-
-
Notifications
You must be signed in to change notification settings - Fork 68
/
dicomparser.py
executable file
·880 lines (739 loc) · 34.1 KB
/
dicomparser.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# dicomparser.py
"""Class that parses and returns formatted DICOM RT data."""
# Copyright (c) 2009-2016 Aditya Panchal
# Copyright (c) 2009-2010 Roy Keyes
# This file is part of dicompyler-core, released under a BSD license.
# See the file license.txt included with this distribution, also
# available at https://github.com/dicompyler/dicompyler-core/
import logging
import numpy as np
try:
from pydicom.dicomio import read_file
from pydicom.dataset import Dataset
from pydicom.pixel_data_handlers.util import pixel_dtype
except ImportError:
from dicom import read_file
from dicom.dataset import Dataset
import random
from numbers import Number
from six import PY2, iterkeys, string_types, BytesIO
from six.moves import range
from dicompylercore import dvh, util
from dicompylercore.config import pil_available, shapely_available
if pil_available:
from PIL import Image
if shapely_available:
from shapely.geometry import Polygon
logger = logging.getLogger('dicompylercore.dicomparser')
class DicomParser:
"""Parses DICOM / DICOM RT files."""
def __init__(self, dataset, memmap_pixel_array=False):
self.memmap_pixel_array = memmap_pixel_array
if isinstance(dataset, Dataset):
self.ds = dataset
elif isinstance(dataset, (string_types, BytesIO)):
try:
with open(dataset, "rb") as fp:
self.ds = read_file(fp, defer_size=100, force=True,
stop_before_pixels=memmap_pixel_array)
if memmap_pixel_array:
self.offset = fp.tell() + 8
except:
# Raise the error for the calling method to handle
raise
else:
# Sometimes DICOM files may not have headers,
# but they should always have a SOPClassUID
# to declare what type of file it is.
# If the file doesn't have a SOPClassUID,
# then it probably isn't DICOM.
if not "SOPClassUID" in self.ds:
raise AttributeError
else:
raise AttributeError
if memmap_pixel_array:
self.filename = dataset
self.pixel_array = self.get_pixel_array
else:
if "PixelData" in self.ds:
self.pixel_array = self.ds.pixel_array
######################## SOP Class and Instance Methods #######################
def GetSOPClassUID(self):
"""Determine the SOP Class UID of the current file."""
uid = getattr(self.ds, 'SOPClassUID', None)
if (uid == '1.2.840.10008.5.1.4.1.1.481.2'):
return 'rtdose'
elif (uid == '1.2.840.10008.5.1.4.1.1.481.3'):
return 'rtss'
elif (uid == '1.2.840.10008.5.1.4.1.1.481.5'):
return 'rtplan'
elif (uid == '1.2.840.10008.5.1.4.1.1.2'):
return 'ct'
else:
return None
def GetSOPInstanceUID(self):
"""Determine the SOP Class UID of the current file."""
return getattr(self.ds, 'SOPInstanceUID', None)
def GetStudyInfo(self):
"""Return the study information of the current file."""
return {'description': getattr(self.ds, 'StudyDescription',
'No description'),
'date': getattr(self.ds, 'StudyDate', None),
'time': getattr(self.ds, 'StudyTime', None),
'id': getattr(self.ds, 'StudyInstanceUID',
str(random.randint(0, 65535)))}
def GetSeriesDateTime(self):
"""Return the series date/time information."""
dt = {'date': getattr(self.ds, 'SeriesDate', None),
'time': getattr(self.ds, 'SeriesTime', None)}
if dt['date'] is None:
dt['date'] = getattr(self.ds, 'InstanceCreationDate', None)
if dt['time'] is None:
dt['time'] = getattr(self.ds, 'InstanceCreationTime', None)
return dt
def GetSeriesInfo(self):
"""Return the series information of the current file."""
series = {'description': getattr(self.ds, 'SeriesDescription',
'No description'),
'id': getattr(self.ds, 'SeriesInstanceUID', None),
'study': getattr(self.ds, 'SeriesInstanceUID', None),
'referenceframe': getattr(self.ds, 'FrameOfReferenceUID',
str(random.randint(0, 65535))),
'modality': getattr(self.ds, 'Modality', 'OT')}
series.update(self.GetSeriesDateTime())
series['study'] = getattr(self.ds, 'StudyInstanceUID', series['study'])
return series
def GetReferencedSeries(self):
"""Return the SOP Class UID of the referenced series."""
if "ReferencedFrameOfReferenceSequence" in self.ds:
frame = self.ds.ReferencedFrameOfReferenceSequence
if "RTReferencedStudySequence" in frame[0]:
study = frame[0].RTReferencedStudySequence[0]
if "RTReferencedSeriesSequence" in study:
if "SeriesInstanceUID" in \
study.RTReferencedSeriesSequence[0]:
series = study.RTReferencedSeriesSequence[0]
return series.SeriesInstanceUID
else:
return ''
def GetFrameOfReferenceUID(self):
"""Determine the Frame of Reference UID of the current file."""
if 'FrameOfReferenceUID' in self.ds:
# Some Files contain a Ref FoR but do not contain an FoR themselves
if not self.ds.FrameOfReferenceUID == '':
return self.ds.FrameOfReferenceUID
if 'ReferencedFrameOfReferenceSequence' in self.ds:
return self.ds.ReferencedFrameOfReferenceSequence[0].FrameOfReferenceUID
else:
return ''
def GetReferencedStructureSet(self):
"""Return the SOP Class UID of the referenced structure set."""
if "ReferencedStructureSetSequence" in self.ds:
return self.ds.ReferencedStructureSetSequence[0].ReferencedSOPInstanceUID
else:
return ''
def GetReferencedRTPlan(self):
"""Return the SOP Class UID of the referenced RT plan."""
if "ReferencedRTPlanSequence" in self.ds:
return self.ds.ReferencedRTPlanSequence[0].ReferencedSOPInstanceUID
else:
return ''
def GetDemographics(self):
"""Return the patient demographics from a DICOM file."""
# Set up some sensible defaults for demographics
patient = {'name': 'None',
'id': 'None',
'birth_date': None,
'gender': 'Other'}
if 'PatientName' in self.ds:
if PY2:
self.ds.decode()
name = self.ds.PatientName
patient['name'] = str(name)
patient['given_name'] = name.given_name
patient['middle_name'] = name.middle_name
patient['family_name'] = name.family_name
if 'PatientID' in self.ds:
patient['id'] = self.ds.PatientID
if 'PatientSex' in self.ds:
if (self.ds.PatientSex == 'M'):
patient['gender'] = 'M'
elif (self.ds.PatientSex == 'F'):
patient['gender'] = 'F'
else:
patient['gender'] = 'O'
if 'PatientBirthDate' in self.ds:
if len(self.ds.PatientBirthDate):
patient['birth_date'] = str(self.ds.PatientBirthDate)
return patient
############################### Image Methods #################################
def GetImageData(self):
"""Return the image data from a DICOM file."""
data = {}
if 'ImagePositionPatient' in self.ds:
data['position'] = self.ds.ImagePositionPatient
if 'ImageOrientationPatient' in self.ds:
data['orientation'] = self.ds.ImageOrientationPatient
if 'PixelSpacing' in self.ds:
data['pixelspacing'] = self.ds.PixelSpacing
else:
data['pixelspacing'] = [1, 1]
data['rows'] = self.ds.Rows
data['columns'] = self.ds.Columns
data['samplesperpixel'] = self.ds.SamplesPerPixel
data['photometricinterpretation'] = self.ds.PhotometricInterpretation
data['littlendian'] = \
self.ds.file_meta.TransferSyntaxUID.is_little_endian
if 'PatientPosition' in self.ds:
data['patientposition'] = self.ds.PatientPosition
data['frames'] = self.GetNumberOfFrames()
return data
def GetPixelArray(self):
"""Generate a memory mapped numpy accessor to the pixel array."""
if self.memmap_pixel_array is False:
return self.pixel_array
data = self.GetImageData()
filename = self.filename
dtype = pixel_dtype(self.ds)
offset = self.offset
frames = int(data['frames'])
shape = (int(self.GetNumberOfFrames()),
data['rows'], data['columns']) if frames > 1 \
else (data['rows'], data['columns'])
def get_pixel_array(filename, dtype, offset, shape):
array = np.memmap(
filename,
dtype=dtype,
mode="r",
offset=offset,
shape=shape
)
yield array
del array
return list(get_pixel_array(filename, dtype, offset, shape))[0]
get_pixel_array = property(GetPixelArray)
def GetImageLocation(self):
"""Calculate the location of the current image slice."""
ipp = self.ds.ImagePositionPatient
iop = self.ds.ImageOrientationPatient
normal = []
normal.append(iop[1] * iop[5] - iop[2] * iop[4])
normal.append(iop[2] * iop[3] - iop[0] * iop[5])
normal.append(iop[0] * iop[4] - iop[1] * iop[3])
loc = 0
for i in range(0, len(normal)):
loc += normal[i] * ipp[i]
# The image location is inverted for Feet First images
if 'PatientPosition' in self.ds:
if ('ff' in self.ds.PatientPosition.lower()):
loc = loc * -1
return loc
def GetImageOrientationType(self):
"""Get the orientation of the current image slice."""
if 'ImageOrientationPatient' in self.ds:
iop = np.array(self.ds.ImageOrientationPatient)
orientations = [
["SA", np.array([1, 0, 0, 0, 1, 0])], # supine axial
["PA", np.array([-1, 0, 0, 0, -1, 0])], # prone axial
["SS", np.array([0, 1, 0, 0, 0, -1])], # supine sagittal
["PS", np.array([0, -1, 0, 0, 0, -1])], # prone sagittal
["SC", np.array([1, 0, 0, 0, 0, -1])], # supine coronal
["PC", np.array([-1, 0, 0, 0, 0, -1])] # prone coronal
]
for o in orientations:
if (not np.any(np.array(np.round(iop - o[1]), dtype=np.int32))):
return o[0]
# Return N/A if the orientation was not found or could not be determined
return "NA"
def GetNumberOfFrames(self):
"""Return the number of frames in a DICOM image file."""
frames = 1
if 'NumberOfFrames' in self.ds:
frames = self.ds.NumberOfFrames.real
else:
if "PixelData" not in self.ds:
return 0
else:
if (self.pixel_array.ndim > 2):
if (self.ds.SamplesPerPixel == 1) and not \
(self.ds.PhotometricInterpretation == 'RGB'):
frames = self.pixel_array.shape[0]
return frames
def GetRescaleInterceptSlope(self):
"""Return the rescale intercept and slope if present."""
intercept, slope = 0, 1
if ('RescaleIntercept' in self.ds and 'RescaleSlope' in self.ds):
intercept = self.ds.RescaleIntercept if \
isinstance(self.ds.RescaleIntercept, Number) else 0
slope = self.ds.RescaleSlope if \
isinstance(self.ds.RescaleSlope, Number) else 1
return intercept, slope
def GetImage(self, window=0, level=0, size=None, background=False,
frames=0):
"""Return the image from a DICOM image storage file."""
if not pil_available:
print("Python imaging library not available." + \
" Cannot generate images.")
return
# Return a black image if the Numpy pixel array cannot be accessed
try:
self.pixel_array
except:
return Image.new('L', size)
# Samples per pixel are > 1 & RGB format
if (self.ds.SamplesPerPixel > 1) and \
(self.ds.PhotometricInterpretation == 'RGB'):
# Little Endian
if self.ds.file_meta.TransferSyntaxUID.is_little_endian:
im = Image.frombuffer('RGB', (self.ds.Columns, self.ds.Rows),
self.ds.PixelData, 'raw', 'RGB', 0, 1)
# Big Endian
else:
im = Image.fromarray(np.rollaxis(
self.pixel_array.transpose(), 0, 2))
# Otherwise the image is monochrome
else:
if ((window == 0) and (level == 0)):
window, level = self.GetDefaultImageWindowLevel()
# Rescale the slope and intercept of the image if present
intercept, slope = self.GetRescaleInterceptSlope()
# Get the requested frame if multi-frame
if (frames > 0):
pixel_array = self.pixel_array[frames]
else:
pixel_array = self.pixel_array
rescaled_image = pixel_array * slope + intercept
image = self.GetLUTValue(rescaled_image, window, level)
im = Image.fromarray(image).convert('L')
# Resize the image if a size is provided
if size:
im.thumbnail(size, Image.ANTIALIAS)
# Add a black background if requested
if background:
bg = Image.new('RGBA', size, (0, 0, 0, 255))
bg.paste(im, ((size[0] - im.size[0]) // 2,
(size[1] - im.size[1]) // 2))
return bg
return im
def GetDefaultImageWindowLevel(self):
"""Determine the default window/level for the DICOM image."""
window, level = 0, 0
if ('WindowWidth' in self.ds) and ('WindowCenter' in self.ds):
if isinstance(self.ds.WindowWidth, float):
window = self.ds.WindowWidth
elif isinstance(self.ds.WindowWidth, list):
if (len(self.ds.WindowWidth) > 1):
window = self.ds.WindowWidth[1]
if isinstance(self.ds.WindowCenter, float):
level = self.ds.WindowCenter
elif isinstance(self.ds.WindowCenter, list):
if (len(self.ds.WindowCenter) > 1):
level = self.ds.WindowCenter[1]
if ((window, level) == (0, 0)):
wmax = 0
wmin = 0
# Rescale the slope and intercept of the image if present
intercept, slope = self.GetRescaleInterceptSlope()
pixel_array = self.pixel_array * slope + intercept
if (pixel_array.max() > wmax):
wmax = pixel_array.max()
if (pixel_array.min() < wmin):
wmin = pixel_array.min()
# Default window is the range of the data array
window = int(wmax - wmin)
# Default level is the range midpoint minus the window minimum
level = int(window / 2 - abs(wmin))
return window, level
def GetLUTValue(self, data, window, level):
"""Apply the RGB Look-Up Table for the data and window/level value."""
lutvalue = util.piecewise(data,
[data <= (level - 0.5 - (window - 1) / 2),
data > (level - 0.5 + (window - 1) / 2)],
[0, 255, lambda data:
((data - (level - 0.5)) / (window-1) + 0.5) *
(255 - 0)])
# Convert the resultant array to an unsigned 8-bit array to create
# an 8-bit grayscale LUT since the range is only from 0 to 255
return np.array(lutvalue, dtype=np.uint8)
def GetPatientToPixelLUT(self):
"""Get the image transformation matrix from the DICOM standard Part 3
Section C.7.6.2.1.1"""
di = self.ds.PixelSpacing[0]
dj = self.ds.PixelSpacing[1]
orientation = self.ds.ImageOrientationPatient
position = self.ds.ImagePositionPatient
m = np.matrix(
[[orientation[0]*di, orientation[3]*dj, 0, position[0]],
[orientation[1]*di, orientation[4]*dj, 0, position[1]],
[orientation[2]*di, orientation[5]*dj, 0, position[2]],
[0, 0, 0, 1]])
x = []
y = []
for i in range(0, self.ds.Columns):
imat = m * np.matrix([[i], [0], [0], [1]])
x.append(float(imat[0]))
for j in range(0, self.ds.Rows):
jmat = m * np.matrix([[0], [j], [0], [1]])
y.append(float(jmat[1]))
return (np.array(x), np.array(y))
########################## RT Structure Set Methods ###########################
def GetStructureInfo(self):
"""Return the patient demographics from a DICOM file."""
structure = {}
structure['label'] = getattr(self.ds, 'StructureSetLabel', '')
structure['date'] = getattr(self.ds, 'StructureSetDate', '')
structure['time'] = getattr(self.ds, 'StructureSetTime', '')
structure['numcontours'] = len(self.ds.ROIContourSequence)
return structure
def GetStructures(self):
"""Returns a dictionary of structures (ROIs)."""
structures = {}
# Determine whether this is RT Structure Set file
if not (self.GetSOPClassUID() == 'rtss'):
return structures
# Locate the name and number of each ROI
if 'StructureSetROISequence' in self.ds:
for item in self.ds.StructureSetROISequence:
data = {}
number = int(item.ROINumber)
data['id'] = number
data['name'] = item.ROIName
logger.debug("Found ROI #%s: %s", str(number), data['name'])
structures[number] = data
# Determine the type of each structure (PTV, organ, external, etc)
if 'RTROIObservationsSequence' in self.ds:
for item in self.ds.RTROIObservationsSequence:
number = item.ReferencedROINumber
if number in structures:
structures[number]['type'] = item.RTROIInterpretedType
# The coordinate data of each ROI is stored within ROIContourSequence
if 'ROIContourSequence' in self.ds:
for roi in self.ds.ROIContourSequence:
number = roi.ReferencedROINumber
# Generate a random color for the current ROI
structures[number]['color'] = np.array((
random.randint(0, 255),
random.randint(0, 255),
random.randint(0, 255)), dtype=int)
# Get the RGB color triplet for the current ROI if it exists
if 'ROIDisplayColor' in roi:
# Make sure the color is not none
if not (roi.ROIDisplayColor is None):
color = roi.ROIDisplayColor
# Otherwise decode values separated by forward slashes
else:
value = roi[0x3006, 0x002a].repval
color = value.strip("'").split("/")
# Try to convert the detected value to a color triplet
try:
structures[number]['color'] = \
np.array(color, dtype=int)
# Otherwise fail and fallback on the random color
except:
logger.debug(
"Unable to decode display color for ROI #%s",
str(number))
# Determine whether the ROI has any contours present
if 'ContourSequence' in roi:
structures[number]['empty'] = False
else:
structures[number]['empty'] = True
return structures
def GetStructureCoordinates(self, roi_number):
"""Get the list of coordinates for each plane of the structure."""
planes = {}
# The coordinate data of each ROI is stored within ROIContourSequence
if 'ROIContourSequence' in self.ds:
for roi in self.ds.ROIContourSequence:
if (roi.ReferencedROINumber == int(roi_number)):
if 'ContourSequence' in roi:
# Locate the contour sequence for each referenced ROI
for c in roi.ContourSequence:
# For each plane, initialize a new plane dict
plane = dict()
# Determine all the plane properties
plane['type'] = c.ContourGeometricType
plane['num_points'] = int(c.NumberOfContourPoints)
plane['data'] = \
self.GetContourPoints(c.ContourData)
# Add each plane to the planes dict
# of the current ROI
z = str(round(plane['data'][0][2], 2)) + '0'
if z not in planes:
planes[z] = []
planes[z].append(plane)
return planes
def GetContourPoints(self, array):
"""Parses an array of xyz points & returns a array of point dicts."""
n = 3
return [array[i:i+n] for i in range(0, len(array), n)]
def CalculatePlaneThickness(self, planesDict):
"""Calculates the plane thickness for each structure."""
planes = []
# Iterate over each plane in the structure
for z in iterkeys(planesDict):
planes.append(float(z))
planes.sort()
# Determine the thickness
thickness = 10000
for n in range(0, len(planes)):
if (n > 0):
newThickness = planes[n] - planes[n-1]
if (newThickness < thickness):
thickness = newThickness
# If the thickness was not detected, set it to 0
if (thickness == 10000):
thickness = 0
return thickness
def CalculateStructureVolume(self, coords, thickness):
"""Calculates the volume of the given structure.
Parameters
----------
coords : dict
Coordinates of each plane of the structure
thickness : float
Thickness of the structure
"""
if not shapely_available:
print("Shapely library not available." +
" Please install to calculate.")
return 0
class Within(Polygon):
def __init__(self, o):
self.o = o
def __lt__(self, other):
return self.o.within(other.o)
s = 0
for i, z in enumerate(sorted(coords.items())):
# Skip contour data if it is not CLOSED_PLANAR
if z[1][0]['type'] != 'CLOSED_PLANAR':
continue
polygons = []
contours = [[x[0:2] for x in c['data']] for c in z[1]]
for contour in contours:
p = Polygon(contour)
polygons.append(p)
# Sort polygons according whether they are contained
# by the previous polygon
if len(polygons) > 1:
ordered_polygons = sorted(polygons, key=Within, reverse=True)
else:
ordered_polygons = polygons
for ip, p in enumerate(ordered_polygons):
pa = 0
if ((i == 0) or (i == len(coords.items()) - 1)) and \
not (len(coords.items()) == 1):
pa += (p.area // 2)
else:
pa += p.area
# Subtract the volume if polygon is contained within the parent
# and is not the parent itself
if p.within(ordered_polygons[0]) and \
(p != ordered_polygons[0]):
s -= pa
else:
s += pa
vol = s * thickness / 1000
return vol
############################## RT Dose Methods ###############################
def HasDVHs(self):
"""Returns whether dose-volume histograms (DVHs) exist."""
if not "DVHSequence" in self.ds:
return False
else:
return True
def GetDVHs(self):
"""Returns cumulative dose-volume histograms (DVHs)."""
self.dvhs = {}
if self.HasDVHs():
for item in self.ds.DVHSequence:
# Make sure that the DVH has a referenced structure / ROI
if not 'DVHReferencedROISequence' in item:
continue
number = item.DVHReferencedROISequence[0].ReferencedROINumber
logger.debug("Found DVH for ROI #%s", str(number))
self.dvhs[number] = dvh.DVH.from_dicom_dvh(self.ds, number)
return self.dvhs
def GetDoseGrid(self, z=0, threshold=0.5):
"""Return the 2d dose grid for the given slice position (mm).
Parameters
----------
z : int, optional
Slice position in mm, by default 0
threshold : float, optional
Threshold in mm to determine the max difference from z
to the closest dose slice without using interpolation,
by default 0.5
Returns
-------
np.array
An numpy 2d array of dose points
"""
# If this is a multi-frame dose pixel array,
# determine the offset for each frame
if 'GridFrameOffsetVector' in self.ds:
pixel_array = self.GetPixelArray()
z = float(z)
# Get the initial dose grid position (z) in patient coordinates
ipp = self.ds.ImagePositionPatient
iop = self.ds.ImageOrientationPatient
gfov = self.ds.GridFrameOffsetVector
# Add the position to the offset vector to determine the
# z coordinate of each dose plane
planes = (iop[0] * iop[4] * np.array(gfov)) + ipp[2]
frame = -1
# Check to see if the requested plane exists in the array
if (np.amin(np.fabs(planes - z)) < threshold):
frame = np.argmin(np.fabs(planes - z))
# Return the requested dose plane, since it was found
if not (frame == -1):
return pixel_array[frame]
# Check if the requested plane is within the dose grid boundaries
elif ((z < np.amin(planes)) or (z > np.amax(planes))):
return np.array([])
# The requested plane was not found, so interpolate between planes
else:
# Determine the upper and lower bounds
umin = np.fabs(planes - z)
ub = np.argmin(umin)
lmin = umin.copy()
# Change the min value to the max so we can find the 2nd min
lmin[ub] = np.amax(umin)
lb = np.argmin(lmin)
# Fractional distance of dose plane between upper & lower bound
fz = (z - planes[lb]) / (planes[ub] - planes[lb])
plane = self.InterpolateDosePlanes(
pixel_array[ub], pixel_array[lb], fz)
return plane
else:
return np.array([])
def InterpolateDosePlanes(self, uplane, lplane, fz):
"""Interpolates a dose plane between two bounding planes at the given
relative location.
:param uplane: Upper dose plane boundary.
:param uplane: Lower dose plane boundary.
:param fz: Fractional distance from the bottom to the top,
where the new plane is located.
E.g. if fz = 1, the plane is at the upper plane,
fz = 0, it is at the lower plane.
:return: An numpy 2d array of the interpolated dose plane.
"""
# A simple linear interpolation
doseplane = fz*uplane + (1.0 - fz)*lplane
return doseplane
def GetIsodosePoints(self, z=0, level=100, threshold=0.5):
"""Return points for the given isodose level and slice position
from the dose grid.
:param z: Slice position in mm.
:param threshold: Threshold in mm to determine the max difference
from z to the closest dose slice without
using interpolation.
:param level: Isodose level in scaled form
(multiplied by self.ds.DoseGridScaling)
:return: An array of tuples representing isodose points.
"""
plane = self.GetDoseGrid(z, threshold)
isodose = (plane >= level).nonzero()
return list(zip(isodose[1].tolist(), isodose[0].tolist()))
def GetDoseData(self):
"""Return the dose data from a DICOM RT Dose file."""
data = self.GetImageData()
data['doseunits'] = getattr(self.ds, 'DoseUnits', '')
data['dosetype'] = getattr(self.ds, 'DoseType', '')
data['dosecomment'] = getattr(self.ds, 'DoseComment', '')
data['dosesummationtype'] = getattr(self.ds, 'DoseSummationType', '')
data['dosegridscaling'] = getattr(self.ds, 'DoseGridScaling', '')
dosemax = 0
for x in range(data["frames"]):
pixel_array = self.GetPixelArray()
newmax = pixel_array[x].max()
dosemax = newmax if newmax > dosemax else dosemax
if self.memmap_pixel_array:
del pixel_array
data['dosemax'] = float(dosemax)
data['lut'] = self.GetPatientToPixelLUT()
data['fraction'] = ''
if "ReferencedRTPlanSequence" in self.ds:
plan = self.ds.ReferencedRTPlanSequence[0]
if "ReferencedFractionGroupSequence" in plan:
data['fraction'] = \
plan.ReferencedFractionGroupSequence[0].ReferencedFractionGroupNumber
return data
def GetReferencedBeamNumber(self):
"""Return the referenced beam number (if it exists) from RT Dose."""
beam = None
if "ReferencedRTPlanSequence" in self.ds:
rp = self.ds.ReferencedRTPlanSequence[0]
if "ReferencedFractionGroupSequence" in rp:
rf = rp.ReferencedFractionGroupSequence[0]
if "ReferencedBeamSequence" in rf:
if "ReferencedBeamNumber" in rf.ReferencedBeamSequence[0]:
beam = \
rf.ReferencedBeamSequence[0].ReferencedBeamNumber
return beam
############################## RT Plan Methods ###############################
def GetPlan(self):
"""Returns the plan information."""
self.plan = {}
self.plan['label'] = getattr(self.ds, 'RTPlanLabel', '')
self.plan['date'] = getattr(self.ds, 'RTPlanDate', '')
self.plan['time'] = getattr(self.ds, 'RTPlanTime', '')
self.plan['name'] = ''
self.plan['rxdose'] = 0
if "DoseReferenceSequence" in self.ds:
for item in self.ds.DoseReferenceSequence:
if item.DoseReferenceStructureType == 'SITE':
self.plan['name'] = "N/A"
if "DoseReferenceDescription" in item:
self.plan['name'] = item.DoseReferenceDescription
if 'TargetPrescriptionDose' in item:
rxdose = item.TargetPrescriptionDose * 100
if (rxdose > self.plan['rxdose']):
self.plan['rxdose'] = rxdose
elif item.DoseReferenceStructureType == 'VOLUME':
if 'TargetPrescriptionDose' in item:
self.plan['rxdose'] = item.TargetPrescriptionDose * 100
if (("FractionGroupSequence" in self.ds) and (self.plan['rxdose'] == 0)):
fg = self.ds.FractionGroupSequence[0]
if ("ReferencedBeamSequence" in fg) and \
("NumberOfFractionsPlanned" in fg):
beams = fg.ReferencedBeamSequence
fx = fg.NumberOfFractionsPlanned
for beam in beams:
if "BeamDose" in beam:
self.plan['rxdose'] += beam.BeamDose * fx * 100
self.plan['rxdose'] = round(self.plan['rxdose'])
self.plan['brachy'] = False
if ("BrachyTreatmentTechnique" in self.ds) or \
("BrachyTreatmentType" in self.ds):
self.plan['brachy'] = True
return self.plan
def GetReferencedBeamsInFraction(self, fx=0):
"""Return the referenced beams from the specified fraction."""
beams = {}
if ("BeamSequence" in self.ds):
bdict = self.ds.BeamSequence
elif ("IonBeamSequence" in self.ds):
bdict = self.ds.IonBeamSequence
else:
return beams
# Obtain the beam information
for b in bdict:
beam = {}
beam['name'] = b.BeamName if "BeamName" in b else ""
beam['description'] = b.BeamDescription \
if "BeamDescription" in b else ""
beams[b.BeamNumber.real] = beam
# Obtain the referenced beam info from the fraction info
if ("FractionGroupSequence" in self.ds):
fg = self.ds.FractionGroupSequence[fx]
if ("ReferencedBeamSequence" in fg):
rb = fg.ReferencedBeamSequence
nfx = fg.NumberOfFractionsPlanned
for b in rb:
if "BeamDose" in b:
beams[b.ReferencedBeamNumber]['dose'] = \
b.BeamDose * nfx * 100
return beams