| Next changeset 1:9340cbc7796c (2020-03-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab" |
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added:
idr_download_by_ids.py idr_download_by_ids.xml test-data/ids.txt test-data/test1.tiff |
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| diff -r 000000000000 -r 57aa9597cd31 idr_download_by_ids.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idr_download_by_ids.py Sat Feb 08 13:24:39 2020 -0500 |
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| b'@@ -0,0 +1,271 @@\n+import argparse\n+import os\n+import sys\n+\n+from matplotlib import pyplot as plt\n+from omero.gateway import BlitzGateway # noqa\n+from omero.constants.namespaces import NSBULKANNOTATIONS # noqa\n+\n+\n+def warn(message, image_identifier):\n+ print(\n+ \'ImageSpecWarning for {0}: {1}\'\n+ .format(image_identifier, message),\n+ file=sys.stderr\n+ )\n+\n+\n+def find_channel_index(image, channel_name):\n+ channel_name = channel_name.lower()\n+ for n, channel in enumerate(image.getChannels()):\n+ if channel_name == channel.getLabel().lower():\n+ return n\n+ # Check map annotation for information (this is necessary for some images)\n+ for ann in image.listAnnotations(NSBULKANNOTATIONS):\n+ pairs = ann.getValue()\n+ for p in pairs:\n+ if p[0] == "Channels":\n+ channels = p[1].replace(" ", "").split(";")\n+ for n, c in enumerate(channels):\n+ for value in c.split(\':\'):\n+ if channel_name == value.lower():\n+ return n\n+ return -1\n+\n+\n+def get_clipping_region(image, x, y, w, h):\n+ # If the (x, y) coordinate falls outside the image boundaries, we\n+ # cannot just shift it because that would render the meaning of\n+ # w and h undefined (should width and height be decreased or the whole\n+ # region be shifted to keep them fixed?).\n+ # It may be better to abort in this situation.\n+ if x < 0 or y < 0:\n+ raise ValueError(\n+ \'Too small upper left coordinate ({0}, {1}) for clipping region.\'\n+ .format(x, y)\n+ )\n+ size_x = image.getSizeX()\n+ size_y = image.getSizeY()\n+ if x >= size_x or y >= size_y:\n+ raise ValueError(\n+ \'Upper left coordinate ({0}, {1}) of clipping region lies \'\n+ \'outside of image.\'\n+ .format(x, y)\n+ )\n+ # adjust width and height to the image dimensions\n+ if w <= 0 or x + w > size_x:\n+ w = size_x - x\n+ if h <= 0 or y + h > size_y:\n+ h = size_y - y\n+ return [x, y, w, h]\n+\n+\n+def confine_plane(image, z):\n+ if z < 0:\n+ z = 0\n+ else:\n+ max_z = image.getSizeZ() - 1\n+ if z > max_z:\n+ z = max_z\n+ return z\n+\n+\n+def confine_frame(image, t):\n+ if t < 0:\n+ t = 0\n+ else:\n+ max_t = image.getSizeT() - 1\n+ if t > max_t:\n+ t = max_t\n+ return t\n+\n+\n+def download_plane_as_tiff(image, tile, z, c, t, fname):\n+ pixels = image.getPrimaryPixels()\n+ selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile)\n+\n+ if fname[-5:] != \'.tiff\':\n+ fname += \'.tiff\'\n+ plt.imsave(fname, selection)\n+\n+\n+def download_image_data(\n+ image_ids,\n+ channel=None, z_stack=0, frame=0,\n+ coord=(0, 0), width=0, height=0, region_spec=\'rectangle\',\n+ skip_failed=False\n+):\n+\n+ # connect to idr\n+ conn = BlitzGateway(\'public\', \'public\',\n+ host=\'idr.openmicroscopy.org\',\n+ secure=True)\n+ conn.connect()\n+\n+ try:\n+ prefix = \'image-\'\n+ for image_id in image_ids:\n+ if image_id[:len(prefix)] == prefix:\n+ image_id = image_id[len(prefix):]\n+ image_id = int(image_id)\n+ image = conn.getObject("Image", image_id)\n+\n+ if image is None:\n+ image_warning_id = \'Image-ID: {0}\'.format(image_id)\n+ if skip_failed:\n+ warn(\n+ \'Unable to find an image with this ID in the \'\n+ \'database. Skipping download!\',\n+ image_warning_id\n+ )\n+ continue\n+ raise ValueError(\n+ \'{0}: Unable to find an image with this ID in the \'\n+ \'database. Aborting!\'\n+ .format(image_warning_id)\n+ )\n+\n+ image_name = os.path.splitext(image.getN'..b'\'\n+ \'frame {1} instead.\'\n+ .format(ori_frame, frame),\n+ image_warning_id\n+ )\n+ # Get the channel index. If the index is not valid, skip the image\n+ if channel is None:\n+ channel_index = 0\n+ num_channels = image.getSizeC()\n+ if num_channels > 1:\n+ warn(\n+ \'No specific channel selected for multi-channel \'\n+ \'image. Using first of {0} channels.\'\n+ .format(num_channels),\n+ image_warning_id\n+ )\n+ else:\n+ channel_index = find_channel_index(image, channel)\n+ if channel_index == -1:\n+ raise ValueError(\n+ \'"{0}" is not a known channel name for image {1}\'\n+ .format(channel, image.getName())\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+ download_plane_as_tiff(image, tile, z_stack, channel_index, frame, fname)\n+ finally:\n+ # Close the connection\n+ conn.close()\n+\n+\n+def _center_to_ul(center_x, center_y, width, height):\n+ if width > 0:\n+ ext_x = (width - 1) // 2\n+ ul_x = max([center_x - ext_x, 0])\n+ width = center_x + ext_x + 1 - ul_x\n+ else:\n+ ul_x = 0\n+ if height > 0:\n+ ext_y = (height - 1) // 2\n+ ul_y = max([center_y - ext_y, 0])\n+ height = center_y + ext_y + 1 - ul_y\n+ else:\n+ ul_y = 0\n+ return ul_x, ul_y, width, height\n+\n+\n+if __name__ == "__main__":\n+ p = argparse.ArgumentParser()\n+ p.add_argument(\n+ \'image_ids\', nargs=\'*\', default=[],\n+ help=\'one or more IDR image ids for which to retrieve data (default: \'\n+ \'read ids from stdin).\'\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+ \'left unspecified)\'\n+ )\n+ region = p.add_mutually_exclusive_group()\n+ region.add_argument(\n+ \'--rectangle\', nargs=4, type=int, default=argparse.SUPPRESS,\n+ help=\'specify a clipping region for the image as x y width height, \'\n+ \'where x and y give the upper left coordinate of the rectangle \'\n+ \'to clip to. Set width and height to 0 to extend the rectangle \'\n+ \'to the actual size of the image.\'\n+ )\n+ region.add_argument(\n+ \'--center\', nargs=4, type=int, default=argparse.SUPPRESS,\n+ help=\'specify a clipping region for the image as x y width height, \'\n+ \'where x and y define the center of a width x height rectangle. \'\n+ \'Set either width or height to 0 to extend the region to the \'\n+ \'actual size of the image along the x- or y-axis.\\n\'\n+ \'Note: Even values for width and height will be rounded down to \'\n+ \'the nearest odd number.\'\n+ )\n+ p.add_argument(\n+ \'-f\', \'--frame\', type=int, default=0\n+ )\n+ p.add_argument(\n+ \'-z\', \'--z-stack\', type=int, default=0\n+ )\n+ p.add_argument(\n+ \'--skip-failed\', action=\'store_true\'\n+ )\n+ args = p.parse_args()\n+ if not args.image_ids:\n+ args.image_ids = sys.stdin.read().split()\n+ if \'center\' in args:\n+ args.coord, args.width, args.height = (\n+ args.center[:2], args.center[2], args.center[3]\n+ )\n+ args.region_spec = \'center\'\n+ del args.center\n+ elif \'rectangle\' in args:\n+ args.coord, args.width, args.height = (\n+ args.rectangle[:2], args.rectangle[2], args.rectangle[3]\n+ )\n+ args.region_spec = \'rectangle\'\n+ del args.rectangle\n+ download_image_data(**vars(args))\n' |
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| diff -r 000000000000 -r 57aa9597cd31 idr_download_by_ids.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idr_download_by_ids.xml Sat Feb 08 13:24:39 2020 -0500 |
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| b'@@ -0,0 +1,257 @@\n+<?xml version="1.0"?>\n+<tool id="idr_download_by_ids" name="IDR Download" version="0.9" profile="18.09">\n+ <description>- download images from the Image Data Resource using image IDs</description>\n+ <macros>\n+ <xml name="region_spec" token_pos="upper-left corner">\n+ <param name="x_coord" type="integer" value="0" min="0"\n+ label="x-coordinate of region @POS@" />\n+ <param name="y_coord" type="integer" value="0" min="0"\n+ label="y-coordinate of region @POS@" />\n+ <param name="width" type="integer" value="0" min="0"\n+ label="Region width"\n+ help="Set to zero to extend the rectangle maximally along the x-axis of the image" />\n+ <param name="height" type="integer" value="0" min="0"\n+ label="Region height"\n+ help="Set to zero to extend the rectangle maximally along the y-axis of the image" />\n+ </xml>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="5.6.0">python-omero</requirement>\n+ <requirement type="package" version="3.1.3">matplotlib</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ mkdir downloads && cd downloads &&\n+ #if str($image_ids.source) == \'link\':\n+ python -c \'print("${image_ids.id_spec}".replace(",", "|").split("?show=")[-1].replace("|", "\\n"))\'\n+ ## https://idr.openmicroscopy.org/webclient/?show=image-3426274|image-3426275|image-3426276|image-3426277\n+ #else:\n+ cat \'${image_ids.id_spec}\'\n+ #end if\n+ | python \'$__tool_directory__/idr_download_by_ids.py\' \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+ #end if\n+ $skip_failed\n+\n+ 2> >(tee -a $out_log >&2)\n+ ]]></command>\n+<inputs>\n+ <conditional name="image_ids">\n+ <param name="source" type="select" label="How would you like to specify the IDs of images to download?">\n+ <option value="link">As text (comma-separated list of IDs or a valid IDR link)</option>\n+ <option value="dataset">As a dataset (one image ID per line)</option>\n+ </param>\n+ <when value="link">\n+ <param name="id_spec" type="text"\n+ label="Image IDs to download"\n+ help="You can enter a single image-id, or a comma (or \'|\')-separated list of IDs. Alternatively, you can paste here a link to an image selection obtained through the IDR webclient.">\n+ <sanitizer>\n+ <valid><add value="|" /></valid>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ <when value="dataset">\n+ <param name="id_spec" type="data" format="txt"\n+ label="Select a dataset with image IDs (one per line)" />\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 '..b' </output_collection>\n+ <output name="out_log">\n+ <assert_contents>\n+ <has_text text="(ID: 9036710): Specified image plane (4) is out of bounds"/>\n+ <has_n_lines n="1"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_failure="true">\n+ <!-- Test behavior with non-existing image-ID 9036708999 -->\n+ <param name="source" value="link" />\n+ <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" />\n+ <param name="channel" value="Spo20(51-91)" />\n+ <param name="z_section" value="4" />\n+ <conditional name="clip_image">\n+ <param name="select" value="" />\n+ </conditional>\n+ <param name="frame" value="20" />\n+ </test>\n+ <test>\n+ <!-- Repeat test with non-existing image-ID 9036708999,\n+ but use skip-failed option -->\n+ <param name="source" value="link" />\n+ <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" />\n+ <param name="channel" value="Spo20(51-91)" />\n+ <param name="z_section" value="4" />\n+ <conditional name="clip_image">\n+ <param name="select" value="" />\n+ </conditional>\n+ <param name="frame" value="20" />\n+ <param name="skip_failed" value="true" />\n+ <output_collection name="output_file" type="list" count="2">\n+ <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_9036711_0_0_1024_1024">\n+ <assert_contents>\n+ <has_size value="4194510" />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output name="out_log">\n+ <assert_contents>\n+ <has_text text="9036708999: Unable to find an image with this ID in the database. Skipping download!" />\n+ <has_text text="(ID: 9036710): Specified image plane (4) is out of bounds" />\n+ <has_n_lines n="2"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Download image data from the IDR_ (Image Data Resource) - a public repository\n+of reference image datasets from published scientific studies.\n+\n+.. _IDR: https://idr.openmicroscopy.org/about/\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Input**\n+\n+A set of image IDs as can be obtained from the IDR webclient_ like this:\n+\n+1. select the images you want to download\n+2. click on the \'Link\' button on the top right of the page and copy the provided\n+ URL\n+3. paste the URL into the input field of this tool, for example: ::\n+\n+ https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711\n+\n+Alternatively, you can simply provide a list of known image IDs in the text\n+input field (comma or \'|\'-separated ), or as an input file (each ID on a\n+separate line).\n+\n+Most images in the IDR have more than two dimensions. Thus, there are\n+parameters available which allow you to select a particular recording channel,\n+z-plane or time frame to download.\n+You can also select a region which will be used to crop the images, rather\n+than downloading the entire file.\n+\n+.. _webclient: https://idr.openmicroscopy.org/\n+\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Output**\n+\n+Downloaded images will be saved in TIFF format. If you selected multiple image\n+IDs to download, these will be saved as elements of a collection.\n+\n+The accompanying error log dataset may hold valuable information about requests\n+that could not be fulfilled exactly as specified, or that were found to be\n+ambiguous.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1038/nmeth.4326</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 57aa9597cd31 test-data/ids.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ids.txt Sat Feb 08 13:24:39 2020 -0500 |
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| @@ -0,0 +1,1 @@ +1884807 |
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| diff -r 000000000000 -r 57aa9597cd31 test-data/test1.tiff |
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| Binary file test-data/test1.tiff has changed |