| Previous 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 a9a143bae95eb6c553fd3d5955c2adb34352480f |
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modified:
idr_download_by_ids.py idr_download_by_ids.xml |
| b |
| diff -r 4b794652dcdc -r f92941d1a85e idr_download_by_ids.py --- a/idr_download_by_ids.py Wed Nov 08 12:57:25 2023 +0000 +++ b/idr_download_by_ids.py Thu Sep 26 12:32:17 2024 +0000 |
| [ |
| b'@@ -4,35 +4,50 @@\n import sys\n import tarfile\n from contextlib import ExitStack\n+from itertools import product\n from tempfile import TemporaryDirectory\n \n-from libtiff import TIFF\n+import numpy\n from omero.cli import cli_login\n-from omero.gateway import BlitzGateway # noqa\n-from omero.constants.namespaces import NSBULKANNOTATIONS # noqa\n+from omero.constants.namespaces import NSBULKANNOTATIONS\n+from omero.gateway import _ImageWrapper, BlitzGateway\n+from tifffile import imwrite\n \n \n-def warn(message, image_identifier, warn_skip=False):\n+def warn(message: str, image_identifier: str, warn_skip: bool = False) -> None:\n+ """Print an error `message` to stderr and\n+ - prefix with the `image_identifier`\n+ - suffix with \'Skipping download!\' if `warn_skip` is True\n+\n+ Args:\n+ message (string): Message to print to stderr\n+ image_identifier (string): Image identifier\n+ warn_skip (bool, optional): Whether \'skipping download\' should be suffix to the message. Defaults to False.\n+ """\n message = message.rstrip()\n if warn_skip:\n- if message[-1] in [\'.\', \'!\', \'?\']:\n- skip_msg = \' Skipping download!\'\n+ if message[-1] in [".", "!", "?"]:\n+ skip_msg = " Skipping download!"\n else:\n- skip_msg = \'. Skipping download!\'\n+ skip_msg = ". Skipping download!"\n else:\n- skip_msg = \'\'\n+ skip_msg = ""\n print(\n- \'ImageSpecWarning for {0}: {1}{2}\'\n- .format(\n- image_identifier,\n- message,\n- skip_msg\n- ),\n- file=sys.stderr\n+ "ImageSpecWarning for {0}: {1}{2}".format(image_identifier, message, skip_msg),\n+ file=sys.stderr,\n )\n \n \n-def find_channel_index(image, channel_name):\n+def find_channel_index(image: _ImageWrapper, channel_name: str) -> int:\n+ """Identify the channel index from the `image` and the `channel_name`\n+\n+ Args:\n+ image (_ImageWrapper): image wrapper on which the channel should be identified\n+ channel_name (string): name of the channel to look for\n+\n+ Returns:\n+ int: Index of the channel or -1 if was not found.\n+ """\n channel_name = channel_name.lower()\n for n, channel in enumerate(image.getChannelLabels()):\n if channel_name == channel.lower():\n@@ -44,13 +59,31 @@\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+ 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+def get_clipping_region(\n+ image: _ImageWrapper, x: int, y: int, w: int, h: int\n+) -> list[int]:\n+ """Check `x`, `y` and adjust `w`, `h` to image size to be able to crop the `image` with these coordinates\n+\n+ Args:\n+ image (_ImageWrapper): image wrapper on which region want to be cropped\n+ x (int): left x coordinate\n+ y (int): top y coordinate\n+ w (int): width\n+ h (int): height\n+\n+ Raises:\n+ ValueError: if the x or y coordinates are negative.\n+ ValueError: if the x or y coordinates are larger than the width or height of the image.\n+\n+ Returns:\n+ list[int]: new [x, y, width, height] adjusted to the image\n+ """\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@@ -58,16 +91,16 @@\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+ "Too small upper left coordinate ({0}, {1}) for clipping region.".format(\n+ x, y\n+ '..b'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+ "--center",\n+ nargs=4,\n+ type=int,\n+ 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+ region.add_argument(\n+ "--download-original",\n+ dest="download_original",\n+ action="store_true",\n+ help="download the original file uploaded to omero",\n+ )\n+ region.add_argument(\n+ "--download-full",\n+ dest="download_full",\n+ action="store_true",\n+ help="download the full image on omero",\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- p.add_argument(\n- \'--download-tar\', action=\'store_true\'\n+ "-c",\n+ "--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), ignored with `--download-original` and "\n+ "`--download-full`",\n )\n p.add_argument(\n- \'-oh\', \'--omero-host\', type=str, default="idr.openmicroscopy.org"\n- )\n- p.add_argument(\n- \'--omero-secured\', action=\'store_true\', default=True\n+ "-f",\n+ "--frame",\n+ type=int,\n+ default=0,\n+ help="index of the frame to retrive data for (first frame is 0),"\n+ " ignored with `--download-original` and `--download-full`",\n )\n p.add_argument(\n- \'-cf\', \'--config-file\', dest=\'config_file\', default=None\n+ "-z",\n+ "--z-stack",\n+ type=int,\n+ default=0,\n+ help="index of the slice to retrive data for (first slice is 0),"\n+ " ignored with `--download-original` and `--download-full`",\n )\n- p.add_argument(\n- \'--dataset\', action=\'store_true\'\n- )\n+ p.add_argument("--skip-failed", action="store_true")\n+ p.add_argument("--download-tar", action="store_true")\n+ p.add_argument("-oh", "--omero-host", type=str, default="idr.openmicroscopy.org")\n+ p.add_argument("--omero-secured", action="store_true", default=True)\n+ p.add_argument("-cf", "--config-file", dest="config_file", default=None)\n+ p.add_argument("--dataset", action="store_true")\n args = p.parse_args()\n if not args.image_ids_or_dataset_id:\n args.image_ids_or_dataset_id = sys.stdin.read().split()\n if args.dataset and len(args.image_ids_or_dataset_id) > 1:\n warn("Multiple dataset ids provided. Only the first one will be used.")\n- if \'center\' in args:\n+ if "center" in args:\n args.coord, args.width, args.height = (\n- args.center[:2], args.center[2], args.center[3]\n+ args.center[:2],\n+ args.center[2],\n+ args.center[3],\n )\n- args.region_spec = \'center\'\n+ args.region_spec = "center"\n del args.center\n- elif \'rectangle\' in args:\n+ elif "rectangle" in args:\n args.coord, args.width, args.height = (\n- args.rectangle[:2], args.rectangle[2], args.rectangle[3]\n+ args.rectangle[:2],\n+ args.rectangle[2],\n+ args.rectangle[3],\n )\n- args.region_spec = \'rectangle\'\n+ args.region_spec = "rectangle"\n del args.rectangle\n download_image_data(**vars(args))\n' |
| b |
| diff -r 4b794652dcdc -r f92941d1a85e idr_download_by_ids.xml --- a/idr_download_by_ids.xml Wed Nov 08 12:57:25 2023 +0000 +++ b/idr_download_by_ids.xml Thu Sep 26 12:32:17 2024 +0000 |
| [ |
| b'@@ -1,5 +1,5 @@\n <?xml version="1.0"?>\n-<tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.44.1" profile="18.09">\n+<tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.45" profile="18.09">\n <description></description>\n <macros>\n <xml name="region_spec" token_pos="upper-left corner">\n@@ -19,8 +19,8 @@\n <edam_operation>operation_3443</edam_operation>\n </edam_operations>\n <requirements>\n- <requirement type="package" version="5.10.1">omero-py</requirement>\n- <requirement type="package" version="0.4.2">pylibtiff</requirement>\n+ <requirement type="package" version="5.19.4">omero-py</requirement>\n+ <requirement type="package" version="2024.9.20">tifffile</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n \n@@ -51,6 +51,8 @@\n #end if\n #if $image_region.original == "original":\n --download-original\n+ #elif $image_region.original == "full":\n+ --download-full\n #else:\n #set $channel = str($image_region.channel).strip()\n #if $channel:\n@@ -87,7 +89,7 @@\n }\n ]]></configfile>\n </configfiles>\n-<inputs>\n+ <inputs>\n <conditional name="omero_instance_type">\n <param name="omero_instance" type="select" label="Which OMERO instance to connect?"\n help="By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you \n@@ -135,9 +137,11 @@\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="full">Whole TIFF (all channels, all frames, all stacks)</option>\n <option value="original">Original file (file uploaded to omero, only available for private instances)</option>\n </param>\n <when value="original"/>\n+ <when value="full"/>\n <when value="TIFF">\n <param name="channel" type="text"\n label="Name of the channel to download"\n@@ -182,7 +186,7 @@\n </data> \n </outputs>\n <tests>\n- <test>\n+ <test expect_num_outputs="2">\n <conditional name="omero_instance_type">\n <param name="omero_instance" value="idr" />\n </conditional>\n@@ -202,10 +206,10 @@\n </conditional>\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" ftype="tiff" file="test0.tiff"/>\n+ <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff" compare="image_diff" />\n </output_collection>\n </test>\n- <test>\n+ <test expect_num_outputs="2">\n <conditional name="omero_instance_type">\n <param name="omero_instance" value="idr" />\n </conditional>\n@@ -225,10 +229,10 @@\n </conditional>\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" ftype="tiff" file="test1.tiff"/>\n+ <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff" compare="image_diff"/>\n </output_collection>\n </test>\n- <test>\n+ <test expect_num_outputs="2">\n <conditional name="omero_instance_type">\n <param name="omero_instance" value="idr" />\n </conditional>\n@@ -248,10 +252,10 @@\n </conditiona'..b'ro_instance_type">\n <param name="omero_instance" value="idr" />\n </conditional>\n@@ -426,27 +446,43 @@\n <output_collection name="output_file" type="list" count="4">\n <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">\n <assert_contents>\n- <has_size value="2097286" />\n+ <has_size size="2097286" />\n+ <has_image_width width="1024" />\n+ <has_image_height height="1024" />\n+ <has_image_mean_intensity mean_intensity="145.310" />\n+ <has_image_center_of_mass center_of_mass="527.499, 480.704" />\n </assert_contents>\n </element>\n <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D__9036708__0__0__1024__1024">\n <assert_contents>\n- <has_size value="2097286" />\n+ <has_size size="2097286" />\n+ <has_image_width width="1024" />\n+ <has_image_height height="1024" />\n+ <has_image_mean_intensity mean_intensity="147.025" />\n+ <has_image_center_of_mass center_of_mass="528.977, 480.691" />\n </assert_contents>\n </element>\n <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D_zproj__9036710__0__0__1024__1024">\n <assert_contents>\n- <has_size value="2097286" />\n+ <has_size size="2097286" />\n+ <has_image_width width="1024" />\n+ <has_image_height height="1024" />\n+ <has_image_mean_intensity mean_intensity="210.787" />\n+ <has_image_center_of_mass center_of_mass="534.629, 473.267" />\n </assert_contents>\n </element>\n <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_REF__9036709__0__0__1024__1024">\n <assert_contents>\n- <has_size value="2097286" />\n+ <has_size size="2097286" />\n+ <has_image_width width="1024" />\n+ <has_image_height height="1024" />\n+ <has_image_mean_intensity mean_intensity="3816.051" />\n+ <has_image_center_of_mass center_of_mass="512.274, 503.186" />\n </assert_contents>\n </element>\n </output_collection>\n </test>\n- <test>\n+ <test expect_num_outputs="2">\n <conditional name="omero_instance_type">\n <param name="omero_instance" value="idr" />\n </conditional>\n@@ -462,6 +498,24 @@\n <output_collection name="output_file" type="list" count="0">\n </output_collection>\n </test>\n+ <test expect_num_outputs="2">\n+ <conditional name="omero_instance_type">\n+ <param name="omero_instance" value="idr" />\n+ </conditional>\n+ <param name="source" value="link" />\n+ <param name="id_spec" value="1229801" />\n+ <param name="download_tar" value="false" />\n+ <conditional name="image_region">\n+ <param name="original" value="full"/> \n+ </conditional>\n+ <output_collection name="output_file" type="list" count="1">\n+ <element name="JL_120731_S6A_[Well_A-1;_Field_#1]__1229801__full">\n+ <assert_contents>\n+ <has_size size="91592058" />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n </tests>\n <help><![CDATA[\n Download image data from the IDR_ (Image Data Resource) - a public repository\n' |