MAXIBONE

Source code for SRμCT Bone tomography analysis project.

How to build

For GPU support, ensure the NVIDIA HPC SDK is in your path

Clone the repository

git clone [email protected]:jamesavery/maxibone.git

Determine python version

python --version

Verify that the first line of src/Makefile is set to the correct python version. Otherwise, change it to the correct version.

Change to the source directory

cd maxibone/src/

Install the Python generic dependencies

make pip_generic

Install the Python dependencies for the GPU

make pip_cuda

Build the project

make -j

Edit the paths in src/config/paths.py to point to the correct data directories

Start running the processing scripts

The scripts should be run from the src directory. Most of them only need the sample name as argument. For example:

python3 processing_steps/0400_h5tobin.py 770c_pag

Each script has a help message that can be displayed by running it with the -h flag:

python3 processing_steps/0400_h5tobin.py -h

Outputs:

usage: 0400_h5tobin.py [-h] [-c CHUNK_SIZE] [--disable-plotting] [-v VERBOSE] [--version] sample [sample_scale] [y_cutoff]

Converts a 16-bit HDF5 file to a 16-bit binary file. The binary file can be read faster than the HDF5 file, if it is stored on a fast disk.

positional arguments:
  sample                The name of the sample volume to be processed.
  sample_scale          The scale of the sample volume to be processed. Default is 1.
  y_cutoff              The y-coordinate to cut the volume at. Default is 0.

options:
  -h, --help            show this help message and exit
  -c CHUNK_SIZE, --chunk-size CHUNK_SIZE
                        The size of the z-axis of the chunks to be processed. Default is 64.
  --disable-plotting    Disable plotting the results of the script.
  -v VERBOSE, --verbose VERBOSE
                        Set the verbosity level of the script. Default is 1. Generally, 0 is no output, 1 is progress / some text output, 2 is helper/core function output, and 3 is extreme debugging.
  --version             Print the version of the script and exit.

For more information, please visit github.com/jamesavery/maxibone