# 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.
import logging
from os import getcwd, makedirs, path
from pathlib import Path
from shutil import copy
from typing import Union
from monai.deploy.core import Operator
# @md.input("saved_images_folder", DataPath, IOType.DISK)
# If `pip_packages` is specified, the definition will be aggregated with the package dependency list of other
# operators and the application in packaging time.
# @md.env(pip_packages=[])
[docs]class PublisherOperator(Operator):
"""This Operator publishes the input and segment mask images for the 3rd party Render Server.
It takes as input the folder path to the input and mask images, in nii, nii.gz, or mhd,
generates the render config file and the meta data file, then save all in the `publish` folder of the app.
"""
# The default input folder for saveing the generated DICOM instance file.
DEFAULT_INPUT_FOLDER = Path(getcwd()) / "input"
# The default output folder for saveing the generated DICOM instance file.
DEFAULT_OUTPUT_FOLDER = Path(getcwd()) / "output"
[docs] def __init__(
self,
*args,
input_folder: Union[str, Path],
output_folder: Union[str, Path],
**kwargs,
):
"""Class to write DICOM Encapsulated PDF Instance with PDF bytes in memory or in a file.
Args:
input_folder (str or Path): The folder to read the input and segment mask files.
output_folder (str or Path): The folder to save the published files.
"""
self._logger = logging.getLogger("{}.{}".format(__name__, type(self).__name__))
# Need to get the input folder in init until the execution context supports input path.
self.input_folder = Path(input_folder) if input_folder else PublisherOperator.DEFAULT_INPUT_FOLDER
# Need to get the output folder in init until the execution context supports output path.
# Not trying to create the folder to avoid exception on init
self.output_dir = Path(output_folder) if output_folder else PublisherOperator.DEFAULT_OUTPUT_FOLDER
super().__init__(*args, **kwargs)
[docs] def compute(self, op_input, op_output, context):
saved_images_folder = op_input.get("saved_images_folder").path
if not self.input_folder.is_dir():
raise ValueError("Expected a folder path for saved_image_folder input")
density_path, mask_path = self._find_density_and_mask_files(saved_images_folder)
subs = {"DENSITY_FILE": path.basename(density_path), "MASK_FILE": path.basename(mask_path)}
publish_folder_path = context.output.get().path.joinpath("publish")
makedirs(publish_folder_path, exist_ok=True)
print(f"App publish folder: {publish_folder_path}")
# Copy over the density and mask files
copy(density_path, publish_folder_path)
copy(mask_path, publish_folder_path)
# Generate the config_render.json from template
with open(path.join(publish_folder_path, "config_render.json"), "w") as config_render_file:
config_render_file.write(CONFIG_RENDER_TXT)
# Replace the file name in the CONFIG_META_TXT and save as config.meta
config_meta_txt = CONFIG_META_TXT.replace("DENSITY_FILE", subs["DENSITY_FILE"]).replace(
"MASK_FILE", subs["MASK_FILE"]
)
with open(path.join(publish_folder_path, "config.meta"), "w") as config_meta_file:
config_meta_file.write(config_meta_txt)
def _find_density_and_mask_files(self, folder_path):
density_path = None
mask_path = None
for matched_file in Path(folder_path).rglob("*"):
# Need to get the file name in str
f_name = str(matched_file)
if path.isfile(f_name):
if f_name.lower().endswith("_seg.nii.gz"):
mask_path = f_name
print(f"Mask file path: {mask_path}")
elif f_name.lower().endswith(".nii.gz"):
density_path = f_name
print(f"Density file path: {density_path}")
if density_path and mask_path:
return density_path, mask_path
raise ValueError("Cannot find both density and mask nii.gz files.")
CONFIG_META_TXT = """
{
"data": [
{
"file": "DENSITY_FILE",
"order": "DXYZ"
},
{
"file": "MASK_FILE",
"order": "MXYZ"
}
],
"name": "BTCV_highres",
"settings": "config_render.json"
}
"""
CONFIG_RENDER_TXT = """
{
"BackgroundLight": {
"bottomColor": {
"x": 1,
"y": 1,
"z": 1
},
"enable": "SWITCH_ENABLE",
"horizonColor": {
"x": 1,
"y": 1,
"z": 1
},
"intensity": 1,
"show": "SWITCH_DISABLE",
"topColor": {
"x": 1,
"y": 1,
"z": 1
}
},
"Camera": {
"eye": {
"x": 0.25439594946576577,
"y": 0.28691943829298083,
"z": 0.7147179382378706
},
"fieldOfView": 30,
"lookAt": {
"x": -0.03195509341043604,
"y": 0.006501020775334048,
"z": -0.016047870948873777
},
"name": "Cinematic",
"pixelAspectRatio": 1,
"up": {
"x": -0.11501682740802115,
"y": 0.9416680547756795,
"z": -0.31627899713554536
}
},
"CameraAperture": {
"aperture": 0.0051,
"autoFocus": "SWITCH_ENABLE",
"enable": "SWITCH_ENABLE",
"focusDistance": 9.999999999999999e-06
},
"Cameras": [
{
"eye": {
"x": 0.25439594946576577,
"y": 0.28691943829298083,
"z": 0.7147179382378706
},
"fieldOfView": 30,
"lookAt": {
"x": -0.03195509341043604,
"y": 0.006501020775334048,
"z": -0.016047870948873777
},
"name": "Cinematic",
"pixelAspectRatio": 1,
"up": {
"x": -0.11501682740802115,
"y": 0.9416680547756795,
"z": -0.31627899713554536
}
},
{
"eye": {
"x": 0,
"y": 10,
"z": 0
},
"fieldOfView": 30,
"lookAt": {
"x": 0,
"y": 0,
"z": 0
},
"name": "SliceTop",
"pixelAspectRatio": 1,
"up": {
"x": 0,
"y": 0,
"z": 1
}
},
{
"eye": {
"x": 0,
"y": 0,
"z": -10
},
"fieldOfView": 30,
"lookAt": {
"x": 0,
"y": 0,
"z": 0
},
"name": "SliceFront",
"pixelAspectRatio": 1,
"up": {
"x": 0,
"y": 1,
"z": 0
}
},
{
"eye": {
"x": 10,
"y": 0,
"z": 0
},
"fieldOfView": 30,
"lookAt": {
"x": 0,
"y": 0,
"z": 0
},
"name": "SliceRight",
"pixelAspectRatio": 1,
"up": {
"x": 0,
"y": 1,
"z": 0
}
},
{
"eye": {
"x": 0,
"y": 10,
"z": 0
},
"fieldOfView": 30,
"lookAt": {
"x": 0,
"y": 0,
"z": 0
},
"name": "SliceOblique",
"pixelAspectRatio": 1,
"up": {
"x": 0,
"y": 0,
"z": 1
}
}
],
"DataCrop": {
"limits": [
{
"max": 1,
"min": 0
},
{
"max": 0.89,
"min": 0.06
},
{
"max": 1,
"min": 0
},
{
"max": 1,
"min": 0.18
}
]
},
"DataView": {},
"Light": [
{
"color": {
"x": 1,
"y": 1,
"z": 1
},
"direction": {
"x": -0.3694435400514917,
"y": -0.8703544378686093,
"z": -0.3255681544571566
},
"enable": "SWITCH_ENABLE",
"index": 0,
"intensity": 1.1,
"position": {
"x": 0.4,
"y": 1,
"z": 0.85
},
"size": 0.1
}
],
"PostProcessDenoise": {
"depthWeight": 3,
"enableIterationLimit": "SWITCH_ENABLE",
"iterationLimit": 500,
"method": "AI",
"noiseThreshold": 0.01,
"radius": 1,
"spatialWeight": 0.05
},
"PostProcessTonemap": {
"enable": "SWITCH_ENABLE",
"exposure": 0.5
},
"RenderSettings": {
"interpolationMode": "CATMULLROM",
"maxIterations": 1000,
"shadowStepSize": 1,
"stepSize": 1
},
"TransferFunction": {
"blendingProfile": "MAXIMUM_OPACITY",
"components": [
{
"activeRegions": [
0
],
"diffuseEnd": {
"x": 1,
"y": 0.8549019607843137,
"z": 0.6980392156862745
},
"diffuseStart": {
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"z": 0.9215686274509803
},
"emissiveEnd": {
"x": 0,
"y": 0,
"z": 0
},
"emissiveStart": {
"x": 0,
"y": 0,
"z": 0
},
"emissiveStrength": 0,
"opacity": 1,
"opacityProfile": "SQUARE",
"opacityTransition": 0.06,
"range": {
"max": 0.778,
"min": 0.521
},
"roughness": 9.8,
"specularEnd": {
"x": 1,
"y": 1,
"z": 1
},
"specularStart": {
"x": 1,
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}
},
{
"activeRegions": [
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],
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"emissiveEnd": {
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},
"emissiveStrength": 0,
"opacity": 0.5,
"opacityProfile": "SQUARE",
"opacityTransition": 0.01,
"range": {
"max": 0.599,
"min": 0.465
},
"roughness": 90,
"specularEnd": {
"x": 1,
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},
"specularStart": {
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}
},
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}
],
"densityScale": 710,
"globalOpacity": 1,
"gradientScale": 110,
"shadingProfile": "HYBRID"
},
"View": {
"cameraName": "Cinematic",
"mode": "CINEMATIC"
}
}
"""