Function reference
Configuration¶
Package-wide defaults, validated and overridable.
| rcparams | Package-wide defaults, in one validated mapping. |
Data Model¶
Core classes representing a GE exam and its series.
| GEExam.ExamBase | Base class for a GE exam, loading series metadata and providing series access. |
| GEExam.DMIExam | Exam containing anatomical, MRS, and MRSI series for a DMI acquisition. |
| GEExam.MS_DMIExam | DMI exam for a multi-slice acquisition with a single MRSI and two MRS series. |
| GEExam.DMIinjExam | DMI exam for an intravenous injection, splitting series into pre-/post-injection. |
| GESeries.NiiBase | Wraps a NIfTI image with orientation-aware loading, display, and I/O helpers. |
| GESeries.MRISeries | A reconstructed MRI series, loaded as a NIfTI (found by its sidecar’s SeriesNumber). |
| GESeries | An MRI series with the associated raw reconstructed .mat data loaded. |
| GESeries.MRSISeries | A raw MRSI series: spectroscopic imaging spectra, fitting, and voxel maps. |
| GESeries.MRSSeries | A single-voxel MRS series: FIDs, spectra, averaging, and fitting. |
| GESeries | An MRS washin series: repeated spectra fitted and grouped over time. |
Data Loading & File Handling¶
Loading raw/reconstructed data and general file helpers.
NIfTI & Imaging¶
DICOM/NIfTI conversion and image utilities.
| utils.nifti | |
| utils | Fractional occupancy of a high-resolution mask on a coarse (MRSI) voxel grid. |
| utils.images |
Plotting¶
Plotting for images and spectra.
| plotting.images | |
| plotting.spectra | |
| utils.spectra | |
| plotting.saving | Saving matplotlib figures with per-context (poster/talk/paper) presets. |
Fitting¶
Spectral fitting, wrapping xmris/pyAMARES.
MATLAB Bridge¶
MATLAB Engine setup and invocation.