Updated the README

Author: carljohnsen

Diff for: README.md

@@ -1,2 +1,69 @@
 # 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
+```sh
+git clone [email protected]:jamesavery/maxibone.git
+```
+
+## Determine python version
+```sh
+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
+```sh
+cd maxibone/src/
+```
+
+## Install the Python generic dependencies
+```sh
+make pip_generic
+```
+
+## Install the Python dependencies for the GPU
+```sh
+make pip_cuda
+```
+
+## Build the project
+```sh
+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:
+```sh
+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:
+```sh
+python3 processing_steps/0400_h5tobin.py -h
+```
+Outputs:
+```txt
+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
+```