def _create_images_result(self, *, interface):
base_dir = Path(
safe_join(self._output_directory, interface.relative_path))
output_files = [f for f in base_dir.glob("*") if f.is_file()]
if not output_files:
raise ComponentException(f"{interface.relative_path} is empty")
importer_result = import_images(
input_directory=base_dir,
builders=[image_builder_mhd, image_builder_tiff],
recurse_subdirectories=False,
)
if len(importer_result.new_images) == 0:
raise ComponentException(
f"No images imported from {interface.relative_path}")
elif len(importer_result.new_images) > 1:
raise ComponentException(
f"Only 1 image should be produced in {interface.relative_path}, "
f"we found {len(importer_result.new_images)}")
try:
civ = interface.create_instance(
image=next(iter(importer_result.new_images)))
except ValidationError:
raise ComponentException(
f"The image produced in {interface.relative_path} is not valid"
)
return civ
def _copy_output_files(self, *, container, base_dir: Path):
output_files = {
base_dir / Path(f)
for f in container.exec_run(f"find {base_dir} -type f")
.output.decode()
.splitlines()
}
if not output_files:
raise ValueError("Output directory is empty")
job = SubmissionToAnnotationSetJob.objects.get(pk=self._job_id)
annotationset = AnnotationSet.objects.create(
creator=job.submission.creator,
base=job.base,
submission=job.submission,
kind=AnnotationSet.PREDICTION,
)
if self.__was_unzipped:
with TemporaryDirectory() as tmpdir:
input_files = set()
for file in output_files:
tmpfile = Path(
safe_join(tmpdir, file.relative_to(base_dir))
)
tmpfile.parent.mkdir(parents=True, exist_ok=True)
with open(tmpfile, "wb") as outfile:
infile = get_file(container=container, src=file)
buffer = True
while buffer:
buffer = infile.read(1024)
outfile.write(buffer)
input_files.add(tmpfile)
importer_result = import_images(files=input_files,)
annotationset.images.add(*importer_result.new_images)
else:
if not len(output_files) == 1:
raise RuntimeError("This submission has too many files.")
f = get_file(container=container, src=output_files.pop())
annotationset.labels = process_csv_file(f)
annotationset.save()
def _copy_output_files(self, *, container, base_dir: Path):
found_files = container.exec_run(f"find {base_dir} -type f")
if found_files.exit_code != 0:
logger.warning(f"Error listing {base_dir}")
return
output_files = [
base_dir / Path(f)
for f in found_files.output.decode().splitlines()
]
if not output_files:
logger.warning("Output directory is empty")
return
with TemporaryDirectory() as tmpdir:
input_files = set()
for file in output_files:
tmpfile = Path(safe_join(tmpdir, file.relative_to(base_dir)))
tmpfile.parent.mkdir(parents=True, exist_ok=True)
with open(tmpfile, "wb") as outfile:
infile = get_file(container=container, src=file)
buffer = True
while buffer:
buffer = infile.read(1024)
outfile.write(buffer)
input_files.add(tmpfile)
importer_result = import_images(
files=input_files,
builders=[image_builder_mhd, image_builder_tiff],
)
default_output_interface = ComponentInterface.objects.get(
slug=DEFAULT_OUTPUT_INTERFACE_SLUG
)
job = Job.objects.get(pk=self._job_id)
for image in importer_result.new_images:
civ = ComponentInterfaceValue.objects.create(
interface=default_output_interface, image=image
)
job.outputs.add(civ)
def _create_images_result(self, *, reader, job):
# TODO JM in the future this will be a file, not a directory
base_dir = Path(self.output_path)
found_files = reader.exec_run(f"find {base_dir} -type f")
if found_files.exit_code != 0:
logger.warning(f"Error listing {base_dir}")
return
output_files = [
base_dir / Path(f)
for f in found_files.output.decode().splitlines()
]
if not output_files:
logger.warning("Output directory is empty")
return
with TemporaryDirectory() as tmpdir:
input_files = set()
for file in output_files:
temp_file = Path(safe_join(tmpdir, file.relative_to(base_dir)))
temp_file.parent.mkdir(parents=True, exist_ok=True)
with open(temp_file, "wb") as outfile:
infile = get_file(container=reader, src=file)
buffer = True
while buffer:
buffer = infile.read(1024)
outfile.write(buffer)
input_files.add(temp_file)
importer_result = import_images(
files=input_files,
builders=[image_builder_mhd, image_builder_tiff],
)
for image in importer_result.new_images:
civ = ComponentInterfaceValue.objects.create(
interface=self, image=image
)
job.outputs.add(civ)
def _create_images_result(self, *, interface, reader):
base_dir = Path(safe_join("/output/", interface.relative_path))
found_files = reader.exec_run(f"find {base_dir} -type f")
if found_files.exit_code != 0:
raise ComponentException(f"Error listing {base_dir}")
output_files = [
base_dir / Path(f)
for f in found_files.output.decode().splitlines()
]
if not output_files:
raise ComponentException(f"{base_dir} is empty")
with TemporaryDirectory() as tmpdir:
for file in output_files:
temp_file = Path(safe_join(tmpdir, file.relative_to(base_dir)))
temp_file.parent.mkdir(parents=True, exist_ok=True)
get_file(container=reader, src=file, dest=temp_file)
importer_result = import_images(
input_directory=tmpdir,
builders=[image_builder_mhd, image_builder_tiff],
)
if len(importer_result.new_images) == 0:
raise ComponentException(f"No images imported from {base_dir}")
elif len(importer_result.new_images) > 1:
raise ComponentException(
f"Only 1 image should be produced in {base_dir}, "
f"we found {len(importer_result.new_images)}")
try:
civ = interface.create_instance(
image=next(iter(importer_result.new_images)))
except ValidationError:
raise ComponentException(
f"The image produced in {base_dir} is not valid")
return civ
