comparison idr_download_by_ids.py @ 11:cbd605a24336 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"

10:4aed70472589

import tarfile
from contextlib import ExitStack
from tempfile import TemporaryDirectory

from libtiff import TIFF
from omero.gateway import BlitzGateway  # noqa
from omero.constants.namespaces import NSBULKANNOTATIONS  # noqa


def warn(message, image_identifier, warn_skip=False):

    return selection


def download_image_data(
    image_ids_or_dataset_id, dataset=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
):

            if omero_username == "" or omero_password == "":
                omero_username = 'public'
                omero_password = 'public'

    if region_spec not in ['rectangle', 'center']:
        raise ValueError(
            'Got unknown value "{0}" as region_spec argument'
            .format(region_spec)
        )
    with ExitStack() as exit_stack:

                raise ValueError(
                    '{0}: Unable to find an image with this ID in the '
                    'database. Aborting!'
                    .format(image_warning_id)
                )

            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
                )

                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)
                    )

                ori_z, z_stack = z_stack, confine_plane(image, z_stack)
                ori_frame, frame = frame, confine_frame(image, frame)
                num_channels = image.getSizeC()
                if channel is None:
                    channel_index = 0
                else:
                    channel_index = find_channel_index(image, channel)
            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

            # 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 '
                    '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
                )

            # 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
                )

            # 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
                    )
            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.',
                            image_warning_id,
                            warn_skip=True
                        )
                        continue
                    else:
                        raise ValueError(
                            '"{0}" is not a known channel name for image {1}. '
                            'Aborting!'
                            .format(channel, image_warning_id)
                        )

            # 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)

                if download_tar:
                    fname = os.path.join(tempdir, fname)
                try:
                    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:
                if skip_failed:
                    # respect skip_failed on unexpected errors
                    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

        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(
        '-c', '--channel',
        help='name of the channel to retrieve data for '
             '(note: the first channel of each image will be downloaded if '
             'left unspecified)'
    )

11:cbd605a24336

import tarfile
from contextlib import ExitStack
from tempfile import TemporaryDirectory

from libtiff import TIFF
from omero.cli import cli_login
from omero.gateway import BlitzGateway  # noqa
from omero.constants.namespaces import NSBULKANNOTATIONS  # noqa


def warn(message, image_identifier, warn_skip=False):

    return selection


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
):

            if omero_username == "" or omero_password == "":
                omero_username = 'public'
                omero_password = 'public'

    if not download_original and region_spec not in ['rectangle', 'center']:
        raise ValueError(
            'Got unknown value "{0}" as region_spec argument'
            .format(region_spec)
        )
    with ExitStack() as exit_stack:

                raise ValueError(
                    '{0}: Unable to find an image with this ID in the '
                    'database. Aborting!'
                    .format(image_warning_id)
                )
            if not 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
                    )

                    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)
                        )

                    ori_z, z_stack = z_stack, confine_plane(image, z_stack)
                    ori_frame, frame = frame, confine_frame(image, frame)
                    num_channels = image.getSizeC()
                    if channel is None:
                        channel_index = 0
                    else:
                        channel_index = find_channel_index(image, channel)
                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

                # 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 '
                        '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
                    )

                # 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
                    )

                # 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
                        )
                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.',
                                image_warning_id,
                                warn_skip=True
                            )
                            continue
                        else:
                            raise ValueError(
                                '"{0}" is not a known channel name for image {1}. '
                                'Aborting!'
                                .format(channel, image_warning_id)
                            )

                # 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)

                    if download_tar:
                        fname = os.path.join(tempdir, fname)
                    try:
                        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:
                    if skip_failed:
                        # 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
                    # 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):
    if width > 0:
        ext_x = (width - 1) // 2

        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)'
    )