Mercurial > repos > iuc > idr_download_by_ids

annotate idr_download_by_ids.py @ 2:17b1cd0f4812 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
1 import argparse
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
2 import os
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
3 import sys
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
4
2
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
5 from libtiff import TIFF
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
6 from omero.gateway import BlitzGateway # noqa
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
7 from omero.constants.namespaces import NSBULKANNOTATIONS # noqa
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
8
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
9
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
10 def warn(message, image_identifier):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
11 print(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
12 'ImageSpecWarning for {0}: {1}'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
13 .format(image_identifier, message),
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
14 file=sys.stderr
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
15 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
16
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
17
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
18 def find_channel_index(image, channel_name):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
19 channel_name = channel_name.lower()
2
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
20 for n, channel in enumerate(image.getChannelLabels()):
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
21 if channel_name == channel.lower():
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
22 return n
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
23 # Check map annotation for information (this is necessary for some images)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
24 for ann in image.listAnnotations(NSBULKANNOTATIONS):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
25 pairs = ann.getValue()
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
26 for p in pairs:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
27 if p[0] == "Channels":
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
28 channels = p[1].replace(" ", "").split(";")
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
29 for n, c in enumerate(channels):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
30 for value in c.split(':'):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
31 if channel_name == value.lower():
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
32 return n
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
33 return -1
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
34
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
35
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
36 def get_clipping_region(image, x, y, w, h):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
37 # If the (x, y) coordinate falls outside the image boundaries, we
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
38 # cannot just shift it because that would render the meaning of
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
39 # w and h undefined (should width and height be decreased or the whole
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
40 # region be shifted to keep them fixed?).
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
41 # It may be better to abort in this situation.
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
42 if x < 0 or y < 0:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
43 raise ValueError(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
44 'Too small upper left coordinate ({0}, {1}) for clipping region.'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
45 .format(x, y)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
46 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
47 size_x = image.getSizeX()
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
48 size_y = image.getSizeY()
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
49 if x >= size_x or y >= size_y:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
50 raise ValueError(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
51 'Upper left coordinate ({0}, {1}) of clipping region lies '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
52 'outside of image.'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
53 .format(x, y)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
54 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
55 # adjust width and height to the image dimensions
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
56 if w <= 0 or x + w > size_x:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
57 w = size_x - x
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
58 if h <= 0 or y + h > size_y:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
59 h = size_y - y
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
60 return [x, y, w, h]
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
61
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
62
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
63 def confine_plane(image, z):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
64 if z < 0:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
65 z = 0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
66 else:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
67 max_z = image.getSizeZ() - 1
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
68 if z > max_z:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
69 z = max_z
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
70 return z
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
71
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
72
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
73 def confine_frame(image, t):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
74 if t < 0:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
75 t = 0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
76 else:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
77 max_t = image.getSizeT() - 1
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
78 if t > max_t:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
79 t = max_t
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
80 return t
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
81
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
82
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
83 def download_plane_as_tiff(image, tile, z, c, t, fname):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
84 pixels = image.getPrimaryPixels()
2
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
85 try:
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
86 selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile)
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
87 except Exception:
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
88 warning = '{0} (ID: {1})'.format(image.getName(),
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
89 image.getId())
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
90 warn('Could not download the requested region', warning)
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
91 return
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
92
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
93 if fname[-5:] != '.tiff':
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
94 fname += '.tiff'
2
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
95 try:
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
96 tiff = TIFF.open(fname, mode='w')
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
97 tiff.write_image(selection)
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
98 finally:
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
99 tiff.close()
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
100
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
101
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
102 def download_image_data(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
103 image_ids,
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
104 channel=None, z_stack=0, frame=0,
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
105 coord=(0, 0), width=0, height=0, region_spec='rectangle',
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
106 skip_failed=False
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
107 ):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
108
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
109 # connect to idr
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
110 conn = BlitzGateway('public', 'public',
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
111 host='idr.openmicroscopy.org',
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
112 secure=True)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
113 conn.connect()
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
114
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
115 try:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
116 prefix = 'image-'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
117 for image_id in image_ids:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
118 if image_id[:len(prefix)] == prefix:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
119 image_id = image_id[len(prefix):]
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
120 image_id = int(image_id)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
121 image = conn.getObject("Image", image_id)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
122
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
123 if image is None:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
124 image_warning_id = 'Image-ID: {0}'.format(image_id)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
125 if skip_failed:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
126 warn(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
127 'Unable to find an image with this ID in the '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
128 'database. Skipping download!',
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
129 image_warning_id
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
130 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
131 continue
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
132 raise ValueError(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
133 '{0}: Unable to find an image with this ID in the '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
134 'database. Aborting!'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
135 .format(image_warning_id)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
136 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
137
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
138 image_name = os.path.splitext(image.getName())[0]
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
139 image_warning_id = '{0} (ID: {1})'.format(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
140 image_name, image_id
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
141 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
142
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
143 if region_spec == 'rectangle':
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
144 tile = get_clipping_region(image, *coord, width, height)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
145 elif region_spec == 'center':
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
146 tile = get_clipping_region(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
147 image,
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
148 *_center_to_ul(*coord, width, height)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
149 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
150 else:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
151 raise ValueError(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
152 'Got unknown value "{0}" as region_spec argument'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
153 .format(region_spec)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
154 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
155 if tile[2] < width or tile[3] < height:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
156 # The downloaded image region will have smaller dimensions
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
157 # than the specified width x height.
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
158 warn(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
159 'Downloaded image dimensions ({0} x {1}) will be smaller '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
160 'than the specified width and height ({2} x {3}).'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
161 .format(tile[2], tile[3], width, height),
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
162 image_warning_id
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
163 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
164
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
165 ori_z, z_stack = z_stack, confine_plane(image, z_stack)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
166 if z_stack != ori_z:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
167 warn(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
168 'Specified image plane ({0}) is out of bounds. Using {1} '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
169 'instead.'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
170 .format(ori_z, z_stack),
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
171 image_warning_id
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
172 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
173
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
174 ori_frame, frame = frame, confine_frame(image, frame)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
175 if frame != ori_frame:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
176 warn(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
177 'Specified image frame ({0}) is out of bounds. Using '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
178 'frame {1} instead.'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
179 .format(ori_frame, frame),
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
180 image_warning_id
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
181 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
182 # Get the channel index. If the index is not valid, skip the image
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
183 if channel is None:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
184 channel_index = 0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
185 num_channels = image.getSizeC()
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
186 if num_channels > 1:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
187 warn(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
188 'No specific channel selected for multi-channel '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
189 'image. Using first of {0} channels.'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
190 .format(num_channels),
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
191 image_warning_id
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
192 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
193 else:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
194 channel_index = find_channel_index(image, channel)
2
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
195 if channel_index == -1 or channel_index >= image.getSizeC():
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
196 raise ValueError(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
197 '"{0}" is not a known channel name for image {1}'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
198 .format(channel, image.getName())
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
199 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
200
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
201 # download and save the region as TIFF
1
9340cbc7796c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit c496b34c7f6265cccd9326fd239542d9e625c1a4"
iuc
parents: 0
diff changeset
202 fname = '__'.join(
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
203 [image_name, str(image_id)] + [str(x) for x in tile]
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
204 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
205 download_plane_as_tiff(image, tile, z_stack, channel_index, frame, fname)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
206 finally:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
207 # Close the connection
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
208 conn.close()
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
209
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
210
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
211 def _center_to_ul(center_x, center_y, width, height):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
212 if width > 0:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
213 ext_x = (width - 1) // 2
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
214 ul_x = max([center_x - ext_x, 0])
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
215 width = center_x + ext_x + 1 - ul_x
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
216 else:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
217 ul_x = 0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
218 if height > 0:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
219 ext_y = (height - 1) // 2
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
220 ul_y = max([center_y - ext_y, 0])
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
221 height = center_y + ext_y + 1 - ul_y
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
222 else:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
223 ul_y = 0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
224 return ul_x, ul_y, width, height
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
225
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
226
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
227 if __name__ == "__main__":
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
228 p = argparse.ArgumentParser()
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
229 p.add_argument(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
230 'image_ids', nargs='*', default=[],
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
231 help='one or more IDR image ids for which to retrieve data (default: '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
232 'read ids from stdin).'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
233 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
234 p.add_argument(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
235 '-c', '--channel',
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
236 help='name of the channel to retrieve data for '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
237 '(note: the first channel of each image will be downloaded if '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
238 'left unspecified)'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
239 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
240 region = p.add_mutually_exclusive_group()
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
241 region.add_argument(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
242 '--rectangle', nargs=4, type=int, default=argparse.SUPPRESS,
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
243 help='specify a clipping region for the image as x y width height, '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
244 'where x and y give the upper left coordinate of the rectangle '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
245 'to clip to. Set width and height to 0 to extend the rectangle '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
246 'to the actual size of the image.'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
247 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
248 region.add_argument(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
249 '--center', nargs=4, type=int, default=argparse.SUPPRESS,
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
250 help='specify a clipping region for the image as x y width height, '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
251 'where x and y define the center of a width x height rectangle. '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
252 'Set either width or height to 0 to extend the region to the '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
253 'actual size of the image along the x- or y-axis.\n'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
254 'Note: Even values for width and height will be rounded down to '
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
255 'the nearest odd number.'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
256 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
257 p.add_argument(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
258 '-f', '--frame', type=int, default=0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
259 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
260 p.add_argument(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
261 '-z', '--z-stack', type=int, default=0
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262 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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263 p.add_argument(
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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264 '--skip-failed', action='store_true'
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265 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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266 args = p.parse_args()
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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267 if not args.image_ids:
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268 args.image_ids = sys.stdin.read().split()
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269 if 'center' in args:
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270 args.coord, args.width, args.height = (
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271 args.center[:2], args.center[2], args.center[3]
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272 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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273 args.region_spec = 'center'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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274 del args.center
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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275 elif 'rectangle' in args:
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276 args.coord, args.width, args.height = (
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277 args.rectangle[:2], args.rectangle[2], args.rectangle[3]
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278 )
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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279 args.region_spec = 'rectangle'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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280 del args.rectangle
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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281 download_image_data(**vars(args))