar: - archive.add(fname, os.path.basename(fname)) - os.remove(fname) - except Exception as e: - if skip_failed: + # 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 + ) + original_image_name = image.getFileset().listFiles()[0].getName() + fname = image_name + "__" + str(image_id) + os.path.splitext(original_image_name)[1] + fname = fname.replace(' ', '_') + fname = fname.replace('/', '_') + download_directory = "./" + if download_tar: + download_directory = tempdir + with cli_login("-u", omero_username, "-s", omero_host, "-w", omero_password) as cli: + cli.invoke(["download", f"Image:{image_id}", download_directory]) + if cli.rv != 0: + raise Exception("Download failed.") + # This will download to download_directory/original_image_name + os.rename(os.path.join(download_directory, original_image_name), + os.path.join(download_directory, fname)) + # move image into tarball + if download_tar: + archive.add(os.path.join(download_directory, fname), + os.path.basename(fname)) + os.remove(os.path.join(download_directory, fname)) + except Exception as e: # respect skip_failed on unexpected errors - warn(str(e), image_warning_id, warn_skip=True) - continue - else: - raise + if skip_failed: + warn(str(e), image_warning_id, warn_skip=True) + continue + else: + raise def _center_to_ul(center_x, center_y, width, height): @@ -369,6 +406,10 @@ 'read ids from stdin).' ) p.add_argument( + '--download-original', dest='download_original', action='store_true', + help="download the original file uploaded to omero" + ) + p.add_argument( '-c', '--channel', help='name of the channel to retrieve data for ' '(note: the first channel of each image will be downloaded if '
--- a/idr_download_by_ids.xml Wed Nov 24 21:01:02 2021 +0000 +++ b/idr_download_by_ids.xml Sat Jan 15 12:25:29 2022 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="idr_download_by_ids" name="IDR/OMERO Download" version="0.43" profile="18.09"> +<tool id="idr_download_by_ids" name="IDR/OMERO Download" version="0.44" profile="18.09"> <description>- download images from any OMERO instance using image IDs</description> <macros> <xml name="region_spec" token_pos="upper-left corner"> @@ -46,14 +46,18 @@ #if str($image_ids.source) == 'omeroDatasetID': --dataset #end if - #set $channel = str($channel).strip() - #if $channel: - -c '$channel' - #end if - -f $frame - -z $z_section - #if str($clip_image.select): - ${clip_image.select} ${clip_image.x_coord} ${clip_image.y_coord} ${clip_image.width} ${clip_image.height} + #if $image_region.original == "original": + --download-original + #else: + #set $channel = str($image_region.channel).strip() + #if $channel: + -c '$channel' + #end if + -f $image_region.frame + -z $image_region.z_section + #if str($image_region.clip_image.select): + ${image_region.clip_image.select} ${image_region.clip_image.x_coord} ${image_region.clip_image.y_coord} ${image_region.clip_image.width} ${image_region.clip_image.height} + #end if #end if $skip_failed $download_tar @@ -124,26 +128,36 @@ <param name="id_dataset_omero" type="integer" min = "0" value = "9059" label="Dataset ID"/> </when> </conditional> - <param name="channel" type="text" - label="Name of the channel to download" - help="For all image IDs only the specified channel will be downloaded. If left empty, the first channel (whatever this is) will be downloaded by default." /> - <param name="z_section" type="integer" value="0" min="0" - label="z-plane of images to download" /> - <param name="frame" type="integer" value="0" min="0" - label="Image frame to download" /> - <conditional name="clip_image"> - <param name="select" type="select" - label="Limit the download to a selected region of the image?"> - <option value="">No, download the entire image plane</option> - <option value="--rectangle">Specify a region using its upper-left corner</option> - <option value="--center">Specify a width x height region around a central point</option> + + <conditional name="image_region"> + <param name="original" type="select" label="Which images do you want to download?"> + <option value="TIFF" selected="true">Exported TIFF (single channel, single stack)</option> + <option value="original">Original file (file uploaded to omero, only available for private instances)</option> </param> - <when value="" /> - <when value="--rectangle"> - <expand macro="region_spec" /> - </when> - <when value="--center"> - <expand macro="region_spec" pos="center" /> + <when value="original"/> + <when value="TIFF"> + <param name="channel" type="text" + label="Name of the channel to download" + help="For all image IDs only the specified channel will be downloaded. If left empty, the first channel (whatever this is) will be downloaded by default." /> + <param name="z_section" type="integer" value="0" min="0" + label="z-plane of images to download" /> + <param name="frame" type="integer" value="0" min="0" + label="Image frame to download" /> + <conditional name="clip_image"> + <param name="select" type="select" + label="Limit the download to a selected region of the image?"> + <option value="">No, download the entire image plane</option> + <option value="--rectangle">Specify a region using its upper-left corner</option> + <option value="--center">Specify a width x height region around a central point</option> + </param> + <when value="" /> + <when value="--rectangle"> + <expand macro="region_spec" /> + </when> + <when value="--center"> + <expand macro="region_spec" pos="center" /> + </when> + </conditional> </when> </conditional> <param name="skip_failed" type="boolean" checked="false" truevalue="--skip-failed" falsevalue="" @@ -171,15 +185,18 @@ </conditional> <param name="source" value="dataset" /> <param name="id_spec" value="ids.txt" /> - <param name="channel" value="PCNT" /> - <conditional name="clip_image"> - <param name="select" value="--rectangle" /> - <param name="x_coord" value="3" /> - <param name="y_coord" value="3" /> - <param name="width" value="5" /> - <param name="height" value="5" /> + <conditional name="image_region"> + <param name="original" value="TIFF"/> + <param name="channel" value="PCNT" /> + <conditional name="clip_image"> + <param name="select" value="--rectangle" /> + <param name="x_coord" value="3" /> + <param name="y_coord" value="3" /> + <param name="width" value="5" /> + <param name="height" value="5" /> + </conditional> + <param name="frame" value="0" /> </conditional> - <param name="frame" value="0" /> <param name="download_tar" value="false" /> <output_collection name="output_file" type="list"> <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff"/> @@ -191,15 +208,18 @@ </conditional> <param name="source" value="link" /> <param name="id_spec" value="1884807" /> - <param name="channel" value="PCNT" /> - <conditional name="clip_image"> - <param name="select" value="--rectangle" /> - <param name="x_coord" value="3" /> - <param name="y_coord" value="3" /> - <param name="width" value="5" /> - <param name="height" value="5" /> + <conditional name="image_region"> + <param name="original" value="TIFF"/> + <param name="channel" value="PCNT" /> + <conditional name="clip_image"> + <param name="select" value="--rectangle" /> + <param name="x_coord" value="3" /> + <param name="y_coord" value="3" /> + <param name="width" value="5" /> + <param name="height" value="5" /> + </conditional> + <param name="frame" value="2" /> </conditional> - <param name="frame" value="2" /> <param name="download_tar" value="false" /> <output_collection name="output_file" type="list"> <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff"/> @@ -211,15 +231,18 @@ </conditional> <param name="source" value="link" /> <param name="id_spec" value="1884807" /> - <param name="channel" value="PCNT" /> - <conditional name="clip_image"> - <param name="select" value="--center" /> - <param name="x_coord" value="5" /> - <param name="y_coord" value="5" /> - <param name="width" value="5" /> - <param name="height" value="5" /> + <conditional name="image_region"> + <param name="original" value="TIFF"/> + <param name="channel" value="PCNT" /> + <conditional name="clip_image"> + <param name="select" value="--center" /> + <param name="x_coord" value="5" /> + <param name="y_coord" value="5" /> + <param name="width" value="5" /> + <param name="height" value="5" /> + </conditional> + <param name="frame" value="2" /> </conditional> - <param name="frame" value="2" /> <param name="download_tar" value="false" /> <output_collection name="output_file" type="list"> <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test2.tiff"/> @@ -231,12 +254,15 @@ </conditional> <param name="source" value="link" /> <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711" /> - <param name="channel" value="Spo20(51-91)" /> - <param name="z_section" value="4" /> - <conditional name="clip_image"> - <param name="select" value="" /> + <conditional name="image_region"> + <param name="original" value="TIFF"/> + <param name="channel" value="Spo20(51-91)" /> + <param name="z_section" value="4" /> + <conditional name="clip_image"> + <param name="select" value="" /> + </conditional> + <param name="frame" value="20" /> </conditional> - <param name="frame" value="20" /> <param name="download_tar" value="false" /> <output_collection name="output_file" type="list" count="3"> <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024"> @@ -259,12 +285,15 @@ <!-- Test behavior with non-existing image-ID 9036708999 --> <param name="source" value="link" /> <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" /> - <param name="channel" value="Spo20(51-91)" /> - <param name="z_section" value="4" /> - <conditional name="clip_image"> - <param name="select" value="" /> + <conditional name="image_region"> + <param name="original" value="TIFF"/> + <param name="channel" value="Spo20(51-91)" /> + <param name="z_section" value="4" /> + <conditional name="clip_image"> + <param name="select" value="" /> + </conditional> + <param name="frame" value="20" /> </conditional> - <param name="frame" value="20" /> <param name="download_tar" value="false" /> </test> <test> @@ -275,12 +304,15 @@ </conditional> <param name="source" value="link" /> <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" /> - <param name="channel" value="Spo20(51-91)" /> - <param name="z_section" value="4" /> - <conditional name="clip_image"> - <param name="select" value="" /> + <conditional name="image_region"> + <param name="original" value="TIFF"/> + <param name="channel" value="Spo20(51-91)" /> + <param name="z_section" value="4" /> + <conditional name="clip_image"> + <param name="select" value="" /> + </conditional> + <param name="frame" value="20" /> </conditional> - <param name="frame" value="20" /> <param name="skip_failed" value="true" /> <param name="download_tar" value="false" /> <output_collection name="output_file" type="list" count="2"> @@ -305,15 +337,18 @@ <!-- Test for download images in a tarball --> <param name="source" value="dataset" /> <param name="id_spec" value="ids_tar.txt" /> - <param name="channel" value="Hoechst" /> - <conditional name="clip_image"> - <param name="select" value="--rectangle" /> - <param name="x_coord" value="0" /> - <param name="y_coord" value="0" /> - <param name="width" value="671" /> - <param name="height" value="511" /> + <conditional name="image_region"> + <param name="original" value="TIFF"/> + <param name="channel" value="Hoechst" /> + <conditional name="clip_image"> + <param name="select" value="--rectangle" /> + <param name="x_coord" value="0" /> + <param name="y_coord" value="0" /> + <param name="width" value="671" /> + <param name="height" value="511" /> + </conditional> + <param name="frame" value="0" /> </conditional> - <param name="frame" value="0" /> <output name="output_tar"> <assert_contents> <has_size value="1382400" /> @@ -335,15 +370,18 @@ </conditional> <param name="source" value="dataset" /> <param name="id_spec" value="ids.txt" /> - <param name="channel" value="PCNT" /> - <conditional name="clip_image"> - <param name="select" value="--rectangle" /> - <param name="x_coord" value="3" /> - <param name="y_coord" value="3" /> - <param name="width" value="5" /> - <param name="height" value="5" /> + <conditional name="image_region"> + <param name="original" value="TIFF"/> + <param name="channel" value="PCNT" /> + <conditional name="clip_image"> + <param name="select" value="--rectangle" /> + <param name="x_coord" value="3" /> + <param name="y_coord" value="3" /> + <param name="width" value="5" /> + <param name="height" value="5" /> + </conditional> + <param name="frame" value="0" /> </conditional> - <param name="frame" value="0" /> <param name="download_tar" value="false" /> <output_collection name="output_file" type="list"> <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff"/> @@ -357,15 +395,18 @@ </conditional> <param name="source" value="dataset" /> <param name="id_spec" value="ids.txt" /> - <param name="channel" value="PCNT" /> - <conditional name="clip_image"> - <param name="select" value="--rectangle" /> - <param name="x_coord" value="3" /> - <param name="y_coord" value="3" /> - <param name="width" value="5" /> - <param name="height" value="5" /> + <conditional name="image_region"> + <param name="original" value="TIFF"/> + <param name="channel" value="PCNT" /> + <conditional name="clip_image"> + <param name="select" value="--rectangle" /> + <param name="x_coord" value="3" /> + <param name="y_coord" value="3" /> + <param name="width" value="5" /> + <param name="height" value="5" /> + </conditional> + <param name="frame" value="0" /> </conditional> - <param name="frame" value="0" /> <param name="download_tar" value="false" /> <assert_stderr> <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" /> @@ -402,6 +443,22 @@ </element> </output_collection> </test> + <test> + <conditional name="omero_instance_type"> + <param name="omero_instance" value="idr" /> + </conditional> + <!-- Test for download all original files from a dataset --> + <!-- Impossible in idr: --> + <param name="source" value="omeroDatasetID" /> + <param name="id_dataset_omero" value="9059" /> + <param name="skip_failed" value="true" /> + <param name="download_tar" value="false" /> + <conditional name="image_region"> + <param name="original" value="original"/> + </conditional> + <output_collection name="output_file" type="list" count="0"> + </output_collection> + </test> </tests> <help><![CDATA[ Download image data from the IDR_ (Image Data Resource) - a public repository