def get_dvh(structure, dose, roi, limit=None, callback=None):
"""Calculate a cumulative DVH in Gy from a DICOM RT Structure Set & Dose.
Parameters
----------
structure : pydicom Dataset
DICOM RT Structure Set used to determine the structure data.
dose : pydicom Dataset
DICOM RT Dose used to determine the dose grid.
roi : int
The ROI number used to uniquely identify the structure in the structure
set.
limit : int, optional
Dose limit in cGy as a maximum bin for the histogram.
callback : function, optional
A function that will be called at every iteration of the calculation.
"""
from dicompylercore import dicomparser
rtss = dicomparser.DicomParser(structure)
rtdose = dicomparser.DicomParser(dose)
structures = rtss.GetStructures()
s = structures[roi]
s['planes'] = rtss.GetStructureCoordinates(roi)
s['thickness'] = rtss.CalculatePlaneThickness(s['planes'])
hist = calculate_dvh(s, rtdose, limit, callback)
return dvh.DVH(
counts=hist,
bins=(np.arange(0, 2) if
(hist.size == 1) else np.arange(0, hist.size + 1) / 100),
dvh_type='differential',
dose_units='gy',
name=s['name']).cumulative
def test_raw_data_dvh(self):
"""Test if a DVH can be created from raw data."""
self.assertEqual(dvh.DVH.from_data(1, 1), dvh.DVH([1], [1]))
self.assertEqual(
repr(dvh.DVH.from_data(1, 1)),
"DVH(cumulative, 1 bins: [0:1] Gy, volume: 1 cm3, "
"name: None, rx_dose: 0 Gy)")
assert_array_equal(dvh.DVH.from_data(0, 1).bins, array([0, 0]))
assert_array_equal(dvh.DVH.from_data(5, 2).bins, array([0, 2, 4, 5]))
def get_dvh(structure,
dose,
roi,
limit=None,
calculate_full_volume=True,
use_structure_extents=False,
interpolation_resolution=None,
interpolation_segments_between_planes=0,
thickness=None,
callback=None):
"""Calculate a cumulative DVH in Gy from a DICOM RT Structure Set & Dose.
Parameters
----------
structure : pydicom Dataset
DICOM RT Structure Set used to determine the structure data.
dose : pydicom Dataset
DICOM RT Dose used to determine the dose grid.
roi : int
The ROI number used to uniquely identify the structure in the structure
set.
limit : int, optional
Dose limit in cGy as a maximum bin for the histogram.
calculate_full_volume : bool, optional
Calculate the full structure volume including contours outside of the
dose grid.
use_structure_extents : bool, optional
Limit the DVH calculation to the in-plane structure boundaries.
interpolation_resolution : tuple or float, optional
Resolution in mm (row, col) to interpolate structure and dose data to.
If float is provided, original dose grid pixel spacing must be square.
interpolation_segments_between_planes : integer, optional
Number of segments to interpolate between structure slices.
thickness : float, optional
Structure thickness used to calculate volume of a voxel.
callback : function, optional
A function that will be called at every iteration of the calculation.
"""
from dicompylercore import dicomparser
rtss = dicomparser.DicomParser(structure)
rtdose = dicomparser.DicomParser(dose)
structures = rtss.GetStructures()
s = structures[roi]
s['planes'] = rtss.GetStructureCoordinates(roi)
s['thickness'] = thickness if thickness else rtss.CalculatePlaneThickness(
s['planes'])
calcdvh = calculate_dvh(s, rtdose, limit, calculate_full_volume,
use_structure_extents, interpolation_resolution,
interpolation_segments_between_planes, callback)
return dvh.DVH(counts=calcdvh.histogram,
bins=(np.arange(0, 2) if (calcdvh.histogram.size == 1) else
np.arange(0, calcdvh.histogram.size + 1) / 100),
dvh_type='differential',
dose_units='Gy',
notes=calcdvh.notes,
name=s['name']).cumulative
def test_dose_constraint_with_zero_volume(self):
subject = dvh.DVH(array([0, 0]), array([0, 1]))
subject.dose_constraint(1)
def test_dvh_statistics_with_zero_volume(self):
subject = dvh.DVH(array([0, 0]), array([0, 1]))
self.assertEqual(subject.max, 0)
self.assertEqual(subject.min, 0)
self.assertEqual(subject.mean, 0)
def test_dose_constraint_with_no_counts(self):
subject = dvh.DVH(array([]), array([0]))
subject.dose_constraint(1)
def test_dvh_statistics_with_no_counts(self):
subject = dvh.DVH(array([]), array([0]))
self.assertEqual(subject.max, 0)
self.assertEqual(subject.min, 0)
self.assertEqual(subject.mean, 0)