Mercurial > repos > iuc > idr_download_by_ids

comparison idr_download_by_ids.py @ 11:cbd605a24336 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
author iuc
date Sat, 15 Jan 2022 12:25:29 +0000
parents 4aed70472589
children f92941d1a85e
comparison
equal deleted inserted replaced
10:4aed70472589 11:cbd605a24336
5 import tarfile 5 import tarfile
6 from contextlib import ExitStack 6 from contextlib import ExitStack
7 from tempfile import TemporaryDirectory 7 from tempfile import TemporaryDirectory
8 8
9 from libtiff import TIFF 9 from libtiff import TIFF
10 from omero.cli import cli_login
10 from omero.gateway import BlitzGateway # noqa 11 from omero.gateway import BlitzGateway # noqa
11 from omero.constants.namespaces import NSBULKANNOTATIONS # noqa 12 from omero.constants.namespaces import NSBULKANNOTATIONS # noqa
12 13
13 14
14 def warn(message, image_identifier, warn_skip=False): 15 def warn(message, image_identifier, warn_skip=False):
109 return selection 110 return selection
110 111
111 112
112 def download_image_data( 113 def download_image_data(
113 image_ids_or_dataset_id, dataset=False, 114 image_ids_or_dataset_id, dataset=False,
115 download_original=False,
114 channel=None, z_stack=0, frame=0, 116 channel=None, z_stack=0, frame=0,
115 coord=(0, 0), width=0, height=0, region_spec='rectangle', 117 coord=(0, 0), width=0, height=0, region_spec='rectangle',
116 skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None 118 skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None
117 ): 119 ):
118 120
127 129
128 if omero_username == "" or omero_password == "": 130 if omero_username == "" or omero_password == "":
129 omero_username = 'public' 131 omero_username = 'public'
130 omero_password = 'public' 132 omero_password = 'public'
131 133
132 if region_spec not in ['rectangle', 'center']: 134 if not download_original and region_spec not in ['rectangle', 'center']:
133 raise ValueError( 135 raise ValueError(
134 'Got unknown value "{0}" as region_spec argument' 136 'Got unknown value "{0}" as region_spec argument'
135 .format(region_spec) 137 .format(region_spec)
136 ) 138 )
137 with ExitStack() as exit_stack: 139 with ExitStack() as exit_stack:
222 raise ValueError( 224 raise ValueError(
223 '{0}: Unable to find an image with this ID in the ' 225 '{0}: Unable to find an image with this ID in the '
224 'database. Aborting!' 226 'database. Aborting!'
225 .format(image_warning_id) 227 .format(image_warning_id)
226 ) 228 )
227 229 if not download_original:
228 try: 230 try:
229 # try to extract image properties 231 # try to extract image properties
230 # if anything goes wrong here skip the image 232 # if anything goes wrong here skip the image
231 # or abort. 233 # or abort.
232 image_name = os.path.splitext(image.getName())[0] 234 image_name = os.path.splitext(image.getName())[0]
233 image_warning_id = '{0} (ID: {1})'.format( 235 image_warning_id = '{0} (ID: {1})'.format(
234 image_name, image_id 236 image_name, image_id
237 )
238
239 if region_spec == 'rectangle':
240 tile = get_clipping_region(image, *coord, width, height)
241 elif region_spec == 'center':
242 tile = get_clipping_region(
243 image,
244 *_center_to_ul(*coord, width, height)
245 )
246
247 ori_z, z_stack = z_stack, confine_plane(image, z_stack)
248 ori_frame, frame = frame, confine_frame(image, frame)
249 num_channels = image.getSizeC()
250 if channel is None:
251 channel_index = 0
252 else:
253 channel_index = find_channel_index(image, channel)
254 except Exception as e:
255 # respect skip_failed on unexpected errors
256 if skip_failed:
257 warn(str(e), image_warning_id, warn_skip=True)
258 continue
259 else:
260 raise
261
262 # region sanity checks and warnings
263 if tile[2] < width or tile[3] < height:
264 # The downloaded image region will have smaller dimensions
265 # than the specified width x height.
266 warn(
267 'Downloaded image dimensions ({0} x {1}) will be smaller '
268 'than the specified width and height ({2} x {3}).'
269 .format(tile[2], tile[3], width, height),
270 image_warning_id
271 )
272
273 # z-stack sanity checks and warnings
274 if z_stack != ori_z:
275 warn(
276 'Specified image plane ({0}) is out of bounds. Using {1} '
277 'instead.'
278 .format(ori_z, z_stack),
279 image_warning_id
280 )
281
282 # frame sanity checks and warnings
283 if frame != ori_frame:
284 warn(
285 'Specified image frame ({0}) is out of bounds. Using '
286 'frame {1} instead.'
287 .format(ori_frame, frame),
288 image_warning_id
289 )
290
291 # channel index sanity checks and warnings
292 if channel is None:
293 if num_channels > 1:
294 warn(
295 'No specific channel selected for multi-channel '
296 'image. Using first of {0} channels.'
297 .format(num_channels),
298 image_warning_id
299 )
300 else:
301 if channel_index == -1 or channel_index >= num_channels:
302 if skip_failed:
303 warn(
304 str(channel)
305 + ' is not a known channel name for this image.',
306 image_warning_id,
307 warn_skip=True
308 )
309 continue
310 else:
311 raise ValueError(
312 '"{0}" is not a known channel name for image {1}. '
313 'Aborting!'
314 .format(channel, image_warning_id)
315 )
316
317 # download and save the region as TIFF
318 fname = '__'.join(
319 [image_name, str(image_id)] + [str(x) for x in tile]
235 ) 320 )
236 321 try:
237 if region_spec == 'rectangle': 322 if fname[-5:] != '.tiff':
238 tile = get_clipping_region(image, *coord, width, height) 323 fname += '.tiff'
239 elif region_spec == 'center': 324
240 tile = get_clipping_region( 325 fname = fname.replace(' ', '_')
241 image, 326
242 *_center_to_ul(*coord, width, height) 327 im_array = get_image_array(image, tile, z_stack, channel_index, frame)
243 ) 328
244 329 if download_tar:
245 ori_z, z_stack = z_stack, confine_plane(image, z_stack) 330 fname = os.path.join(tempdir, fname)
246 ori_frame, frame = frame, confine_frame(image, frame) 331 try:
247 num_channels = image.getSizeC() 332 tiff = TIFF.open(fname, mode='w')
248 if channel is None: 333 tiff.write_image(im_array)
249 channel_index = 0 334 finally:
250 else: 335 tiff.close()
251 channel_index = find_channel_index(image, channel) 336 # move image into tarball
252 except Exception as e: 337 if download_tar:
253 # respect skip_failed on unexpected errors 338 archive.add(fname, os.path.basename(fname))
254 if skip_failed: 339 os.remove(fname)
255 warn(str(e), image_warning_id, warn_skip=True) 340 except Exception as e:
256 continue 341 if skip_failed:
257 else: 342 # respect skip_failed on unexpected errors
258 raise 343 warn(str(e), image_warning_id, warn_skip=True)
259 344 continue
260 # region sanity checks and warnings 345 else:
261 if tile[2] < width or tile[3] < height: 346 raise
262 # The downloaded image region will have smaller dimensions
263 # than the specified width x height.
264 warn(
265 'Downloaded image dimensions ({0} x {1}) will be smaller '
266 'than the specified width and height ({2} x {3}).'
267 .format(tile[2], tile[3], width, height),
268 image_warning_id
269 )
270
271 # z-stack sanity checks and warnings
272 if z_stack != ori_z:
273 warn(
274 'Specified image plane ({0}) is out of bounds. Using {1} '
275 'instead.'
276 .format(ori_z, z_stack),
277 image_warning_id
278 )
279
280 # frame sanity checks and warnings
281 if frame != ori_frame:
282 warn(
283 'Specified image frame ({0}) is out of bounds. Using '
284 'frame {1} instead.'
285 .format(ori_frame, frame),
286 image_warning_id
287 )
288
289 # channel index sanity checks and warnings
290 if channel is None:
291 if num_channels > 1:
292 warn(
293 'No specific channel selected for multi-channel '
294 'image. Using first of {0} channels.'
295 .format(num_channels),
296 image_warning_id
297 )
298 else: 347 else:
299 if channel_index == -1 or channel_index >= num_channels: 348 try:
349 # try to extract image properties
350 # if anything goes wrong here skip the image
351 # or abort.
352 image_name = os.path.splitext(image.getName())[0]
353 image_warning_id = '{0} (ID: {1})'.format(
354 image_name, image_id
355 )
356 original_image_name = image.getFileset().listFiles()[0].getName()
357 fname = image_name + "__" + str(image_id) + os.path.splitext(original_image_name)[1]
358 fname = fname.replace(' ', '_')
359 fname = fname.replace('/', '_')
360 download_directory = "./"
361 if download_tar:
362 download_directory = tempdir
363 with cli_login("-u", omero_username, "-s", omero_host, "-w", omero_password) as cli:
364 cli.invoke(["download", f"Image:{image_id}", download_directory])
365 if cli.rv != 0:
366 raise Exception("Download failed.")
367 # This will download to download_directory/original_image_name
368 os.rename(os.path.join(download_directory, original_image_name),
369 os.path.join(download_directory, fname))
370 # move image into tarball
371 if download_tar:
372 archive.add(os.path.join(download_directory, fname),
373 os.path.basename(fname))
374 os.remove(os.path.join(download_directory, fname))
375 except Exception as e:
376 # respect skip_failed on unexpected errors
300 if skip_failed: 377 if skip_failed:
301 warn( 378 warn(str(e), image_warning_id, warn_skip=True)
302 str(channel)
303 + ' is not a known channel name for this image.',
304 image_warning_id,
305 warn_skip=True
306 )
307 continue 379 continue
308 else: 380 else:
309 raise ValueError( 381 raise
310 '"{0}" is not a known channel name for image {1}. '
311 'Aborting!'
312 .format(channel, image_warning_id)
313 )
314
315 # download and save the region as TIFF
316 fname = '__'.join(
317 [image_name, str(image_id)] + [str(x) for x in tile]
318 )
319 try:
320 if fname[-5:] != '.tiff':
321 fname += '.tiff'
322
323 fname = fname.replace(' ', '_')
324
325 im_array = get_image_array(image, tile, z_stack, channel_index, frame)
326
327 if download_tar:
328 fname = os.path.join(tempdir, fname)
329 try:
330 tiff = TIFF.open(fname, mode='w')
331 tiff.write_image(im_array)
332 finally:
333 tiff.close()
334 # move image into tarball
335 if download_tar:
336 archive.add(fname, os.path.basename(fname))
337 os.remove(fname)
338 except Exception as e:
339 if skip_failed:
340 # respect skip_failed on unexpected errors
341 warn(str(e), image_warning_id, warn_skip=True)
342 continue
343 else:
344 raise
345 382
346 383
347 def _center_to_ul(center_x, center_y, width, height): 384 def _center_to_ul(center_x, center_y, width, height):
348 if width > 0: 385 if width > 0:
349 ext_x = (width - 1) // 2 386 ext_x = (width - 1) // 2
367 help='one or more IDR image ids or a single dataset id' 404 help='one or more IDR image ids or a single dataset id'
368 'for which to retrieve data (default: ' 405 'for which to retrieve data (default: '
369 'read ids from stdin).' 406 'read ids from stdin).'
370 ) 407 )
371 p.add_argument( 408 p.add_argument(
409 '--download-original', dest='download_original', action='store_true',
410 help="download the original file uploaded to omero"
411 )
412 p.add_argument(
372 '-c', '--channel', 413 '-c', '--channel',
373 help='name of the channel to retrieve data for ' 414 help='name of the channel to retrieve data for '
374 '(note: the first channel of each image will be downloaded if ' 415 '(note: the first channel of each image will be downloaded if '
375 'left unspecified)' 416 'left unspecified)'
376 ) 417 )