PyViz grew out of a necessity to be able to easily view volumetric image data common to CT/MRI scans in the medical field. This project is implemented in python using matplotlib for image rendering. It is a simple slice-by-slice viewer that supports re-orienting the view into the 3 orthogonal cartesian planes, referred to as axial, coronal, and sagittal by the medical community.
This project currently supports the following types of data:
- raw/bin - linear packing of float/double data, assumed to be in C-major ordering (z-index: slowest, x-index: fastest)
- npy/npz - currently supports automatic unpacking of the first array in the .npz file. Future versions will allow selection of other arrays
- dicom - either as a single dicom slice (.dcm file) or as a directory containing all slices in a series. (required: pydicom, pymedimage)
The functionality can be easily extended for other proprietary formats as well.
Open a terminal window and enter:
pip3 install git+git://github.com/ryanneph/PyViz.git#egg=PyVizOpen a terminal window and enter:
pip3 install --upgrade git+git://github.com/ryanneph/PyViz.git#egg=PyVizOpen a terminal window and enter:
git clone https://github.com/ryanneph/PyViz.git
cd PyViz
pip3 install -e --process-dependency-links .PyViz can be run directly by opening a terminal and running:
cd PyViz
python3 pyviz/gui.pyor can be run from any location after installation by opening a terminal and running:
pyviz- Select a directory which will be recursively searched for
.bin/.raw/.dcmfiles - For dicom files, simply select from the list and the array size will be automatically detected
- To open a dicom series (stack of 2D slices), navigate to the parent of the directory containing the
.dcmfiles and select the containing directory from the list in the gui window. - For raw/bin files, first enter the X, Y, Z array sizes into the text fields below the list, then select the file
Please open an issue describing a problem or contact Ryan Neph at neph320@gmail.com to get involved.