Merge pull request #53 from CBICA/main

Main to ge-dev

.github/workflows/macos_build.yml

@@ -1,4 +1,4 @@
-name: NiChart_DLMUSE building test for macos
+name: MacOS Build
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
@@ -11,21 +11,20 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
       - name: Set-up miniconda for macos and ubuntu
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: 3.8
+          python-version: 3.12
           miniconda-version: "latest"
       - name: Create conda env
-        run: conda create -n NCP python=3.8
+        run: conda create -n NCP python=3.12
       - name: Install pip
         run: conda run -n NCP conda install pip
       - name: Build NiChart_DLMUSE from source
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls NiChart_DLMUSE*)
-          pip install "$WHEEL_FILE"
+          pip install -r requirements.txt
+          python3 -m pip install -e .

.github/workflows/macos_tests.yml

@@ -0,0 +1,28 @@
+name: macos build
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["macos-13"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install spare scores
+        run: |
+          python -m pip cache purge
+          pip install -r requirements.txt
+          pip install setuptools twine wheel
+          python -m pip install .
+      - name: Run unit tests
+        run: |
+          cd tests/ && pytest --cov=../ --cov-report=xml
+      - name: Upload Coverage to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: CBICA/NiChart_DLMUSE

.github/workflows/pre-commit.yml

@@ -12,6 +12,6 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
       - run: pip3 install pre-commit
       - run: pre-commit run --files NiChart_DLMUSE/*

.github/workflows/python-publish.yml

@@ -0,0 +1,40 @@
+name: Upload Python Package
+
+on: workflow_dispatch
+
+permissions:
+  contents: read
+  id-token: write # Allow GitHub to mint tokens
+
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest # Can use macos-latest if needed
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.x"
+
+      - name: Install dependencies
+        run: |
+          pip install setuptools
+          pip install twine
+          pip install wheel
+          sudo apt-get install jq
+
+      - name: Clean previous builds
+        run: rm -rf dist
+
+      - name: Build package
+        run: python setup.py sdist bdist_wheel
+
+      - name: Publish package to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: twine upload --repository-url https://upload.pypi.org/legacy/ dist/*

.github/workflows/sphinx-docs.yml

@@ -5,12 +5,12 @@ on:
 
 jobs:
   build-docs:
-    runs-on: macos-13
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.12"
       - name: Set-up miniconda for macos and ubuntu
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -24,7 +24,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install -r requirements.txt
-          brew install python-setuptools
+          pip install setuptools
           pip install sphinx sphinx_rtd_theme sphinx-tabs sphinx_toolbox
       - name: Sphinx build
         run: |

.github/workflows/ubuntu_build.yml

@@ -1,4 +1,4 @@
-name: NiChart_DLMUSE building test for ubuntu
+name: Ubuntu Build
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
@@ -11,21 +11,20 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
       - name: Set-up miniconda for macos and ubuntu
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: 3.8
+          python-version: 3.12
           miniconda-version: "latest"
       - name: Create conda env
-        run: conda create -n NCP python=3.8
+        run: conda create -n NCP python=3.12
       - name: Install pip
         run: conda run -n NCP conda install pip
       - name: Build NiChart_DLMUSE from source
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls NiChart_DLMUSE*)
-          pip install "$WHEEL_FILE"
+          pip install -r requirements.txt
+          python3 -m pip install -e .

.github/workflows/ubuntu_tests.yml

@@ -0,0 +1,23 @@
+name: ubuntu tests
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["ubuntu-latest"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install spare scores
+        run: |
+          python -m pip cache purge
+          pip install -r requirements.txt
+          pip install setuptools twine wheel
+          python -m pip install .
+      - name: Run unit tests
+        run: |
+          cd tests && pytest

Dockerfile

@@ -1,30 +1,38 @@
-FROM pytorch/pytorch:2.0.1-cuda11.7-cudnn8-runtime
-
-LABEL IMAGE="NiChart_DLMUSE"
-LABEL VERSION="0.1.7"
-LABEL CI_IGNORE="True"
-
-RUN apt-get update && \
-    apt-get -y install gcc \
-    mono-mcs \
-    gnupg2 \
-    git \
-    htop \
-    zip \
-    unzip \
-    g++ && \ 
-    apt-key del 3bf863cc && \ 
-    apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub && \ 
-    rm -rf /var/lib/apt/lists/* && \
-    pip install --upgrade pip && \ 
-    pip install Cmake
-
-# RUN mkdir /NiChart_DLMUSE 
-# COPY ./ /NiChart_DLMUSE/
-# RUN cd /NiChart_DLMUSE && pip install .
-
-RUN cd / && \
-    git clone https://github.com/CBICA/NiChart_DLMUSE && \
-    cd /NiChart_DLMUSE && pip install . 
-
-CMD ["NiChart_DLMUSE" ]
+
+## Suggested pull command (run from anywhere):
+## CUDA_VERSION=11.8 docker pull cbica/nichart_dlmuse:1.0.1-cuda${CUDA_VERSION}
+## OR
+## docker pull cbica/nichart_dlmuse:1.0.1
+
+## Suggested automatic inference run time command 
+## Place input in /path/to/input/on/host.
+## Replace -d cuda with -d mps or -d cpu as needed, or don't pass at all to automatically use CUDA.
+## Each "/path/to/.../on/host" is a placeholder, use your actual paths!
+## docker run -it --name DLMUSE_inference --rm 
+##    --mount type=bind,source=/path/to/input/on/host,target=/input,readonly 
+##    --mount type=bind,source=/path/to/output/on/host,target=/output
+##    --gpus all cbica/nichart_dlmuse:1.0.1 -d cuda
+
+## Suggested build command (run from the top-level repo directory):
+## CUDA_VERSION=11.8 docker build --build-arg CUDA_VERSION=${CUDA_VERSION} 
+##      -t cbica/nichart_dlmuse:1.0.1-cuda${CUDA_VERSION} .
+## OR
+## docker build -t cbica/nichart_dlmuse:1.0.1 .
+
+ARG NICHART_DLMUSE_VERSION="1.0.1"
+ARG CUDA_VERSION="11.8"
+ARG TORCH_VERSION="2.4.1"
+ARG CUDNN_VERSION="9"
+
+## This base image is generally the smallest with all prereqs.
+FROM pytorch/pytorch:${TORCH_VERSION}-cuda${CUDA_VERSION}-cudnn${CUDNN_VERSION}-runtime
+
+WORKDIR /app
+COPY . /app/ 
+
+RUN pip install .
+RUN mkdir /dummyinput && mkdir /dummyoutput
+## Cache DLMUSE and DLICV models with an empty job so no download is needed later
+RUN DLMUSE -i /dummyinput -o /dummyoutput && DLICV -i /dummyinput -o /dummyoutput
+ENTRYPOINT ["NiChart_DLMUSE", "-i", "/input", "-o", "/output"]
+CMD ["-d", "cuda"]

NiChart_DLMUSE/CalcROIVol.py

@@ -1,11 +1,15 @@
 import csv as csv
+import logging
 import os
 from typing import Any
 
 import nibabel as nib
 import numpy as np
 import pandas as pd
 
+logger = logging.getLogger(__name__)
+logging.basicConfig(filename="pipeline.log", encoding="utf-8", level=logging.DEBUG)
+
 
 def calc_roi_volumes(mrid: Any, in_img: Any, label_indices: Any) -> pd.DataFrame:
     """
@@ -150,7 +154,7 @@ def combine_roi_csv(
             df_tmp = pd.read_csv(in_csv)
             dfs.append(df_tmp)
         except:
-            print("Skip subject, out csv missing: " + in_csv)
+            logging.info("Skip subject, out csv missing: " + in_csv)
     if len(dfs) > 0:
         df_out = pd.concat(dfs)
     df_out.to_csv(out_csv, index=False)

NiChart_DLMUSE/RelabelROI.py

@@ -11,7 +11,9 @@ def relabel_rois(
 ) -> None:
     """
     Convert labels in input roi image to new labels based on the mapping
+    print()
     The mapping file should contain numeric indices for the mapping
+    irint()
     between the input roi image (from) and output roi image (to)
     """
 

NiChart_DLMUSE/ReorientImage.py

@@ -1,3 +1,4 @@
+import logging
 import os
 from typing import Any
 
@@ -7,13 +8,16 @@
 
 IMG_EXT = ".nii.gz"
 
+logger = logging.getLogger(__name__)
+logging.basicConfig(filename="pipeline.log", encoding="utf-8", level=logging.DEBUG)
+
 
 def reorient_img(in_img: Any, ref: Any, out_img: Any) -> None:
     """
     Reorient image
     """
     if os.path.exists(out_img):
-        print("Out file exists, skip reorientation ...")
+        logging.info("Out file exists, skip reorientation ...")
 
     else:
         # Read input img