def runInpainting(self, image, mask, folder):
basename = os.path.splitext(image['name'])[0]
outPath = VolumePath(basename + '_result.jpg')
artifactPath = VolumePath('job_artifacts')
job = docker_run.delay(
'zachmullen/inpainting:latest',
container_args=[
GirderFileIdToVolume(image['_id']),
GirderFileIdToVolume(mask['_id']), outPath, '--artifacts-dir',
artifactPath, '--progress-pipe',
ProgressPipe()
],
girder_job_title='Inpainting: %s' % image['name'],
girder_result_hooks=[
GirderUploadVolumePathToFolder(outPath,
folder['_id'],
upload_kwargs={
'reference':
json.dumps({
'inpaintedImage':
True,
'folderId':
str(folder['_id']),
})
}),
# GirderUploadVolumePathJobArtifact(artifactPath)
]).job
folder['inpaintingJobId'] = job['_id']
Folder().save(folder)
job['inpaintingImageId'] = image['_id']
job['inpaintingMaskId'] = mask['_id']
job['inpaintingFolderId'] = folder['_id']
return Job().save(job)
def run_albany(self, params):
"""Run albany on a folder that is on girder.
Will store the output in the specified output folder.
"""
inputFolderId = params.get('inputFolderId')
outputFolderId = params.get('outputFolderId')
filename = 'input.yaml'
folder_name = 'workingDir'
volume = GirderFolderIdToVolume(inputFolderId,
volume=TemporaryVolume.default,
folder_name=folder_name)
outputDir = inputFolderId + '/' + folder_name + '/output.exo'
volumepath = VolumePath(outputDir, volume=TemporaryVolume.default)
result = docker_run.delay(ALBANY_IMAGE,
pull_image=False,
container_args=[filename],
entrypoint='/usr/local/albany/bin/AlbanyT',
remove_container=True,
working_dir=volume,
girder_result_hooks=[
GirderUploadVolumePathToFolder(
volumepath, outputFolderId)
])
# Set the multiscale meta data and return the job
jobId = result.job['_id']
return utils.setMultiscaleMetaData(jobId, inputFolderId,
outputFolderId)
def run_dream3d(self, params):
"""Run Dream3D on a folder that is on girder.
Will store the output in the specified output folder.
"""
inputFolderId = params.get('inputFolderId')
outputFolderId = params.get('outputFolderId')
folder_name = 'workingDir'
volume = GirderFolderIdToVolume(inputFolderId,
volume=TemporaryVolume.default,
folder_name=folder_name)
outputDir = inputFolderId + '/' + folder_name + '/output'
volumepath = VolumePath(outputDir, volume=TemporaryVolume.default)
result = docker_run.delay(
DREAM3D_IMAGE,
pull_image=False,
container_args=[
'-c', 'bash /root/runPipelineRunner $(ls *.json | head -1)'
],
remove_container=True,
working_dir=volume,
entrypoint='bash',
girder_result_hooks=[
GirderUploadVolumePathToFolder(volumepath, outputFolderId)
])
# Set the multiscale meta data and return the job
jobId = result.job['_id']
return utils.setMultiscaleMetaData(jobId, inputFolderId,
outputFolderId)
def test_docker_run(self, params):
result = docker_run.delay(
TEST_IMAGE,
pull_image=True,
container_args=['stdio', '-m', 'hello docker!'],
remove_container=True)
return result.job
def selectBest(initWorkingSetName,
stepName,
requestInfo,
jobId,
outputFolder,
imageFiles,
dsmFile):
"""
Run a Girder Worker job to select the best image pair.
Requirements:
- Danesfield Docker image is available on host
:param initWorkingSetName: The name of the top-level working set.
:type initWorkingSetName: str
:param stepName: The name of the step.
:type stepName: str (DanesfieldStep)
:param requestInfo: HTTP request and authorization info.
:type requestInfo: RequestInfo
:param jobId: Job ID.
:type jobId: str
:param outputFolder: Output folder document.
:type outputFolder: dict
:param imageFiles: List of image files.
:type imageFiles: list[dict]
:param file: DSM image file document.
:type file: dict
:returns: Job document.
"""
gc = createGirderClient(requestInfo)
# Docker container arguments
containerArgs = list(itertools.chain(
[
'danesfield/tools/select_best.py',
'--dsm', GirderFileIdToVolume(dsmFile['_id'], gc=gc)
],
[
GirderFileIdToVolume(imageFile['_id'], gc=gc)
for imageFile in imageFiles
]
))
asyncResult = docker_run.delay(
**createDockerRunArguments(
image=DockerImage.DANESFIELD,
containerArgs=containerArgs,
jobTitle='[%s] Select best' % initWorkingSetName,
jobType=stepName,
user=requestInfo.user
)
)
# Add info for job event listeners
job = asyncResult.job
job = addJobInfo(job, jobId=jobId, stepName=stepName)
return job
def _runUtm(folder, paramsFile, outputFolder):
outpath = VolumePath('__results__')
return docker_run.delay('samuelgerber/utm', container_args=[
GirderFolderIdToVolume(folder['_id']),
GirderFileIdToVolume(paramsFile['_id']),
'--workingfolder', outpath
], girder_job_title='UTM: ' + folder['name'], girder_result_hooks=[
GirderUploadVolumePathToFolder(outpath, outputFolder['_id'])
]).job
def test_docker_run_progress_pipe(self, params):
progressions = params.get('progressions')
progress_pipe = ProgressPipe()
result = docker_run.delay(
TEST_IMAGE, pull_image=True,
container_args=['progress', '-p', progress_pipe, '--progressions', progressions],
remove_container=True)
return result.job
def test_docker_run_girder_file_to_volume(self, params):
file_id = params.get('fileId')
result = docker_run.delay(
TEST_IMAGE, pull_image=True,
container_args=['read_write', '-i', GirderFileIdToVolume(file_id),
'-o', Connect(NamedOutputPipe('out'), HostStdOut())],
remove_container=True)
return result.job
def test_docker_run_cancel(self, params):
mode = params.get('mode')
result = docker_run.delay(
TEST_IMAGE, pull_image=True, container_args=[mode],
remove_container=True)
assert wait_for_status(self.getCurrentUser(), result.job, JobStatus.RUNNING)
result.revoke()
return result.job
def test_docker_run_file_upload_to_item(self, params):
item_id = params.get('itemId')
contents = params.get('contents')
volumepath = VolumePath('test_file')
result = docker_run.delay(
TEST_IMAGE, pull_image=True,
container_args=['write', '-p', volumepath, '-m', contents],
remove_container=True,
girder_result_hooks=[GirderUploadVolumePathToItem(volumepath, item_id)])
return result.job
def test_docker_run_mount_volume(self, params):
fixture_dir = params.get('fixtureDir')
filename = 'read.txt'
mount_dir = '/mnt/test'
mount_path = os.path.join(mount_dir, filename)
volumes = {fixture_dir: {'bind': mount_dir, 'mode': 'ro'}}
result = docker_run.delay(TEST_IMAGE,
pull_image=True,
container_args=['read', '-p', mount_path],
remove_container=True,
volumes=volumes)
return result.job
def test_docker_run_mount_idiomatic_volume(self, params):
fixture_dir = params.get('fixtureDir')
filename = 'read.txt'
mount_dir = '/mnt/test'
mount_path = os.path.join(mount_dir, filename)
volume = BindMountVolume(fixture_dir, mount_path, 'ro')
volumepath = VolumePath(filename, volume)
result = docker_run.delay(
TEST_IMAGE, pull_image=True, container_args=['read', '-p', volumepath],
remove_container=True, volumes=[volume])
return result.job
def test_docker_run_temporary_volume_root(self, params):
prefix = params.get('prefix')
root = os.path.join(tempfile.gettempdir(), prefix)
# We set the mode to 0o777 because the worker container is
# running as the 'worker' user and needs to be able to have
# read/write access to the TemporaryVolume
volume = TemporaryVolume(host_dir=root, mode=0o777)
result = docker_run.delay(
TEST_IMAGE, pull_image=True, container_args=['print_path', '-p', volume],
remove_container=True, volumes=[volume])
return result.job
def test_docker_run_girder_file_to_named_pipe_on_temp_vol(self, params):
"""
This is a simplified version of test_docker_run_girder_file_to_named_pipe
it uses the TemporaryVolume, rather than having to setup the volumes
'manually', this is the approach we should encourage.
"""
file_id = params.get('fileId')
pipe_name = 'input_pipe'
connect = Connect(GirderFileIdToStream(file_id), NamedInputPipe(pipe_name))
result = docker_run.delay(
TEST_IMAGE, pull_image=True, container_args=['read', '-p', connect],
remove_container=True)
return result.job
def test_docker_run_girder_file_to_named_pipe(self, params):
tmp_dir = params.get('tmpDir')
file_id = params.get('fileId')
mount_dir = '/mnt/girder_worker/data'
pipe_name = 'input_pipe'
volumes = {tmp_dir: {'bind': mount_dir, 'mode': 'rw'}}
connect = Connect(GirderFileIdToStream(file_id),
NamedInputPipe(pipe_name, mount_dir, tmp_dir))
result = docker_run.delay(TEST_IMAGE,
pull_image=True,
container_args=['read', '-p', connect],
remove_container=True,
volumes=volumes)
return result.job
def test_docker_run_named_pipe_output(self, params):
tmp_dir = params.get('tmpDir')
message = params.get('message')
mount_dir = '/mnt/girder_worker/data'
pipe_name = 'output_pipe'
volumes = {tmp_dir: {'bind': mount_dir, 'mode': 'rw'}}
connect = Connect(NamedOutputPipe(pipe_name, mount_dir, tmp_dir),
HostStdOut())
result = docker_run.delay(
TEST_IMAGE,
pull_image=True,
container_args=['write', '-p', connect, '-m', message],
remove_container=True,
volumes=volumes)
return result.job
def test_docker_run_transfer_encoding_stream(self, params):
item_id = params.get('itemId')
file_id = params.get('fileId')
delimiter = params.get('delimiter')
headers = {
'Girder-Token': str(Token().createToken(getCurrentUser())['_id'])
}
url = '%s/%s?itemId=%s&delimiter=%s' % (
getApiUrl(), 'integration_tests/docker/input_stream', item_id, delimiter)
container_args = [
'read_write',
'-i', GirderFileIdToVolume(file_id),
'-o', Connect(NamedOutputPipe('out'),
ChunkedTransferEncodingStream(url, headers))
]
result = docker_run.delay(
TEST_IMAGE, pull_image=True, container_args=container_args,
remove_container=True)
return result.job
def _createThumbnail(item):
# Remove previously attached thumbnails
_removeThumbnails(item, saveItem=True)
outdir = VolumePath('__thumbnails_output__')
return docker_run.delay(
'girder/dicom_thumbnailer:latest',
container_args=[
'--slices',
str(THUMB_SLICES), '--width',
str(THUMB_WIDTH), '--height',
str(THUMB_HEIGHT),
GirderItemIdToVolume(item['_id'], item_name=item['name']), outdir
],
girder_job_title='DICOM thumbnail generation: %s' % item['name'],
girder_result_hooks=[
GirderUploadVolumePathToItem(
outdir,
item['_id'],
upload_kwargs={
'reference': json.dumps({'interactive_thumbnail': True})
})
]).job
def _createThumbnail(item, preset):
# Remove previously attached thumbnails
_removeThumbnails(item, saveItem=True)
outdir = VolumePath('__thumbnails_output__')
return docker_run.delay(
'zachmullen/3d_thumbnails:latest',
container_args=[
'--angle-step',
str(_ANGLE_STEP), '--width',
str(_SIZE), '--height',
str(_SIZE), '--preset', preset,
GirderItemIdToVolume(item['_id'], item_name=item['name']), outdir
],
girder_job_title='Interactive thumbnail generation: %s' % item['name'],
girder_result_hooks=[
GirderUploadVolumePathToItem(
outdir,
item['_id'],
upload_kwargs={
'reference': json.dumps({'interactive_thumbnail': True})
})
]).job
def run_smtk_mesh_placement(self, params):
"""Run an smtk mesh placement on a folder that is on girder.
Will store the output in the specified output folder.
"""
inputFolderId = params.get('inputFolderId')
outputFolderId = params.get('outputFolderId')
folder_name = 'workingDir'
volume = GirderFolderIdToVolume(inputFolderId,
volume=TemporaryVolume.default,
folder_name=folder_name)
outputDir = inputFolderId + '/' + folder_name + '/output/'
volumepath = VolumePath(outputDir, volume=TemporaryVolume.default)
result = docker_run.delay(
SMTK_IMAGE,
pull_image=False,
container_args=[
'-c',
('. ~/setupEnvironment; '
'python /usr/local/afrl-automation/runner.py input.json; '
'mkdir output; '
'mv input.yaml output/; '
'mv elastic.yaml output/;'
'mv *BC.exo output/')
],
entrypoint='bash',
remove_container=True,
working_dir=volume,
girder_result_hooks=[
GirderUploadVolumePathToFolder(volumepath, outputFolderId)
])
# Set the multiscale meta data and return the job
jobId = result.job['_id']
return utils.setMultiscaleMetaData(jobId, inputFolderId,
outputFolderId)
def runMetrics(initWorkingSetName, stepName, requestInfo, jobId, outputFolder,
referenceFolder, referencePrefix, dtmFile, dsmFile, clsFile,
mtlFile):
"""
Run a Girder Worker job to compute metrics on output files.
Requirements:
- Danesfield Docker image is available on host
:param initWorkingSetName: The name of the top-level working set.
:type initWorkingSetName: str
:param stepName: The name of the step.
:type stepName: str (DanesfieldStep)
:param requestInfo: HTTP request and authorization info.
:type requestInfo: RequestInfo
:param jobId: Job ID.
:type jobId: str
:param outputFolder: Output folder document.
:type outputFolder: dict
:param referenceFolder: Reference directory.
:type referenceFolder: dict
:param referencePrefix: Reference file prefix.
:type referencePrefix: str
:param dtmFile: DTM file document.
:type dtmFile: dict
:param dsmFile: DSM file document.
:type dsmFile: dict
:param clsFile: CLS file document.
:type clsFile: dict
:param mtlFile: MTL file document.
:type mtlFile: dict
:returns: Job document.
"""
gc = createGirderClient(requestInfo)
if referencePrefix == "STANDARD":
# We know that there's no reference data with this selection
containerArgs = ['echo', 'No ground truth selected for scoring']
asyncResult = docker_run.delay(
**createDockerRunArguments(image=DockerImage.DANESFIELD,
containerArgs=containerArgs,
jobTitle='[%s] Run metrics' %
initWorkingSetName,
jobType=stepName,
user=requestInfo.user))
else:
# Otherwise we assume the reference data exists, and try to
# run the metrics
outputVolumePath = VolumePath('__output__')
# Docker container arguments
containerArgs = [
'danesfield/tools/run_metrics.py', '--output-dir',
outputVolumePath, '--ref-dir',
GirderFolderIdToVolume(referenceFolder['_id'], gc=gc),
'--ref-prefix', referencePrefix, '--dsm',
GirderFileIdToVolume(dsmFile['_id'], gc=gc), '--cls',
GirderFileIdToVolume(clsFile['_id'], gc=gc), '--mtl',
GirderFileIdToVolume(mtlFile['_id'], gc=gc), '--dtm',
GirderFileIdToVolume(dtmFile['_id'], gc=gc)
]
# Result hooks
# - Upload output files to output folder
# - Provide upload metadata
upload_kwargs = createUploadMetadata(jobId, stepName)
resultHooks = [
GirderUploadVolumePathToFolder(outputVolumePath,
outputFolder['_id'],
upload_kwargs=upload_kwargs,
gc=gc)
]
asyncResult = docker_run.delay(
**createDockerRunArguments(image=DockerImage.DANESFIELD,
containerArgs=containerArgs,
jobTitle='[%s] Run metrics' %
initWorkingSetName,
jobType=stepName,
user=requestInfo.user,
resultHooks=resultHooks))
# Add info for job event listeners
job = asyncResult.job
job = addJobInfo(job, jobId=jobId, stepName=stepName)
return job
def unetSemanticSegmentation(initWorkingSetName, stepName, requestInfo, jobId,
outputFolder, dsmFile, dtmFile, msiImageFile,
rgbImageFile, configFile, modelFile):
"""
Run a Girder Worker job to segment buildings using UNet semantic
segmentation.
Requirements:
- Danesfield Docker image is available on host
:param initWorkingSetName: The name of the top-level working set.
:type initWorkingSetName: strps
:param stepName: The name of the step.
:type stepName: str (DanesfieldStep)
:param requestInfo: HTTP request and authorization info.
:type requestInfo: RequestInfo
:param jobId: Job ID.
:type jobId: str
:param outputFolder: Output folder document.
:type outputFolder: dict
:param dsmFile: DSM file document.
:type dsmFile: dict
:param dtmFile: DTM file document.
:type dtmFile: dict
:param msiImageFile: Pansharpened MSI image file document.
:type msiImageFile: dict
:param rgbImageFile: RGB image file document.
:type rgbImageFile: dict
:param configFile: Configuration file document.
:type configFile: dict
:param modelFile: Model file document.
:type modelFile: dict
:returns: Job document.
"""
gc = createGirderClient(requestInfo)
# Set output directory
outputVolumePath = VolumePath('.')
# Docker container arguments
containerArgs = [
'danesfield/tools/kwsemantic_segment.py',
# Configuration file
GirderFileIdToVolume(configFile['_id'], gc=gc),
# Model file
GirderFileIdToVolume(modelFile['_id'], gc=gc),
# RGB image
GirderFileIdToVolume(rgbImageFile['_id'], gc=gc),
# DSM
GirderFileIdToVolume(dsmFile['_id'], gc=gc),
# DTM
GirderFileIdToVolume(dtmFile['_id'], gc=gc),
# MSI image
GirderFileIdToVolume(msiImageFile['_id'], gc=gc),
# Output directory
outputVolumePath,
# Output file prefix
'semantic'
]
# Result hooks
# - Upload output files to output folder
# - Provide upload metadata
upload_kwargs = createUploadMetadata(jobId, stepName)
resultHooks = [
GirderUploadVolumePathToFolder(outputVolumePath,
outputFolder['_id'],
upload_kwargs=upload_kwargs,
gc=gc)
]
asyncResult = docker_run.delay(
**createDockerRunArguments(image=DockerImage.DANESFIELD,
containerArgs=containerArgs,
jobTitle=(
'[%s] UNet semantic segmentation: %s' %
(initWorkingSetName, dsmFile['name'])),
jobType=stepName,
user=requestInfo.user,
resultHooks=resultHooks))
# Add info for job event listeners
job = asyncResult.job
job = addJobInfo(job, jobId=jobId, stepName=stepName)
return job
def computeNdvi(initWorkingSetName, stepName, requestInfo, jobId, outputFolder,
imageFiles, outputNdviFilename):
"""
Run a Girder Worker job to compute the NDVI from a set of images
Requirements:
- Danesfield Docker image is available on host
:param initWorkingSetName: The name of the top-level working set.
:type initWorkingSetName: str
:param stepName: The name of the step.
:type stepName: str (DanesfieldStep)
:param requestInfo: HTTP request and authorization info.
:type requestInfo: RequestInfo
:param jobId: Job ID.
:type jobId: str
:param outputFolder: Output folder document.
:type outputFolder: dict
:param imageFiles: List of pansharpened image files.
:type imageFiles: list[dict]
:param outputNdviFilename: Filename for output NDVI
:type outputNdviFilename: str
:returns: Job document.
"""
gc = createGirderClient(requestInfo)
# Set output file names
ndviOutputVolumePath = VolumePath(outputNdviFilename)
# Docker container arguments
containerArgs = list(
itertools.chain([
'danesfield/tools/compute_ndvi.py',
], [
GirderFileIdToVolume(imageFile['_id'], gc=gc)
for imageFile in imageFiles
], [ndviOutputVolumePath]))
# Result hooks
# - Upload output files to output folder
# - Provide upload metadata
upload_kwargs = createUploadMetadata(jobId, stepName)
resultHooks = [
GirderUploadVolumePathToFolder(ndviOutputVolumePath,
outputFolder['_id'],
upload_kwargs=upload_kwargs,
gc=gc)
]
asyncResult = docker_run.delay(
**createDockerRunArguments(image=DockerImage.DANESFIELD,
containerArgs=containerArgs,
jobTitle='[%s] Compute NDVI' %
initWorkingSetName,
jobType=stepName,
user=requestInfo.user,
resultHooks=resultHooks))
# Add info for job event listeners
job = asyncResult.job
job = addJobInfo(job, jobId=jobId, stepName=stepName)
return job
def runPhotomorph(self, folder, maskRect):
user = self.getCurrentUser()
mp4Out = VolumePath('__output_mp4s__/')
gifOut = VolumePath('__output_gifs__/')
parent = Folder().load(folder['parentId'],
level=AccessType.WRITE,
exc=True,
user=user)
outputFolder = Folder().createFolder(parent,
'_output',
public=False,
creator=user,
reuseExisting=True)
outputMp4 = Folder().createFolder(outputFolder,
'mp4s',
public=False,
creator=user,
reuseExisting=True)
outputGif = Folder().createFolder(outputFolder,
'gifs',
public=False,
creator=user,
reuseExisting=True)
parent['photomorphOutputFolderId'] = outputFolder['_id']
parent['photomorphOutputItems'] = {}
parent['photomorphMaskRect'] = maskRect
parent['photomorphJobStatus'] = JobStatus.QUEUED
parent['photomorphOutputItems'] = {'gif': [], 'mp4': []}
job = docker_run.delay(
'zachmullen/photomorph:latest',
container_args=[
'--mp4-out', mp4Out, '--gif-out', gifOut, '--mask-rect',
','.join(str(i) for i in itertools.chain(*maskRect)),
GirderFolderIdToVolume(folder['_id'], folder_name='_input')
],
girder_job_title='Timelapse creation: %s' % parent['name'],
girder_result_hooks=[
GirderUploadVolumePathToFolder(mp4Out,
outputMp4['_id'],
upload_kwargs={
'reference':
json.dumps({
'photomorph':
True,
'folderId':
str(parent['_id']),
'resultType':
'mp4'
})
}),
GirderUploadVolumePathToFolder(gifOut,
outputGif['_id'],
upload_kwargs={
'reference':
json.dumps({
'photomorph':
True,
'folderId':
str(parent['_id']),
'resultType':
'gif'
})
})
]).job
parent['photomorphJobId'] = job['_id']
Folder().save(parent)
job['photomorphId'] = parent['_id']
return Job().save(job)
def getRoadVector(initWorkingSetName,
stepName,
requestInfo,
jobId,
outputFolder,
left,
bottom,
right,
top):
"""
Run a Girder Worker job to segment buildings by comparing a DSM to a DTM.
Requirements:
- Danesfield Docker image is available on host
:param initWorkingSetName: The name of the top-level working set.
:type initWorkingSetName: str
:param stepName: The name of the step.
:type stepName: str (DanesfieldStep)
:param requestInfo: HTTP request and authorization info.
:type requestInfo: RequestInfo
:param jobId: Job ID.
:type jobId: str
:param outputFolder: Output folder document.
:type outputFolder: dict
:param left: Longitude of left / westernmost side of bounding box
:type left: float
:param bottom: Latitude of bottom / southernmost side of bounding box
:type bottom: float
:param right: Longitude of right / easternmost side of bounding box
:type right: float
:param top: Latitude of top / northernmost side of bounding box
:type top: float
:returns: Job document.
"""
gc = createGirderClient(requestInfo)
# Set output file names
outputVolumePath = VolumePath('__output__')
# Docker container arguments
containerArgs = [
'danesfield/tools/get_road_vector.py',
'--left', str(left),
'--bottom', str(bottom),
'--right', str(right),
'--top', str(top),
'--output-dir', outputVolumePath,
]
# Result hooks
# - Upload output files to output folder
# - Provide upload metadata
upload_kwargs = createUploadMetadata(jobId, stepName)
resultHooks = [
GirderUploadVolumePathToFolder(
outputVolumePath,
outputFolder['_id'],
upload_kwargs=upload_kwargs,
gc=gc)
]
asyncResult = docker_run.delay(
**createDockerRunArguments(
image=DockerImage.DANESFIELD,
containerArgs=containerArgs,
jobTitle='[%s] Get OSM road vector data' % initWorkingSetName,
jobType=stepName,
user=requestInfo.user,
resultHooks=resultHooks
)
)
# Add info for job event listeners
job = asyncResult.job
job = addJobInfo(job, jobId=jobId, stepName=stepName)
return job
def generateDsm(initWorkingSetName, stepName, requestInfo, jobId, outputFolder,
pointCloudFile, outputPrefix):
"""
Run a Girder Worker job to generate a Digital Surface Model (DSM)
from a point cloud.
Requirements:
- Danesfield Docker image is available on host
:param initWorkingSetName: The name of the top-level working set.
:type initWorkingSetName: str
:param stepName: The name of the step.
:type stepName: str (DanesfieldStep)
:param requestInfo: HTTP request and authorization info.
:type requestInfo: RequestInfo
:param jobId: Job ID.
:type jobId: str
:param outputFolder: Output folder document.
:type outputFolder: dict
:param pointCloudFile: Point cloud file document.
:type pointCloudFile: dict
:param outputPrefix: The prefix of the output file name.
:type outputPrefix: str
:returns: Job document.
"""
gc = createGirderClient(requestInfo)
# Set output file name based on point cloud file
dsmName = outputPrefix + '_P3D_DSM.tif'
outputVolumePath = VolumePath(dsmName)
# Docker container arguments
containerArgs = [
'danesfield/tools/generate_dsm.py', outputVolumePath,
'--source_points',
GirderFileIdToVolume(pointCloudFile['_id'], gc=gc)
]
# Result hooks
# - Upload output files to output folder
# - Provide upload metadata
upload_kwargs = createUploadMetadata(jobId, stepName)
resultHooks = [
GirderUploadVolumePathToFolder(outputVolumePath,
outputFolder['_id'],
upload_kwargs=upload_kwargs,
gc=gc)
]
asyncResult = docker_run.delay(
**createDockerRunArguments(image=DockerImage.DANESFIELD,
containerArgs=containerArgs,
jobTitle=('[%s] Generate DSM: %s' %
(initWorkingSetName,
pointCloudFile['name'])),
jobType=stepName,
user=requestInfo.user,
resultHooks=resultHooks))
# Add info for job event listeners
job = asyncResult.job
job = addJobInfo(job, jobId=jobId, stepName=stepName)
return job
def test_docker_run_raises_exception(self, params):
result = docker_run.delay(
TEST_IMAGE, pull_image=True, container_args=['raise_exception'], remove_container=True)
return result.job
def textureMapping(initWorkingSetName, stepName, requestInfo, jobId,
outputFolder, objFiles, imageFiles, dsmFile, dtmFile):
"""
Run a Girder Worker job to run texture mapping.
Requirements:
- Danesfield Docker image is available on host
:param initWorkingSetName: The name of the top-level working set.
:type initWorkingSetName: str
:param stepName: The name of the step.
:type stepName: str (DanesfieldStep)
:param requestInfo: HTTP request and authorization info.
:type requestInfo: RequestInfo
:param jobId: Job ID.
:type jobId: str
:param outputFolder: Output folder document.
:type outputFolder: dict
:param objFiles: List of OBJ files.
:type objFiles: list[dict]
:param imageFiles: List of cropped and pansharpened image files.
:type imageFiles: list[dict]
:param dsmFile: DSM file document.
:type dsmFile: dict
:param dtmFile: DTM file document.
:type dtmFile: dict
:returns: Job document.
"""
gc = createGirderClient(requestInfo)
# Set output directory
outputVolumePath = VolumePath('__output__')
# Set output path for occlusion mesh
occlusionMeshName = 'xxxx.obj'
occlusionMeshVolumePath = VolumePath(occlusionMeshName)
containerArgs = [
'danesfield/tools/texture_mapping.py',
GirderFileIdToVolume(dsmFile['_id'], gc=gc),
GirderFileIdToVolume(dtmFile['_id'], gc=gc), outputVolumePath,
occlusionMeshVolumePath, '--crops'
]
containerArgs.extend(
[GirderFileIdToVolume(f['_id'], gc=gc) for f in imageFiles])
containerArgs.append('--buildings')
containerArgs.extend(
[GirderFileIdToVolume(f['_id'], gc=gc) for f in objFiles])
# Result hooks
# - Upload output files to output folder
# - Provide upload metadata
upload_kwargs = createUploadMetadata(jobId, stepName)
resultHooks = [
GirderUploadVolumePathToFolder(outputVolumePath,
outputFolder['_id'],
upload_kwargs=upload_kwargs,
gc=gc),
GirderUploadVolumePathToFolder(occlusionMeshVolumePath,
outputFolder['_id'],
upload_kwargs=upload_kwargs,
gc=gc)
]
asyncResult = docker_run.delay(
**createDockerRunArguments(image=DockerImage.DANESFIELD,
containerArgs=containerArgs,
jobTitle='[%s] Texture mapping' %
initWorkingSetName,
jobType=stepName,
user=requestInfo.user,
resultHooks=resultHooks))
# Add info for job event listeners
job = asyncResult.job
job = addJobInfo(job, jobId=jobId, stepName=stepName)
return job
def generatePointCloud(initWorkingSetName,
stepName,
requestInfo,
jobId,
outputFolder,
imageFiles,
longitude,
latitude,
longitudeWidth,
latitudeWidth):
"""
Run a Girder Worker job to generate a 3D point cloud from 2D images.
Requirements:
- P3D Girder Worker Docker image is available on host
- Host folder /mnt/GTOPO30 contains GTOPO 30 data
:param initWorkingSetName: The name of the top-level working set.
:type initWorkingSetName: str
:param stepName: The name of the step.
:type stepName: str (DanesfieldStep)
:param requestInfo: HTTP request and authorization info.
:type requestInfo: RequestInfo
:param jobId: Job ID.
:type jobId: str
:param outputFolder: Output folder document.
:type outputFolder: dict
:param imageFiles: List of input image files.
:type imageFiles: list[dict]
:param longitude:
:type longitude:
:param latitude:
:type latitude:
:param longitudeWidth:
:type longitudeWidth:
:param latitudeWidth:
:type latitudeWidth:
:returns: Job document.
"""
gc = createGirderClient(requestInfo)
# Docker volumes
volumes = [
BindMountVolume(host_path='/mnt/GTOPO30',
container_path='/P3D/GTOPO30',
mode='ro')
]
outputVolumePath = VolumePath('__output__')
# Docker container arguments
# TODO: Consider a solution where args are written to a file, in
# case of very long command lines
containerArgs = list(itertools.chain(
[
'python', '/P3D/RTN_distro/scripts/generate_point_cloud.pyc',
'--out', outputVolumePath,
'--longitude', str(longitude),
'--latitude', str(latitude),
'--longitudeWidth', str(longitudeWidth),
'--latitudeWidth', str(latitudeWidth),
'--firstProc', '0',
'--threads', '8',
'--images'
],
[GirderFileIdToVolume(imageFile['_id'], gc=gc)
for imageFile in imageFiles],
))
# Result hooks
# - Upload output files to output folder
# - Provide upload metadata
upload_kwargs = createUploadMetadata(jobId, stepName)
resultHooks = [
GirderUploadVolumePathToFolder(
outputVolumePath,
outputFolder['_id'],
upload_kwargs=upload_kwargs,
gc=gc)
]
asyncResult = docker_run.delay(
volumes=volumes,
**createDockerRunArguments(
image=DockerImage.P3D,
containerArgs=containerArgs,
jobTitle='[%s] Generate point cloud' % initWorkingSetName,
jobType=stepName,
user=requestInfo.user,
resultHooks=resultHooks
)
)
# Add info for job event listeners
job = asyncResult.job
job = addJobInfo(job, jobId=jobId, stepName=stepName)
return job
def segmentByHeight(initWorkingSetName, stepName, requestInfo, jobId,
outputFolder, dsmFile, dtmFile, ndviFile, roadVectorFile):
"""
Run a Girder Worker job to segment buildings by comparing a DSM to a DTM.
Requirements:
- Danesfield Docker image is available on host
:param initWorkingSetName: The name of the top-level working set.
:type initWorkingSetName: str
:param stepName: The name of the step.
:type stepName: str (DanesfieldStep)
:param requestInfo: HTTP request and authorization info.
:type requestInfo: RequestInfo
:param jobId: Job ID.
:type jobId: str
:param outputFolder: Output folder document.
:type outputFolder: dict
:param dsmFile: DSM file document.
:type dsmFile: dict
:param dtmFile: DTM file document.
:type dtmFile: dict
:param ndviFile: NDVI file document.
:type ndviFile: dict
:param roadVectorFile: Road vector file.
:type roadVectorFile: dict
:returns: Job document.
"""
gc = createGirderClient(requestInfo)
# Set output file names
# TODO: Danesfield master script hardcodes these without any
# prefix; do the same here
thresholdOutputVolumePath = VolumePath('threshold_CLS.tif')
roadRasterOutputVolumePath = VolumePath('road_rasterized.tif')
roadBridgeRasterOutputVolumePath = VolumePath('road_rasterized_bridge.tif')
# Docker container arguments
containerArgs = [
'danesfield/tools/segment_by_height.py',
# DSM
GirderFileIdToVolume(dsmFile['_id'], gc=gc),
# DTM
GirderFileIdToVolume(dtmFile['_id'], gc=gc),
# Threshold output image
thresholdOutputVolumePath,
# Normalized Difference Vegetation Index image
'--input-ndvi',
GirderFileIdToVolume(ndviFile['_id'], gc=gc),
'--road-vector',
GirderFileIdToVolume(roadVectorFile['_id'], gc=gc),
'--road-rasterized',
roadRasterOutputVolumePath,
'--road-rasterized-bridge',
roadBridgeRasterOutputVolumePath
]
# Result hooks
# - Upload output files to output folder
# - Provide upload metadata
upload_kwargs = createUploadMetadata(jobId, stepName)
resultHooks = [
GirderUploadVolumePathToFolder(thresholdOutputVolumePath,
outputFolder['_id'],
upload_kwargs=upload_kwargs,
gc=gc)
]
asyncResult = docker_run.delay(
**createDockerRunArguments(image=DockerImage.DANESFIELD,
containerArgs=containerArgs,
jobTitle='[%s] Segment by height: %s' %
(initWorkingSetName, dsmFile['name']),
jobType=stepName,
user=requestInfo.user,
resultHooks=resultHooks))
# Add info for job event listeners
job = asyncResult.job
job = addJobInfo(job, jobId=jobId, stepName=stepName)
return job
