Source code for large_image_tasks.tasks

import logging
import os
import shutil
import sys
import time

from import app
from girder_worker.utils import girder_job

@girder_job(title='Create a pyramidal tiff using vips', type='large_image_tiff')
def create_tiff(self, inputFile, outputName=None, outputDir=None, quality=90,
                tileSize=256, **kwargs):
    Take a source input file, readable by vips, and output a pyramidal tiff

    :param inputFile: the path to the input file or base file of a set.
    :param outputName: the name of the output file.  If None, the name is
        based on the input name and current date and time.  May be a full path.
    :param outputDir: the location to store the output.  If unspecified, the
        inputFile's directory is used.  If the outputName is a fully qualified
        path, this is ignored.
    :param quality: a jpeg quality passed to vips.  0 is small, 100 is high
        quality.  90 or above is recommended.
    :param tileSize: the horizontal and vertical tile size.
    Optional parameters that can be specified in kwargs:
    :param compression: one of 'jpeg', 'deflate' (zip), 'lzw', 'packbits', or
    :param level: compression level for zstd, 1-22 (default is 10).
    :param predictor: one of 'none', 'horizontal', or 'float' used for lzw and
    :param inputName: if no output name is specified, and this is specified,
        this is used as the basis of the output name instead of extracting the
        name from the inputFile path.
    :returns: output path.
    import large_image_converter

    logger = logging.getLogger('large-image-converter')
    if not len(logger.handlers):
    if not logger.level:

    if '_concurrency' not in kwargs:
        kwargs['_concurrency'] = -2
    inputPath = os.path.abspath(os.path.expanduser(inputFile))
    geospatial = large_image_converter.is_geospatial(inputPath)
    inputName = kwargs.get('inputName', os.path.basename(inputPath))
    suffix = large_image_converter.format_hook('adjust_params', geospatial, kwargs, **kwargs)
    suffix = suffix or ('.tiff' if not geospatial else '.geo.tiff')
    if not outputName:
        outputName = os.path.splitext(inputName)[0] + suffix
        if outputName.endswith('.geo' + suffix):
            outputName = outputName[:len(outputName) - len(suffix) - 4] + suffix
        if outputName == inputName:
            outputName = (os.path.splitext(inputName)[0] + '.' +
                          time.strftime('%Y%m%d-%H%M%S') + suffix)
    renameOutput = outputName
    if not outputName.endswith(suffix):
        outputName += suffix
    if not outputDir:
        outputDir = os.path.dirname(inputPath)
    outputPath = os.path.join(outputDir, outputName)
        inputPath, outputPath, quality=quality, tileSize=tileSize, **kwargs)
    if not os.path.exists(outputPath):
        raise Exception('Conversion command failed to produce output')
    if renameOutput != outputName:
        renamePath = os.path.join(outputDir, renameOutput)
        shutil.move(outputPath, renamePath)
        outputPath = renamePath'Created a file of size %d' % os.path.getsize(outputPath))
    return outputPath

[docs]class JobLogger(logging.Handler): def __init__(self, level=logging.NOTSET, job=None, *args, **kwargs): self._job = job super().__init__(level=level, *args, **kwargs)
[docs] def emit(self, record): from girder_jobs.models.job import Job self._job = Job().updateJob(self._job, log=self.format(record).rstrip() + '\n')
[docs]def convert_image_job(job): import tempfile from girder_jobs.constants import JobStatus from girder_jobs.models.job import Job from girder.constants import AccessType from girder.models.file import File from girder.models.folder import Folder from girder.models.item import Item from girder.models.upload import Upload from girder.models.user import User kwargs = job['kwargs'] item = Item().load(kwargs.pop('itemId'), force=True) fileObj = File().load(kwargs.pop('fileId'), force=True) userId = kwargs.pop('userId', None) user = User().load(userId, force=True) if userId else None folder = Folder().load(kwargs.pop('folderId', item['folderId']), user=user, level=AccessType.WRITE) name = kwargs.pop('name', None) job = Job().updateJob( job, log='Started large image conversion\n', status=JobStatus.RUNNING) logger = logging.getLogger('large-image-converter') handler = JobLogger(job=job) logger.addHandler(handler) # We could increase the default logging level here # logger.setLevel(logging.DEBUG) try: inputPath = None if not fileObj.get('imported'): try: inputPath = File().getGirderMountFilePath(fileObj) except Exception: pass inputPath = inputPath or File().getLocalFilePath(fileObj) with tempfile.TemporaryDirectory() as tempdir: dest = create_tiff( inputFile=inputPath, inputName=fileObj['name'], outputDir=tempdir, **kwargs, ) job = Job().updateJob(job, log='Storing result\n') with open(dest, 'rb') as fobj: fileObj = Upload().uploadFromFile( fobj, size=os.path.getsize(dest), name=name or os.path.basename(dest), parentType='folder', parent=folder, user=user, ) job = Job().load(job['_id'], force=True) job.setdefault('results', {}) job['results'].setdefault('file', []) job['results']['file'].append(fileObj['_id']) job = Job().save(job) except Exception as exc: status = JobStatus.ERROR logger.exception('Failed in large image conversion') job = Job().updateJob( job, log='Failed in large image conversion (%s)\n' % exc, status=status) else: status = JobStatus.SUCCESS job = Job().updateJob( job, log='Finished large image conversion\n', status=status) finally: logger.removeHandler(handler)
[docs]def cache_tile_frames_job(job): from girder_jobs.constants import JobStatus from girder_jobs.models.job import Job from girder_large_image.models.image_item import ImageItem from girder import logger kwargs = job['kwargs'] item = ImageItem().load(kwargs.pop('itemId'), force=True) job = Job().updateJob( job, log='Started caching tile frames\n', status=JobStatus.RUNNING) try: for entry in kwargs.get('tileFramesList'): job = Job().load(job['_id'], force=True) if job['status'] == JobStatus.CANCELED: return job = Job().updateJob(job, log='Caching %r\n' % entry) ImageItem().tileFrames(item, checkAndCreate=True, **entry) job = Job().updateJob(job, log='Finished caching tile frames\n', status=JobStatus.SUCCESS) except Exception as exc: logger.exception('Failed caching tile frames') job = Job().updateJob( job, log='Failed caching tile frames (%s)\n' % exc, status=JobStatus.ERROR)