Merge pull request #1 from andreped/dev

Started setting up the app + docker builds [no ci]

.dockerignore

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+venv/

.github/workflows/deploy.yml

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+name: Sync to Hugging Face hub
+on:
+  push:
+    branches: [ main ]
+
+  # to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  sync-to-hub:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          lfs: true
+      - name: Push to hub
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: git push https://andreped:$HF_TOKEN@huggingface.co/spaces/andreped/neukit main

.github/workflows/filesize.yml

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+name: Check file size
+on:               # or directly `on: [push]` to run the action on every push on any branch
+  pull_request:
+    branches: [ main ]
+
+  # to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  sync-to-hub:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check large files
+        uses: ActionsDesk/lfs-warning@v2.0
+        with:
+          filesizelimit: 10485760 # this is 10MB so we can sync to HF Spaces

.gitignore

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+venv/

Dockerfile

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+# read the doc: https://huggingface.co/docs/hub/spaces-sdks-docker
+# you will also find guides on how best to write your Dockerfile
+
+# creates virtual ubuntu in docker image
+FROM ubuntu:22.04
+
+# set language, format and stuff
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+
+# NOTE: using -y is conveniently to automatically answer yes to all the questions
+# installing python3 with a specific version
+RUN apt-get update -y
+RUN apt-get upgrade -y
+RUN apt install software-properties-common -y
+RUN add-apt-repository ppa:deadsnakes/ppa -y
+RUN apt update
+RUN apt install python3.7 -y
+RUN apt install python3.7-distutils -y
+RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.7 1
+
+# installing other libraries
+RUN apt-get install python3-pip -y && \
+    apt-get -y install sudo
+RUN apt-get install curl -y
+RUN apt-get install nano -y
+RUN apt-get update && apt-get install -y git
+RUN apt-get install libblas-dev -y && apt-get install liblapack-dev -y
+RUN apt-get install gfortran -y
+RUN apt-get install libpng-dev -y
+RUN apt-get install python3-dev -y
+# RUN apt-get -y install cmake curl
+
+WORKDIR /code
+
+# install dependencies
+COPY ./requirements.txt /code/requirements.txt
+RUN pip install --no-cache-dir --upgrade -r /code/requirements.txt
+
+# resolve issue with tf==2.4 and gradio dependency collision issue
+RUN pip install --force-reinstall typing_extensions==4.0.0
+
+# Install wget
+RUN apt install wget -y && \
+    apt install unzip
+
+# Set up a new user named "user" with user ID 1000
+RUN useradd -m -u 1000 user
+
+# Switch to the "user" user
+USER user
+
+# Set home to the user's home directory
+ENV HOME=/home/user \
+    PATH=/home/user/.local/bin:$PATH
+
+# Set the working directory to the user's home directory
+WORKDIR $HOME/app
+
+# Copy the current directory contents into the container at $HOME/app setting the owner to the user
+COPY --chown=user . $HOME/app
+
+# Download pretrained parenchyma model
+RUN wget "https://github.com/raidionics/Raidionics-models/releases/download/1.2.0/Raidionics-MRI_Meningioma-ONNX-v12.zip" && \
+    unzip "Raidionics-MRI_Meningioma-ONNX-v12.zip" && mkdir -p resources/models/ && mv MRI_Meningioma/ resources/models/MRI_Meningioma/
+
+# Download test sample
+RUN pip install gdown && gdown "https://drive.google.com/uc?id=1shjSrFjS4PHE5sTku30PZTLPZpGu24o3"
+
+# CMD ["/bin/bash"]
+CMD ["python3", "demo/app.py"]

README.md

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-# neurokit
+---
+title: 'neukit: automatic meningioma segmentation from T1-weighted MRI'
+colorFrom: indigo
+colorTo: indigo
+sdk: docker
+app_port: 7860
+emoji: 🔎
+pinned: false
+license: mit
+app_file: app.py
+---
+
+# neukit
+
+## Usage
+
+The software will be made openly available on Hugging Face spaces very soon. Stay tuned for more!
+
+## Setup
+
+For development of this software, follow these steps to build the docker image and run the app through it:
+
+```
+docker build -t neukit ..
+docker run -it -p 7860:7860 neukit
+```
+
+Then open `http://127.0.0.1:7860` in your favourite internet browser to view the demo.

app.py

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+from neukit.gui import WebUI
+
+
+def main():
+    print("Launching demo...")
+
+    # cwd = "/Users/andreped/workspace/livermask/"  # local testing -> macOS
+    cwd = "/home/user/app/"  # production -> docker
+
+    model_name = "model.h5"  # assumed to lie in `cwd` directory
+    class_name = "parenchyma"
+
+    # initialize and run app
+    app = WebUI(model_name=model_name, class_name=class_name, cwd=cwd)
+    app.run()
+
+
+if __name__ == "__main__":
+    main()

neukit/gui.py

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+import gradio as gr
+from .utils import load_ct_to_numpy, load_pred_volume_to_numpy
+from .compute import run_model
+from .convert import nifti_to_glb
+
+
+class WebUI:
+    def __init__(self, model_name:str = None, class_name:str = None, cwd:str = None):
+        # global states
+        self.images = []
+        self.pred_images = []
+
+        # @TODO: This should be dynamically set based on chosen volume size
+        self.nb_slider_items = 100
+
+        self.model_name = model_name
+        self.class_name = class_name
+        self.cwd = cwd
+
+        # define widgets not to be rendered immediantly, but later on
+        self.slider = gr.Slider(1, self.nb_slider_items, value=1, step=1, label="Which 2D slice to show")
+        self.volume_renderer = gr.Model3D(
+            clear_color=[0.0, 0.0, 0.0, 0.0],
+            label="3D Model",
+            visible=True
+        ).style(height=512)
+
+    def combine_ct_and_seg(self, img, pred):
+        return (img, [(pred, self.class_name)])
+
+    def upload_file(self, file):
+        return file.name
+
+    def load_mesh(self, mesh_file_name, model_name):
+        path = mesh_file_name.name
+        run_model(path, model_name)
+        nifti_to_glb("prediction-livermask.nii")
+        self.images = load_ct_to_numpy(path)
+        self.pred_images = load_pred_volume_to_numpy("./prediction-livermask.nii")
+        self.slider = self.slider.update(value=2)
+        return "./prediction.obj"
+
+    def get_img_pred_pair(self, k):
+        k = int(k) - 1
+        out = [gr.AnnotatedImage.update(visible=False)] * self.nb_slider_items
+        out[k] = gr.AnnotatedImage.update(self.combine_ct_and_seg(self.images[k], self.pred_images[k]), visible=True)
+        return out
+
+    def run(self):
+        with gr.Blocks() as demo:
+
+            with gr.Row().style(equal_height=True):
+                file_output = gr.File(
+                    file_types=[".nii", ".nii.nz"],
+                    file_count="single"
+                ).style(full_width=False, size="sm")
+                file_output.upload(self.upload_file, file_output, file_output)
+
+                run_btn = gr.Button("Run analysis").style(full_width=False, size="sm")
+                run_btn.click(
+                    fn=lambda x: self.load_mesh(x, model_name=self.cwd + self.model_name),
+                    inputs=file_output,
+                    outputs=self.volume_renderer
+                )
+
+            with gr.Row().style(equal_height=True):
+                gr.Examples(
+                    examples=[self.cwd + "test-volume.nii"],
+                    inputs=file_output,
+                    outputs=file_output,
+                    fn=self.upload_file,
+                    cache_examples=True,
+                )
+
+            with gr.Row().style(equal_height=True):
+                with gr.Box():
+                    image_boxes = []
+                    for i in range(self.nb_slider_items):
+                        visibility = True if i == 1 else False
+                        t = gr.AnnotatedImage(visible=visibility)\
+                            .style(color_map={self.class_name: "#ffae00"}, height=512, width=512)
+                        image_boxes.append(t)
+
+                    self.slider.change(self.get_img_pred_pair, self.slider, image_boxes)
+
+                with gr.Box():
+                    self.volume_renderer.render()
+
+            with gr.Row():
+                self.slider.render()
+
+        # sharing app publicly -> share=True: https://gradio.app/sharing-your-app/
+        # inference times > 60 seconds -> need queue(): https://github.com/tloen/alpaca-lora/issues/60#issuecomment-1510006062
+        demo.queue().launch(server_name="0.0.0.0", server_port=7860, share=True)

neukit/utils.py

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+import numpy as np
+import nibabel as nib
+from nibabel.processing import resample_to_output
+from skimage.measure import marching_cubes
+
+
+def load_ct_to_numpy(data_path):
+    if type(data_path) != str:
+        data_path = data_path.name
+
+    image = nib.load(data_path)
+    data = image.get_fdata()
+
+    data = np.rot90(data, k=1, axes=(0, 1))
+
+    data[data < -150] = -150
+    data[data > 250] = 250
+
+    data = data - np.amin(data)
+    data = data / np.amax(data) * 255
+    data = data.astype("uint8")
+
+    print(data.shape)
+    return [data[..., i] for i in range(data.shape[-1])]
+
+
+def load_pred_volume_to_numpy(data_path):
+    if type(data_path) != str:
+        data_path = data_path.name
+
+    image = nib.load(data_path)
+    data = image.get_fdata()
+
+    data = np.rot90(data, k=1, axes=(0, 1))
+
+    data[data > 0] = 1
+    data = data.astype("uint8")
+
+    print(data.shape)
+    return [data[..., i] for i in range(data.shape[-1])]
+
+
+def nifti_to_glb(path, output="prediction.obj"):
+    # load NIFTI into numpy array
+    image = nib.load(path)
+    resampled = resample_to_output(image, [1, 1, 1], order=1)
+    data = resampled.get_fdata().astype("uint8")
+
+    # extract surface
+    verts, faces, normals, values = marching_cubes(data, 0)
+    faces += 1
+
+    with open(output, 'w') as thefile:
+        for item in verts:
+            thefile.write("v {0} {1} {2}\n".format(item[0],item[1],item[2]))
+
+        for item in normals:
+            thefile.write("vn {0} {1} {2}\n".format(item[0],item[1],item[2]))
+
+        for item in faces:
+            thefile.write("f {0}//{0} {1}//{1} {2}//{2}\n".format(item[0],item[1],item[2]))

requirements.txt

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+raidionicsrads @ https://github.com/dbouget/raidionics_rads_lib/releases/download/v1.1.0/raidionicsrads-1.1.0-py3-none-manylinux1_x86_64.whl
+onnxruntime-gpu==1.12.1
+gradio==3.32.0