Update to headless whippersnappy

.dockerignore

@@ -0,0 +1,74 @@
+# Python Build Artifacts
+.Python
+**/__pycache__/
+**/*.py[cod]
+**/build/
+**/develop-eggs/
+**/dist/
+**/downloads/
+**/eggs/
+**/.eggs/
+**/lib/
+**/lib64/
+**/parts/
+**/sdist/
+**/var/
+**/wheels/
+**/*.egg-info/
+**/.installed.cfg
+**/*.egg
+**/MANIFEST
+
+# Test & Coverage Files
+.pytest_cache/
+.ruff_cache/
+.tox/
+.nox/
+coverage.xml
+.coverage
+.coverage.*
+htmlcov/
+junit-results.xml
+tests/
+
+# Version Control
+.git/
+.gitignore
+.gitattributes
+.github/
+
+# Editor / IDE Files
+.ipynb_checkpoints
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# Virtual Environments
+venv/
+.venv/
+env/
+.env/
+
+# Docker Files
+.dockerignore
+docker
+docker/Dockerfile
+
+# Singularity files
+singularity
+*sif
+
+# Local Config Files
+.env
+*.env.*
+*.pem
+*.key
+
+# OS files
+.DS_Store
+Thumbs.db
+
+# Documentation
+howto*

.github/workflows/build.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     name: ${{ matrix.os }} - py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}-latest
     defaults:

.github/workflows/code-style.yml

@@ -15,10 +15,10 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
-      - name: Setup Python 3.10
+      - name: Setup Python 3.13
         uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version: '3.13'
           architecture: 'x64'
       - name: Install dependencies
         run: |
@@ -28,8 +28,3 @@ jobs:
         run: ruff check .
       - name: Run codespell
         uses: codespell-project/actions-codespell@master
-        with:
-          check_filenames: true
-          check_hidden: true
-          skip: './.git,./build,./.mypy_cache,./.pytest_cache'
-          ignore_words_file: ./.codespellignore

.github/workflows/doc.yml

@@ -20,10 +20,10 @@ jobs:
         uses: actions/checkout@v6
         with:
           path: ./main
-      - name: Setup Python 3.10
+      - name: Setup Python 3.13
         uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version: '3.13'
           architecture: 'x64'
       - name: Install package
         run: |

.github/workflows/publish.yml

@@ -11,10 +11,10 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
-      - name: Setup Python 3.10
+      - name: Setup Python 3.13
         uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version: '3.13'
           architecture: 'x64'
       - name: Install dependencies
         run: |

.gitignore

@@ -1,13 +1,19 @@
-#
-misc
-deprecated
-testing
+# tests
+tests
+.pytest_cache/
+.ruff_cache/
+junit-results.xml
+coverage.xml
 
-# macOS
+# OS files
 .DS_Store
+Thumbs.db
 
-#
-.flake8
+# documentation
+howto*
+
+# images
+*sif
 
 #
 .ipynb_checkpoints
@@ -22,19 +28,19 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+.installed.cfg
 build/
-develop-eggs/
 dist/
 downloads/
+develop-eggs/
 eggs/
 .eggs/
+*.egg-info/
+*.egg
 lib/
 lib64/
 parts/
 sdist/
 var/
 wheels/
-*.egg-info/
-.installed.cfg
-*.egg
 MANIFEST

README.md

@@ -465,7 +465,7 @@ ___
 - At least one structural MR image that was processed with Freesurfer 6.0, 7.x,
   or FastSurfer 1.1 or later (including the surface pipeline).
 
-- A Python version >= 3.8 is required to run this script.
+- A Python version >= 3.10 is required to run this script.
 
 - Required packages include (among others) the nibabel and skimage package for
   the core functionality, plus the matplotlib, pandas, and transform3d

docker/Docker.md

@@ -6,16 +6,18 @@ The docker image will be based on Ubuntu, contain the fsqc scripts, the lapy and
 
 ## Build fsqc Docker image
 
-To build the docker image, execute the following command after traversing into the *docker* directory of this repository:
+To build the docker image, first download the software from its GitHub repository at `https://github.com/Deep-MI/fsqc`, or clone it directly via `git clone https://github.com/Deep-MI/fsqc`.
+
+Next, execute the following **docker** command from the project's main directory, i.e. `fsqc` (not `fsqc/fsqc`):
 
 ```bash
-docker build --rm -t deepmi/fsqcdocker -f Dockerfile .
+docker build --rm -t deepmi/fsqcdocker -f docker/Dockerfile .
 ```
-The name of the image will be `deepmi/fsqcdocker`, and it will be built from the `Dockerfile` configuration file from the *docker* directory. You have some flexibility in choosing the name, so this is just an example.
+The name of the image will be `deepmi/fsqcdocker`, and it will be built from the `Dockerfile` configuration file from the *docker* directory. You have some flexibility in choosing the name, so this is just an example. Note that the `fsqc` directory will be the *build context* for creating the docker image; if you do not want to include any particular files or directories into the image, add them to the `.dockerignore` file.
 
 The `--rm` flag will remove intermediate containers after a successful build; `-t` specifies the name of the image, and `-f` indicates the configuration file from which to build.
 
-Take a look at the contents of the [`Dockerfile`](Dockerfile) to see what is done during the build process: essentially, it is getting the Ubuntu 22.04 image, installing additional packages from the distribution, downloading the fsqc toolbox, and setting the necessary environment variables. Unless the `Dockerfile` changes, the build process has to be done only once.
+Take a look at the contents of the [`Dockerfile`](Dockerfile) to see what is done during the build process: essentially, it is getting the Python3.11 image, installing additional packages, copying and installing the fsqc toolbox, and setting the necessary environment variables. Unless the `Dockerfile` changes, the build process has to be done only once.
 
 ## Download the Docker image
 

docker/Dockerfile

@@ -1,45 +1,57 @@
 # get OS
-FROM ubuntu:22.04
-
-# update OS
-RUN apt-get update
+FROM python:3.11
 
 # get additional packages
-RUN apt-get install -y --no-install-recommends \
-    gcc \
-    git \
+RUN apt-get update && apt-get install -y --no-install-recommends \
     time \
     zlib1g-dev \
     libjpeg-dev \
-    python3 \
-    python3-dev \
-    python3-pip \
-    python3-setuptools \
-    python3-wheel \
     libxcb-xinerama0 \
-    xvfb \    
-    libopengl0 \
-    libegl1-mesa
-
-# clone fsqc
-RUN git clone https://github.com/Deep-MI/fsqc.git /app/fsqc
+    libegl1 \
+    libgl1 \
+    libfontconfig1 && \
+  apt-get clean && \
+  rm -rf /var/lib/apt/lists/*
 
 # upgrade pip
-RUN pip3 install --upgrade pip
+RUN pip install --upgrade pip
+
+# 
+RUN mkdir -p /app/fsqc
 
-# install additional python packages (not necessary if using pip install)
-RUN pip3 install -r /app/fsqc/requirements.txt
+#
+COPY pyproject.toml /app/fsqc
+COPY setup.py /app/fsqc
+COPY requirements.txt /app/fsqc
+COPY DESCRIPTION.md /app/fsqc
+COPY LICENSE /app/fsqc
+COPY VERSION /app/fsqc
+COPY fsqc /app/fsqc/fsqc
+COPY run_fsqc /app/fsqc
+
+# install fsqc as a package
+RUN pip install /app/fsqc
 
 # Add other environment variables
 ENV OMP_NUM_THREADS=1
 ENV MPLCONFIGDIR=/tmp/mplconfigdir
 
-# Set the working directory to /app
-WORKDIR /app
+# Suppress Mesa's shader-cache warning ("Failed to create //.cache …") that
+# appears when running as a non-standard user inside Docker where $HOME is
+# unset or points to a non-writable directory.
+ENV MESA_SHADER_CACHE_DISABLE=1
+
+# In order to find NVIDIA GPUs (--gpus all)
+ENV NVIDIA_VISIBLE_DEVICES=all
+ENV NVIDIA_DRIVER_CAPABILITIES=all
 
-# Set entrypoint (non-interactive mode)
-ENTRYPOINT ["python3", "/app/fsqc/run_fsqc"]
+# Register the NVIDIA EGL ICD so libEGL finds the GPU driver
+RUN mkdir -p /usr/share/glvnd/egl_vendor.d && \
+    echo '{"file_format_version":"1.0.0","ICD":{"library_path":"libEGL_nvidia.so.0"}}' \
+    > /usr/share/glvnd/egl_vendor.d/10_nvidia.json
 
-## Run app when the container launches (interactive mode)
-#CMD ["/bin/bash"]
+# Set the working directory to /app
+WORKDIR /app
 
+# Set entrypoint
+ENTRYPOINT ["run_fsqc"]

fsqc/createScreenshots.py

@@ -208,7 +208,7 @@ def computeLayout(n):
 
         lut = np.concatenate((lut, lutAdd), axis=0)
 
-    lutEnum = dict(zip(lut[:, 0], range(len(lut[:, 0]))))
+    lutEnum = dict(zip(lut[:, 0], range(len(lut[:, 0])), strict=True))
 
     lutTab = np.array(lut[:, (2, 3, 4, 5)] / 255, dtype="float32")
     lutTab[:, 3] = 1

fsqc/createSurfacePlots.py

@@ -30,8 +30,7 @@ def createSurfacePlots(SUBJECT, SUBJECTS_DIR, SURFACES_OUTDIR, VIEWS, FASTSURFER
 
     import os
 
-    from whippersnappy import snap1
-    from whippersnappy.utils.types import ViewType
+    from whippersnappy import ViewType, snap1
 
     # -----------------------------------------------------------------------------
     # import surfaces and overlays

fsqc/fsqcMain.py

@@ -323,7 +323,7 @@ def get_help(print_help=True, return_help=False):
     At least one subject whose structural MR image was processed with Freesurfer
     6.0 or later, or FastSurfer v1.1 or later (including the surface pipeline).
 
-    A Python version >= 3.8 is required to run this script.
+    A Python version >= 3.10 is required to run this script.
 
     Required packages include (among others) the nibabel and skimage package for
     the core functionality, plus the the matplotlib, pandas, and transform3d
@@ -2438,7 +2438,8 @@ def _do_fsqc(argsDict):
                                         "fornixShapeEV{:0>3}".format,
                                         range(FORNIX_N_EIGEN),
                                     ),
-                                    fornixShapeOutput,
+                                    fornixShapeOutput, 
+                                    strict=True,
                                 )
                             )
                         }
@@ -2455,7 +2456,8 @@ def _do_fsqc(argsDict):
                                         "fornixShapeEV{:0>3}".format,
                                         range(FORNIX_N_EIGEN),
                                     ),
-                                    np.full(FORNIX_N_EIGEN, np.nan),
+                                    np.full(FORNIX_N_EIGEN, np.nan), 
+                                    strict=True,
                                 )
                             )
                         }
@@ -2486,7 +2488,8 @@ def _do_fsqc(argsDict):
                                         "fornixShapeEV{:0>3}".format,
                                         range(FORNIX_N_EIGEN),
                                     ),
-                                    fornixShapeOutput,
+                                    fornixShapeOutput, 
+                                    strict=True,
                                 )
                             )
                         }
@@ -2899,7 +2902,8 @@ def _do_fsqc(argsDict):
                                 map(
                                     "fornixShapeEV{:0>3}".format, range(FORNIX_N_EIGEN)
                                 ),
-                                fornixShapeOutput,
+                                fornixShapeOutput, 
+                                strict=True,
                             )
                         )
                     }