6. Functions

6.1. dictwriter functions

dicom_conversion.conversion_dictwriter.parse_args(startpatient, endpatient, sourcedir, miscdir, modalitylist, ROIs, maxdelineationdelay, maxstudydelay)

Parsing function that declares relevant variables for later use.

Parameters:

  • startpatient – Starting point

  • endpatient – End point

  • sourcedir – directory for location of dicom files

  • miscdir – directory for miscellaneous output

  • modalitylist – list of relevant modalities

  • ROIs – list of relevant regions of interest

  • maxdelineationdelay – maximum allowed number of days between scan and delineation

  • maxstudydelay – maximum allowed number of days between primary and secondary study

Returns:

parsing arguments

dicom_conversion.conversion_dictwriter.main(args)

produces a dictionary consisting of patient studies, ROIs, Modalities and apertaining dates.

Parameters:

args – arguement object from parse_args

Returns:

excel dictionary

6.2. filewriter functions

dicom_conversion.conversion_filewriter.parse_args(targetdir, miscdir, modalitylist, ROIs, includered, includeorange, includeyellow)

Parsing function that declares relevant variables for later use.

Parameters:

  • targetdir – directory for output nifti files

  • miscdir – directory for miscellanous output

  • modalitylist – list of relevant modalities

  • ROIs – list of relevant regions of interest

  • includered – boolean variable which includes red flagged patients if True

  • includeorange – boolean variable which includes orange flagged patients if True

  • includeyellow – boolean variable which includes yellow flagged patients if True

Returns:

parsing arguments

dicom_conversion.conversion_filewriter.main(args)

produces converted nifti-files using an excel dictionary.

Parameters:

args – arguement object from parse_args

Returns:

nifti-files

6.3. Helper functions for the conversion scripts

dicom_conversion.conversion_functions.read_dicts_from_excel(filepath, include_red, include_orange, include_yellow)

Read dictionaries from Excel-file via JSON.

Parameters:

  • filepath – directory for excel-file

  • include_red – boolean variable which includes red flagged patients if True

  • include_orange – boolean variable which includes orange flagged patients if True

  • include_yellow – boolean variable which includes yellow flagged patients if True

Returns:

series dictionary

dicom_conversion.conversion_functions.highlight_rows(row, list_flagged)

flags patients with error codes.

Parameters:

  • row – row of the flagged patient

  • list_flagged – list of flagged patients.

Returns:

formatting options

6.4. evaluation functions

evaluation.parse_args(startpatient, endpatient, sourcedir, miscdir, margin, flaggingthreshold)

Parsing function that declares relevant variables for later use.

Parameters:

  • startpatient – Starting point

  • endpatient – End point

  • sourcedir – directory for location of registered images

  • miscdir – directory for miscellaneous output

  • margin – number of additional slices that should be removed

  • flaggingthreshold – evaluation threshold for flagging images

Returns:

parsing arguments

evaluation.main(args)

Calculates evaluation metric on registered images and flags low perfoming images.

Parameters:

args – arguement object from parse_args

Returns:

excel-file containing evaluation scores.

evaluation.getCropParameters(moving, marginsize=0)

Finds the cropbox for an MR-scan, i.e. a cropbox around all voxels with values greater than or equal to 1.

Parameters:

  • moving – the MR-scan to find a cropbox in

  • marginsize – margin to crop away in addition to cropbox. Default 0

Returns:

a list containing where to crop in all 6 spatial directions

evaluation.calcMI(fixed, moving)

Calculates Mutual Information between two images.

Parameters:

  • fixed – the fixed image, usually a CT-scan

  • moving – the moving image, usually a PT- or MR-scan

Returns:

the Mutual Information value as a float.

evaluation.resample(image, tx=0.0, ty=0.0, tz=0.0, def_value=0.0)

Applies a directional shift in an image.

Parameters:

  • image – the image to shift

  • tx – the number of voxels to shift by along the x-axis. Default 0.0

  • ty – the number of voxels to shift by along the y-axis. Default 0.0

  • tz – the number of voxels to shift by along the z-axis. Default 0.0

  • def_value – the default voxel value to use. Default 0.0

Returns:

image shifted as specified.

6.5. registration functions

registration.register_rigid_bspline.parse_args(sourcedir, targetdir, startpatient, endpatient)

Parsing function that declares relevant variables for later use.

Parameters:

  • sourcedir – directory for images that needs to be registered

  • targetdir – directory for nifti-files output

  • startpatient – starting point

  • endpatient – end point

Returns:

parsing arguments

registration.register_rigid_bspline.main(args)

Executes rigid and deformable registration on nifti images.

Parameters:

  • sourcedir – directory for images that needs to be registered

  • targetdir – directory for nifti-files output

  • startpatient – starting point

  • endpatient – end point

Returns:

parsing arguements