| Previous changeset 10:4aed70472589 (2021-11-24) Next changeset 12:4b794652dcdc (2023-11-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f" |
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modified:
idr_download_by_ids.py idr_download_by_ids.xml |
| b |
| diff -r 4aed70472589 -r cbd605a24336 idr_download_by_ids.py --- 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 |
| [ |
| b'@@ -7,6 +7,7 @@\n from tempfile import TemporaryDirectory\n \n from libtiff import TIFF\n+from omero.cli import cli_login\n from omero.gateway import BlitzGateway # noqa\n from omero.constants.namespaces import NSBULKANNOTATIONS # noqa\n \n@@ -111,6 +112,7 @@\n \n def download_image_data(\n image_ids_or_dataset_id, dataset=False,\n+ download_original=False,\n channel=None, z_stack=0, frame=0,\n coord=(0, 0), width=0, height=0, region_spec=\'rectangle\',\n skip_failed=False, download_tar=False, omero_host=\'idr.openmicroscopy.org\', omero_secured=False, config_file=None\n@@ -129,7 +131,7 @@\n omero_username = \'public\'\n omero_password = \'public\'\n \n- if region_spec not in [\'rectangle\', \'center\']:\n+ if not download_original and region_spec not in [\'rectangle\', \'center\']:\n raise ValueError(\n \'Got unknown value "{0}" as region_spec argument\'\n .format(region_spec)\n@@ -224,124 +226,159 @@\n \'database. Aborting!\'\n .format(image_warning_id)\n )\n+ if not download_original:\n+ try:\n+ # try to extract image properties\n+ # if anything goes wrong here skip the image\n+ # or abort.\n+ image_name = os.path.splitext(image.getName())[0]\n+ image_warning_id = \'{0} (ID: {1})\'.format(\n+ image_name, image_id\n+ )\n \n- try:\n- # try to extract image properties\n- # if anything goes wrong here skip the image\n- # or abort.\n- image_name = os.path.splitext(image.getName())[0]\n- image_warning_id = \'{0} (ID: {1})\'.format(\n- image_name, image_id\n- )\n+ if region_spec == \'rectangle\':\n+ tile = get_clipping_region(image, *coord, width, height)\n+ elif region_spec == \'center\':\n+ tile = get_clipping_region(\n+ image,\n+ *_center_to_ul(*coord, width, height)\n+ )\n+\n+ ori_z, z_stack = z_stack, confine_plane(image, z_stack)\n+ ori_frame, frame = frame, confine_frame(image, frame)\n+ num_channels = image.getSizeC()\n+ if channel is None:\n+ channel_index = 0\n+ else:\n+ channel_index = find_channel_index(image, channel)\n+ except Exception as e:\n+ # respect skip_failed on unexpected errors\n+ if skip_failed:\n+ warn(str(e), image_warning_id, warn_skip=True)\n+ continue\n+ else:\n+ raise\n \n- if region_spec == \'rectangle\':\n- tile = get_clipping_region(image, *coord, width, height)\n- elif region_spec == \'center\':\n- tile = get_clipping_region(\n- image,\n- *_center_to_ul(*coord, width, height)\n+ # region sanity checks and warnings\n+ if tile[2] < width or tile[3] < height:\n+ # The downloaded image region will have smaller dimensions\n+ # than the specified width x height.\n+ warn(\n+ \'Downloaded image dimensions ({0} x {1}) will be smaller \'\n+ \'than the specified width and height ({2} x {3}).\'\n+ .format(tile[2], tile[3], width, height),\n+ image_warning_id\n+ )\n+\n+ # z-stack sanity checks and warnings\n+ if z_stack != ori_z:\n+ warn(\n+ \'Specified image plane ({0}) is out of bounds. Using {1} \''..b' # respect skip_failed on unexpected errors\n+ warn(str(e), image_warning_id, warn_skip=True)\n continue\n else:\n- raise ValueError(\n- \'"{0}" is not a known channel name for image {1}. \'\n- \'Aborting!\'\n- .format(channel, image_warning_id)\n- )\n-\n- # download and save the region as TIFF\n- fname = \'__\'.join(\n- [image_name, str(image_id)] + [str(x) for x in tile]\n- )\n- try:\n- if fname[-5:] != \'.tiff\':\n- fname += \'.tiff\'\n-\n- fname = fname.replace(\' \', \'_\')\n-\n- im_array = get_image_array(image, tile, z_stack, channel_index, frame)\n-\n- if download_tar:\n- fname = os.path.join(tempdir, fname)\n+ raise\n+ else:\n try:\n- tiff = TIFF.open(fname, mode=\'w\')\n- tiff.write_image(im_array)\n- finally:\n- tiff.close()\n- # move image into tarball\n- if download_tar:\n- archive.add(fname, os.path.basename(fname))\n- os.remove(fname)\n- except Exception as e:\n- if skip_failed:\n+ # try to extract image properties\n+ # if anything goes wrong here skip the image\n+ # or abort.\n+ image_name = os.path.splitext(image.getName())[0]\n+ image_warning_id = \'{0} (ID: {1})\'.format(\n+ image_name, image_id\n+ )\n+ original_image_name = image.getFileset().listFiles()[0].getName()\n+ fname = image_name + "__" + str(image_id) + os.path.splitext(original_image_name)[1]\n+ fname = fname.replace(\' \', \'_\')\n+ fname = fname.replace(\'/\', \'_\')\n+ download_directory = "./"\n+ if download_tar:\n+ download_directory = tempdir\n+ with cli_login("-u", omero_username, "-s", omero_host, "-w", omero_password) as cli:\n+ cli.invoke(["download", f"Image:{image_id}", download_directory])\n+ if cli.rv != 0:\n+ raise Exception("Download failed.")\n+ # This will download to download_directory/original_image_name\n+ os.rename(os.path.join(download_directory, original_image_name),\n+ os.path.join(download_directory, fname))\n+ # move image into tarball\n+ if download_tar:\n+ archive.add(os.path.join(download_directory, fname),\n+ os.path.basename(fname))\n+ os.remove(os.path.join(download_directory, fname))\n+ except Exception as e:\n # respect skip_failed on unexpected errors\n- warn(str(e), image_warning_id, warn_skip=True)\n- continue\n- else:\n- raise\n+ if skip_failed:\n+ warn(str(e), image_warning_id, warn_skip=True)\n+ continue\n+ else:\n+ raise\n \n \n def _center_to_ul(center_x, center_y, width, height):\n@@ -369,6 +406,10 @@\n \'read ids from stdin).\'\n )\n p.add_argument(\n+ \'--download-original\', dest=\'download_original\', action=\'store_true\',\n+ help="download the original file uploaded to omero"\n+ )\n+ p.add_argument(\n \'-c\', \'--channel\',\n help=\'name of the channel to retrieve data for \'\n \'(note: the first channel of each image will be downloaded if \'\n' |
| b |
| diff -r 4aed70472589 -r cbd605a24336 idr_download_by_ids.xml --- 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 |
| [ |
| b'@@ -1,5 +1,5 @@\n <?xml version="1.0"?>\n-<tool id="idr_download_by_ids" name="IDR/OMERO Download" version="0.43" profile="18.09">\n+<tool id="idr_download_by_ids" name="IDR/OMERO Download" version="0.44" profile="18.09">\n <description>- download images from any OMERO instance using image IDs</description>\n <macros>\n <xml name="region_spec" token_pos="upper-left corner">\n@@ -46,14 +46,18 @@\n #if str($image_ids.source) == \'omeroDatasetID\':\n --dataset\n #end if\n- #set $channel = str($channel).strip()\n- #if $channel:\n- -c \'$channel\'\n- #end if\n- -f $frame\n- -z $z_section\n- #if str($clip_image.select):\n- ${clip_image.select} ${clip_image.x_coord} ${clip_image.y_coord} ${clip_image.width} ${clip_image.height}\n+ #if $image_region.original == "original":\n+ --download-original\n+ #else:\n+ #set $channel = str($image_region.channel).strip()\n+ #if $channel:\n+ -c \'$channel\'\n+ #end if\n+ -f $image_region.frame\n+ -z $image_region.z_section\n+ #if str($image_region.clip_image.select):\n+ ${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}\n+ #end if\n #end if\n $skip_failed\n $download_tar\n@@ -124,26 +128,36 @@\n <param name="id_dataset_omero" type="integer" min = "0" value = "9059" label="Dataset ID"/>\n </when>\n </conditional>\n- <param name="channel" type="text"\n- label="Name of the channel to download"\n- 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." />\n- <param name="z_section" type="integer" value="0" min="0"\n- label="z-plane of images to download" />\n- <param name="frame" type="integer" value="0" min="0"\n- label="Image frame to download" />\n- <conditional name="clip_image">\n- <param name="select" type="select"\n- label="Limit the download to a selected region of the image?">\n- <option value="">No, download the entire image plane</option>\n- <option value="--rectangle">Specify a region using its upper-left corner</option>\n- <option value="--center">Specify a width x height region around a central point</option>\n+\n+ <conditional name="image_region">\n+ <param name="original" type="select" label="Which images do you want to download?">\n+ <option value="TIFF" selected="true">Exported TIFF (single channel, single stack)</option>\n+ <option value="original">Original file (file uploaded to omero, only available for private instances)</option>\n </param>\n- <when value="" />\n- <when value="--rectangle">\n- <expand macro="region_spec" />\n- </when>\n- <when value="--center">\n- <expand macro="region_spec" pos="center" />\n+ <when value="original"/>\n+ <when value="TIFF">\n+ <param name="channel" type="text"\n+ label="Name of the channel to download"\n+ 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." />\n+ <param name="z_section" type="integer" value="0" min="0"\n+ label="z-plane of images to download" />\n+ <param name="frame" type="integer" value="0" min="0"\n+ label="Image frame to download" />\n+ <conditional name="clip_image">\n+ <param name="select" type="select"\n+ label="Limit the download to a selected'..b'\n </conditional>\n- <param name="frame" value="0" />\n <output name="output_tar">\n <assert_contents>\n <has_size value="1382400" />\n@@ -335,15 +370,18 @@\n </conditional>\n <param name="source" value="dataset" />\n <param name="id_spec" value="ids.txt" />\n- <param name="channel" value="PCNT" />\n- <conditional name="clip_image">\n- <param name="select" value="--rectangle" />\n- <param name="x_coord" value="3" />\n- <param name="y_coord" value="3" />\n- <param name="width" value="5" />\n- <param name="height" value="5" />\n+ <conditional name="image_region">\n+ <param name="original" value="TIFF"/> \n+ <param name="channel" value="PCNT" />\n+ <conditional name="clip_image">\n+ <param name="select" value="--rectangle" />\n+ <param name="x_coord" value="3" />\n+ <param name="y_coord" value="3" />\n+ <param name="width" value="5" />\n+ <param name="height" value="5" />\n+ </conditional>\n+ <param name="frame" value="0" />\n </conditional>\n- <param name="frame" value="0" />\n <param name="download_tar" value="false" />\n <output_collection name="output_file" type="list">\n <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff"/>\n@@ -357,15 +395,18 @@\n </conditional>\n <param name="source" value="dataset" />\n <param name="id_spec" value="ids.txt" />\n- <param name="channel" value="PCNT" />\n- <conditional name="clip_image">\n- <param name="select" value="--rectangle" />\n- <param name="x_coord" value="3" />\n- <param name="y_coord" value="3" />\n- <param name="width" value="5" />\n- <param name="height" value="5" />\n+ <conditional name="image_region">\n+ <param name="original" value="TIFF"/> \n+ <param name="channel" value="PCNT" />\n+ <conditional name="clip_image">\n+ <param name="select" value="--rectangle" />\n+ <param name="x_coord" value="3" />\n+ <param name="y_coord" value="3" />\n+ <param name="width" value="5" />\n+ <param name="height" value="5" />\n+ </conditional>\n+ <param name="frame" value="0" />\n </conditional>\n- <param name="frame" value="0" />\n <param name="download_tar" value="false" />\n <assert_stderr>\n <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" />\n@@ -402,6 +443,22 @@\n </element>\n </output_collection>\n </test>\n+ <test>\n+ <conditional name="omero_instance_type">\n+ <param name="omero_instance" value="idr" />\n+ </conditional>\n+ <!-- Test for download all original files from a dataset -->\n+ <!-- Impossible in idr: -->\n+ <param name="source" value="omeroDatasetID" />\n+ <param name="id_dataset_omero" value="9059" />\n+ <param name="skip_failed" value="true" />\n+ <param name="download_tar" value="false" />\n+ <conditional name="image_region">\n+ <param name="original" value="original"/> \n+ </conditional>\n+ <output_collection name="output_file" type="list" count="0">\n+ </output_collection>\n+ </test>\n </tests>\n <help><![CDATA[\n Download image data from the IDR_ (Image Data Resource) - a public repository\n' |