Startup

After installing, PySeus can be invoced in the command line via pyseus [file]. Alternatively, you can call PySeus directly from any python script:

import pyseus

pyseus.load()  # starts the PySeus GUI
pyseus.load(data)  # starts the GUI and loads [data]
pyseus.load(path)  # starts the GUI and loads [path]

Supported formats

PySeus supports the following data formats:

Python lists / arrays: PySeus will accept any 2 to 5 dimensional data.

Numpy nd-arrays: PySeus will accept nd-arrays and .npy files. .npz files are currently not supported.

HDF5 files: PySeus will accept HDF5 files; if multiple datasets are present within a file, a selection dialog is displayed.

DICOM files: PySeus will accept .DCM files and attempt to load slices and scans form the base and parent directories. DICOMDIR files are currently not supported.

NIfTI files: Pyseus will accept NIfTI-1 and NIfTI-2 .nii files.

If you need to extend PySeus to use other file formats, see Development / Formats.

Data conventions

Some formats, like NumPy and HDF5 allow for a lot of freedom in how the data is structured; in these cases, PySeus interprets data like this:

Two dimensional data is interpreted as a single slice, the first dimension being the y-axis.

Three dimensional data is interpreted as a set of slices, where the first dimension is the slice index.

Four dimensional data is interpreted as a set of scans, where the first dimension is the scan index.

Five dimensional data is interpreted as a set of scans, where the first two dimensions are merged for the scan index.