comparison idr_download_by_ids.py @ 4:11036f6197d6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"

3:381f248febba

import argparse
import os
import sys

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):

        if t > max_t:
            t = max_t
    return t


def download_plane_as_tiff(image, tile, z, c, t, fname):
    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)
        return

    if fname[-5:] != '.tiff':
        fname += '.tiff'
    try:
        fname = fname.replace(' ', '_')
        tiff = TIFF.open(fname, mode='w')
        tiff.write_image(selection)
    finally:
        tiff.close()


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
):
    # basic argument sanity checks and adjustments
    prefix = 'image-'
    # normalize image ids by stripping off prefix if it exists
    image_ids = [

    # connect to idr
    conn = BlitzGateway('public', 'public',
                        host='idr.openmicroscopy.org',
                        secure=True)
    conn.connect()

    try:
        for image_id in image_ids:
            image_warning_id = 'Image-ID: {0}'.format(image_id)
            try:

            # download and save the region as TIFF
            fname = '__'.join(
                [image_name, str(image_id)] + [str(x) for x in tile]
            )
            try:
                download_plane_as_tiff(image, tile, z_stack, channel_index, frame, 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
    finally:
        # Close the connection
        conn.close()


def _center_to_ul(center_x, center_y, width, height):

        '-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 = (

4:11036f6197d6

import argparse
import os
import sys
import tarfile

from libtiff import TIFF
from PIL import Image
from tempfile import TemporaryFile
from omero.gateway import BlitzGateway  # noqa
from omero.constants.namespaces import NSBULKANNOTATIONS  # noqa


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

        if t > max_t:
            t = max_t
    return t


def get_image_array(image, tile, z, c, t):
    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)
        return

    return 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, download_tar=False
):
    # basic argument sanity checks and adjustments
    prefix = 'image-'
    # normalize image ids by stripping off prefix if it exists
    image_ids = [

    # connect to idr
    conn = BlitzGateway('public', 'public',
                        host='idr.openmicroscopy.org',
                        secure=True)
    conn.connect()

    if download_tar:
        # create an archive file to write images to
        archive = tarfile.open('images.tar', mode='w')

    try:
        for image_id in image_ids:
            image_warning_id = 'Image-ID: {0}'.format(image_id)
            try:

            # 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)

                # pack images into tarball
                if download_tar:
                    tar_img = Image.fromarray(im_array)
                    # Use TemporaryFile() for intermediate storage of images.
                    # TO DO: could this be improved by using
                    # SpooledTemporaryFile with a suitable max_size?
                    with TemporaryFile() as buf:
                        tar_img.save(buf, format='TIFF')
                        tarinfo = tarfile.TarInfo(name=fname)
                        buf.seek(0, 2)
                        tarinfo.size = buf.tell()
                        buf.seek(0)
                        archive.addfile(tarinfo=tarinfo, fileobj=buf)
                else:  # save image as individual file
                    try:
                        tiff = TIFF.open(fname, mode='w')
                        tiff.write_image(im_array)
                    finally:
                        tiff.close()
            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

    finally:
        # close the archive file,if it is created
        if download_tar:
            archive.close()
        # Close the connection
        conn.close()


def _center_to_ul(center_x, center_y, width, height):

        '-z', '--z-stack', type=int, default=0
    )
    p.add_argument(
        '--skip-failed', action='store_true'
    )
    p.add_argument(
        '--download-tar', 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 = (