Mercurial > repos > iuc > idr_download_by_ids
changeset 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 | 4b794652dcdc |
| children | |
| files | idr_download_by_ids.py idr_download_by_ids.xml |
| diffstat | 2 files changed, 475 insertions(+), 223 deletions(-) [+] |
line wrap: on
line diff
--- a/idr_download_by_ids.py Wed Nov 08 12:57:25 2023 +0000 +++ b/idr_download_by_ids.py Thu Sep 26 12:32:17 2024 +0000 @@ -4,35 +4,50 @@ 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 # noqa +from omero.constants.namespaces import NSBULKANNOTATIONS +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 ['.', '!', '?']: - skip_msg = ' Skipping download!' + if message[-1] in [".", "!", "?"]: + skip_msg = " Skipping download!" else: - skip_msg = '. Skipping download!' + skip_msg = ". Skipping download!" else: - skip_msg = '' + skip_msg = "" print( - 'ImageSpecWarning for {0}: {1}{2}' - .format( - image_identifier, - message, - skip_msg - ), - file=sys.stderr + "ImageSpecWarning for {0}: {1}{2}".format(image_identifier, message, skip_msg), + file=sys.stderr, ) -def find_channel_index(image, channel_name): +def find_channel_index(image: _ImageWrapper, channel_name: str) -> int: + """Identify the channel index from the `image` and the `channel_name` + + Args: + image (_ImageWrapper): image wrapper on which the channel should be identified + 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(): @@ -44,13 +59,31 @@ 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 @@ -58,16 +91,16 @@ # 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) + "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) + "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: @@ -77,7 +110,16 @@ 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: @@ -87,7 +129,16 @@ 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: @@ -97,65 +148,155 @@ 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(), - image.getId()) - warn('Could not download the requested region', warning) + warning = "{0} (ID: {1})".format(image.getName(), image.getId()) + 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, - download_original=False, - channel=None, z_stack=0, frame=0, - coord=(0, 0), width=0, height=0, region_spec='rectangle', - skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None -): + image_ids_or_dataset_id: str, + dataset: bool = False, + download_original: bool = False, + download_full: bool = False, + 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_password = 'public' + omero_username = "public" + omero_password = "public" else: # other omero instance with open(config_file) as f: cfg = json.load(f) - omero_username = cfg['username'] - omero_password = cfg['password'] + omero_username = cfg["username"] + omero_password = cfg["password"] if omero_username == "" or omero_password == "": - omero_username = 'public' - omero_password = 'public' + omero_username = "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' - .format(region_spec) + 'Got unknown value "{0}" as region_spec argument'.format(region_spec) ) with ExitStack() as exit_stack: conn = exit_stack.enter_context( BlitzGateway( - omero_username, omero_password, - host=omero_host, - secure=omero_secured + omero_username, omero_password, 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( - tarfile.open('images.tar', mode='w') - ) - tempdir = exit_stack.enter_context( - TemporaryDirectory() - ) + archive = exit_stack.enter_context(tarfile.open("images.tar", mode="w")) + 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: @@ -175,28 +316,26 @@ if image_ids is None: if skip_failed: warn( - 'Unable to find a dataset with this ID in the ' - 'database.', + "Unable to find a dataset with this ID in the " "database.", dataset_warning_id, - warn_skip=True + warn_skip=True, ) else: raise ValueError( - '{0}: Unable to find a dataset with this ID in the ' - 'database. Aborting!' - .format(dataset_warning_id) + "{0}: Unable to find a dataset with this ID in the " + "database. Aborting!".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: @@ -215,33 +354,106 @@ if image is None: if skip_failed: warn( - 'Unable to find an image with this ID in the ' - 'database.', + "Unable to find an image with this ID in the database.", image_warning_id, - warn_skip=True + warn_skip=True, ) continue raise ValueError( - '{0}: Unable to find an image with this ID in the ' - 'database. Aborting!' - .format(image_warning_id) + "{0}: Unable to find an image with this ID in the " + "database. Aborting!".format(image_warning_id) + ) + 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" ) - if not download_original: + # 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] - image_warning_id = '{0} (ID: {1})'.format( - image_name, image_id + original_image_name = image.getFileset().listFiles()[0].getName() + fname = ( + image_name + + "__" + + str(image_id) + + 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), ) - - if region_spec == 'rectangle': + # 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, - *_center_to_ul(*coord, width, height) + image, *_center_to_ul(*coord, width, height) ) ori_z, z_stack = z_stack, confine_plane(image, z_stack) @@ -264,75 +476,65 @@ # 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 + "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, ) # z-stack sanity checks and warnings 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 + "Specified image plane ({0}) is out of bounds. Using {1} " + "instead.".format(ori_z, z_stack), + image_warning_id, ) # frame sanity checks and warnings if frame != ori_frame: warn( - 'Specified image frame ({0}) is out of bounds. Using ' - 'frame {1} instead.' - .format(ori_frame, frame), - image_warning_id + "Specified image frame ({0}) is out of bounds. Using " + "frame {1} instead.".format(ori_frame, frame), + 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 ' - 'image. Using first of {0} channels.' - .format(num_channels), - image_warning_id + "No specific channel selected for multi-channel " + "image. Using first of {0} channels.".format(num_channels), + 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!' - .format(channel, image_warning_id) + "Aborting!".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': - fname += '.tiff' - - fname = fname.replace(' ', '_') - - im_array = get_image_array(image, tile, z_stack, channel_index, frame) + im_array = get_image_array( + image, tile, z_stack, channel_index, frame + ) if download_tar: fname = os.path.join(tempdir, fname) - try: - tiff = TIFF.open(fname, mode='w') - tiff.write_image(im_array) - finally: - tiff.close() + imwrite(fname, im_array) # move image into tarball if download_tar: archive.add(fname, os.path.basename(fname)) @@ -344,44 +546,20 @@ continue else: raise - else: - try: - # try to extract image properties - # 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 - ) - original_image_name = image.getFileset().listFiles()[0].getName() - fname = image_name + "__" + str(image_id) + 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 -def _center_to_ul(center_x, center_y, width, height): +def _center_to_ul(center_x: int, center_y: int, width: int, height: int) -> list[int]: + """Convert the center coordinates (`center_x`, `center_y`), `width`, `height` to upper left coordinates, width, height + + Args: + center_x (int): x coordinate of center + center_y (int): y coordinate of center + width (int): width + height (int): height + + Returns: + list[int]: [x, y, width, height] where x,y are the upper left coordinates + """ if width > 0: ext_x = (width - 1) // 2 ul_x = max([center_x - ext_x, 0]) @@ -400,77 +578,97 @@ if __name__ == "__main__": p = argparse.ArgumentParser() p.add_argument( - 'image_ids_or_dataset_id', nargs='*', default=[], - help='one or more IDR image ids or a single dataset id' - 'for which to retrieve data (default: ' - 'read ids from stdin).' - ) - p.add_argument( - '--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)' + "image_ids_or_dataset_id", + nargs="*", + default=[], + help="one or more IDR image ids or a single dataset id" + "for which to retrieve data (default: " + "read ids from stdin).", ) 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.' + "--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.' + "--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 + 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( - '-z', '--z-stack', type=int, default=0 - ) - p.add_argument( - '--skip-failed', action='store_true' - ) - p.add_argument( - '--download-tar', action='store_true' + "-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( - '-oh', '--omero-host', type=str, default="idr.openmicroscopy.org" - ) - p.add_argument( - '--omero-secured', action='store_true', default=True + "-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( - '-cf', '--config-file', dest='config_file', default=None + "-z", + "--z-stack", + type=int, + default=0, + help="index of the slice to retrive data for (first slice is 0)," + " ignored with `--download-original` and `--download-full`", ) - p.add_argument( - '--dataset', action='store_true' - ) + p.add_argument("--skip-failed", action="store_true") + p.add_argument("--download-tar", action="store_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("-cf", "--config-file", dest="config_file", default=None) + 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.center[3], ) - args.region_spec = 'center' + 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.rectangle[3], ) - args.region_spec = 'rectangle' + args.region_spec = "rectangle" del args.rectangle download_image_data(**vars(args))
--- a/idr_download_by_ids.xml Wed Nov 08 12:57:25 2023 +0000 +++ b/idr_download_by_ids.xml Thu Sep 26 12:32:17 2024 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.44.1" profile="18.09"> +<tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.45" profile="18.09"> <description></description> <macros> <xml name="region_spec" token_pos="upper-left corner"> @@ -19,8 +19,8 @@ <edam_operation>operation_3443</edam_operation> </edam_operations> <requirements> - <requirement type="package" version="5.10.1">omero-py</requirement> - <requirement type="package" version="0.4.2">pylibtiff</requirement> + <requirement type="package" version="5.19.4">omero-py</requirement> + <requirement type="package" version="2024.9.20">tifffile</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -51,6 +51,8 @@ #end if #if $image_region.original == "original": --download-original + #elif $image_region.original == "full": + --download-full #else: #set $channel = str($image_region.channel).strip() #if $channel: @@ -87,7 +89,7 @@ } ]]></configfile> </configfiles> -<inputs> + <inputs> <conditional name="omero_instance_type"> <param name="omero_instance" type="select" label="Which OMERO instance to connect?" help="By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you @@ -135,9 +137,11 @@ <conditional name="image_region"> <param name="original" type="select" label="Which images do you want to download?"> <option value="TIFF" selected="true">Exported TIFF (single channel, single stack)</option> + <option value="full">Whole TIFF (all channels, all frames, all stacks)</option> <option value="original">Original file (file uploaded to omero, only available for private instances)</option> </param> <when value="original"/> + <when value="full"/> <when value="TIFF"> <param name="channel" type="text" label="Name of the channel to download" @@ -182,7 +186,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="2"> <conditional name="omero_instance_type"> <param name="omero_instance" value="idr" /> </conditional> @@ -202,10 +206,10 @@ </conditional> <param name="download_tar" value="false" /> <output_collection name="output_file" type="list"> - <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff"/> + <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff" compare="image_diff" /> </output_collection> </test> - <test> + <test expect_num_outputs="2"> <conditional name="omero_instance_type"> <param name="omero_instance" value="idr" /> </conditional> @@ -225,10 +229,10 @@ </conditional> <param name="download_tar" value="false" /> <output_collection name="output_file" type="list"> - <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff"/> + <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff" compare="image_diff"/> </output_collection> </test> - <test> + <test expect_num_outputs="2"> <conditional name="omero_instance_type"> <param name="omero_instance" value="idr" /> </conditional> @@ -248,10 +252,10 @@ </conditional> <param name="download_tar" value="false" /> <output_collection name="output_file" type="list"> - <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test2.tiff"/> + <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test2.tiff" compare="image_diff"/> </output_collection> </test> - <test> + <test expect_num_outputs="2"> <conditional name="omero_instance_type"> <param name="omero_instance" value="idr" /> </conditional> @@ -270,7 +274,11 @@ <output_collection name="output_file" type="list" count="3"> <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024"> <assert_contents> - <has_size value="2097286" /> + <has_size size="2097286" /> + <has_image_width width="1024" /> + <has_image_height height="1024" /> + <has_image_mean_intensity mean_intensity="320.868" /> + <has_image_center_of_mass center_of_mass="541.664, 456.743" /> </assert_contents> </element> </output_collection> @@ -299,7 +307,7 @@ </conditional> <param name="download_tar" value="false" /> </test> - <test> + <test expect_num_outputs="2"> <!-- Repeat test with non-existing image-ID 9036708999, but use skip-failed option --> <conditional name="omero_instance_type"> @@ -321,7 +329,11 @@ <output_collection name="output_file" type="list" count="2"> <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024"> <assert_contents> - <has_size value="2097286" /> + <has_size size="2097286" /> + <has_image_width width="1024" /> + <has_image_height height="1024" /> + <has_image_mean_intensity mean_intensity="320.868" /> + <has_image_center_of_mass center_of_mass="541.664, 456.743" /> </assert_contents> </element> </output_collection> @@ -333,7 +345,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="2"> <conditional name="omero_instance_type"> <param name="omero_instance" value="idr" /> </conditional> @@ -354,17 +366,25 @@ </conditional> <output name="output_tar"> <assert_contents> - <has_size value="1382400" /> + <has_size size="1382400" /> <has_archive_member path=".*/*__1828167__0__0__671__511.tiff" > - <has_size value="685896" /> + <has_size size="685896" /> + <has_image_width width="671" /> + <has_image_height height="511" /> + <has_image_mean_intensity mean_intensity="388.711" /> + <has_image_center_of_mass center_of_mass="354.627, 267" /> </has_archive_member> <has_archive_member path=".*/*__1828658__0__0__671__511.tiff" > - <has_size value="685896" /> + <has_size size="685896" /> + <has_image_width width="671" /> + <has_image_height height="511" /> + <has_image_mean_intensity mean_intensity="397.507" /> + <has_image_center_of_mass center_of_mass="346.098, 250.652" /> </has_archive_member> </assert_contents> </output> </test> - <test> + <test expect_num_outputs="2"> <conditional name="omero_instance_type"> <param name="omero_instance" value="priv" /> <param name="omero_host" value="idr.openmicroscopy.org" /> @@ -387,7 +407,7 @@ </conditional> <param name="download_tar" value="false" /> <output_collection name="output_file" type="list"> - <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff"/> + <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff" compare="image_diff"/> </output_collection> </test> <test expect_failure="true"> @@ -415,7 +435,7 @@ <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" /> </assert_stderr > </test> - <test> + <test expect_num_outputs="2"> <conditional name="omero_instance_type"> <param name="omero_instance" value="idr" /> </conditional> @@ -426,27 +446,43 @@ <output_collection name="output_file" type="list" count="4"> <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024"> <assert_contents> - <has_size value="2097286" /> + <has_size size="2097286" /> + <has_image_width width="1024" /> + <has_image_height height="1024" /> + <has_image_mean_intensity mean_intensity="145.310" /> + <has_image_center_of_mass center_of_mass="527.499, 480.704" /> </assert_contents> </element> <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D__9036708__0__0__1024__1024"> <assert_contents> - <has_size value="2097286" /> + <has_size size="2097286" /> + <has_image_width width="1024" /> + <has_image_height height="1024" /> + <has_image_mean_intensity mean_intensity="147.025" /> + <has_image_center_of_mass center_of_mass="528.977, 480.691" /> </assert_contents> </element> <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D_zproj__9036710__0__0__1024__1024"> <assert_contents> - <has_size value="2097286" /> + <has_size size="2097286" /> + <has_image_width width="1024" /> + <has_image_height height="1024" /> + <has_image_mean_intensity mean_intensity="210.787" /> + <has_image_center_of_mass center_of_mass="534.629, 473.267" /> </assert_contents> </element> <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_REF__9036709__0__0__1024__1024"> <assert_contents> - <has_size value="2097286" /> + <has_size size="2097286" /> + <has_image_width width="1024" /> + <has_image_height height="1024" /> + <has_image_mean_intensity mean_intensity="3816.051" /> + <has_image_center_of_mass center_of_mass="512.274, 503.186" /> </assert_contents> </element> </output_collection> </test> - <test> + <test expect_num_outputs="2"> <conditional name="omero_instance_type"> <param name="omero_instance" value="idr" /> </conditional> @@ -462,6 +498,24 @@ <output_collection name="output_file" type="list" count="0"> </output_collection> </test> + <test expect_num_outputs="2"> + <conditional name="omero_instance_type"> + <param name="omero_instance" value="idr" /> + </conditional> + <param name="source" value="link" /> + <param name="id_spec" value="1229801" /> + <param name="download_tar" value="false" /> + <conditional name="image_region"> + <param name="original" value="full"/> + </conditional> + <output_collection name="output_file" type="list" count="1"> + <element name="JL_120731_S6A_[Well_A-1;_Field_#1]__1229801__full"> + <assert_contents> + <has_size size="91592058" /> + </assert_contents> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ Download image data from the IDR_ (Image Data Resource) - a public repository