idr_download_by_ids: idr_download_by

comparison idr_download_by_ids.py @ 0:57aa9597cd31 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"

author	iuc
date	Sat, 08 Feb 2020 13:24:39 -0500
parents
children	9340cbc7796c

comparison

equal deleted inserted replaced

--1:000000000000
+:57aa9597cd31
+import argparse
+import os
+import sys
+from matplotlib import pyplot as plt
+from omero.gateway import BlitzGateway  # noqa
+from omero.constants.namespaces import NSBULKANNOTATIONS  # noqa
+def warn(message, image_identifier):
+print(
+'ImageSpecWarning for {0}: {1}'
+.format(image_identifier, message),
+file=sys.stderr
+)
+def find_channel_index(image, channel_name):
+channel_name = channel_name.lower()
+for n, channel in enumerate(image.getChannels()):
+if channel_name == channel.getLabel().lower():
+return n
+# Check map annotation for information (this is necessary for some images)
+for ann in image.listAnnotations(NSBULKANNOTATIONS):
+pairs = ann.getValue()
+for p in pairs:
+if p[0] == "Channels":
+channels = p[1].replace(" ", "").split(";")
+for n, c in enumerate(channels):
+for value in c.split(':'):
+if channel_name == value.lower():
+return n
+return -1
+def get_clipping_region(image, x, y, w, h):
+# If the (x, y) coordinate falls outside the image boundaries, we
+# cannot just shift it because that would render the meaning of
+# w and h undefined (should width and height be decreased or the whole
+# region be shifted to keep them fixed?).
+# It may be better to abort in this situation.
+if x < 0 or y < 0:
+raise ValueError(
+'Too small upper left coordinate ({0}, {1}) for clipping region.'
+.format(x, y)
+)
+size_x = image.getSizeX()
+size_y = image.getSizeY()
+if x >= size_x or y >= size_y:
+raise ValueError(
+'Upper left coordinate ({0}, {1}) of clipping region lies '
+'outside of image.'
+.format(x, y)
+)
+# adjust width and height to the image dimensions
+if w <= 0 or x + w > size_x:
+w = size_x - x
+if h <= 0 or y + h > size_y:
+h = size_y - y
+return [x, y, w, h]
+def confine_plane(image, z):
+if z < 0:
+z = 0
+else:
+max_z = image.getSizeZ() - 1
+if z > max_z:
+z = max_z
+return z
+def confine_frame(image, t):
+if t < 0:
+t = 0
+else:
+max_t = image.getSizeT() - 1
+if t > max_t:
+t = max_t
+return t
+def download_plane_as_tiff(image, tile, z, c, t, fname):
+pixels = image.getPrimaryPixels()
+selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile)
+if fname[-5:] != '.tiff':
+fname += '.tiff'
+plt.imsave(fname, 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
+):
+# connect to idr
+conn = BlitzGateway('public', 'public',
+host='idr.openmicroscopy.org',
+secure=True)
+conn.connect()
+try:
+prefix = 'image-'
+for image_id in image_ids:
+if image_id[:len(prefix)] == prefix:
+image_id = image_id[len(prefix):]
+image_id = int(image_id)
+image = conn.getObject("Image", image_id)
+if image is None:
+image_warning_id = 'Image-ID: {0}'.format(image_id)
+if skip_failed:
+warn(
+'Unable to find an image with this ID in the '
+'database. Skipping download!',
+image_warning_id
+)
+continue
+raise ValueError(
+'{0}: Unable to find an image with this ID in the '
+'database. Aborting!'
+.format(image_warning_id)
+)
+image_name = os.path.splitext(image.getName())[0]
+image_warning_id = '{0} (ID: {1})'.format(
+image_name, image_id
+)
+if region_spec == 'rectangle':
+tile = get_clipping_region(image, *coord, width, height)
+elif region_spec == 'center':
+tile = get_clipping_region(
+image,
+*_center_to_ul(*coord, width, height)
+)
+else:
+raise ValueError(
+'Got unknown value "{0}" as region_spec argument'
+.format(region_spec)
+)
+if tile[2] < width or tile[3] < height:
+# The downloaded image region will have smaller dimensions
+# than the specified width x height.
+warn(
+'Downloaded image dimensions ({0} x {1}) will be smaller '
+'than the specified width and height ({2} x {3}).'
+.format(tile[2], tile[3], width, height),
+image_warning_id
+)
+ori_z, z_stack = z_stack, confine_plane(image, z_stack)
+if z_stack != ori_z:
+warn(
+'Specified image plane ({0}) is out of bounds. Using {1} '
+'instead.'
+.format(ori_z, z_stack),
+image_warning_id
+)
+ori_frame, frame = frame, confine_frame(image, frame)
+if frame != ori_frame:
+warn(
+'Specified image frame ({0}) is out of bounds. Using '
+'frame {1} instead.'
+.format(ori_frame, frame),
+image_warning_id
+)
+# Get the channel index. If the index is not valid, skip the image
+if channel is None:
+channel_index = 0
+num_channels = image.getSizeC()
+if num_channels > 1:
+warn(
+'No specific channel selected for multi-channel '
+'image. Using first of {0} channels.'
+.format(num_channels),
+image_warning_id
+)
+else:
+channel_index = find_channel_index(image, channel)
+if channel_index == -1:
+raise ValueError(
+'"{0}" is not a known channel name for image {1}'
+.format(channel, image.getName())
+)
+# download and save the region as TIFF
+fname = '_'.join(
+[image_name, str(image_id)] + [str(x) for x in tile]
+)
+download_plane_as_tiff(image, tile, z_stack, channel_index, frame, fname)
+finally:
+# Close the connection
+conn.close()
+def _center_to_ul(center_x, center_y, width, height):
+if width > 0:
+ext_x = (width - 1) // 2
+ul_x = max([center_x - ext_x, 0])
+width = center_x + ext_x + 1 - ul_x
+else:
+ul_x = 0
+if height > 0:
+ext_y = (height - 1) // 2
+ul_y = max([center_y - ext_y, 0])
+height = center_y + ext_y + 1 - ul_y
+else:
+ul_y = 0
+return ul_x, ul_y, width, height
+if __name__ == "__main__":
+p = argparse.ArgumentParser()
+p.add_argument(
+'image_ids', nargs='*', default=[],
+help='one or more IDR image ids for which to retrieve data (default: '
+'read ids from stdin).'
+)
+p.add_argument(
+'-c', '--channel',
+help='name of the channel to retrieve data for '
+'(note: the first channel of each image will be downloaded if '
+'left unspecified)'
+)
+region = p.add_mutually_exclusive_group()
+region.add_argument(
+'--rectangle', nargs=4, type=int, default=argparse.SUPPRESS,
+help='specify a clipping region for the image as x y width height, '
+'where x and y give the upper left coordinate of the rectangle '
+'to clip to. Set width and height to 0 to extend the rectangle '
+'to the actual size of the image.'
+)
+region.add_argument(
+'--center', nargs=4, type=int, default=argparse.SUPPRESS,
+help='specify a clipping region for the image as x y width height, '
+'where x and y define the center of a width x height rectangle. '
+'Set either width or height to 0 to extend the region to the '
+'actual size of the image along the x- or y-axis.\n'
+'Note: Even values for width and height will be rounded down to '
+'the nearest odd number.'
+)
+p.add_argument(
+'-f', '--frame', type=int, default=0
+)
+p.add_argument(
+'-z', '--z-stack', type=int, default=0
+)
+p.add_argument(
+'--skip-failed', action='store_true'
+)
+args = p.parse_args()
+if not args.image_ids:
+args.image_ids = sys.stdin.read().split()
+if 'center' in args:
+args.coord, args.width, args.height = (
+args.center[:2], args.center[2], args.center[3]
+)
+args.region_spec = 'center'
+del args.center
+elif 'rectangle' in args:
+args.coord, args.width, args.height = (
+args.rectangle[:2], args.rectangle[2], args.rectangle[3]
+)
+args.region_spec = 'rectangle'
+del args.rectangle
+download_image_data(**vars(args))

Mercurial > repos > iuc > idr_download_by_ids

comparison idr_download_by_ids.py @ 0:57aa9597cd31 draft