Mercurial > repos > iuc > idr_download_by_ids

comparison idr_download_by_ids.py @ 2:17b1cd0f4812 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
author iuc
date Tue, 14 Apr 2020 10:27:25 -0400
parents 9340cbc7796c
children 381f248febba
comparison
equal deleted inserted replaced
1:9340cbc7796c 2:17b1cd0f4812
1 import argparse 1 import argparse
2 import os 2 import os
3 import sys 3 import sys
4 4
5 from matplotlib import pyplot as plt 5 from libtiff import TIFF
6 from omero.gateway import BlitzGateway # noqa 6 from omero.gateway import BlitzGateway # noqa
7 from omero.constants.namespaces import NSBULKANNOTATIONS # noqa 7 from omero.constants.namespaces import NSBULKANNOTATIONS # noqa
8 8
9 9
10 def warn(message, image_identifier): 10 def warn(message, image_identifier):
15 ) 15 )
16 16
17 17
18 def find_channel_index(image, channel_name): 18 def find_channel_index(image, channel_name):
19 channel_name = channel_name.lower() 19 channel_name = channel_name.lower()
20 for n, channel in enumerate(image.getChannels()): 20 for n, channel in enumerate(image.getChannelLabels()):
21 if channel_name == channel.getLabel().lower(): 21 if channel_name == channel.lower():
22 return n 22 return n
23 # Check map annotation for information (this is necessary for some images) 23 # Check map annotation for information (this is necessary for some images)
24 for ann in image.listAnnotations(NSBULKANNOTATIONS): 24 for ann in image.listAnnotations(NSBULKANNOTATIONS):
25 pairs = ann.getValue() 25 pairs = ann.getValue()
26 for p in pairs: 26 for p in pairs:
80 return t 80 return t
81 81
82 82
83 def download_plane_as_tiff(image, tile, z, c, t, fname): 83 def download_plane_as_tiff(image, tile, z, c, t, fname):
84 pixels = image.getPrimaryPixels() 84 pixels = image.getPrimaryPixels()
85 selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile) 85 try:
86 selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile)
87 except Exception:
88 warning = '{0} (ID: {1})'.format(image.getName(),
89 image.getId())
90 warn('Could not download the requested region', warning)
91 return
86 92
87 if fname[-5:] != '.tiff': 93 if fname[-5:] != '.tiff':
88 fname += '.tiff' 94 fname += '.tiff'
89 plt.imsave(fname, selection) 95 try:
96 tiff = TIFF.open(fname, mode='w')
97 tiff.write_image(selection)
98 finally:
99 tiff.close()
90 100
91 101
92 def download_image_data( 102 def download_image_data(
93 image_ids, 103 image_ids,
94 channel=None, z_stack=0, frame=0, 104 channel=None, z_stack=0, frame=0,
180 .format(num_channels), 190 .format(num_channels),
181 image_warning_id 191 image_warning_id
182 ) 192 )
183 else: 193 else:
184 channel_index = find_channel_index(image, channel) 194 channel_index = find_channel_index(image, channel)
185 if channel_index == -1: 195 if channel_index == -1 or channel_index >= image.getSizeC():
186 raise ValueError( 196 raise ValueError(
187 '"{0}" is not a known channel name for image {1}' 197 '"{0}" is not a known channel name for image {1}'
188 .format(channel, image.getName()) 198 .format(channel, image.getName())
189 ) 199 )
190 200