BrainVisa tools modules¶
brainvisa.tools.aimsGlobals¶
This module provides a few functions using pyaims (soma.aims module), and defines several lists of formats (neuroDiskItems.NamedFormatList
):
- brainvisa.tools.aimsGlobals.anatomistVolumeFormats¶
The name of the list is Anatomist volume formats and it contains the volume formats which are handled by Anatomist.
- brainvisa.tools.aimsGlobals.aimsVolumeFormats¶
- brainvisa.tools.aimsGlobals.vipVolumeFormats¶
The name of the list is Aims readable volume formats and it contains the volume formats which can be read with Aims.
- brainvisa.tools.aimsGlobals.aimsWriteVolumeFormats¶
The name of the list is Aims writable volume formats and it contains the volume formats which can be written with Aims.
- brainvisa.tools.aimsGlobals.aimsImageFormats¶
The name of the list is Aims image formats and it contains the 2D image formats which are readable with Aims.
- brainvisa.tools.aimsGlobals.anatomistMeshFormats¶
The name of the list is Anatomist mesh formats and it contains the mesh formats which are handled by Anatomist.
- brainvisa.tools.aimsGlobals.aimsMeshFormats¶
The name of the list is Aims mesh formats and it contains the mesh formats which are handled by Aims.
- brainvisa.tools.aimsGlobals.aimsTextureFormats¶
The name of the list is Aims texture formats and it contains the texture formats which are handled by Aims.
- brainvisa.tools.aimsGlobals.anatomistTextureFormats¶
The name of the list is Anatomist texture formats and it contains the texture formats which are handled by Anatomist.
- brainvisa.tools.aimsGlobals.html_pdf_formats¶
Formats list for HTML format, and PDF if the wkhtmltopdf tool is installed on the system and available in the PATH.
These global variables are initialized through the function initializeFormatLists()
.
- brainvisa.tools.aimsGlobals.aimsVolumeAttributes(item, writeOnly=0, forceFormat=0)[source]¶
Gets the header attributes of a
DiskItem
if the item is a readable volume.- Parameters
item – the diskitem
writeonly – if True, the function just returns an empty dictionary
forceFormat – if True, the format of the diskitem is not checked
- Returns
a dictionary containing the attributes of the header.
- brainvisa.tools.aimsGlobals.aims_to_bv_formats(formats)[source]¶
Translates formats (single string or list) from AIMS formats names into BrainVISA’s
- brainvisa.tools.aimsGlobals.initializeFormatLists()[source]¶
Initializes several lists of formats. The lists are stored in global variables.
- brainvisa.tools.aimsGlobals.reordered_formats(formats, priority_list=['gz compressed NIFTI-1 image', 'NIFTI-1 image', 'GIS Image', 'MINC image', 'gz compressed MINC image', 'SPM image', 'Z Compressed GIS Image', 'gz Compressed GIS Image', 'ECAT v image', 'ECAT i image', 'FreesurferMGZ', 'FreesurferMGH', 'Z compressed VIDA Image', 'gz compressed VIDA Image', 'Z compressed SPM image', 'gz compressed SPM image', 'Z compressed ECAT v image', 'gz compressed ECAT v image', 'Z compressed ECAT i image', 'gz compressed ECAT i image', 'JPEG image', 'GIF image', 'PNG image', 'MNG image', 'BMP image', 'PBM image', 'PGM image', 'PPM image', 'XBM image', 'XPM image', 'TIFF image', 'TIFF(.tif) image', 'DICOM image', 'Directory', 'FDF image', 'VIDA Image', 'GIFTI file', 'MESH mesh', 'TRI mesh', 'Z compressed MESH mesh', 'gz compressed MESH mesh', 'Z compressed TRI mesh', 'gz compressed TRI mesh', 'PLY mesh', 'Z compressed PLY mesh', 'gz compressed PLY mesh', 'Z compressed GIFTI file', 'gz compressed GIFTI file', 'MNI OBJ mesh', 'Z compressed MNI OBJ mesh', 'gz compressed MNI OBJ mesh', 'Texture', 'Z compressed Texture', 'gz compressed texture', 'Z compressed GIFTI file', 'gz compressed GIFTI file'])[source]¶
Reorder brainvisa formats according to a priority list: set formats from the priority list first (in their order) when they are part of the formats list, then append the remaining ones (in their order also)
brainvisa.tools.mainthreadlife¶
Deprecated module, it has been moved to soma.qt_gui.qtThread: please use soma.qt_gui.qtThread.MainThreadLife now.
brainvisa.tools.matlabValidation¶
brainvisa.tools.spm_conversion¶
brainvisa.tools.spm_registration¶
brainvisa.tools.spm_results¶
brainvisa.tools.spm_run¶
- exception brainvisa.tools.spm_run.Spm8Standalone_error[source]¶
Bases:
RuntimeError
- exception brainvisa.tools.spm_run.Spm8_error[source]¶
Bases:
RuntimeError
- exception brainvisa.tools.spm_run.SpmConfigError[source]¶
Bases:
RuntimeError
brainvisa.tools.spm_segmentation¶
brainvisa.tools.spm_utils¶
brainvisa.tools.DisplayResultsFromSPM¶
brainvisa.tools.displayTitledGrid¶
- class brainvisa.tools.displayTitledGrid.DisplayTitledGrid(objPathMatrix, parent=None, mainColormap='B-W LINEAR', overlayColormap='RAINBOW', customOverlayColormap='Blue-White')[source]¶
Bases:
PyQt5.QtWidgets.QWidget
- brainvisa.tools.displayTitledGrid.displayTitledGrid(transformationManager, parent, inverseRawColumn, objPathMatrix, rowTitles=['raw_space', 'MRI_native_space', 'mask', 'MNI_space'], rowColors=['darkOrange', 'blue', 'MRI', 'blue', 'magenta'], colTitles=['PET', 'MRI', 'grey'], windowTitle='View grid', linkWindows='space', overlaidImages=[], mainColormap='B-W LINEAR', overlayColormap='RAINBOW', customOverlayColormap='Blue-White', rowButtonSubTitles=None)[source]¶
Grid of Anatomist views
Parameters: linkWindows: str
possible values : ‘all’ | none | row
- rowColors: list
default: [‘darkOrange’, ‘blue’, “MRI”, ‘blue’, ‘magenta’] orange = rawSpace, blue = mri space, magenta = mni space