Collection of scripts used in the Bone Imaging Laboratory.

Main branch test status:

• Python All source code is Python, no C++, ergo no compilation
• Examples Please do upload individual, one-off project scripts to the /examples directory!
• Open source The whole world can see your code, and the whole world can contribute back
• Testing Automatically runs tests on a server. So, please write your tests!

# Clone the repository onto your computer and change into the directory.
# ... with SSH authentication
git clone [email protected]:Bonelab/Bonelab.git
# ... or straight HTTPS
git clone https://github.com/Bonelab/Bonelab.git

# setup the environment
conda create -n bl -c numerics88 -c conda-forge python=3 pyqt n88tools simpleitk pbr nose six pydicom gdcm

# ... or start fresh
conda create -n bl -c numerics88 -c conda-forge python=3 n88tools pbr nose

# Activate the environemnt
conda activate bl

# change directory into the Bonelab repo
cd Bonelab

# Install in an 'editable' format
pip install -e .

Install for M1 MACs (instructions from here)

# Clone the repository onto your computer and change into the directory.
# ... with SSH authentication
git clone [email protected]:Bonelab/Bonelab.git
# ... or straight HTTPS
git clone https://github.com/Bonelab/Bonelab.git

# setup the environment
CONDA_SUBDIR=osx-64 conda create -n bl -c numerics88 -c conda-forge python=3 pyqt n88tools simpleitk pbr nose six pydicom gdcm

# ... or start fresh
CONDA_SUBDIR=osx-64 conda create -n bl -c numerics88 -c conda-forge python=3 n88tools pbr nose

# Activate the environemnt
conda activate bl

# Tell conda to always not use the ARM directory for this env
conda env config vars set CONDA_SUBDIR=osx-64

# Deactivate and reactivate
conda deactivate
conda activate bl

# change directory into the Bonelab repo
cd Bonelab

# Install in an 'editable' format
pip install -e .

Installing in an 'editable' format allows changes to the code to be immediately reflected in your programs. This removes the need to run pip install with each change. However, changing entry points in setup.cfg will require re-running pip install.

bonelab.io.download_data

• environment variables for downloading Bonelab test data

bonelab.io.sitk_helpers

• dictionary of file types and casting types for reading and writing 2D raster images with :code:SimpleITK

bonelab.io.vtk_helpers

• utility functions for reading and writing images with vtk and vtkbone
• particularly useful functions for properly writing AIMs!

bonelab.util.aim_calibration_header

• utility functions for parsing calibration coefficients from AIM calibration headers

bonelab.util.echo_arguments

• utility function to use with a command-line application, or a function, to automatically print the arguments to the terminal

bonelab.util.multiscale_registration

• utility functions for performing multi-scale Demons registration with SimpleITK

bonelab.util.n88_util

• utility functions for extracting fields from n88models as :code:numpy arrays for visualization or processing

bonelab.util.time_stamp

• utility function for printing a message along with a time stamp, for logging, debugging, etc.

bonelab.util.vtk_util

• utility functions for converting data between vtk.vtkImageData and np.ndarray formats

bonelab.util.write_csv

• utility function for writing data stored in a dictionary to a csv file

Here is a list of all of the command-line apps that get installed along with the bonelab package. For detailed usage instructions, type the command followed by -h into the terminal with the bl environment activated.

# Be at the root
cd Bonelab

# Run tests
nosetests tests/

A collection of example data is provided by the Bone Imaging Laboratory.

These data can be fetched by executing the command blDownloadData in your terminal. Currently, the data is downloaded into the user's directory under the directory ~/.bldata. Please see blDownloadData -h for additional information.

Contributions or changes to the repository should be made using the trunk and branch development style. You first create a branch:

git checkout master
git pull
git checkout -b <your-name>/<branch-name>

As you develop locally, periodically run the tests to ensure your changes haven't broken anything:

nosetests tests/

Once you are satisfied with your changes, use the web interface to submit a pull request. Get someone more senior (/ Steve) to review your changes, and merge once review is done.

To add a new command-line application, do the following:

• Add file with main function in bonelab.cli
• Add entry point to setup.cfg that points to the new file
• Rerun pip install -e .
• Add tests to tests.cli, test_cli_setup.py and, if appropriate, add other tests.

If you're going to add something, please do add at least unit tests so that as other people edit the repository we can be sure they don't break your code.

Also make sure you document your new cool stuff in the README (this file) so that other people in the lab know about it!