Mercurial > repos > iuc > idr_download_by_ids

comparison idr_download_by_ids.py @ 6:5c743356df83 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bf331f8e60e7bc1daf1cd71d2068062d925e7ffa"
author iuc
date Mon, 06 Jul 2020 19:33:59 -0400
parents e08b1dc0480c
children f067504aa92a
comparison
equal deleted inserted replaced
5:e08b1dc0480c 6:5c743356df83
1 import argparse 1 import argparse
2 import os 2 import os
3 import sys 3 import sys
4 import tarfile 4 import tarfile
5 import time 5 from contextlib import ExitStack
6 from tempfile import TemporaryFile 6 from tempfile import TemporaryDirectory
7 7
8 from libtiff import TIFF 8 from libtiff import TIFF
9 from PIL import Image
10 from omero.gateway import BlitzGateway # noqa 9 from omero.gateway import BlitzGateway # noqa
11 from omero.constants.namespaces import NSBULKANNOTATIONS # noqa 10 from omero.constants.namespaces import NSBULKANNOTATIONS # noqa
12 11
13 12
14 def warn(message, image_identifier, warn_skip=False): 13 def warn(message, image_identifier, warn_skip=False):
127 raise ValueError( 126 raise ValueError(
128 'Got unknown value "{0}" as region_spec argument' 127 'Got unknown value "{0}" as region_spec argument'
129 .format(region_spec) 128 .format(region_spec)
130 ) 129 )
131 130
132 # connect to idr 131 with ExitStack() as exit_stack:
133 conn = BlitzGateway('public', 'public', 132 # connect to idr
134 host='idr.openmicroscopy.org', 133 conn = exit_stack.enter_context(
135 secure=True) 134 BlitzGateway(
136 conn.connect() 135 'public', 'public',
137 136 host='idr.openmicroscopy.org',
138 if download_tar: 137 secure=True
139 # create an archive file to write images to 138 )
140 archive = tarfile.open('images.tar', mode='w') 139 )
141 140 # exit_stack.callback(conn.connect().close)
142 try: 141 if download_tar:
142 # create an archive file to write images to
143 archive = exit_stack.enter_context(
144 tarfile.open('images.tar', mode='w')
145 )
146 tempdir = exit_stack.enter_context(
147 TemporaryDirectory()
148 )
149
143 for image_id in image_ids: 150 for image_id in image_ids:
144 image_warning_id = 'Image-ID: {0}'.format(image_id) 151 image_warning_id = 'Image-ID: {0}'.format(image_id)
145 try: 152 try:
146 image_id = int(image_id) 153 image_id = int(image_id)
147 except ValueError: 154 except ValueError:
269 276
270 fname = fname.replace(' ', '_') 277 fname = fname.replace(' ', '_')
271 278
272 im_array = get_image_array(image, tile, z_stack, channel_index, frame) 279 im_array = get_image_array(image, tile, z_stack, channel_index, frame)
273 280
274 # pack images into tarball
275 if download_tar: 281 if download_tar:
276 tar_img = Image.fromarray(im_array) 282 fname = os.path.join(tempdir, fname)
277 # Use TemporaryFile() for intermediate storage of images. 283 try:
278 # TO DO: could this be improved by using 284 tiff = TIFF.open(fname, mode='w')
279 # SpooledTemporaryFile with a suitable max_size? 285 tiff.write_image(im_array)
280 with TemporaryFile() as buf: 286 finally:
281 tar_img.save(buf, format='TIFF') 287 tiff.close()
282 tarinfo = tarfile.TarInfo(name=fname) 288 # move image into tarball
283 buf.seek(0, 2) 289 if download_tar:
284 tarinfo.size = buf.tell() 290 archive.add(fname, os.path.basename(fname))
285 tarinfo.mtime = time.time() 291 os.remove(fname)
286 buf.seek(0)
287 archive.addfile(tarinfo=tarinfo, fileobj=buf)
288 else: # save image as individual file
289 try:
290 tiff = TIFF.open(fname, mode='w')
291 tiff.write_image(im_array)
292 finally:
293 tiff.close()
294 except Exception as e: 292 except Exception as e:
295 if skip_failed: 293 if skip_failed:
296 # respect skip_failed on unexpected errors 294 # respect skip_failed on unexpected errors
297 warn(str(e), image_warning_id, warn_skip=True) 295 warn(str(e), image_warning_id, warn_skip=True)
298 continue 296 continue
299 else: 297 else:
300 raise 298 raise
301
302 finally:
303 # close the archive file,if it is created
304 if download_tar:
305 archive.close()
306 # Close the connection
307 conn.close()
308 299
309 300
310 def _center_to_ul(center_x, center_y, width, height): 301 def _center_to_ul(center_x, center_y, width, height):
311 if width > 0: 302 if width > 0:
312 ext_x = (width - 1) // 2 303 ext_x = (width - 1) // 2