Mercurial > repos > iuc > idr_download_by_ids
changeset 4:11036f6197d6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
| author | iuc |
|---|---|
| date | Fri, 15 May 2020 14:54:02 -0400 |
| parents | 381f248febba |
| children | e08b1dc0480c |
| files | idr_download_by_ids.py idr_download_by_ids.xml test-data/ids_tar.txt |
| diffstat | 3 files changed, 86 insertions(+), 12 deletions(-) [+] |
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--- a/idr_download_by_ids.py Wed Apr 22 11:43:18 2020 -0400 +++ b/idr_download_by_ids.py Fri May 15 14:54:02 2020 -0400 @@ -1,8 +1,11 @@ import argparse import os import sys +import tarfile from libtiff import TIFF +from PIL import Image +from tempfile import TemporaryFile from omero.gateway import BlitzGateway # noqa from omero.constants.namespaces import NSBULKANNOTATIONS # noqa @@ -92,7 +95,7 @@ return t -def download_plane_as_tiff(image, tile, z, c, t, fname): +def get_image_array(image, tile, z, c, t): pixels = image.getPrimaryPixels() try: selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile) @@ -102,21 +105,14 @@ warn('Could not download the requested region', warning) return - if fname[-5:] != '.tiff': - fname += '.tiff' - try: - fname = fname.replace(' ', '_') - tiff = TIFF.open(fname, mode='w') - tiff.write_image(selection) - finally: - tiff.close() + return selection def download_image_data( image_ids, channel=None, z_stack=0, frame=0, coord=(0, 0), width=0, height=0, region_spec='rectangle', - skip_failed=False + skip_failed=False, download_tar=False ): # basic argument sanity checks and adjustments prefix = 'image-' @@ -138,6 +134,10 @@ secure=True) conn.connect() + if download_tar: + # create an archive file to write images to + archive = tarfile.open('images.tar', mode='w') + try: for image_id in image_ids: image_warning_id = 'Image-ID: {0}'.format(image_id) @@ -263,7 +263,32 @@ [image_name, str(image_id)] + [str(x) for x in tile] ) try: - download_plane_as_tiff(image, tile, z_stack, channel_index, frame, fname) + if fname[-5:] != '.tiff': + fname += '.tiff' + + fname = fname.replace(' ', '_') + + im_array = get_image_array(image, tile, z_stack, channel_index, frame) + + # pack images into tarball + if download_tar: + tar_img = Image.fromarray(im_array) + # Use TemporaryFile() for intermediate storage of images. + # TO DO: could this be improved by using + # SpooledTemporaryFile with a suitable max_size? + with TemporaryFile() as buf: + tar_img.save(buf, format='TIFF') + tarinfo = tarfile.TarInfo(name=fname) + buf.seek(0, 2) + tarinfo.size = buf.tell() + buf.seek(0) + archive.addfile(tarinfo=tarinfo, fileobj=buf) + else: # save image as individual file + try: + tiff = TIFF.open(fname, mode='w') + tiff.write_image(im_array) + finally: + tiff.close() except Exception as e: if skip_failed: # respect skip_failed on unexpected errors @@ -271,7 +296,11 @@ continue else: raise + finally: + # close the archive file,if it is created + if download_tar: + archive.close() # Close the connection conn.close() @@ -331,6 +360,9 @@ p.add_argument( '--skip-failed', action='store_true' ) + p.add_argument( + '--download-tar', action='store_true' + ) args = p.parse_args() if not args.image_ids: args.image_ids = sys.stdin.read().split()
--- a/idr_download_by_ids.xml Wed Apr 22 11:43:18 2020 -0400 +++ b/idr_download_by_ids.xml Fri May 15 14:54:02 2020 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="idr_download_by_ids" name="IDR Download" version="0.30" profile="18.09"> +<tool id="idr_download_by_ids" name="IDR Download" version="0.40" 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"> @@ -38,6 +38,7 @@ ${clip_image.select} ${clip_image.x_coord} ${clip_image.y_coord} ${clip_image.width} ${clip_image.height} #end if $skip_failed + $download_tar 2> >(tee -a $out_log >&2) ]]></command> @@ -86,12 +87,20 @@ <param name="skip_failed" type="boolean" checked="false" truevalue="--skip-failed" falsevalue="" label="Skip failed retrievals?" help="By default the tool will fail with an error on the first non-retrievable image ID. Here, you can choose to skip non-retrievable image IDs and continue downloading the available ones instead. The error log will contain warnings about failed IDs in this case." /> + <param name="download_tar" type="boolean" checked="true" truevalue="--download-tar" falsevalue="" + label="Download images in a tarball?" + help="By default, the tool will download a tarball containing individual images into your Galaxy history. This option is strongly recommended, especially for a large number of files. With this option set to No, you will download a collection of images, only suggested for a small number of files." > + </param> </inputs> <outputs> <data name="out_log" format="txt" label="${tool.name} error log" /> <collection name="output_file" type="list"> <discover_datasets pattern="__name_and_ext__" directory="downloads" /> + <filter>not download_tar</filter> </collection> + <data name="output_tar" format="tar" from_work_dir="./downloads/images.tar" label ="Images tarball"> + <filter>download_tar</filter> + </data> </outputs> <tests> <test> @@ -106,6 +115,7 @@ <param name="height" value="5" /> </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" file="test1.tiff"/> </output_collection> @@ -122,6 +132,7 @@ <param name="height" value="5" /> </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" file="test1.tiff"/> </output_collection> @@ -138,6 +149,7 @@ <param name="height" value="5" /> </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" file="test1.tiff"/> </output_collection> @@ -151,6 +163,7 @@ <param name="select" value="" /> </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"> <assert_contents> @@ -175,6 +188,7 @@ <param name="select" value="" /> </conditional> <param name="frame" value="20" /> + <param name="download_tar" value="false" /> </test> <test> <!-- Repeat test with non-existing image-ID 9036708999, @@ -188,6 +202,7 @@ </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"> <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024"> <assert_contents> @@ -203,6 +218,31 @@ </assert_contents> </output> </test> + <test> + <!-- 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> + <param name="frame" value="0" /> + <output name="output_tar"> + <assert_contents> + <has_size value="1382400" /> + <has_archive_member path=".*/*__1828167__0__0__671__511.tiff" > + <has_size value="685884" /> + </has_archive_member> + <has_archive_member path=".*/*__1828658__0__0__671__511.tiff" > + <has_size value="685884" /> + </has_archive_member> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ Download image data from the IDR_ (Image Data Resource) - a public repository