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Update README.md
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m-reuter authored May 2, 2024
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Expand Up @@ -8,25 +8,25 @@ FastSurfer surface models and color overlays and generate screen shots.
- Capture 4x4 surface plots (front & back, left and right)
- OpenGL window for interactive visualization

Note, that currently no off-screen rendering is supported. Even in snap
## Installation:

The `WhipperSnapPy` package can be installed from pypi via
```
python3 -m pip install whippersnappy
```

Note, that currently no off-screen rendering is natively supported. Even in snap
mode an invisible window will be created to render the openGL output
and capture the contents to an image. In order to run this on a headless
server, inside Docker, or via ssh we recommend to install xvfb and run

```
apt update && apt install -y python3 python3-pip xvfb
sudo apt update && apt install -y python3 python3-pip xvfb
pip3 install pyopengl glfw pillow numpy pyrr PyQt5==5.15.6
pip3 install .
pip3 install whippersnappy
xvfb-run whippersnap ...
```

## Installation:

The `WhipperSnapPy` package can be installed from this repository using:
```
python3 -m pip install .
```

## Usage:

### Local:
Expand All @@ -40,7 +40,7 @@ whippersnap -lh $OVERLAY_DIR/$LH_OVERLAY_FILE \
-o $OUTPUT_DIR/whippersnappy_image.png \
```

Note that adding the `--interactive` flag will start an interactive GUI that
Note, that adding the `--interactive` flag will start an interactive GUI that
includes a visualization of one hemisphere side and a simple application through
which color threshold values can be configured.

Expand All @@ -65,7 +65,7 @@ docker run --rm --init --name my_whippersnappy -v $SURF_SUBJECT_DIR:/surf_subjec

In this example: `$SURF_SUBJECT_DIR` contains the surface files, `$OVERLAY_DIR` contains the overlays to be loaded on to the surfaces, `$OUTPUT_DIR` is the local output directory in which the snapshot will be saved, and `${LH/RH}_OVERLAY_FILE` point to the specific overlay files to load.

**Note:** The `--init` flag is needed for the `xvfb-run` tool to be used correctly.
**Note:** The `--init` flag is needed for the `xvfb-run` tool to be used correctly for off screen rendering.


## API Documentation
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