idr_download_by_ids: idr_download_by

comparison idr_download_by_ids.py @ 13:f92941d1a85e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f

author	iuc
date	Thu, 26 Sep 2024 12:32:17 +0000
parents	cbd605a24336
children

comparison

equal deleted inserted replaced

-:4b794652dcdc
+:f92941d1a85e
 import json
 import os
 import sys
 import tarfile
 from contextlib import ExitStack
+from itertools import product
 from tempfile import TemporaryDirectory
-from libtiff import TIFF
+import numpy
 from omero.cli import cli_login
-from omero.gateway import BlitzGateway  # noqa
+from omero.constants.namespaces import NSBULKANNOTATIONS
-from omero.constants.namespaces import NSBULKANNOTATIONS  # noqa
+from omero.gateway import _ImageWrapper, BlitzGateway
+from tifffile import imwrite
-def warn(message, image_identifier, warn_skip=False):
+def warn(message: str, image_identifier: str, warn_skip: bool = False) -> None:
+"""Print an error `message` to stderr and
+- prefix with the `image_identifier`
+- suffix with 'Skipping download!' if `warn_skip` is True
+Args:
+message (string): Message to print to stderr
+image_identifier (string): Image identifier
+warn_skip (bool, optional): Whether 'skipping download' should be suffix to the message. Defaults to False.
+"""
 message = message.rstrip()
 if warn_skip:
-if message[-1] in ['.', '!', '?']:
+if message[-1] in [".", "!", "?"]:
-skip_msg = ' Skipping download!'
+skip_msg = " Skipping download!"
 else:
-skip_msg = '. Skipping download!'
+skip_msg = ". Skipping download!"
 else:
-skip_msg = ''
+skip_msg = ""
 print(
-'ImageSpecWarning for {0}: {1}{2}'
+"ImageSpecWarning for {0}: {1}{2}".format(image_identifier, message, skip_msg),
-.format(
+file=sys.stderr,
-image_identifier,
+)
-message,
-skip_msg
-),
+def find_channel_index(image: _ImageWrapper, channel_name: str) -> int:
-file=sys.stderr
+"""Identify the channel index from the `image` and the `channel_name`
-)
+Args:
+image (_ImageWrapper): image wrapper on which the channel should be identified
-def find_channel_index(image, channel_name):
+channel_name (string): name of the channel to look for
+Returns:
+int: Index of the channel or -1 if was not found.
+"""
 channel_name = channel_name.lower()
 for n, channel in enumerate(image.getChannelLabels()):
 if channel_name == channel.lower():
 return n
 # Check map annotation for information (this is necessary for some images)
 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(':'):
+for value in c.split(":"):
 if channel_name == value.lower():
 return n
 return -1
-def get_clipping_region(image, x, y, w, h):
+def get_clipping_region(
+image: _ImageWrapper, x: int, y: int, w: int, h: int
+) -> list[int]:
+"""Check `x`, `y` and adjust `w`, `h` to image size to be able to crop the `image` with these coordinates
+Args:
+image (_ImageWrapper): image wrapper on which region want to be cropped
+x (int): left x coordinate
+y (int): top y coordinate
+w (int): width
+h (int): height
+Raises:
+ValueError: if the x or y coordinates are negative.
+ValueError: if the x or y coordinates are larger than the width or height of the image.
+Returns:
+list[int]: new [x, y, width, height] adjusted to the image
+"""
 # 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.'
+"Too small upper left coordinate ({0}, {1}) for clipping region.".format(
-.format(x, y)
+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 '
+"Upper left coordinate ({0}, {1}) of clipping region lies "
-'outside of image.'
+"outside of image.".format(x, y)
-.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):
+def confine_plane(image: _ImageWrapper, z: int) -> int:
+"""Adjust/Confine `z` to be among the possible z for the `image`
+Args:
+image (_ImageWrapper): image wrapper for which the z is adjusted
+z (int): plane index that need to be confined
+Returns:
+int: confined 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):
+def confine_frame(image: _ImageWrapper, t: int) -> int:
+"""Adjust/Confine `t` to be among the possible t for the `image`
+Args:
+image (_ImageWrapper): image wrapper for which the t is adjusted
+t (int): frame index that need to be confined
+Returns:
+int: confined t
+"""
 if t < 0:
 t = 0
 else:
 max_t = image.getSizeT() - 1
 if t > max_t:
 t = max_t
 return t
-def get_image_array(image, tile, z, c, t):
+def get_image_array(
+image: _ImageWrapper, tile: list[int], z: int, c: int, t: int
+) -> numpy.ndarray:
+"""Get a 2D numpy array from an `image` wrapper for a given `tile`, `z`, `c`, `t`
+Args:
+image (_ImageWrapper): image wrapper from which values are taken
+tile (list[int]): [x, y, width, height] where x,y is the top left coordinate of the region to crop
+z (int): plane index
+c (int): channel index
+t (int): frame index
+Returns:
+numpy.ndarray: image values of the selected area (2 dimensions)
+"""
 pixels = image.getPrimaryPixels()
 try:
 selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile)
 except Exception:
-warning = '{0} (ID: {1})'.format(image.getName(),
+warning = "{0} (ID: {1})".format(image.getName(), image.getId())
-image.getId())
+warn("Could not download the requested region", warning)
-warn('Could not download the requested region', warning)
 return
 return selection
+def get_full_image_array(image: _ImageWrapper) -> numpy.ndarray:
+"""Get a 5D numpy array with all values from an `image` wrapper
+Args:
+image (_ImageWrapper): image wrapper from which values are taken
+Returns:
+numpy.ndarray: image values in the TZCYX order (5 dimensions)
+"""
+# The goal is to get the image in TZCYX order
+pixels = image.getPrimaryPixels()
+# Get the final tzclist in the order that will make the numpy reshape work
+tzclist = list(
+product(
+range(image.getSizeT()), range(image.getSizeZ()), range(image.getSizeC())
+)
+)
+# As getPlanes requires the indices in the zct order
+# We keep the final order but switch indices
+zctlist = [(z, c, t) for (t, z, c) in tzclist]
+try:
+all_planes = numpy.array(list(pixels.getPlanes(zctlist)))
+all_planes_reshaped = all_planes.reshape(
+image.getSizeT(),
+image.getSizeZ(),
+image.getSizeC(),
+all_planes.shape[-2],
+all_planes.shape[-1],
+)
+except Exception as e:
+warning = "{0} (ID: {1})".format(image.getName(), image.getId())
+warn(f"Could not download the full image \n {e.msg}", warning)
+return
+return all_planes_reshaped
 def download_image_data(
-image_ids_or_dataset_id, dataset=False,
+image_ids_or_dataset_id: str,
-download_original=False,
+dataset: bool = False,
-channel=None, z_stack=0, frame=0,
+download_original: bool = False,
-coord=(0, 0), width=0, height=0, region_spec='rectangle',
+download_full: bool = False,
-skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None
+channel: str = None,
-):
+z_stack: int = 0,
+frame: int = 0,
+coord: tuple[int, int] = (0, 0),
+width: int = 0,
+height: int = 0,
+region_spec: str = "rectangle",
+skip_failed: bool = False,
+download_tar: bool = False,
+omero_host: str = "idr.openmicroscopy.org",
+omero_secured: bool = False,
+config_file: str = None,
+) -> None:
+"""Download the image data of
+either a list of image ids or all images from a dataset.
+The image data can be:
+- a 2D cropped region or
+- a hyperstack written in a tiff file
+- the original image uploaded in omero
+Optionally, the final file can be in a tar
+Args:
+image_ids_or_dataset_id (list[str]): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-'
+dataset (bool, optional): Whether the image_ids_or_dataset_id is a dataset id and all images from this dataset should be retrieved (true) or image_ids_or_dataset_id are individual image ids (false). Defaults to False.
+download_original (bool, optional): Whether the original file uploded to omero should be downloaded (ignored if `download_full` is set to True). Defaults to False.
+download_full (bool, optional): Whether the full image (hyperstack) on omero should be written to TIFF. Defaults to False.
+channel (string, optional): Channel name (ignored if `download_full` or `download_original` is set to True). Defaults to None.
+z_stack (int, optional): Z stack (plane) index (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
+frame (int, optional): T frame index (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
+coord (tuple[int, int], optional): Coordinates of the top left or center of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to (0, 0).
+width (int, optional): Width of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
+height (int, optional): Height of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
+region_spec (str, optional): How the region is specified ('rectangle' = coord is top left or 'center' = the region is center, ignored if `download_full` or `download_original` is set to True). Defaults to "rectangle".
+skip_failed (bool, optional): Do not stop the downloads if one fails. Defaults to False.
+download_tar (bool, optional): Put all downloaded images into a tar file. Defaults to False.
+omero_host (str, optional): omero host url. Defaults to "idr.openmicroscopy.org".
+omero_secured (bool, optional): Whether the omero connects with secure connection. Defaults to False.
+config_file (string, optional): File path with config file with credentials to connect to OMERO. Defaults to None.
+Raises:
+ValueError: If the region_spec is not 'rectangle' nor 'center' and a cropped region is wanted.
+ValueError: If there is no dataset with this number in OMERO
+ValueError: If there is no image with this number in OMERO
+Exception: If the command to download the original image fails
+ValueError: If the channel name could not be identified
+"""
 if config_file is None:  # IDR connection
-omero_username = 'public'
+omero_username = "public"
-omero_password = 'public'
+omero_password = "public"
 else:  # other omero instance
 with open(config_file) as f:
 cfg = json.load(f)
-omero_username = cfg['username']
+omero_username = cfg["username"]
-omero_password = cfg['password']
+omero_password = cfg["password"]
 if omero_username == "" or omero_password == "":
-omero_username = 'public'
+omero_username = "public"
-omero_password = 'public'
+omero_password = "public"
-if not download_original and region_spec not in ['rectangle', 'center']:
+if (
+not download_original
+and not download_full
+and region_spec not in ["rectangle", "center"]
+):
 raise ValueError(
-'Got unknown value "{0}" as region_spec argument'
+'Got unknown value "{0}" as region_spec argument'.format(region_spec)
-.format(region_spec)
 )
 with ExitStack() as exit_stack:
 conn = exit_stack.enter_context(
 BlitzGateway(
-omero_username, omero_password,
+omero_username, omero_password, host=omero_host, secure=omero_secured
-host=omero_host,
-secure=omero_secured
 )
 )
-# exit_stack.callback(conn.connect().close)
 if download_tar:
 # create an archive file to write images to
-archive = exit_stack.enter_context(
+archive = exit_stack.enter_context(tarfile.open("images.tar", mode="w"))
-tarfile.open('images.tar', mode='w')
+tempdir = exit_stack.enter_context(TemporaryDirectory())
-)
-tempdir = exit_stack.enter_context(
-TemporaryDirectory()
-)
 if dataset:
-dataset_warning_id = 'Dataset-ID: {0}'.format(image_ids_or_dataset_id[0])
+dataset_warning_id = "Dataset-ID: {0}".format(image_ids_or_dataset_id[0])
 try:
 dataset_id = int(image_ids_or_dataset_id[0])
 except ValueError:
 image_ids = None
 else:
 image_ids = [image.id for image in dataset.listChildren()]
 if image_ids is None:
 if skip_failed:
 warn(
-'Unable to find a dataset with this ID in the '
+"Unable to find a dataset with this ID in the " "database.",
-'database.',
 dataset_warning_id,
-warn_skip=True
+warn_skip=True,
 )
 else:
 raise ValueError(
-'{0}: Unable to find a dataset with this ID in the '
+"{0}: Unable to find a dataset with this ID in the "
-'database. Aborting!'
+"database. Aborting!".format(dataset_warning_id)
-.format(dataset_warning_id)
 )
 else:
 # basic argument sanity checks and adjustments
-prefix = 'image-'
+prefix = "image-"
 # normalize image ids by stripping off prefix if it exists
 image_ids = [
 iid[len(prefix):] if iid[:len(prefix)] == prefix else iid
 for iid in image_ids_or_dataset_id
 ]
 for image_id in image_ids:
-image_warning_id = 'Image-ID: {0}'.format(image_id)
+image_warning_id = "Image-ID: {0}".format(image_id)
 try:
 image_id = int(image_id)
 except ValueError:
 image = None
 else:
 raise
 if image is None:
 if skip_failed:
 warn(
-'Unable to find an image with this ID in the '
+"Unable to find an image with this ID in the database.",
-'database.',
 image_warning_id,
-warn_skip=True
+warn_skip=True,
 )
 continue
 raise ValueError(
-'{0}: Unable to find an image with this ID in the '
+"{0}: Unable to find an image with this ID in the "
-'database. Aborting!'
+"database. Aborting!".format(image_warning_id)
-.format(image_warning_id)
 )
-if not download_original:
+try:
+# try to extract image name
+# if anything goes wrong here skip the image
+# or abort.
+image_name = os.path.splitext(image.getName())[0]
+image_warning_id = "{0} (ID: {1})".format(image_name, image_id)
+except Exception as e:
+# respect skip_failed on unexpected errors
+if skip_failed:
+warn(str(e), image_warning_id, warn_skip=True)
+continue
+else:
+raise
+if download_full:
+fname = (
+"__".join([image_name.replace(" ", "_"), str(image_id), "full"])
++ ".tiff"
+)
+# download and save the region as TIFF
+try:
+im_array = get_full_image_array(image)
+if download_tar:
+fname = os.path.join(tempdir, fname)
+imwrite(fname, im_array, imagej=True)
+# move image into tarball
+if download_tar:
+archive.add(fname, os.path.basename(fname))
+os.remove(fname)
+except Exception as e:
+if skip_failed:
+# respect skip_failed on unexpected errors
+warn(str(e), image_warning_id, warn_skip=True)
+continue
+else:
+raise
+elif download_original:
 try:
 # try to extract image properties
 # if anything goes wrong here skip the image
 # or abort.
-image_name = os.path.splitext(image.getName())[0]
+original_image_name = image.getFileset().listFiles()[0].getName()
-image_warning_id = '{0} (ID: {1})'.format(
+fname = (
-image_name, image_id
+image_name
-)
++ "__"
++ str(image_id)
-if region_spec == 'rectangle':
++ os.path.splitext(original_image_name)[1]
+)
+fname = fname.replace(" ", "_")
+fname = fname.replace("/", "_")
+download_directory = "./"
+if download_tar:
+download_directory = tempdir
+with cli_login(
+"-u", omero_username, "-s", omero_host, "-w", omero_password
+) as cli:
+cli.invoke(
+["download", f"Image:{image_id}", download_directory]
+)
+if cli.rv != 0:
+raise Exception("Download failed.")
+# This will download to download_directory/original_image_name
+os.rename(
+os.path.join(download_directory, original_image_name),
+os.path.join(download_directory, fname),
+)
+# move image into tarball
+if download_tar:
+archive.add(
+os.path.join(download_directory, fname),
+os.path.basename(fname),
+)
+os.remove(os.path.join(download_directory, fname))
+except Exception as e:
+# respect skip_failed on unexpected errors
+if skip_failed:
+warn(str(e), image_warning_id, warn_skip=True)
+continue
+else:
+raise
+else:
+try:
+# try to extract image properties
+# if anything goes wrong here skip the image
+# or abort.
+if region_spec == "rectangle":
 tile = get_clipping_region(image, *coord, width, height)
-elif region_spec == 'center':
+elif region_spec == "center":
 tile = get_clipping_region(
-image,
+image, *_center_to_ul(*coord, width, height)
-*_center_to_ul(*coord, width, height)
 )
 ori_z, z_stack = z_stack, confine_plane(image, z_stack)
 ori_frame, frame = frame, confine_frame(image, frame)
 num_channels = image.getSizeC()
 # region sanity checks and warnings
 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 '
+"Downloaded image dimensions ({0} x {1}) will be smaller "
-'than the specified width and height ({2} x {3}).'
+"than the specified width and height ({2} x {3}).".format(
-.format(tile[2], tile[3], width, height),
+tile[2], tile[3], width, height
-image_warning_id
+),
+image_warning_id,
 )
 # z-stack sanity checks and warnings
 if z_stack != ori_z:
 warn(
-'Specified image plane ({0}) is out of bounds. Using {1} '
+"Specified image plane ({0}) is out of bounds. Using {1} "
-'instead.'
+"instead.".format(ori_z, z_stack),
-.format(ori_z, z_stack),
+image_warning_id,
-image_warning_id
 )
 # frame sanity checks and warnings
 if frame != ori_frame:
 warn(
-'Specified image frame ({0}) is out of bounds. Using '
+"Specified image frame ({0}) is out of bounds. Using "
-'frame {1} instead.'
+"frame {1} instead.".format(ori_frame, frame),
-.format(ori_frame, frame),
+image_warning_id,
-image_warning_id
 )
 # channel index sanity checks and warnings
 if channel is None:
 if num_channels > 1:
 warn(
-'No specific channel selected for multi-channel '
+"No specific channel selected for multi-channel "
-'image. Using first of {0} channels.'
+"image. Using first of {0} channels.".format(num_channels),
-.format(num_channels),
+image_warning_id,
-image_warning_id
 )
 else:
 if channel_index == -1 or channel_index >= num_channels:
 if skip_failed:
 warn(
 str(channel)
-+ ' is not a known channel name for this image.',
++ " is not a known channel name for this image.",
 image_warning_id,
-warn_skip=True
+warn_skip=True,
 )
 continue
 else:
 raise ValueError(
 '"{0}" is not a known channel name for image {1}. '
-'Aborting!'
+"Aborting!".format(channel, image_warning_id)
-.format(channel, image_warning_id)
 )
+fname = "__".join([image_name, str(image_id)] + [str(x) for x in tile])
+fname += ".tiff"
+fname = fname.replace(" ", "_")
 # download and save the region as TIFF
-fname = '__'.join(
-[image_name, str(image_id)] + [str(x) for x in tile]
-)
 try:
-if fname[-5:] != '.tiff':
+im_array = get_image_array(
-fname += '.tiff'
+image, tile, z_stack, channel_index, frame
+)
-fname = fname.replace(' ', '_')
-im_array = get_image_array(image, tile, z_stack, channel_index, frame)
 if download_tar:
 fname = os.path.join(tempdir, fname)
-try:
+imwrite(fname, im_array)
-tiff = TIFF.open(fname, mode='w')
-tiff.write_image(im_array)
-finally:
-tiff.close()
 # move image into tarball
 if download_tar:
 archive.add(fname, os.path.basename(fname))
 os.remove(fname)
 except Exception as e:
 # respect skip_failed on unexpected errors
 warn(str(e), image_warning_id, warn_skip=True)
 continue
 else:
 raise
-else:
-try:
-# try to extract image properties
+def _center_to_ul(center_x: int, center_y: int, width: int, height: int) -> list[int]:
-# if anything goes wrong here skip the image
+"""Convert the center coordinates (`center_x`, `center_y`), `width`, `height` to upper left coordinates, width, height
-# or abort.
-image_name = os.path.splitext(image.getName())[0]
+Args:
-image_warning_id = '{0} (ID: {1})'.format(
+center_x (int): x coordinate of center
-image_name, image_id
+center_y (int): y coordinate of center
-)
+width (int): width
-original_image_name = image.getFileset().listFiles()[0].getName()
+height (int): height
-fname = image_name + "__" + str(image_id) + os.path.splitext(original_image_name)[1]
-fname = fname.replace(' ', '_')
+Returns:
-fname = fname.replace('/', '_')
+list[int]: [x, y, width, height] where x,y are the upper left coordinates
-download_directory = "./"
+"""
-if download_tar:
-download_directory = tempdir
-with cli_login("-u", omero_username, "-s", omero_host, "-w", omero_password) as cli:
-cli.invoke(["download", f"Image:{image_id}", download_directory])
-if cli.rv != 0:
-raise Exception("Download failed.")
-# This will download to download_directory/original_image_name
-os.rename(os.path.join(download_directory, original_image_name),
-os.path.join(download_directory, fname))
-# move image into tarball
-if download_tar:
-archive.add(os.path.join(download_directory, fname),
-os.path.basename(fname))
-os.remove(os.path.join(download_directory, fname))
-except Exception as e:
-# respect skip_failed on unexpected errors
-if skip_failed:
-warn(str(e), image_warning_id, warn_skip=True)
-continue
-else:
-raise
-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:
 if __name__ == "__main__":
 p = argparse.ArgumentParser()
 p.add_argument(
-'image_ids_or_dataset_id', nargs='*', default=[],
+"image_ids_or_dataset_id",
-help='one or more IDR image ids or a single dataset id'
+nargs="*",
-'for which to retrieve data (default: '
+default=[],
-'read ids from stdin).'
+help="one or more IDR image ids or a single dataset id"
-)
+"for which to retrieve data (default: "
-p.add_argument(
+"read ids from stdin).",
-'--download-original', dest='download_original', action='store_true',
-help="download the original file uploaded to omero"
-)
-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,
+"--rectangle",
-help='specify a clipping region for the image as x y width height, '
+nargs=4,
-'where x and y give the upper left coordinate of the rectangle '
+type=int,
-'to clip to. Set width and height to 0 to extend the rectangle '
+default=argparse.SUPPRESS,
-'to the actual size of the image.'
+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,
+"--center",
-help='specify a clipping region for the image as x y width height, '
+nargs=4,
-'where x and y define the center of a width x height rectangle. '
+type=int,
-'Set either width or height to 0 to extend the region to the '
+default=argparse.SUPPRESS,
-'actual size of the image along the x- or y-axis.\n'
+help="specify a clipping region for the image as x y width height, "
-'Note: Even values for width and height will be rounded down to '
+"where x and y define the center of a width x height rectangle. "
-'the nearest odd number.'
+"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.",
+)
+region.add_argument(
+"--download-original",
+dest="download_original",
+action="store_true",
+help="download the original file uploaded to omero",
+)
+region.add_argument(
+"--download-full",
+dest="download_full",
+action="store_true",
+help="download the full image on omero",
 )
 p.add_argument(
-'-f', '--frame', type=int, default=0
+"-c",
+"--channel",
+help="name of the channel to retrieve data for "
+"(note: the first channel of each image will be downloaded if "
+"left unspecified), ignored with `--download-original` and "
+"`--download-full`",
 )
 p.add_argument(
-'-z', '--z-stack', type=int, default=0
+"-f",
+"--frame",
+type=int,
+default=0,
+help="index of the frame to retrive data for (first frame is 0),"
+" ignored with `--download-original` and `--download-full`",
 )
 p.add_argument(
-'--skip-failed', action='store_true'
+"-z",
-)
+"--z-stack",
-p.add_argument(
+type=int,
-'--download-tar', action='store_true'
+default=0,
-)
+help="index of the slice to retrive data for (first slice is 0),"
-p.add_argument(
+" ignored with `--download-original` and `--download-full`",
-'-oh', '--omero-host', type=str, default="idr.openmicroscopy.org"
+)
-)
+p.add_argument("--skip-failed", action="store_true")
-p.add_argument(
+p.add_argument("--download-tar", action="store_true")
-'--omero-secured', action='store_true', default=True
+p.add_argument("-oh", "--omero-host", type=str, default="idr.openmicroscopy.org")
-)
+p.add_argument("--omero-secured", action="store_true", default=True)
-p.add_argument(
+p.add_argument("-cf", "--config-file", dest="config_file", default=None)
-'-cf', '--config-file', dest='config_file', default=None
+p.add_argument("--dataset", action="store_true")
-)
-p.add_argument(
-'--dataset', action='store_true'
-)
 args = p.parse_args()
 if not args.image_ids_or_dataset_id:
 args.image_ids_or_dataset_id = sys.stdin.read().split()
 if args.dataset and len(args.image_ids_or_dataset_id) > 1:
 warn("Multiple dataset ids provided. Only the first one will be used.")
-if 'center' in args:
+if "center" in args:
 args.coord, args.width, args.height = (
-args.center[:2], args.center[2], args.center[3]
+args.center[:2],
-)
+args.center[2],
-args.region_spec = 'center'
+args.center[3],
+)
+args.region_spec = "center"
 del args.center
-elif 'rectangle' in args:
+elif "rectangle" in args:
 args.coord, args.width, args.height = (
-args.rectangle[:2], args.rectangle[2], args.rectangle[3]
+args.rectangle[:2],
-)
+args.rectangle[2],
-args.region_spec = 'rectangle'
+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 @ 13:f92941d1a85e draft default tip