Updated poetry environment, removed checkpoints to models

.gitignore

@@ -1,3 +1,4 @@
 .pytest_cache
 **/__pycache__/
 *.egg-info
+checkpoints

README.md

@@ -1,24 +1,29 @@
-## Build docker container for preprocessing
-Note that for now, building the container requires a folder called <checkpoints> that contains the FastSurfer segmentation checkpoints
+# Installation
+<details>
+<summary> <b>macOS</b> </summary>
 
+### Install pyenv
+To select the appropriate python version, ```pyenv``` must be installed. On macOS this can be done via brew:
 ```
-docker build \
-    -f docker/preprocess.Dockerfile \
-    -t pyment/preprocessing:1.0.0 \
-    .
+brew update
+brew install pyenv
+```
+After installation we can add pyenv to the ```~/.zshrc```-file to enable terminal shortcuts:
+```
+echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.zshrc
+echo '[[ -d $PYENV_ROOT/bin ]] && export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.zshrc
+echo 'eval "$(pyenv init - zsh)"' >> ~/.zshrc
 ```
 
-## Run docker container for preprocessing
-Running the container for preprocessing requires three volumes:
-- Inputs: A folder containing input data. All nifti-files detected in this folder or one of its subfolders will be processed
-- Outputs: A folder where the preprocessed images will be written.
-- Licenses: A folder containing the freesurfer license
-```
-docker run --rm \
-    --user $(id -u):$(id -g) \
-    --volume <path_to_input>:/input \
-    --volume <path_to_ouput>:/output \
-    --volume <path_to_licenses>:/licenses \
-    --gpus all \
-    pyment/preprocessing:1.0.0
+### Install Python
+The models in this repository expects Python version 3.10.4, which can be set up using ```pyenv```:
+```
+pyenv install 3.10.4
+```
+### Configure Python environment
+Next, we can set up a python environment for running the code in the repository:
+```
+poetry env use 3.10.4
+poetry install
 ```
+</details>

docker/README.md

@@ -0,0 +1,24 @@
+## Build docker container for preprocessing
+Note that for now, building the container requires a folder called <checkpoints> that contains the FastSurfer segmentation checkpoints
+
+```
+docker build \
+    -f docker/preprocess.Dockerfile \
+    -t pyment/preprocessing:1.0.0 \
+    .
+```
+
+## Run docker container for preprocessing
+Running the container for preprocessing requires three volumes:
+- Inputs: A folder containing input data. All nifti-files detected in this folder or one of its subfolders will be processed
+- Outputs: A folder where the preprocessed images will be written.
+- Licenses: A folder containing the freesurfer license
+```
+docker run --rm \
+    --user $(id -u):$(id -g) \
+    --volume <path_to_input>:/input \
+    --volume <path_to_ouput>:/output \
+    --volume <path_to_licenses>:/licenses \
+    --gpus all \
+    pyment/preprocessing:1.0.0
+```

new_packages.txt

@@ -1,17 +0,0 @@
-tomli==2.2.1
-pandas==1.4.2
-packaging==24.1
-typing-extensions==4.12.2
-wheel==0.43
-decorator==5.1.1
-requests==2.32.3
-nibabel==5.2.1
-jupyter==1.1.1
-matplotlib==3.8
-tqdm==4.66.4
-
-plotly==5.24.1
-pytest==8.3.3
-scikit-learn==1.5.1
-xlrd==2.0.1
-pydantic==2.10

pyproject.toml

@@ -17,8 +17,26 @@ packages = [{include = "pyment"}]
 
 [tool.poetry.dependencies]
 python = "3.10.4"
-tensorflow = "2.11.0"
+tensorflow-macos = { version = "2.11", markers = "platform_system == 'Darwin'" }
+tensorflow-metal = { version = "0.7", markers = "platform_system == 'Darwin'" }
+tensorflow = { version = "2.11", markers = "platform_system != 'Darwin'" }
 numpy = "1.22.3"
+tomli = "2.2.1"
+pandas = "1.4.2"
+packaging = "24.1"
+typing-extensions = "4.12.2"
+wheel = "0.43"
+decorator = "5.1.1"
+requests = "2.32.3"
+nibabel = "5.2.1"
+jupyter = "1.1.1"
+matplotlib = "3.8"
+tqdm = "4.66.4"
+plotly = "5.24.1"
+pytest = "8.3.3"
+scikit-learn = "1.5.1"
+xlrd = "2.0.1"
+pydantic = "2.10"
 
 [build-system]
 requires = ["poetry-core>=2.0.0,<3.0.0"]