# Copyright 2021 MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from os import makedirs
from os.path import join
from monai.deploy.core import (
DataPath,
ExecutionContext,
Image,
InputContext,
IOType,
Operator,
OutputContext,
env,
input,
output,
)
from monai.deploy.operators.dicom_data_loader_operator import DICOMDataLoaderOperator
from monai.deploy.operators.dicom_series_to_volume_operator import DICOMSeriesToVolumeOperator
from monai.deploy.utils.importutil import optional_import
PILImage, _ = optional_import("PIL", name="Image")
[docs]@input("image", Image, IOType.IN_MEMORY)
@output("image", DataPath, IOType.DISK)
@env(pip_packages=["Pillow >= 8.0.0"])
class PNGConverterOperator(Operator):
"""
This operator writes out a 3D Volumtric Image to disk in a slice by slice manner
"""
[docs] def compute(self, input: InputContext, output: OutputContext, context: ExecutionContext):
input = input.get("image")
output_dir = output.get().path
output_dir.mkdir(parents=True, exist_ok=True)
self.convert_and_save(input, output_dir)
[docs] def convert_and_save(self, image, path):
"""
extracts the slices in originally acquired direction (often axial)
and saves then in PNG format slice by slice in the specified directory
"""
image_data = image.asnumpy()
image_shape = image_data.shape
num_images = image_shape[0]
for i in range(0, num_images):
input_data = image_data[:, :, i]
pil_image = PILImage.fromarray(input_data)
if pil_image.mode != "RGB":
pil_image = pil_image.convert("RGB")
pil_image.save(join(str(path), join(str(i) + ".png")))
def main():
op1 = DICOMSeriesToVolumeOperator()
data_path = "/home/rahul/medical-images/lung-ct-2/"
out_path = "/home/rahul/monai-output/"
makedirs(out_path, exist_ok=True)
files = []
loader = DICOMDataLoaderOperator()
loader._list_files(
data_path,
files,
)
study_list = loader._load_data(files)
series = study_list[0].get_all_series()[0]
op1.prepare_series(series)
voxels = op1.generate_voxel_data(series)
metadata = op1.create_metadata(series)
image = op1.create_volumetric_image(voxels, metadata)
op2 = PNGConverterOperator()
op2.convert_and_save(image, out_path)
print(series)
# print(metadata.keys())
if __name__ == "__main__":
main()