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- .gitattributes +44 -0
- Dockerfile +80 -0
- dermsynth3d.yml +204 -0
- gradio_app.py +1014 -0
- hf_demo/lesions/006-f-run/lesion_dilated_mask_demo.png +0 -0
- hf_demo/lesions/006-f-run/lesion_dilated_mask_latest.png +0 -0
- hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_1.png +0 -0
- hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_10.png +0 -0
- hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_15.png +0 -0
- hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_2.png +0 -0
- hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_30.png +0 -0
- hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_5.png +0 -0
- hf_demo/lesions/006-f-run/lesion_mask_latest.png +0 -0
- hf_demo/lesions/006-f-run/lesion_mask_lesion_0.png +0 -0
- hf_demo/lesions/006-f-run/lesion_mask_lesion_1.png +0 -0
- hf_demo/lesions/006-f-run/lesion_mask_lesion_10.png +0 -0
- hf_demo/lesions/006-f-run/lesion_mask_lesion_15.png +0 -0
- hf_demo/lesions/006-f-run/lesion_mask_lesion_2.png +0 -0
- hf_demo/lesions/006-f-run/lesion_mask_lesion_30.png +0 -0
- hf_demo/lesions/006-f-run/lesion_mask_lesion_5.png +0 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_demo.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_latest.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_1.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_10.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_15.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_2.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_30.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_5.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_demo.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_latest.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_1.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_10.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_15.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_2.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_30.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_5.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_lesion_0.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_mask.png +0 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_demo.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_latest.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_1.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_10.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_15.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_2.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_30.png +3 -0
- hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_5.png +3 -0
- hf_demo/lesions/221-m-u/lesion_dilated_mask_lesion_1.png +0 -0
- hf_demo/lesions/221-m-u/lesion_dilated_mask_lesion_10.png +0 -0
- hf_demo/lesions/221-m-u/lesion_dilated_mask_lesion_15.png +0 -0
- hf_demo/lesions/221-m-u/lesion_dilated_mask_lesion_2.png +0 -0
.gitattributes
CHANGED
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@@ -33,3 +33,47 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.zst filter=lfs diff=lfs merge=lfs -text
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*tfevents* filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.zst filter=lfs diff=lfs merge=lfs -text
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*tfevents* filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_demo.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_latest.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_1.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_10.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_15.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_2.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_30.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_5.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_demo.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_latest.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_1.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_10.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_15.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_2.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_30.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_5.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_lesion_0.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_demo.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_latest.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_1.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_10.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_15.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_2.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_30.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_5.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_blended_lesion_1.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_blended_lesion_10.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_blended_lesion_15.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_blended_lesion_2.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_blended_lesion_30.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_blended_lesion_5.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_dilated_lesion_1.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_dilated_lesion_10.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_dilated_lesion_15.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_dilated_lesion_2.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_dilated_lesion_30.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_dilated_lesion_5.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_lesion_0.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_pasted_lesion_1.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_pasted_lesion_10.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_pasted_lesion_15.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_pasted_lesion_2.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_pasted_lesion_30.png filter=lfs diff=lfs merge=lfs -text
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hf_demo/lesions/221-m-u/model_highres_0_normalized_pasted_lesion_5.png filter=lfs diff=lfs merge=lfs -text
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Dockerfile
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| 1 |
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FROM nvidia/cuda:11.3.1-cudnn8-runtime-ubuntu20.04
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# FROM pytorch/pytorch:1.12.1-cuda11.3-cudnn8-devel
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RUN echo $CUDA_HOME
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# ENV LD_LIBRARY_PATH /usr/local/cuda/lib64/stubs/:$LD_LIBRARY_PATH
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# ENV CUDA_HOME /usr/local/cuda
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# ENV LD_LIBRARY_PATH /usr/local/cuda/lib64/:$LD_LIBRARY_PATH
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# ENV PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
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# ENV LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64
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# ENV PATH=/opt/conda/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
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# ENV LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64
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#
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ENV DEBIAN_FRONTEND=noninteractive
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ARG UID=1000
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ARG GID=1000
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ARG USER=developer
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ARG GROUP=$USER
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ENV FORCE_CUDA=1
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RUN echo $(nvcc --version)
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# Install necessary packages
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RUN --mount=type=cache,target=/var/cache/apt apt update && apt install -y --no-install-recommends \
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sudo \
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git \
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wget \
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bzip2 \
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ca-certificates \
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libx11-6 \
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python3-opencv \
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vim \
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&& rm -rf /var/lib/apt/lists/*
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## Create a non-root user and group
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RUN addgroup --gid $GID $GROUP
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RUN adduser --disabled-password --gecos '' --uid $UID --gid $GID $USER && \
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adduser $USER sudo && \
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echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
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# RUN useradd -D -mU ${USER} --uid=${UID}
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# Run as this user from now on
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USER $USER:$GID
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# Install Miniconda
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WORKDIR /home/$USER
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RUN wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh \
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&& /bin/bash ~/miniconda.sh -b -p ~/miniconda \
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&& rm ~/miniconda.sh
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ENV PATH=/home/$USER/miniconda/bin:$PATH
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| 53 |
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| 54 |
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RUN git clone --recurse-submodules https://github.com/sfu-mial/DermSynth3D.git
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WORKDIR /home/$USER/DermSynth3D
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| 56 |
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| 57 |
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# Set up conda environment
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COPY . .
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COPY dermsynth3d.yml .
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RUN conda env create -f dermsynth3d.yml && conda clean -afy
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ENV CONDA_DEFAULT_ENV=dermsynth3d
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ENV CONDA_PREFIX=/home/$USER/miniconda/envs/$CONDA_DEFAULT_ENV
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| 63 |
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ENV PATH=$CONDA_PREFIX/bin:$PATH
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| 64 |
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| 65 |
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| 66 |
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RUN echo "source activate $(head -1 dermsynth3d.yml | cut -d' ' -f2)" > ~/.bashrc
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| 67 |
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ENV PATH /home/$USER/miniconda/envs/$(head -1 dermsynth3d.yml | cut -d' ' -f2)/bin:$PATH
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| 68 |
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| 69 |
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# Copy code
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| 70 |
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# COPY data /demo_data
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| 71 |
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# COPY . /home/$USER/DermSynth3D
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| 72 |
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| 73 |
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COPY . .
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| 74 |
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# Test imports
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| 75 |
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# RUN git clone --recurse-submodules https://github.com/sfu-mial/DermSynth3D.git
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#, "python", "scripts/gen_data.py"]
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| 77 |
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WORKDIR /home/$USER/DermSynth3D
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| 78 |
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RUN pip install gradio fire streamlit
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| 79 |
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# CMD ["streamlit", "run", "app.py"]
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| 80 |
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CMD ["gradio", "gradio_app.py"]
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dermsynth3d.yml
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
name: dermsynth3d
|
| 2 |
+
channels:
|
| 3 |
+
- pytorch3d
|
| 4 |
+
- iopath
|
| 5 |
+
- bottler
|
| 6 |
+
- pytorch
|
| 7 |
+
- fvcore
|
| 8 |
+
- pytorch
|
| 9 |
+
- conda-forge
|
| 10 |
+
- defaults
|
| 11 |
+
dependencies:
|
| 12 |
+
- _libgcc_mutex=0.1=conda_forge
|
| 13 |
+
- _openmp_mutex=4.5=2_kmp_llvm
|
| 14 |
+
- brotlipy=0.7.0=py38h27cfd23_1003
|
| 15 |
+
- ca-certificates=2022.12.7=ha878542_0
|
| 16 |
+
- certifi=2022.12.7=py38h06a4308_0
|
| 17 |
+
- cffi=1.15.1=py38h4a40e3a_3
|
| 18 |
+
- charset-normalizer=2.0.4=pyhd3eb1b0_0
|
| 19 |
+
- colorama=0.4.6=pyhd8ed1ab_0
|
| 20 |
+
- cryptography=38.0.1=py38h9ce1e76_0
|
| 21 |
+
- cudatoolkit=11.3.1=h2bc3f7f_2
|
| 22 |
+
- freetype=2.12.1=hca18f0e_1
|
| 23 |
+
- future=0.18.2=pyhd8ed1ab_6
|
| 24 |
+
- fvcore=0.1.5.post20210915=py38
|
| 25 |
+
- idna=3.4=py38h06a4308_0
|
| 26 |
+
- intel-openmp=2021.4.0=h06a4308_3561
|
| 27 |
+
- iopath=0.1.9=py38
|
| 28 |
+
- jbig=2.1=h7f98852_2003
|
| 29 |
+
- jpeg=9e=h166bdaf_2
|
| 30 |
+
- lcms2=2.12=hddcbb42_0
|
| 31 |
+
- ld_impl_linux-64=2.38=h1181459_1
|
| 32 |
+
- lerc=3.0=h295c915_0
|
| 33 |
+
- libblas=3.9.0=12_linux64_mkl
|
| 34 |
+
- libcblas=3.9.0=12_linux64_mkl
|
| 35 |
+
- libdeflate=1.8=h7f8727e_5
|
| 36 |
+
- libffi=3.4.2=h6a678d5_6
|
| 37 |
+
- libgcc-ng=12.2.0=h65d4601_19
|
| 38 |
+
- liblapack=3.9.0=12_linux64_mkl
|
| 39 |
+
- libpng=1.6.39=h753d276_0
|
| 40 |
+
- libprotobuf=3.19.4=h780b84a_0
|
| 41 |
+
- libstdcxx-ng=11.2.0=h1234567_1
|
| 42 |
+
- libtiff=4.3.0=h6f004c6_2
|
| 43 |
+
- libwebp-base=1.2.4=h166bdaf_0
|
| 44 |
+
- libzlib=1.2.13=h166bdaf_4
|
| 45 |
+
- llvm-openmp=15.0.6=he0ac6c6_0
|
| 46 |
+
- lz4-c=1.9.3=h9c3ff4c_1
|
| 47 |
+
- mkl=2021.4.0=h06a4308_640
|
| 48 |
+
- ncurses=6.3=h5eee18b_3
|
| 49 |
+
- ninja=1.11.0=h924138e_0
|
| 50 |
+
- numpy=1.22.3=py38h99721a1_2
|
| 51 |
+
- olefile=0.46=pyh9f0ad1d_1
|
| 52 |
+
- openjpeg=2.5.0=h7d73246_0
|
| 53 |
+
- openssl=1.1.1s=h0b41bf4_1
|
| 54 |
+
- pillow=8.4.0=py38h8e6f84c_0
|
| 55 |
+
- pip=22.3.1=py38h06a4308_0
|
| 56 |
+
- portalocker=2.6.0=py38h578d9bd_1
|
| 57 |
+
- pycparser=2.21=pyhd8ed1ab_0
|
| 58 |
+
- pyopenssl=22.0.0=pyhd3eb1b0_0
|
| 59 |
+
- pysocks=1.7.1=py38h06a4308_0
|
| 60 |
+
- python=3.8.15=h7a1cb2a_2
|
| 61 |
+
- python_abi=3.8=2_cp38
|
| 62 |
+
- pytorch
|
| 63 |
+
- torchvision
|
| 64 |
+
- pytorch3d=0.7.2=py38_cu113_pyt1100
|
| 65 |
+
- pyyaml=6.0=py38h0a891b7_5
|
| 66 |
+
- readline=8.2=h5eee18b_0
|
| 67 |
+
- requests=2.28.1=py38h06a4308_0
|
| 68 |
+
- setuptools=65.5.0=py38h06a4308_0
|
| 69 |
+
- six=1.16.0=pyh6c4a22f_0
|
| 70 |
+
- sleef=3.5.1=h9b69904_2
|
| 71 |
+
- sqlite=3.40.0=h5082296_0
|
| 72 |
+
- tabulate=0.9.0=pyhd8ed1ab_1
|
| 73 |
+
- termcolor=2.1.1=pyhd8ed1ab_0
|
| 74 |
+
- tk=8.6.12=h1ccaba5_0
|
| 75 |
+
- tqdm=4.64.1=pyhd8ed1ab_0
|
| 76 |
+
- typing_extensions=4.4.0=pyha770c72_0
|
| 77 |
+
- urllib3=1.26.13=py38h06a4308_0
|
| 78 |
+
- wheel=0.37.1=pyhd3eb1b0_0
|
| 79 |
+
- xz=5.2.8=h5eee18b_0
|
| 80 |
+
- yacs=0.1.8=pyhd8ed1ab_0
|
| 81 |
+
- yaml=0.2.5=h7f98852_2
|
| 82 |
+
- zlib=1.2.13=h166bdaf_4
|
| 83 |
+
- zstd=1.5.2=h8a70e8d_1
|
| 84 |
+
- pip:
|
| 85 |
+
- absl-py==1.4.0
|
| 86 |
+
- albumentations==1.3.0
|
| 87 |
+
- anyio==3.6.2
|
| 88 |
+
- argon2-cffi==21.3.0
|
| 89 |
+
- argon2-cffi-bindings==21.2.0
|
| 90 |
+
- arrow==1.2.3
|
| 91 |
+
- asttokens==2.2.1
|
| 92 |
+
- attrs==22.2.0
|
| 93 |
+
- babel==2.11.0
|
| 94 |
+
- backcall==0.2.0
|
| 95 |
+
- beautifulsoup4==4.11.1
|
| 96 |
+
- bleach==5.0.1
|
| 97 |
+
- boto3==1.26.47
|
| 98 |
+
- botocore==1.29.47
|
| 99 |
+
- comm==0.1.2
|
| 100 |
+
- contourpy==1.0.6
|
| 101 |
+
- cycler==0.11.0
|
| 102 |
+
- debugpy==1.6.4
|
| 103 |
+
- decorator==5.1.1
|
| 104 |
+
- defusedxml==0.7.1
|
| 105 |
+
- entrypoints==0.4
|
| 106 |
+
- executing==1.2.0
|
| 107 |
+
- fastjsonschema==2.16.2
|
| 108 |
+
- fonttools==4.38.0
|
| 109 |
+
- fqdn==1.5.1
|
| 110 |
+
- imageio==2.23.0
|
| 111 |
+
- importlib-metadata==5.2.0
|
| 112 |
+
- importlib-resources==5.10.2
|
| 113 |
+
- ipykernel==6.19.4
|
| 114 |
+
- ipython==8.7.0
|
| 115 |
+
- ipython-genutils==0.2.0
|
| 116 |
+
- ipywidgets==8.0.4
|
| 117 |
+
- isoduration==20.11.0
|
| 118 |
+
- jedi==0.18.2
|
| 119 |
+
- jinja2==3.1.2
|
| 120 |
+
- jmespath==1.0.1
|
| 121 |
+
- joblib==1.2.0
|
| 122 |
+
- json5==0.9.10
|
| 123 |
+
- jsonpointer==2.3
|
| 124 |
+
- jsonschema==4.17.3
|
| 125 |
+
- jupyter-client==7.4.8
|
| 126 |
+
- jupyter-core==5.1.1
|
| 127 |
+
- jupyter-events==0.5.0
|
| 128 |
+
- jupyter-server==2.0.6
|
| 129 |
+
- jupyter-server-terminals==0.4.3
|
| 130 |
+
- jupyterlab==3.5.2
|
| 131 |
+
- jupyterlab-pygments==0.2.2
|
| 132 |
+
- jupyterlab-server==2.17.0
|
| 133 |
+
- jupyterlab-widgets==3.0.5
|
| 134 |
+
- kiwisolver==1.4.4
|
| 135 |
+
- markupsafe==2.1.1
|
| 136 |
+
- matplotlib==3.6.2
|
| 137 |
+
- matplotlib-inline==0.1.6
|
| 138 |
+
- mistune==2.0.4
|
| 139 |
+
- nbclassic==0.4.8
|
| 140 |
+
- nbclient==0.7.2
|
| 141 |
+
- nbconvert==7.2.7
|
| 142 |
+
- nbformat==5.7.1
|
| 143 |
+
- nest-asyncio==1.5.6
|
| 144 |
+
- networkx==2.8.8
|
| 145 |
+
- nibabel==5.0.0
|
| 146 |
+
- notebook==6.5.2
|
| 147 |
+
- mediapy
|
| 148 |
+
- fire
|
| 149 |
+
- streamlit
|
| 150 |
+
- gradio
|
| 151 |
+
- notebook-shim==0.2.2
|
| 152 |
+
- opencv-python==4.6.0.66
|
| 153 |
+
- opencv-python-headless==4.6.0.66
|
| 154 |
+
- packaging==22.0
|
| 155 |
+
- pandas==1.5.2
|
| 156 |
+
- pandocfilters==1.5.0
|
| 157 |
+
- parso==0.8.3
|
| 158 |
+
- pexpect==4.8.0
|
| 159 |
+
- pickleshare==0.7.5
|
| 160 |
+
- pkgutil-resolve-name==1.3.10
|
| 161 |
+
- platformdirs==2.6.2
|
| 162 |
+
- prometheus-client==0.15.0
|
| 163 |
+
- prompt-toolkit==3.0.36
|
| 164 |
+
- psutil==5.9.4
|
| 165 |
+
- ptyprocess==0.7.0
|
| 166 |
+
- pure-eval==0.2.2
|
| 167 |
+
- pygments==2.13.0
|
| 168 |
+
- pyparsing==3.0.9
|
| 169 |
+
- pyrsistent==0.19.3
|
| 170 |
+
- python-dateutil==2.8.2
|
| 171 |
+
- python-json-logger==2.0.4
|
| 172 |
+
- pytz==2022.7
|
| 173 |
+
- pywavelets==1.4.1
|
| 174 |
+
- pyzmq==24.0.1
|
| 175 |
+
- qudida==0.0.4
|
| 176 |
+
- regex==2022.10.31
|
| 177 |
+
- rfc3339-validator==0.1.4
|
| 178 |
+
- rfc3986-validator==0.1.1
|
| 179 |
+
- rtree==1.0.1
|
| 180 |
+
- s3transfer==0.6.0
|
| 181 |
+
- scikit-image==0.19.3
|
| 182 |
+
- scikit-learn==1.2.0
|
| 183 |
+
- scipy==1.9.3
|
| 184 |
+
- seaborn==0.12.2
|
| 185 |
+
- send2trash==1.8.0
|
| 186 |
+
- sniffio==1.3.0
|
| 187 |
+
- soupsieve==2.3.2.post1
|
| 188 |
+
- stack-data==0.6.2
|
| 189 |
+
- terminado==0.17.1
|
| 190 |
+
- threadpoolctl==3.1.0
|
| 191 |
+
- tornado==6.2
|
| 192 |
+
- traitlets==5.8.0
|
| 193 |
+
- trimesh==3.17.1
|
| 194 |
+
- uri-template==1.2.0
|
| 195 |
+
- wcwidth==0.2.5
|
| 196 |
+
- webcolors==1.12
|
| 197 |
+
- webencodings==0.5.1
|
| 198 |
+
- websocket-client==1.4.2
|
| 199 |
+
- widgetsnbextension==4.0.5
|
| 200 |
+
- zipp==3.11.0
|
| 201 |
+
- streamlit
|
| 202 |
+
- rtree
|
| 203 |
+
- plotly
|
| 204 |
+
prefix: /localhome/asa409/miniconda3/envs/dermsynth3d
|
gradio_app.py
ADDED
|
@@ -0,0 +1,1014 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
from functools import partial
|
| 2 |
+
import gradio as gr
|
| 3 |
+
|
| 4 |
+
from PIL import Image
|
| 5 |
+
import numpy as np
|
| 6 |
+
import gradio as gr
|
| 7 |
+
import torch
|
| 8 |
+
import os
|
| 9 |
+
import fire
|
| 10 |
+
import multiprocessing as mp
|
| 11 |
+
import os, sys
|
| 12 |
+
|
| 13 |
+
sys.path.append(os.path.join(os.path.dirname(__file__), "DermSynth3D"))
|
| 14 |
+
sys.path.append(os.path.join(os.path.dirname(__file__), "DermSynth3D", "dermsynth3d"))
|
| 15 |
+
sys.path.append(os.path.join(os.path.dirname(__file__), "DermSynth3D", "skin3d"))
|
| 16 |
+
|
| 17 |
+
import pandas as pd
|
| 18 |
+
import numpy as np
|
| 19 |
+
from glob import glob
|
| 20 |
+
from PIL import Image
|
| 21 |
+
import torch
|
| 22 |
+
import torch.nn as nn
|
| 23 |
+
import trimesh
|
| 24 |
+
import plotly.graph_objects as go
|
| 25 |
+
from plotly.subplots import make_subplots
|
| 26 |
+
|
| 27 |
+
import math
|
| 28 |
+
from trimesh import transformations as tf
|
| 29 |
+
import os
|
| 30 |
+
from math import pi
|
| 31 |
+
import matplotlib.pyplot as plt
|
| 32 |
+
import plotly
|
| 33 |
+
|
| 34 |
+
import plotly.graph_objects as go
|
| 35 |
+
from skimage import io
|
| 36 |
+
|
| 37 |
+
view_width = 400
|
| 38 |
+
view_height = 400
|
| 39 |
+
|
| 40 |
+
import mediapy as mpy
|
| 41 |
+
|
| 42 |
+
try:
|
| 43 |
+
from pytorch3d.io import load_objs_as_meshes
|
| 44 |
+
from pytorch3d.structures import Meshes
|
| 45 |
+
|
| 46 |
+
from pytorch3d.renderer import (
|
| 47 |
+
look_at_view_transform,
|
| 48 |
+
FoVPerspectiveCameras,
|
| 49 |
+
PointLights,
|
| 50 |
+
DirectionalLights,
|
| 51 |
+
Materials,
|
| 52 |
+
RasterizationSettings,
|
| 53 |
+
MeshRenderer,
|
| 54 |
+
MeshRasterizer,
|
| 55 |
+
SoftPhongShader,
|
| 56 |
+
TexturesUV,
|
| 57 |
+
TexturesVertex,
|
| 58 |
+
)
|
| 59 |
+
|
| 60 |
+
print("Pytorch3d compiled properly")
|
| 61 |
+
except:
|
| 62 |
+
print("Pytorch3d not compiled properly. Install pytorch3d with torch/cuda support")
|
| 63 |
+
|
| 64 |
+
try:
|
| 65 |
+
sys.path.append("./DermSynth3D/")
|
| 66 |
+
sys.path.append("./DermSynth3D/dermsynth3d/")
|
| 67 |
+
sys.path.append("./DermSynth3D/skin3d/")
|
| 68 |
+
from dermsynth3d import BlendLesions, Generate2DViews, SelectAndPaste
|
| 69 |
+
from dermsynth3d.tools.generate2d import Generate2DHelper
|
| 70 |
+
from dermsynth3d.utils.utils import yaml_loader
|
| 71 |
+
from dermsynth3d.utils.utils import random_bound, make_masks
|
| 72 |
+
from dermsynth3d.tools.synthesize import Synthesize2D
|
| 73 |
+
from dermsynth3d.datasets.synth_dataset import SynthesizeDataset
|
| 74 |
+
from dermsynth3d.tools.renderer import (
|
| 75 |
+
MeshRendererPyTorch3D,
|
| 76 |
+
camera_pos_from_normal,
|
| 77 |
+
)
|
| 78 |
+
from dermsynth3d.deepblend.blend3d import Blended3d
|
| 79 |
+
from dermsynth3d.utils.channels import Target
|
| 80 |
+
from dermsynth3d.utils.tensor import (
|
| 81 |
+
pil_to_tensor,
|
| 82 |
+
)
|
| 83 |
+
from dermsynth3d.utils.colorconstancy import shade_of_gray_cc
|
| 84 |
+
from dermsynth3d.datasets.datasets import Fitz17KAnnotations, Background2d
|
| 85 |
+
from skin3d.skin3d.bodytex import BodyTexDataset
|
| 86 |
+
|
| 87 |
+
print("DermSynth3D compiled properly")
|
| 88 |
+
except Exception as e:
|
| 89 |
+
print(e)
|
| 90 |
+
print("DermSynth3D not in the path. Make sure to add it to the path.")
|
| 91 |
+
|
| 92 |
+
_TITLE = """DermSynth3D: A Framework for generating Synthetic Dermatological Images"""
|
| 93 |
+
_DESCRIPTION = """
|
| 94 |
+
**Step 1**. Select the Mesh, texture map and number of lesions from the dropdown or select an example.</br>
|
| 95 |
+
**Step 2**. Selct the number of views to render. </br>
|
| 96 |
+
**Step 3** (optional). Randomize the view parameters by clicking on the checkbox.</br>
|
| 97 |
+
**Step 4**. Click on the Render Views button to render the views. </br>
|
| 98 |
+
"""
|
| 99 |
+
|
| 100 |
+
|
| 101 |
+
deployed = True
|
| 102 |
+
|
| 103 |
+
if deployed:
|
| 104 |
+
print(f"Is CUDA available: {torch.cuda.is_available()}")
|
| 105 |
+
global DEVICE
|
| 106 |
+
DEVICE = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
|
| 107 |
+
if torch.cuda.is_available():
|
| 108 |
+
print(f"CUDA device: {torch.cuda.get_device_name(torch.cuda.current_device())}")
|
| 109 |
+
else:
|
| 110 |
+
print("Running on CPU")
|
| 111 |
+
|
| 112 |
+
global mesh_paths, mesh_names, all_textures, dir_blended_textures, dir_anatomy
|
| 113 |
+
global get_no_lesion_path, get_mesh_path, get_mask_path, get_dilated_lesion_path
|
| 114 |
+
global get_blended_lesion_path, get_pasted_lesion_path, get_texture_module
|
| 115 |
+
global dir_blended_textures, dir_anatomy, dir_background
|
| 116 |
+
|
| 117 |
+
# File path of the bodytex CSV.
|
| 118 |
+
bodytex_csv = "./DermSynth3D/skin3d/data/3dbodytex-1.1-highres/bodytex.csv"
|
| 119 |
+
bodytex_df = pd.read_csv(bodytex_csv, converters={"scan_id": lambda x: str(x)})
|
| 120 |
+
bodytex = BodyTexDataset(
|
| 121 |
+
df=bodytex_df,
|
| 122 |
+
dir_textures="./DermSynth3D/data/3dbodytex-1.1-highres/",
|
| 123 |
+
dir_annotate="./DermSynth3D/skin3d/data/3dbodytex-1.1-highres/annotations/",
|
| 124 |
+
)
|
| 125 |
+
# True to use the blended lesions, False to use the pasted lesions.
|
| 126 |
+
is_blend = True
|
| 127 |
+
background_ds = Background2d(
|
| 128 |
+
dir_images="./DermSynth3D/data/background/IndoorScene/",
|
| 129 |
+
image_filenames=None,
|
| 130 |
+
)
|
| 131 |
+
|
| 132 |
+
|
| 133 |
+
def prepare_ds_renderer(
|
| 134 |
+
randomize,
|
| 135 |
+
mesh_name,
|
| 136 |
+
texture_name,
|
| 137 |
+
num_lesion,
|
| 138 |
+
num_views,
|
| 139 |
+
dist,
|
| 140 |
+
elev,
|
| 141 |
+
azim,
|
| 142 |
+
light_pos,
|
| 143 |
+
light_ac,
|
| 144 |
+
light_dc,
|
| 145 |
+
light_sc,
|
| 146 |
+
mat_sh,
|
| 147 |
+
mat_sc,
|
| 148 |
+
device=DEVICE,
|
| 149 |
+
):
|
| 150 |
+
mesh_filename = get_mesh_path(mesh_name)
|
| 151 |
+
mesh = load_mesh_and_texture(mesh_name, texture_name, num_lesion, device)
|
| 152 |
+
gr.Info("Preparing for Rendering...")
|
| 153 |
+
mesh_renderer = MeshRendererPyTorch3D(mesh, DEVICE, config=None)
|
| 154 |
+
extension = f"lesion_{num_lesion}"
|
| 155 |
+
nevi_exists = os.path.exists(bodytex.annotation_filepath(mesh_name.split("_")[0]))
|
| 156 |
+
gen2d = Generate2DHelper(
|
| 157 |
+
mesh_filename=mesh_filename,
|
| 158 |
+
dir_blended_textures="./hf_demo/lesions/",
|
| 159 |
+
dir_anatomy="./DermSynth3D/data/bodytex_anatomy_labels/",
|
| 160 |
+
fitz_ds=None, # fitz_ds,
|
| 161 |
+
background_ds=background_ds,
|
| 162 |
+
device=device,
|
| 163 |
+
debug=True,
|
| 164 |
+
bodytex=bodytex,
|
| 165 |
+
blended_file_ext=extension, # if num_lesion > 0 else "demo",
|
| 166 |
+
config=None,
|
| 167 |
+
is_blended=is_blend,
|
| 168 |
+
)
|
| 169 |
+
blended3d = Blended3d(
|
| 170 |
+
mesh_filename=os.path.join(
|
| 171 |
+
"./DermSynth3D/data/3dbodytex-1.1-highres/",
|
| 172 |
+
mesh_name,
|
| 173 |
+
"model_highres_0_normalized.obj",
|
| 174 |
+
),
|
| 175 |
+
device=DEVICE,
|
| 176 |
+
dir_blended_textures=dir_blended_textures,
|
| 177 |
+
dir_anatomy=dir_anatomy,
|
| 178 |
+
extension=extension if num_lesion > 0 else "demo",
|
| 179 |
+
)
|
| 180 |
+
normal_texture = load_texture_map(
|
| 181 |
+
mesh, mesh_name, "No Lesion", 0, device
|
| 182 |
+
).maps_padded()
|
| 183 |
+
if num_lesion > 0:
|
| 184 |
+
blended_texture_image = load_texture_map(
|
| 185 |
+
mesh, mesh_name, "Blended Lesion", num_lesion, device
|
| 186 |
+
).maps_padded()
|
| 187 |
+
pasted_texture_image = load_texture_map(
|
| 188 |
+
mesh, mesh_name, "Pasted Lesion", num_lesion, device
|
| 189 |
+
).maps_padded()
|
| 190 |
+
dilated_texture_image = load_texture_map(
|
| 191 |
+
mesh, mesh_name, "Dilated Lesion", num_lesion, device
|
| 192 |
+
).maps_padded()
|
| 193 |
+
|
| 194 |
+
# texture_lesion_mask = blended3d.lesion_texture_mask(astensor=True).to(device)
|
| 195 |
+
# non_skin_texture_mask = blended3d.nonskin_texture_mask(astensor=True).to(device)
|
| 196 |
+
# vertices_to_anatomy = blended3d.vertices_to_anatomy()
|
| 197 |
+
# mesh_renderer.raster_settings = raster_settings
|
| 198 |
+
renderer, cameras, lights, materials = set_rendering_params(
|
| 199 |
+
randomize,
|
| 200 |
+
1, # num_views,
|
| 201 |
+
dist,
|
| 202 |
+
elev,
|
| 203 |
+
azim,
|
| 204 |
+
light_pos,
|
| 205 |
+
light_ac,
|
| 206 |
+
light_dc,
|
| 207 |
+
light_sc,
|
| 208 |
+
mat_sh,
|
| 209 |
+
mat_sc,
|
| 210 |
+
)
|
| 211 |
+
# mesh_renderer.mesh = mesh
|
| 212 |
+
# mesh_renderer.cameras = cameras
|
| 213 |
+
# mesh_renderer.lights = lights
|
| 214 |
+
# mesh_renderer.materials = materials
|
| 215 |
+
# mesh_renderer.renderer = renderer
|
| 216 |
+
gr.Info("Successfully prepared renderer.")
|
| 217 |
+
# render normal images
|
| 218 |
+
gr.Info("Rendering Images...")
|
| 219 |
+
# if num_views > 1:
|
| 220 |
+
# mesh_renderer.mesh = mesh.extend(num_views)
|
| 221 |
+
gr.Info(f"Rendering {num_views} views on {DEVICE}. Please wait...")
|
| 222 |
+
img_count = 0
|
| 223 |
+
view2d = []
|
| 224 |
+
depth2d = []
|
| 225 |
+
anatomy2d = []
|
| 226 |
+
seg2d = []
|
| 227 |
+
view_size = (224, 224)
|
| 228 |
+
while img_count < num_views:
|
| 229 |
+
if randomize:
|
| 230 |
+
gr.Info("Finding suitable parameters...")
|
| 231 |
+
success = gen2d.randomize_parameters(config=None)
|
| 232 |
+
if not success:
|
| 233 |
+
gr.Info("Could not find suitable parameters. Trying again.")
|
| 234 |
+
continue
|
| 235 |
+
else:
|
| 236 |
+
raster_settings = RasterizationSettings(
|
| 237 |
+
image_size=view_size[0],
|
| 238 |
+
blur_radius=0.0,
|
| 239 |
+
faces_per_pixel=1,
|
| 240 |
+
# max_faces_per_bin=100,
|
| 241 |
+
# bin_size=0,
|
| 242 |
+
perspective_correct=True,
|
| 243 |
+
)
|
| 244 |
+
gen2d.mesh_renderer.cameras = cameras
|
| 245 |
+
gen2d.mesh_renderer.lights = lights
|
| 246 |
+
gen2d.mesh_renderer.materials = materials
|
| 247 |
+
gen2d.mesh_renderer.raster_settings = raster_settings
|
| 248 |
+
gen2d.mesh_renderer.initialize_renderer()
|
| 249 |
+
gr.Info("Rasterization in progress...")
|
| 250 |
+
gen2d.mesh_renderer.compute_fragments()
|
| 251 |
+
gr.Info("Successfully rasterized.")
|
| 252 |
+
paste_img, target = gen2d.render_image_and_target(paste_lesion=True)
|
| 253 |
+
if paste_img is None:
|
| 254 |
+
gr.Info(
|
| 255 |
+
"***Not enough skin or unable to paste lesion. Skipping and Retrying."
|
| 256 |
+
)
|
| 257 |
+
print("***Not enough skin or unable to paste lesion. Skipping.")
|
| 258 |
+
continue
|
| 259 |
+
paste_img = (paste_img * 255).astype(np.uint8)
|
| 260 |
+
depth_view = target[:, :, 4]
|
| 261 |
+
depth_img = (depth_view - depth_view.min()) / (
|
| 262 |
+
depth_view.max() - depth_view.min()
|
| 263 |
+
)
|
| 264 |
+
depth_img = (depth_img * 255).astype(np.uint8)
|
| 265 |
+
view2d.append(paste_img)
|
| 266 |
+
depth2d.append(depth_img)
|
| 267 |
+
anatomy2d.append(target[:, :, 5])
|
| 268 |
+
seg2d.append(target[:, :, 3])
|
| 269 |
+
gr.Info(f"Successfully rendered {img_count+1}/{num_views} image+annotations.")
|
| 270 |
+
img_count += 1
|
| 271 |
+
return view2d, depth2d, anatomy2d, seg2d
|
| 272 |
+
|
| 273 |
+
# mesh_renderer.compute_fragments()
|
| 274 |
+
# view2d = mesh_renderer.render_view(asnumpy=True, asRGB=True)
|
| 275 |
+
# gr.Info("Successfully rendered images.")
|
| 276 |
+
# gr.Info("Preparing annotations...")
|
| 277 |
+
# # breakpoint()
|
| 278 |
+
# pix2face = torch.from_numpy(mesh_renderer.pixels_to_face()).to(
|
| 279 |
+
# mesh_renderer.mesh.device
|
| 280 |
+
# )
|
| 281 |
+
# pix2vert = torch.stack(
|
| 282 |
+
# [a[i] for a, i in zip(mesh_renderer.mesh.faces_padded().squeeze(), pix2face)]
|
| 283 |
+
# )
|
| 284 |
+
# pix2vert = pix2vert.detach().cpu().numpy()
|
| 285 |
+
# anatomy_image = [
|
| 286 |
+
# vertices_to_anatomy[pix2vert[i]] * mesh_renderer.body_mask()
|
| 287 |
+
# for i in range(num_views)
|
| 288 |
+
# ]
|
| 289 |
+
# anatomy_image = np.stack(anatomy_image)
|
| 290 |
+
|
| 291 |
+
# anatomy_image = mesh_renderer.anatomy_image(vertices_to_anatomy)
|
| 292 |
+
# depth_img = mesh_renderer.depth_view(asnumpy=True)
|
| 293 |
+
# mesh_renderer.set_texture_image(texture_lesion_mask[:, :, np.newaxis])
|
| 294 |
+
# mask2d = mesh_renderer.render_view(asnumpy=True, asRGB=True)
|
| 295 |
+
# lesion_mask = mesh_renderer.lesion_mask(mask2d[:, :, 0], lesion_mask_id=None)
|
| 296 |
+
# # skin mask
|
| 297 |
+
# mesh_renderer.set_texture_image(non_skin_texture_mask)
|
| 298 |
+
# nonskin_mask = mesh_renderer.render_view(asnumpy=True, asRGB=True)
|
| 299 |
+
# skin_mask = mesh_renderer.skin_mask(nonskin_mask[:, :, 0] > 0.5)
|
| 300 |
+
# segmentation_mask = make_masks(lesion_mask, skin_mask)
|
| 301 |
+
# gr.Info("Successfully prepared annotations.")
|
| 302 |
+
# print(view2d.shape, anatomy_image.shape, depth_img.shape, segmentation_mask.shape)
|
| 303 |
+
# convert anatomy image with labels for each pixel to an image with RGB values
|
| 304 |
+
# map labels to pixels
|
| 305 |
+
|
| 306 |
+
# return (
|
| 307 |
+
# view2d,
|
| 308 |
+
# anatomy_image,
|
| 309 |
+
# depth_img,
|
| 310 |
+
# skin_mask,
|
| 311 |
+
# ) # segmentation_mask
|
| 312 |
+
|
| 313 |
+
|
| 314 |
+
# define the list of all the examples
|
| 315 |
+
def get_examples():
|
| 316 |
+
# setup_paths()
|
| 317 |
+
# get mesh names from here
|
| 318 |
+
mesh_names = globals()["mesh_names"]
|
| 319 |
+
# get the textures
|
| 320 |
+
textures = ["No Lesion", "Pasted Lesion", "Blended Lesion", "Dilated Lesion"]
|
| 321 |
+
lesions = [1, 2, 5, 10]
|
| 322 |
+
examples = []
|
| 323 |
+
for mesh in mesh_names:
|
| 324 |
+
for texture in textures:
|
| 325 |
+
for lesion in lesions:
|
| 326 |
+
if texture == "No Lesion":
|
| 327 |
+
# examples.append([mesh, texture, 0, 4, True])
|
| 328 |
+
examples.append([mesh, texture, 0])
|
| 329 |
+
break
|
| 330 |
+
# examples.append([mesh, texture, lesion, 4, True])
|
| 331 |
+
examples.append([mesh, texture, lesion])
|
| 332 |
+
return examples
|
| 333 |
+
|
| 334 |
+
|
| 335 |
+
import tempfile
|
| 336 |
+
|
| 337 |
+
|
| 338 |
+
def get_trimesh_attrs(mesh_name, tex_name, num_lesion=1):
|
| 339 |
+
mesh_path = get_mesh_path(mesh_name)
|
| 340 |
+
texture_path = get_texture_module(tex_name)(mesh_name, num_lesion)
|
| 341 |
+
texture_img = Image.open(texture_path).convert("RGB")
|
| 342 |
+
tri_mesh = trimesh.load(mesh_path)
|
| 343 |
+
|
| 344 |
+
angle = -math.pi / 2
|
| 345 |
+
direction = [0, 1, 0]
|
| 346 |
+
center = [0, 0, 0]
|
| 347 |
+
rot_matrix = tf.rotation_matrix(angle, direction, center)
|
| 348 |
+
tri_mesh = tri_mesh.apply_transform(rot_matrix)
|
| 349 |
+
tri_mesh.apply_transform(tf.rotation_matrix(math.pi, [0, 0, 1], [-1, -1, -1]))
|
| 350 |
+
|
| 351 |
+
verts, faces = tri_mesh.vertices, tri_mesh.faces
|
| 352 |
+
uvs = tri_mesh.visual.uv
|
| 353 |
+
material = trimesh.visual.texture.SimpleMaterial(image=texture_img)
|
| 354 |
+
vis = trimesh.visual.TextureVisuals(uv=uvs, material=material, image=texture_img)
|
| 355 |
+
tri_mesh.visual = vis
|
| 356 |
+
colors = tri_mesh.visual.to_color()
|
| 357 |
+
vc = colors.vertex_colors # / 255.0
|
| 358 |
+
# timg = tri_mesh.visual.material.image
|
| 359 |
+
|
| 360 |
+
return verts, faces, vc, mesh_name
|
| 361 |
+
|
| 362 |
+
|
| 363 |
+
def plotly_image(image):
|
| 364 |
+
fig = go.Figure()
|
| 365 |
+
fig.add_trace(go.Image(z=image))
|
| 366 |
+
fig.update_layout(
|
| 367 |
+
width=view_width,
|
| 368 |
+
height=view_height,
|
| 369 |
+
margin=dict(l=0, r=0, b=0, t=0, pad=0),
|
| 370 |
+
paper_bgcolor="rgba(0,0,0,0)",
|
| 371 |
+
plot_bgcolor="rgba(0,0,0,0)",
|
| 372 |
+
)
|
| 373 |
+
fig.update_xaxes(showticklabels=False)
|
| 374 |
+
fig.update_yaxes(showticklabels=False)
|
| 375 |
+
fig.update_traces(hoverinfo="none")
|
| 376 |
+
return fig
|
| 377 |
+
|
| 378 |
+
|
| 379 |
+
def plotly_mesh(verts, faces, vc, mesh_name):
|
| 380 |
+
fig = go.Figure(
|
| 381 |
+
data=[
|
| 382 |
+
go.Mesh3d(
|
| 383 |
+
x=verts[:, 0],
|
| 384 |
+
y=verts[:, 1],
|
| 385 |
+
z=verts[:, 2],
|
| 386 |
+
i=faces[:, 0],
|
| 387 |
+
j=faces[:, 1],
|
| 388 |
+
k=faces[:, 2],
|
| 389 |
+
vertexcolor=vc,
|
| 390 |
+
)
|
| 391 |
+
]
|
| 392 |
+
)
|
| 393 |
+
fig.update_layout(scene_aspectmode="manual", scene_aspectratio=dict(x=1, y=1, z=1))
|
| 394 |
+
fig.update_layout(scene=dict(xaxis=dict(visible=False), yaxis=dict(visible=False)))
|
| 395 |
+
fig.update_layout(scene=dict(zaxis=dict(visible=False)))
|
| 396 |
+
fig.update_layout(scene=dict(camera=dict(up=dict(x=1, y=0, z=1))))
|
| 397 |
+
fig.update_layout(scene=dict(camera=dict(eye=dict(x=-2, y=-2, z=-1))))
|
| 398 |
+
# disable hover info
|
| 399 |
+
fig.update_traces(hoverinfo="none")
|
| 400 |
+
return fig
|
| 401 |
+
|
| 402 |
+
|
| 403 |
+
def load_texture_map(mesh, mesh_name, texture_name, num_lesion, device=DEVICE):
|
| 404 |
+
verts = mesh.verts_packed().detach().cpu().numpy()
|
| 405 |
+
faces = mesh.faces_packed().detach().cpu().numpy()
|
| 406 |
+
normals = mesh.verts_normals_packed().detach().cpu().numpy()
|
| 407 |
+
texture_path = get_texture_module(texture_name)(mesh_name, num_lesion)
|
| 408 |
+
texture_img = Image.open(texture_path).convert("RGB")
|
| 409 |
+
texture_tensor = torch.from_numpy(np.array(texture_img)).to(DEVICE)
|
| 410 |
+
tmap = TexturesUV(
|
| 411 |
+
maps=texture_tensor.float().to(device=mesh.device).unsqueeze(0),
|
| 412 |
+
verts_uvs=mesh.textures.verts_uvs_padded(),
|
| 413 |
+
faces_uvs=mesh.textures.faces_uvs_padded(),
|
| 414 |
+
)
|
| 415 |
+
return tmap
|
| 416 |
+
|
| 417 |
+
|
| 418 |
+
def load_mesh_and_texture(mesh_name, texture_name, num_lesion=1, device=DEVICE):
|
| 419 |
+
"""
|
| 420 |
+
Load a mesh and its corresponding texture.
|
| 421 |
+
|
| 422 |
+
Args:
|
| 423 |
+
mesh_name (str): The name of the mesh.
|
| 424 |
+
texture_name (str): The name of the texture module.
|
| 425 |
+
num_lesion (int, optional): The number of lesions. Defaults to 1.
|
| 426 |
+
device (torch.device, optional): The device to load the mesh and texture on. Defaults to DEVICE.
|
| 427 |
+
|
| 428 |
+
Returns:
|
| 429 |
+
new_mesh (Meshes): The loaded mesh with texture.
|
| 430 |
+
"""
|
| 431 |
+
mesh_path = get_mesh_path(mesh_name)
|
| 432 |
+
texture_path = get_texture_module(texture_name)(mesh_name, num_lesion)
|
| 433 |
+
gr.Info("Loading mesh and texture...")
|
| 434 |
+
mesh = load_objs_as_meshes([mesh_path], device=device)
|
| 435 |
+
tmap = load_texture_map(mesh, mesh_name, texture_name, num_lesion, device)
|
| 436 |
+
new_mesh = Meshes(
|
| 437 |
+
verts=mesh.verts_padded(), faces=mesh.faces_padded(), textures=tmap
|
| 438 |
+
)
|
| 439 |
+
return new_mesh
|
| 440 |
+
|
| 441 |
+
|
| 442 |
+
def setup_cameras(dist, elev, azim, device=DEVICE):
|
| 443 |
+
gr.Info("Setting up cameras...")
|
| 444 |
+
R, T = look_at_view_transform(dist, elev, azim, degrees=True)
|
| 445 |
+
cameras = FoVPerspectiveCameras(device=device, R=R, T=T, fov=30.0, znear=0.01)
|
| 446 |
+
return cameras
|
| 447 |
+
|
| 448 |
+
|
| 449 |
+
def setup_lights(
|
| 450 |
+
light_pos, ambient_color, diffuse_color, specular_color, device=DEVICE
|
| 451 |
+
):
|
| 452 |
+
gr.Info("Setting up lights...")
|
| 453 |
+
lights = PointLights(
|
| 454 |
+
device=device,
|
| 455 |
+
location=light_pos,
|
| 456 |
+
ambient_color=ambient_color,
|
| 457 |
+
diffuse_color=diffuse_color,
|
| 458 |
+
specular_color=specular_color,
|
| 459 |
+
)
|
| 460 |
+
return lights
|
| 461 |
+
|
| 462 |
+
|
| 463 |
+
def setup_materials(shininess, specularity, device=DEVICE):
|
| 464 |
+
gr.Info("Setting up materials...")
|
| 465 |
+
materials = Materials(
|
| 466 |
+
device=device,
|
| 467 |
+
specular_color=specularity, # [[specularity, specularity, specularity]],
|
| 468 |
+
shininess=shininess.reshape(-1), # [shininess],
|
| 469 |
+
)
|
| 470 |
+
return materials
|
| 471 |
+
|
| 472 |
+
|
| 473 |
+
def setup_renderer(cameras, lights, materials, device=DEVICE):
|
| 474 |
+
global raster_settings
|
| 475 |
+
raster_settings = RasterizationSettings(
|
| 476 |
+
image_size=128,
|
| 477 |
+
blur_radius=0.0,
|
| 478 |
+
faces_per_pixel=1,
|
| 479 |
+
# max_faces_per_bin=100,
|
| 480 |
+
# bin_size=0,
|
| 481 |
+
perspective_correct=True,
|
| 482 |
+
)
|
| 483 |
+
renderer = MeshRenderer(
|
| 484 |
+
rasterizer=MeshRasterizer(cameras=cameras, raster_settings=raster_settings),
|
| 485 |
+
shader=SoftPhongShader(
|
| 486 |
+
device=device, cameras=cameras, lights=lights, materials=materials
|
| 487 |
+
),
|
| 488 |
+
)
|
| 489 |
+
return renderer
|
| 490 |
+
|
| 491 |
+
|
| 492 |
+
def render_images(renderer, mesh, lights, cameras, materials, nviews, device=DEVICE):
|
| 493 |
+
meshes = mesh.extend(nviews)
|
| 494 |
+
gr.Info("Rendering Images...")
|
| 495 |
+
images = renderer(meshes, lights=lights, cameras=cameras, materials=materials)
|
| 496 |
+
gr.Info("Successfully rendered images.")
|
| 497 |
+
images = images[..., :3]
|
| 498 |
+
images = (images - images.min()) / (images.max() - images.min())
|
| 499 |
+
return images
|
| 500 |
+
fragments = MeshRasterizer(cameras=cameras, raster_settings=raster_settings)(meshes)
|
| 501 |
+
# print(images.shape)
|
| 502 |
+
# breakpoint()
|
| 503 |
+
return images
|
| 504 |
+
|
| 505 |
+
|
| 506 |
+
def randomize_view_params(randomize, num_views):
|
| 507 |
+
dist = torch.rand(num_views).uniform_(0.0, 10.0)
|
| 508 |
+
elev = torch.rand(num_views).uniform_(-90, 90)
|
| 509 |
+
azim = torch.rand(num_views).uniform_(-90, 90)
|
| 510 |
+
light_pos = torch.rand(num_views, 3).uniform_(0.0, 2.0)
|
| 511 |
+
light_ac = torch.rand(num_views, 3).uniform_(0.0, 1.0)
|
| 512 |
+
light_dc = torch.rand(num_views, 3).uniform_(0.0, 1.0)
|
| 513 |
+
light_sc = torch.rand(num_views, 3).uniform_(0.0, 1.0)
|
| 514 |
+
mat_sh = torch.rand(num_views, 1).uniform_(0, 100)
|
| 515 |
+
mat_sc = torch.rand(num_views, 3).uniform_(0.0, 1.0)
|
| 516 |
+
gr.Info("Randomized view parameters...")
|
| 517 |
+
return (
|
| 518 |
+
dist,
|
| 519 |
+
elev,
|
| 520 |
+
azim,
|
| 521 |
+
light_pos,
|
| 522 |
+
light_ac,
|
| 523 |
+
light_dc,
|
| 524 |
+
light_sc,
|
| 525 |
+
mat_sh,
|
| 526 |
+
mat_sc,
|
| 527 |
+
)
|
| 528 |
+
|
| 529 |
+
|
| 530 |
+
def sample_camera_params(num_views, dist, elev, azim):
|
| 531 |
+
gr.Info("Setting up cameras...")
|
| 532 |
+
dist = torch.linspace(dist - num_views // 2, dist + num_views // 2, num_views)
|
| 533 |
+
elev = torch.linspace(elev - num_views // 2, elev + num_views // 2, num_views)
|
| 534 |
+
azim = torch.linspace(azim - num_views // 2, azim + num_views // 2, num_views)
|
| 535 |
+
cameras = setup_cameras(dist, elev, azim)
|
| 536 |
+
|
| 537 |
+
return cameras
|
| 538 |
+
|
| 539 |
+
|
| 540 |
+
def sample_light_params(num_views, light_pos, light_ac, light_dc, light_sc):
|
| 541 |
+
gr.Info("Setting up lights...")
|
| 542 |
+
light_pos = (
|
| 543 |
+
torch.linspace(
|
| 544 |
+
light_pos - num_views // 2, light_pos + num_views // 2, num_views
|
| 545 |
+
)
|
| 546 |
+
.reshape(-1, 1)
|
| 547 |
+
.repeat(1, 3)
|
| 548 |
+
)
|
| 549 |
+
light_ac = (
|
| 550 |
+
torch.linspace(light_ac - num_views // 2, light_ac + num_views // 2, num_views)
|
| 551 |
+
.reshape(-1, 1)
|
| 552 |
+
.repeat(1, 3)
|
| 553 |
+
)
|
| 554 |
+
light_dc = (
|
| 555 |
+
torch.linspace(light_dc - num_views // 2, light_dc + num_views // 2, num_views)
|
| 556 |
+
.reshape(-1, 1)
|
| 557 |
+
.repeat(1, 3)
|
| 558 |
+
)
|
| 559 |
+
light_sc = (
|
| 560 |
+
torch.linspace(light_sc - num_views // 2, light_sc + num_views // 2, num_views)
|
| 561 |
+
.reshape(-1, 1)
|
| 562 |
+
.repeat(1, 3)
|
| 563 |
+
)
|
| 564 |
+
lights = setup_lights(light_pos, light_ac, light_dc, light_sc)
|
| 565 |
+
return lights
|
| 566 |
+
|
| 567 |
+
|
| 568 |
+
def sample_material_params(num_views, mat_sh, mat_sc):
|
| 569 |
+
gr.Info("Setting up materials...")
|
| 570 |
+
mat_sh = (
|
| 571 |
+
torch.linspace(mat_sh - num_views // 2, mat_sh + num_views // 2, num_views)
|
| 572 |
+
.reshape(-1, 1)
|
| 573 |
+
.repeat(1, 1)
|
| 574 |
+
)
|
| 575 |
+
mat_sc = (
|
| 576 |
+
torch.linspace(mat_sc - num_views // 2, mat_sc + num_views // 2, num_views)
|
| 577 |
+
.reshape(-1, 1)
|
| 578 |
+
.repeat(1, 3)
|
| 579 |
+
)
|
| 580 |
+
materials = setup_materials(mat_sh, mat_sc)
|
| 581 |
+
return materials
|
| 582 |
+
|
| 583 |
+
|
| 584 |
+
def set_rendering_params(
|
| 585 |
+
randomize,
|
| 586 |
+
num_views,
|
| 587 |
+
dist,
|
| 588 |
+
elev,
|
| 589 |
+
azim,
|
| 590 |
+
light_pos,
|
| 591 |
+
light_ac,
|
| 592 |
+
light_dc,
|
| 593 |
+
light_sc,
|
| 594 |
+
mat_sh,
|
| 595 |
+
mat_sc,
|
| 596 |
+
):
|
| 597 |
+
if randomize:
|
| 598 |
+
(
|
| 599 |
+
dist,
|
| 600 |
+
elev,
|
| 601 |
+
azim,
|
| 602 |
+
light_pos,
|
| 603 |
+
light_ac,
|
| 604 |
+
light_dc,
|
| 605 |
+
light_sc,
|
| 606 |
+
mat_sh,
|
| 607 |
+
mat_sc,
|
| 608 |
+
) = randomize_view_params(randomize, num_views)
|
| 609 |
+
cameras = setup_cameras(dist, elev, azim)
|
| 610 |
+
lights = setup_lights(light_pos, light_ac, light_dc, light_sc)
|
| 611 |
+
materials = setup_materials(mat_sh, mat_sc)
|
| 612 |
+
else:
|
| 613 |
+
cameras = sample_camera_params(num_views, dist, elev, azim)
|
| 614 |
+
lights = sample_light_params(num_views, light_pos, light_ac, light_dc, light_sc)
|
| 615 |
+
materials = sample_material_params(num_views, mat_sh, mat_sc)
|
| 616 |
+
|
| 617 |
+
renderer = setup_renderer(cameras, lights, materials)
|
| 618 |
+
return renderer, cameras, lights, materials
|
| 619 |
+
|
| 620 |
+
|
| 621 |
+
def process_examples(mesh_name, tex_name, n_lesion):
|
| 622 |
+
mesh_path = get_mesh_path(mesh_name)
|
| 623 |
+
texture_path = get_texture_module(tex_name)(mesh_name, n_lesion)
|
| 624 |
+
mesh_to_view = plotly_mesh(*get_trimesh_attrs(mesh_name, tex_name, n_lesion))
|
| 625 |
+
# mesh = load_mesh_and_texture(mesh_name, tex_name, n_lesion)
|
| 626 |
+
return mesh_to_view, texture_path, n_lesion
|
| 627 |
+
|
| 628 |
+
|
| 629 |
+
def update_plots(mesh_name, texture_name, num_lesion):
|
| 630 |
+
if num_lesion > 0 and texture_name == "No Lesion":
|
| 631 |
+
gr.Warning(
|
| 632 |
+
f"Cannot display '{texture_name}' texture map with {num_lesion} lesions! Please change the texture. Meanwhile, not updating the display."
|
| 633 |
+
)
|
| 634 |
+
return default_mesh_plot, default_texture, num_lesion
|
| 635 |
+
elif num_lesion == 0 and texture_name != "No Lesion":
|
| 636 |
+
go.Warning(
|
| 637 |
+
f"Cannot display '{texture_name}' texture map with {num_lesion} lesions! Please increase the number of lesions."
|
| 638 |
+
)
|
| 639 |
+
return default_mesh_plot, default_texture, num_lesion
|
| 640 |
+
mesh_path = get_mesh_path(mesh_name)
|
| 641 |
+
texture_path = get_texture_module(texture_name)(mesh_name, num_lesion)
|
| 642 |
+
mesh_to_view = plotly_mesh(*get_trimesh_attrs(mesh_name, texture_name, num_lesion))
|
| 643 |
+
gr.Info("Successfully updated mesh and texture.")
|
| 644 |
+
return mesh_to_view, texture_path, num_lesion
|
| 645 |
+
|
| 646 |
+
|
| 647 |
+
def run_demo():
|
| 648 |
+
# get the defined examples
|
| 649 |
+
all_examples = get_examples()
|
| 650 |
+
|
| 651 |
+
mesh_block = gr.Plot(
|
| 652 |
+
label="Selected Mesh",
|
| 653 |
+
value=default_mesh_plot,
|
| 654 |
+
# scale=1,
|
| 655 |
+
)
|
| 656 |
+
texture_block = gr.Image(
|
| 657 |
+
value=default_texture,
|
| 658 |
+
type="pil",
|
| 659 |
+
image_mode="RGB",
|
| 660 |
+
height="auto",
|
| 661 |
+
width="auto",
|
| 662 |
+
label="Selected Texture",
|
| 663 |
+
)
|
| 664 |
+
num_lesions = gr.Radio(
|
| 665 |
+
choices=[0, 1, 2, 5, 10],
|
| 666 |
+
label="Number of Lesions",
|
| 667 |
+
value=0,
|
| 668 |
+
interactive=True,
|
| 669 |
+
)
|
| 670 |
+
num_views = gr.Slider(2, 32, 4, label="Number of Views", step=2, interactive=True)
|
| 671 |
+
randomize = gr.Checkbox(
|
| 672 |
+
label="Randomize View Parameters", value=True, interactive=True
|
| 673 |
+
)
|
| 674 |
+
render_button = gr.Button("Render Views")
|
| 675 |
+
|
| 676 |
+
select_mesh = gr.Dropdown(
|
| 677 |
+
choices=mesh_names,
|
| 678 |
+
value=mesh_names[0],
|
| 679 |
+
interactive=True,
|
| 680 |
+
label="Input Mesh",
|
| 681 |
+
info="Select the mesh to render",
|
| 682 |
+
)
|
| 683 |
+
select_texture = gr.Dropdown(
|
| 684 |
+
choices=["No Lesion", "Pasted Lesion", "Blended Lesion", "Dilated Lesion"],
|
| 685 |
+
value="No Lesion",
|
| 686 |
+
interactive=True,
|
| 687 |
+
label="Input Texture",
|
| 688 |
+
info="Select the texture to use for the mesh.",
|
| 689 |
+
)
|
| 690 |
+
# compose demo layout and data flow
|
| 691 |
+
with gr.Blocks(
|
| 692 |
+
title=_TITLE, analytics_enabled=True, theme=gr.themes.Base()
|
| 693 |
+
) as demo:
|
| 694 |
+
with gr.Row():
|
| 695 |
+
with gr.Column(scale=1):
|
| 696 |
+
gr.Markdown(f"# {_TITLE}")
|
| 697 |
+
gr.Markdown(_DESCRIPTION)
|
| 698 |
+
|
| 699 |
+
# User input panel
|
| 700 |
+
with gr.Row(variant="panel"):
|
| 701 |
+
with gr.Column(scale=1):
|
| 702 |
+
select_mesh.render()
|
| 703 |
+
select_texture.render()
|
| 704 |
+
num_lesions.render()
|
| 705 |
+
num_views.render()
|
| 706 |
+
randomize.render()
|
| 707 |
+
|
| 708 |
+
with gr.Column(scale=1):
|
| 709 |
+
mesh_block.render()
|
| 710 |
+
with gr.Column(scale=1):
|
| 711 |
+
texture_block.render()
|
| 712 |
+
|
| 713 |
+
gr.on(
|
| 714 |
+
triggers=[
|
| 715 |
+
select_mesh.change,
|
| 716 |
+
select_texture.change,
|
| 717 |
+
num_lesions.change,
|
| 718 |
+
],
|
| 719 |
+
inputs=[select_mesh, select_texture, num_lesions],
|
| 720 |
+
outputs=[mesh_block, texture_block, num_lesions],
|
| 721 |
+
fn=update_plots,
|
| 722 |
+
)
|
| 723 |
+
|
| 724 |
+
# @gr.on(
|
| 725 |
+
# inputs=[
|
| 726 |
+
# select_mesh,
|
| 727 |
+
# select_texture,
|
| 728 |
+
# num_lesions,
|
| 729 |
+
# ],
|
| 730 |
+
# outputs=[
|
| 731 |
+
# mesh_block,
|
| 732 |
+
# texture_block,
|
| 733 |
+
# num_lesions,
|
| 734 |
+
# ],
|
| 735 |
+
# triggers=[
|
| 736 |
+
# select_mesh.change,
|
| 737 |
+
# select_texture.change,
|
| 738 |
+
# num_lesions.change,
|
| 739 |
+
# ],
|
| 740 |
+
# )
|
| 741 |
+
# def update(m, t, l):
|
| 742 |
+
# return update_plots(m, t, l)
|
| 743 |
+
|
| 744 |
+
# rendering choices
|
| 745 |
+
with gr.Row(variant="panel"):
|
| 746 |
+
with gr.Column(scale=1):
|
| 747 |
+
render_button.render()
|
| 748 |
+
with gr.Column(scale=1):
|
| 749 |
+
with gr.Accordion("Configure View Parameters", open=False):
|
| 750 |
+
# setup cameras
|
| 751 |
+
with gr.Accordion("Camera Parameters", open=False):
|
| 752 |
+
dist = gr.Slider(
|
| 753 |
+
minimum=0.0,
|
| 754 |
+
maximum=10.0,
|
| 755 |
+
value=0.5,
|
| 756 |
+
step=0.5,
|
| 757 |
+
interactive=True,
|
| 758 |
+
label="Distance",
|
| 759 |
+
)
|
| 760 |
+
elev = gr.Slider(
|
| 761 |
+
label="Elevation",
|
| 762 |
+
interactive=True,
|
| 763 |
+
minimum=-90,
|
| 764 |
+
maximum=90,
|
| 765 |
+
value=0,
|
| 766 |
+
step=10,
|
| 767 |
+
)
|
| 768 |
+
azim = gr.Slider(
|
| 769 |
+
label="Azimuth",
|
| 770 |
+
interactive=True,
|
| 771 |
+
minimum=-90,
|
| 772 |
+
maximum=90,
|
| 773 |
+
value=90,
|
| 774 |
+
step=10,
|
| 775 |
+
)
|
| 776 |
+
# setup lights
|
| 777 |
+
with gr.Accordion("Lighting Parameters", open=False):
|
| 778 |
+
light_pos = gr.Slider(
|
| 779 |
+
label="Light Position",
|
| 780 |
+
interactive=True,
|
| 781 |
+
minimum=0.0,
|
| 782 |
+
maximum=2.0,
|
| 783 |
+
value=0.5,
|
| 784 |
+
step=0.1,
|
| 785 |
+
)
|
| 786 |
+
light_ac = gr.Slider(
|
| 787 |
+
label="Ambient Color",
|
| 788 |
+
minimum=0.0,
|
| 789 |
+
maximum=1.0,
|
| 790 |
+
interactive=True,
|
| 791 |
+
value=0.5,
|
| 792 |
+
step=0.1,
|
| 793 |
+
)
|
| 794 |
+
light_dc = gr.Slider(
|
| 795 |
+
label="Diffuse Color",
|
| 796 |
+
minimum=0.0,
|
| 797 |
+
maximum=1.0,
|
| 798 |
+
interactive=True,
|
| 799 |
+
value=0.5,
|
| 800 |
+
step=0.1,
|
| 801 |
+
)
|
| 802 |
+
light_sc = gr.Slider(
|
| 803 |
+
label="Specular Color",
|
| 804 |
+
minimum=0.0,
|
| 805 |
+
maximum=1.0,
|
| 806 |
+
interactive=True,
|
| 807 |
+
value=0.5,
|
| 808 |
+
step=0.1,
|
| 809 |
+
)
|
| 810 |
+
# setup material parameters
|
| 811 |
+
with gr.Accordion("Material Parameters", open=False):
|
| 812 |
+
mat_sh = gr.Slider(
|
| 813 |
+
label="Shininess",
|
| 814 |
+
interactive=True,
|
| 815 |
+
minimum=0,
|
| 816 |
+
maximum=100,
|
| 817 |
+
value=50,
|
| 818 |
+
step=10,
|
| 819 |
+
)
|
| 820 |
+
mat_sc = gr.Slider(
|
| 821 |
+
label="Specularity",
|
| 822 |
+
minimum=0.0,
|
| 823 |
+
interactive=True,
|
| 824 |
+
maximum=1.0,
|
| 825 |
+
value=0.5,
|
| 826 |
+
step=0.1,
|
| 827 |
+
)
|
| 828 |
+
|
| 829 |
+
update_view_btn = gr.Button("Update View Parameters")
|
| 830 |
+
|
| 831 |
+
gr.on(
|
| 832 |
+
triggers=[
|
| 833 |
+
update_view_btn.click,
|
| 834 |
+
dist.change,
|
| 835 |
+
elev.change,
|
| 836 |
+
azim.change,
|
| 837 |
+
light_pos.change,
|
| 838 |
+
light_ac.change,
|
| 839 |
+
light_dc.change,
|
| 840 |
+
light_sc.change,
|
| 841 |
+
mat_sh.change,
|
| 842 |
+
mat_sc.change,
|
| 843 |
+
],
|
| 844 |
+
inputs=[randomize],
|
| 845 |
+
outputs=[randomize],
|
| 846 |
+
fn=lambda x: False,
|
| 847 |
+
show_progress="hidden",
|
| 848 |
+
queue=False,
|
| 849 |
+
scroll_to_output=True,
|
| 850 |
+
)
|
| 851 |
+
# rendered views panel
|
| 852 |
+
with gr.Row(variant="panel"):
|
| 853 |
+
render_block = gr.Gallery(
|
| 854 |
+
label="Rendered Views", columns=4, height="auto", object_fit="contain"
|
| 855 |
+
)
|
| 856 |
+
|
| 857 |
+
@gr.on(
|
| 858 |
+
triggers=[render_button.click],
|
| 859 |
+
inputs=[
|
| 860 |
+
randomize,
|
| 861 |
+
select_mesh,
|
| 862 |
+
select_texture,
|
| 863 |
+
num_lesions,
|
| 864 |
+
num_views,
|
| 865 |
+
dist,
|
| 866 |
+
elev,
|
| 867 |
+
azim,
|
| 868 |
+
light_pos,
|
| 869 |
+
light_ac,
|
| 870 |
+
light_dc,
|
| 871 |
+
light_sc,
|
| 872 |
+
mat_sh,
|
| 873 |
+
mat_sc,
|
| 874 |
+
],
|
| 875 |
+
outputs=[render_block],
|
| 876 |
+
)
|
| 877 |
+
def render_views(
|
| 878 |
+
randomize,
|
| 879 |
+
select_mesh,
|
| 880 |
+
select_texture,
|
| 881 |
+
num_lesions,
|
| 882 |
+
num_views,
|
| 883 |
+
dist,
|
| 884 |
+
elev,
|
| 885 |
+
azim,
|
| 886 |
+
light_pos,
|
| 887 |
+
light_ac,
|
| 888 |
+
light_dc,
|
| 889 |
+
light_sc,
|
| 890 |
+
mat_sh,
|
| 891 |
+
mat_sc,
|
| 892 |
+
):
|
| 893 |
+
renderer, cameras, lights, materials = set_rendering_params(
|
| 894 |
+
randomize,
|
| 895 |
+
num_views,
|
| 896 |
+
dist,
|
| 897 |
+
elev,
|
| 898 |
+
azim,
|
| 899 |
+
light_pos,
|
| 900 |
+
light_ac,
|
| 901 |
+
light_dc,
|
| 902 |
+
light_sc,
|
| 903 |
+
mat_sh,
|
| 904 |
+
mat_sc,
|
| 905 |
+
)
|
| 906 |
+
# gr.Info("Loading mesh and texture...")
|
| 907 |
+
# mesh = load_mesh_and_texture(select_mesh, select_texture, num_lesions)
|
| 908 |
+
# cameras
|
| 909 |
+
# images = render_images(
|
| 910 |
+
# renderer, mesh, lights, cameras, materials, num_views
|
| 911 |
+
# )
|
| 912 |
+
# return [_ for _ in images.detach().cpu().numpy()]
|
| 913 |
+
view2d, anatomy, depth, segmentation = prepare_ds_renderer(
|
| 914 |
+
randomize,
|
| 915 |
+
select_mesh,
|
| 916 |
+
select_texture,
|
| 917 |
+
num_lesions,
|
| 918 |
+
num_views,
|
| 919 |
+
dist,
|
| 920 |
+
elev,
|
| 921 |
+
azim,
|
| 922 |
+
light_pos,
|
| 923 |
+
light_ac,
|
| 924 |
+
light_dc,
|
| 925 |
+
light_sc,
|
| 926 |
+
mat_sh,
|
| 927 |
+
mat_sc,
|
| 928 |
+
)
|
| 929 |
+
return view2d
|
| 930 |
+
|
| 931 |
+
# examples panel when the iuser does not want to input
|
| 932 |
+
with gr.Row(variant="panel"):
|
| 933 |
+
with gr.Column(scale=1):
|
| 934 |
+
gr.Examples(
|
| 935 |
+
examples=all_examples,
|
| 936 |
+
inputs=[
|
| 937 |
+
select_mesh,
|
| 938 |
+
select_texture,
|
| 939 |
+
num_lesions,
|
| 940 |
+
],
|
| 941 |
+
outputs=[
|
| 942 |
+
mesh_block,
|
| 943 |
+
texture_block,
|
| 944 |
+
num_lesions,
|
| 945 |
+
],
|
| 946 |
+
cache_examples=False,
|
| 947 |
+
fn=update_plots,
|
| 948 |
+
label="Meshes and Textures for Demo (Click to start)",
|
| 949 |
+
)
|
| 950 |
+
|
| 951 |
+
demo.queue(max_size=10)
|
| 952 |
+
demo.launch(
|
| 953 |
+
share=True,
|
| 954 |
+
max_threads=mp.cpu_count(),
|
| 955 |
+
show_error=True,
|
| 956 |
+
show_api=False,
|
| 957 |
+
)
|
| 958 |
+
|
| 959 |
+
|
| 960 |
+
def get_texture_module(tex_type):
|
| 961 |
+
if tex_type == "No Lesion":
|
| 962 |
+
return get_no_lesion_path
|
| 963 |
+
elif tex_type == "Pasted Lesion":
|
| 964 |
+
return get_pasted_lesion_path
|
| 965 |
+
elif tex_type == "Blended Lesion":
|
| 966 |
+
return get_blended_lesion_path
|
| 967 |
+
elif tex_type == "Dilated Lesion":
|
| 968 |
+
return get_dilated_lesion_path
|
| 969 |
+
else:
|
| 970 |
+
raise ValueError(f"Texture type {tex_type} not supported!")
|
| 971 |
+
|
| 972 |
+
|
| 973 |
+
if __name__ == "__main__":
|
| 974 |
+
# setup_paths()
|
| 975 |
+
mesh_paths = glob("./DermSynth3D//data/3dbodytex-1.1-highres/*/*.obj")
|
| 976 |
+
mesh_names = [os.path.basename(os.path.dirname(x)) for x in mesh_paths]
|
| 977 |
+
# get the textures
|
| 978 |
+
all_textures = glob("./DermSynth3D//data/3dbodytex-1.1-highres/*/*.png")
|
| 979 |
+
dir_blended_textures = "./hf_demo/lesions/"
|
| 980 |
+
dir_anatomy = "./DermSynth3D/data/bodytex_anatomy_labels/"
|
| 981 |
+
dir_background = "./DermSynth3D/data/background/IndoorScene/"
|
| 982 |
+
get_no_lesion_path = lambda x, y: os.path.join(
|
| 983 |
+
"./DermSynth3D/data/3dbodytex-1.1-highres", x, "model_highres_0_normalized.png"
|
| 984 |
+
)
|
| 985 |
+
get_mesh_path = lambda x: os.path.join(
|
| 986 |
+
"./DermSynth3D/data/3dbodytex-1.1-highres", x, "model_highres_0_normalized.obj"
|
| 987 |
+
)
|
| 988 |
+
# get the textures with the lesions
|
| 989 |
+
get_mask_path = lambda x: os.path.join(
|
| 990 |
+
"./hf_demo/lesions/", x, "model_highres_0_normalized_mask.png"
|
| 991 |
+
)
|
| 992 |
+
get_dilated_lesion_path = lambda x, y: os.path.join(
|
| 993 |
+
"./hf_demo/lesions/",
|
| 994 |
+
x,
|
| 995 |
+
f"model_highres_0_normalized_dilated_lesion_{y}.png",
|
| 996 |
+
)
|
| 997 |
+
get_blended_lesion_path = lambda x, y: os.path.join(
|
| 998 |
+
"./hf_demo/lesions/",
|
| 999 |
+
x,
|
| 1000 |
+
f"model_highres_0_normalized_blended_lesion_{y}.png",
|
| 1001 |
+
)
|
| 1002 |
+
get_pasted_lesion_path = lambda x, y: os.path.join(
|
| 1003 |
+
"./hf_demo/lesions/",
|
| 1004 |
+
x,
|
| 1005 |
+
f"model_highres_0_normalized_pasted_lesion_{y}.png",
|
| 1006 |
+
)
|
| 1007 |
+
default_mesh_plot = plotly_mesh(*get_trimesh_attrs(mesh_names[0], "No Lesion", 0))
|
| 1008 |
+
default_texture = Image.open(all_textures[0]).convert("RGB").resize((512, 512))
|
| 1009 |
+
new_values = {
|
| 1010 |
+
"default_mesh_plot": default_mesh_plot,
|
| 1011 |
+
"default_texture": default_texture,
|
| 1012 |
+
}
|
| 1013 |
+
globals().update(new_values)
|
| 1014 |
+
run_demo()
|
hf_demo/lesions/006-f-run/lesion_dilated_mask_demo.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_dilated_mask_latest.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_1.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_10.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_15.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_2.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_30.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_dilated_mask_lesion_5.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_mask_latest.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_mask_lesion_0.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_mask_lesion_1.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_mask_lesion_10.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_mask_lesion_15.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_mask_lesion_2.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_mask_lesion_30.png
ADDED
|
hf_demo/lesions/006-f-run/lesion_mask_lesion_5.png
ADDED
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_demo.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_latest.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_1.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_10.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_15.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_2.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_30.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_blended_lesion_5.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_demo.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_latest.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_1.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_10.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_15.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_2.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_30.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_dilated_lesion_5.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_lesion_0.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_mask.png
ADDED
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_demo.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_latest.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_1.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_10.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_15.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_2.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_30.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/006-f-run/model_highres_0_normalized_pasted_lesion_5.png
ADDED
|
Git LFS Details
|
hf_demo/lesions/221-m-u/lesion_dilated_mask_lesion_1.png
ADDED
|
hf_demo/lesions/221-m-u/lesion_dilated_mask_lesion_10.png
ADDED
|
hf_demo/lesions/221-m-u/lesion_dilated_mask_lesion_15.png
ADDED
|
hf_demo/lesions/221-m-u/lesion_dilated_mask_lesion_2.png
ADDED
|