forked from ricgambino/XNAT-PIC
-
Notifications
You must be signed in to change notification settings - Fork 0
/
bruker2dicom_converter.py
653 lines (581 loc) · 42.3 KB
/
bruker2dicom_converter.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
# -*- coding: utf-8 -*-
"""
Created on Dec 7 2021
@author: Riccardo Gambino
"""
from glob import glob
import os, re, time
import numpy as np
import datetime, shutil
import dateutil.parser
from pip import main
from pydicom.dataset import Dataset, FileDataset
import pydicom.uid
from read_visupars import read_visupars_parameters
from cest_dict import add_cest_dict
from read_method import read_method_parameters
import tkinter as tk
import tkinter.ttk as ttk
from tkinter import messagebox, HORIZONTAL
import sys, traceback
from ProgressBar import App
def update_progress_bar(current_step, max_step, bar_length):
loc_bar = int(current_step * bar_length / max_step)
return loc_bar
def bruker2dicom(folder_to_convert, dst_folder, master):
# Tag entries for cest acquisition
add_cest_dict()
parameters = 0
PV_version = ''
list_path = sorted(os.listdir(folder_to_convert))
# Check for 'results' folder into list_path
if hasattr(master, 'results_flag') is False:
master.results_flag = 0
if not os.path.isdir(dst_folder):
os.makedirs(dst_folder)
start_time = time.time()
for i, path in enumerate(list_path, 1):
if 'Results' not in path:
current_path = os.path.join(folder_to_convert, path).replace('\\', '/')
if os.path.isdir(current_path):
# Check for existing dseq paths into the current folder
dseq_file = glob(current_path + '/**/2dseq', recursive=True)
# Check for non-empty list, so we could be sure that 2dseq file exists
if dseq_file != []:
# Open and record configuration parameters from visu_pars, reco, acqp and method files
dseq_path = dseq_file[0].replace('\\', '/')
visu_pars_path = glob(current_path + '/**/**/visu_pars', recursive=True)[0].replace('\\', '/')
with open(visu_pars_path, "r"):
parameters = read_visupars_parameters(visu_pars_path)
reco_path = '/'.join(dseq_path.split('/')[:-1]) + '/' + "reco"
with open(reco_path, "r"):
reco_parameters = read_method_parameters(reco_path)
method_path = current_path + '/' + "method"
with open(method_path, "r"):
method_parameters = read_method_parameters(method_path)
acqp_path = current_path + '/' + "acqp"
with open(acqp_path, "r"):
acqp_parameters = read_visupars_parameters(acqp_path)
try:
PV_version = parameters.get("VisuCreatorVersion")
if PV_version == '':
PV_version = acqp_parameters.get("ACQ_sw_version")
except Exception as e:
messagebox.showerror("XNAT-PIC - Bruker2Dicom", e)
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_tb(exc_traceback)
sys.exit(1)
filename_little_endian = "MRIm"
img_type = parameters.get("VisuCoreWordType")
img_endianness = parameters.get("VisuCoreByteOrder")
img_frames = parameters.get("VisuCoreFrameCount")
img_dims = parameters.get("VisuCoreSize")
core_ext = parameters.get("VisuCoreExtent")
if isinstance(parameters.get("VisuCoreDataSlope"), str) and isinstance(parameters.get("VisuCoreDataOffs"), str):
slope = float(parameters.get("VisuCoreDataSlope")[parameters.get("VisuCoreDataSlope").find('(') \
+ 1 : parameters.get("VisuCoreDataSlope").find(')')])
intercept = float(parameters.get("VisuCoreDataOffs")[parameters.get("VisuCoreDataOffs").find('(') \
+ 1 : parameters.get("VisuCoreDataOffs").find(')')])
else:
slope = parameters.get("VisuCoreDataSlope")
intercept = parameters.get("VisuCoreDataOffs")
# Check endianness and precision
if img_type == "_32BIT_SGN_INT" and img_endianness == "littleEndian":
data_precision = np.dtype("<i4")
elif img_type == "_32BIT_SGN_INT" and img_endianness == "bigEndian":
data_precision = np.dtype(">i4")
elif img_type == "_16BIT_SGN_INT" and img_endianness == "littleEndian":
data_precision = np.dtype("<i2")
elif img_type == "_16BIT_SGN_INT" and img_endianness == "bigEndian":
data_precision = np.dtype(">i2")
else:
messagebox.showerror(
"Error!", "Image data precision is neither 16 nor 32 bit!"
)
os._exit(0)
raw_data = open(dseq_path, "rb")
img_data_precision = np.fromfile(raw_data, dtype=data_precision)
raw_data.close()
res = current_path
# head2, _ = os.path.split(res)
rel_path = os.path.relpath(res, folder_to_convert)
# parent_folder = os.path.basename(head2)
dst_path = os.path.join(dst_folder, 'MR', rel_path).replace('\\', '/')
if not os.path.isdir(dst_path):
os.makedirs(dst_path)
os.chdir(dst_path)
if img_type == "_16BIT_SGN_INT" and img_endianness == "littleEndian":
# img = np.array(img_data_precision,np.uint16)
if np.size(slope) == 1:
img_data_corrected = img_data_precision * slope
img_data_corrected += intercept
else:
img_data_corrected = img_data_precision * slope[0]
img_data_corrected += intercept[0]
factor = ((2 ** 16) - 1) / (np.amax(img_data_corrected))
img_float = img_data_corrected * factor
img = np.array(img_float, np.uint16)
# if 32 bit, slope and intercept correction
elif img_type == "_32BIT_SGN_INT" and img_endianness == "littleEndian":
if np.size(slope) == 1:
img_data_corrected = img_data_precision * slope
img_data_corrected += intercept
else:
img_data_corrected = img_data_precision * slope[0]
img_data_corrected += intercept[0]
factor = ((2 ** 16) - 1) / (np.amax(img_data_corrected))
img_float = img_data_corrected * factor
img = np.array(img_float, np.uint16)
else:
messagebox.showerror(
"Error!",
"The image you are trying to convert is neither 16 bit nor 32 bit!",
)
os._exit(0)
# Populate required values for file meta information
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = "1.2.840.10008.5.1.4.1.1.4"
file_meta.MediaStorageSOPInstanceUID = parameters.get("VisuUid")
file_meta.ImplementationClassUID = "1.2.276.0.7230010.3.0.3.5.3"
file_meta.ImplementationVersionName = 'OFFIS_DCMTK_353'
# Create the FileDataset instance (initially no data elements, but file_meta supplied)
img_data = FileDataset(filename_little_endian, {}, file_meta=file_meta, preamble=b"\0" * 128)
img_data.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian
# This group is responsible for describing how to read the pixels
nframes = parameters.get("VisuCoreFrameCount")
img_data.NumberOfFrames = parameters.get("VisuCoreFrameCount")
img_data.SamplesPerPixel = 1
img_data.PhotometricInterpretation = "MONOCHROME2"
img_data.PixelRepresentation = 0 # unsigned (0)
img_data.BitsAllocated = 16
img_data.BitsStored = 16
img_data.HighBit = 15
img_data.Columns = int(img_dims[0])
img_data.Rows = int(img_dims[1])
img_data.PixelSpacing = [core_ext[0]/img_dims[0], core_ext[1]/img_dims[1]]
img_data.WindowCenterWidthExplanation = "MinMax"
# PixelData contains the raw bytes exactly as found in the file
img_data.PixelData = img.tobytes()
img_data[0x7FE0, 0x0010].VR = "OW"
# The dicom_dict entry for LargestImagePixelValue uses an ambiguous VR (Value Representation).
# It can either be an unsigned short integer (US) or a signed short integer (SS).
# In order to properly write the data to the file,
# you have to explicitly tell it which one you want to use.
img_data.WindowWidth = int(np.amax(img) + 1)
img_data.WindowCenter = int((np.amax(img) + 1) / 2)
img_data[0x0028, 0x1050].VR = "DS"
img_data[0x0028, 0x1051].VR = "DS"
img_data.SmallestImagePixelValue = int(np.amin(img_data.pixel_array))
img_data.LargestImagePixelValue = int(np.amax(img_data.pixel_array))
img_data[0x0028, 0x0106].VR = "US"
img_data[0x0028, 0x0107].VR = "US"
# Loop over the number of frames found in img_data
for iteration, layer in enumerate(img_data.pixel_array, 0):
layer = np.reshape(layer, int(img_dims[0]) * int(img_dims[1]))
# Populate required values for file meta information
file_meta_temp = Dataset()
file_meta_temp.MediaStorageSOPClassUID = "1.2.840.10008.5.1.4.1.1.4"
file_meta_temp.MediaStorageSOPInstanceUID = parameters.get("VisuUid") + ".%s" % (iteration)
file_meta_temp.ImplementationClassUID = "1.2.276.0.7230010.3.0.3.5.3"
file_meta_temp.ImplementationVersionName = 'OFFIS_DCMTK_353'
# Create the FileDataset instance (initially no data elements, but file_meta supplied)
ds_temp = FileDataset(filename_little_endian, {}, file_meta=file_meta_temp, \
preamble=b"\0" * 128)
ds_temp.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian
# Add the data elements -- Check DICOM standard
ds_temp.ImageType = ["ORIGINAL", "PRIMARY", "OTHER"]
# if ('treated' in root):
# appendix='treated'
# elif ('untreated' in root):
# appendix='untreated'
# patient_type=re.findall('/[^/]*trea[^/]*/[^/]*/',root)
# if len(patient_type)!=0:
# group=patient_type[0].split('/')[1]
# timepoint=patient_type[0].split('/')[2]
# ds.PatientName = parameters.get("VisuSubjectName")+'_'+group+'_'+timepoint
# else:
# ds.PatientName= parameters.get("VisuSubjectName")
# head_ID, _ = os.path.split(head2)
############### Get common parameters among PV versions ###################
ds_temp.PatientName = parameters.get("VisuSubjectName")
ds_temp.PatientID = parameters.get("VisuSubjectId")
ds_temp.PatientBirthDate = parameters.get("VisuSubjectBirthDate")
ds_temp.PatientSex = parameters.get("VisuSubjectSex")
ds_temp.PatientWeight = parameters.get("VisuSubjectWeight")
ds_temp.PatientComments = parameters.get("VisuSubjectComment")
ds_temp.PatientSpeciesDescription = parameters.get("VisuSubjectType")
ds_temp.ReferringPhysicianName = ' '.join(parameters.get("VisuStudyReferringPhysician"))
ds_temp.PatientBreedDescription = None
ds_temp.PatientBreedCodeSequence = None
ds_temp.ResponsiblePerson = None
ds_temp.BreedRegistrationSequence = None
ds_temp.ResponsibleOrganization = ' '.join(parameters.get("VisuInstitution"))
ds_temp.StudyID = parameters.get("VisuStudyId")
ds_temp.SeriesNumber = os.path.basename(res)
ds_temp.Modality = str("MR")
ds_temp.ScanningSequence = str("RM")
ds_temp.SequenceVariant = str("None")
ds_temp.SequenceName = ' '.join(parameters.get("VisuAcqSequenceName"))
ds_temp.ProtocolName = parameters.get("VisuAcquisitionProtocol")
ds_temp.SeriesDescription = parameters.get("VisuAcquisitionProtocol")
if np.size(parameters.get("VisuAcqRepetitionTime")) > 1 and np.size(parameters.get("VisuAcqRepetitionTime")) == nframes:
ds_temp.RepetitionTime = str(np.array(parameters.get("VisuAcqRepetitionTime"), dtype=int)[iteration])
elif np.size(parameters.get("VisuAcqRepetitionTime")) > 1 and np.size(parameters.get("VisuAcqRepetitionTime")) != nframes:
r_step = int(nframes/np.size(parameters.get("VisuAcqRepetitionTime")))
repetition_time = []
for t in range(0,np.size(parameters.get("VisuAcqRepetitionTime"))):
for kk in range(0,r_step):
repetition_time.append(parameters.get("VisuAcqRepetitionTime")[t])
ds_temp.RepetitionTime=str(np.array(repetition_time,dtype=float)[iteration])
else:
ds_temp.RepetitionTime=parameters.get("VisuAcqRepetitionTime")
if np.size(parameters.get("VisuAcqEchoTime")) > 1 and np.size(parameters.get("VisuAcqEchoTime")) == nframes:
ds_temp.EchoTime=str(np.array(parameters.get("VisuAcqEchoTime"),dtype=float)[iteration])
elif np.size(parameters.get("VisuAcqEchoTime")) > 1 and np.size(parameters.get("VisuAcqEchoTime")) != nframes:
e_step = int(nframes/np.size(parameters.get("VisuAcqEchoTime")))
echo_time = []
for t in range(0,np.size(parameters.get("VisuAcqEchoTime"))):
for kk in range(0,e_step):
echo_time.append(parameters.get("VisuAcqEchoTime")[t])
ds_temp.EchoTime=str(np.array(echo_time,dtype=float)[iteration])
else:
ds_temp.EchoTime=parameters.get("VisuAcqEchoTime")
ds_temp.AcquisitionDuration=parameters.get("VisuAcqScanTime")
ds_temp.NumberOfAverages = str(parameters.get("VisuAcqNumberOfAverages"))
ds_temp.ImagingFrequency = parameters.get("VisuAcqImagingFrequency")
ds_temp.ImagedNucleus = parameters.get("VisuAcqImagedNucleus")
ds_temp.NumberOfPhaseEncodingSteps = parameters.get("VisuAcqPhaseEncSteps")
ds_temp.EchoTrainLength = parameters.get("VisuAcqEchoTrainLength")
ds_temp.PixelBandwidth = parameters.get("VisuAcqPixelBandwidth")
ds_temp.FlipAngle = str(parameters.get("VisuAcqFlipAngle"))
ds_temp.PatientPosition = parameters.get("VisuSubjectPosition")
ds_temp.PatientOrientation = method_parameters.get("PVM_SPackArrReadOrient")[0][1:]
ds_temp.StationName = parameters.get("VisuStation")
ds_temp.InstitutionName = " ".join(parameters.get("VisuInstitution"))
ds_temp.Manufacturer = parameters.get("ORIGIN")
ds_temp.SeriesInstanceUID = parameters.get("VisuUid")
ds_temp.FrameOfReferenceUID = parameters.get("VisuUid") + ".%s" % (iteration)
ds_temp.StudyInstanceUID = parameters.get("VisuStudyUid")
ds_temp.SOPInstanceUID = parameters.get("VisuUid") + ".%s" % (iteration)
ds_temp.SOPClassUID = "1.2.840.10008.5.1.4.1.1.4"
ds_temp.AcquisitionNumber = iteration + 1
ds_temp.InstanceNumber = iteration + 1
ds_temp.MRAcquisitionType = str(parameters.get("VisuCoreDim")) + "D"
ds_temp.SoftwareVersions = str(parameters.get("VisuCreator")) + " " + str(parameters.get("VisuCreatorVersion"))
ds_temp.PercentPhaseFieldOfView = "100"
if parameters.get("VisuCoreOrientation").shape[0] == 1:
ds_temp.ImagePositionPatient = list(map(str, parameters.get("VisuCorePosition")[0]))
ds_temp.ImageOrientationPatient = list(map(str, parameters.get("VisuCoreOrientation")[0][0:6]))
ds_temp.SliceThickness = parameters.get("VisuCoreFrameThickness")
ds_temp.NumberOfFrames = 1
ds_temp.ImagesInAcquisition = parameters.get("VisuCoreFrameCount")
ds_temp.SliceLocation = parameters.get("VisuCorePosition")[0][2]
elif parameters.get("VisuCoreOrientation").shape[0] != nframes:
p = int(nframes / parameters.get("VisuCorePosition").shape[0])
visucoreposition = np.tile(parameters.get("VisuCorePosition"), (p, 1))
visucoreorientation = np.tile(parameters.get("VisuCoreOrientation"), (p, 1))
ds_temp.ImagePositionPatient = list(map(str, visucoreposition[iteration - 1]))
ds_temp.ImageOrientationPatient = list(map(str, visucoreorientation[iteration - 1][0:6]))
ds_temp.SliceThickness = parameters.get("VisuCoreFrameThickness")
ds_temp.NumberOfFrames = 1
ds_temp.ImagesInAcquisition = parameters.get("VisuCoreFrameCount")
ds_temp.SliceLocation = list(map(str, visucoreposition[iteration]))[2]
else:
ds_temp.ImagePositionPatient = list(map(str, parameters.get("VisuCorePosition")[iteration - 1]))
ds_temp.ImageOrientationPatient = list(map(str, parameters.get("VisuCoreOrientation")[iteration - 1][0:6]))
ds_temp.SliceThickness = parameters.get("VisuCoreFrameThickness")
ds_temp.NumberOfFrames = 1
ds_temp.ImagesInAcquisition = parameters.get("VisuCoreFrameCount")
ds_temp.SliceLocation = list(map(str, parameters.get("VisuCorePosition")[iteration - 1]))[2]
# Get other parameters which differ among PV versions
if PV_version == "5.1":
########################### ParaVision 5.1 ##############################
studydate = parameters.get("VisuStudyDate").date()
studytime = parameters.get("VisuStudyDate").time()
ds_temp.StudyDate = studydate.strftime("%Y%m%d")
ds_temp.StudyTime = studytime.strftime("%H%M%S")
acquisitiondate = parameters.get("VisuAcqDate").date()
acquisitiontime = parameters.get("VisuAcqDate").time()
ds_temp.AcquisitionDate = acquisitiondate.strftime("%Y%m%d")
ds_temp.AcquisitionTime = acquisitiontime.strftime("%H%M%S")
VisuAcqImagePhaseEncDir = parameters.get("VisuAcqImagePhaseEncDir")
ds_temp.Columns = int(img_dims[0])
ds_temp.Rows = int(img_dims[1])
if np.size(VisuAcqImagePhaseEncDir) == 1:
ds_temp.InPlanePhaseEncodingDirection = parameters.get("VisuAcqImagePhaseEncDir").split("_")[0]
else:
ds_temp.InPlanePhaseEncodingDirection = parameters.get("VisuAcqImagePhaseEncDir")[0].split("_")[0]
if ds_temp.InPlanePhaseEncodingDirection == "row":
acqmat = np.pad(parameters.get("VisuAcqSize"), 1, "constant")
ds_temp.AcquisitionMatrix = list(np.array(acqmat, dtype=int))
ds_temp.PixelSpacing = [core_ext[0] / img_dims[0], core_ext[1] / img_dims[1]]
pixel_spacing = [core_ext[0] / img_dims[0], core_ext[1] / img_dims[1]]
ds_temp.PixelSpacing = pixel_spacing[::-1]
elif ds_temp.InPlanePhaseEncodingDirection == "col":
acqmat = np.insert(parameters.get("VisuAcqSize"), 1, [0, 0])
ds_temp.AcquisitionMatrix = list(np.flip(np.array(acqmat, dtype=int), 0))
ds_temp.PixelSpacing = [core_ext[1] / img_dims[1], core_ext[0] / img_dims[0]]
gamma = 42.5756
Bo = round(ds_temp.ImagingFrequency / gamma)
ds_temp.MagneticFieldStrength = Bo
elif PV_version == "6.0.1":
########################### ParaVision 6.0.1 ##############################
s = parameters.get("VisuStudyDate")
date = re.sub("\ |\<|\>", "", s)
studydate = dateutil.parser.parse(date)
ds_temp.StudyDate = studydate.strftime("%Y%m%d")
ds_temp.StudyTime = studydate.strftime("%H%M%S")
t = parameters.get("VisuAcqDate")
acqdate = re.sub("\ |\<|\>", "", t)
acquisitiondate = dateutil.parser.parse(acqdate)
ds_temp.AcquisitionDate = acquisitiondate.strftime("%Y%m%d")
ds_temp.AcquisitionTime = acquisitiondate.strftime("%H%M%S")
ds_temp.InPlanePhaseEncodingDirection = parameters.get("VisuAcqGradEncoding")
if ds_temp.InPlanePhaseEncodingDirection[0] == "read_enc":
ds_temp.Columns = int(img_dims[0])
ds_temp.Rows = int(img_dims[1])
acqmat = np.pad(parameters.get("VisuAcqSize"), 1, "constant")
ds_temp.AcquisitionMatrix = list(np.array(acqmat, dtype=int))
ds_temp.PixelSpacing = [core_ext[1] / img_dims[1], core_ext[0] / img_dims[0]]
elif ds_temp.InPlanePhaseEncodingDirection[0] == "phase_enc":
ds_temp.Columns = int(img_dims[1])
ds_temp.Rows = int(img_dims[0])
acqmat = np.insert(parameters.get("VisuAcqSize"), 1, [0, 0])
ds_temp.AcquisitionMatrix = list(np.flip(np.array(acqmat, dtype=int), 0)) # check
ds_temp.PixelSpacing = [core_ext[0] / img_dims[0], core_ext[1] / img_dims[1]]
gamma = 42.5756
Bo = round(ds_temp.ImagingFrequency / gamma)
ds_temp.MagneticFieldStrength = Bo
elif '360' in PV_version:
########################### ParaVision 360 ##############################
VisuStudyDate = parameters.get("VisuStudyDate")
StudyDate=re.sub('\ |\<|\>', '', VisuStudyDate )
StudyDate = dateutil.parser.parse(StudyDate)
ds_temp.StudyDate = StudyDate.strftime("%Y%m%d")
ds_temp.StudyTime = StudyDate.strftime("%H%M%S")
VisuAcqDate = parameters.get("VisuAcqDate")
AcqDate = re.sub('\ |\<|\>', '', VisuAcqDate)
AcqDate = dateutil.parser.parse(AcqDate)
ds_temp.AcquisitionDate = AcqDate.strftime("%Y%m%d")
ds_temp.AcquisitionTime = AcqDate.strftime("%H%M%S")
ds_temp.InPlanePhaseEncodingDirection = parameters.get("VisuAcqGradEncoding")
if ds_temp.InPlanePhaseEncodingDirection[0] == 'read_enc':
ds_temp.Columns = int(img_dims[0])
ds_temp.Rows = int(img_dims[1])
acqmat = np.pad(parameters.get("VisuAcqSize"),1,'constant')
ds_temp.AcquisitionMatrix = list(np.array(acqmat,dtype=int))
ds_temp.PixelSpacing = [core_ext[1]/img_dims[1],core_ext[0]/img_dims[0]]
elif ds_temp.InPlanePhaseEncodingDirection[0] == 'phase_enc':
ds_temp.Columns = int(img_dims[1])
ds_temp.Rows = int(img_dims[0])
acqmat = np.insert(parameters.get("VisuAcqSize"),1,[0,0])
ds_temp.AcquisitionMatrix = list(np.flip(np.array(acqmat,dtype=int),0))
ds_temp.PixelSpacing = ([core_ext[0]/img_dims[0],core_ext[1]/img_dims[1]])
ds_temp.MagneticFieldStrength = parameters.get('VisuMagneticFieldStrength')
# DCE acquisition
if "DCE" in ds_temp.ProtocolName:
NRepetitions = method_parameters.get("PVM_NRepetitions")
enc_matrix = str(method_parameters.get("PVM_EncMatrix"))
enc_step = float(re.findall('[0-9]+',enc_matrix)[1])
total_scan_time = ds_temp.RepetitionTime * NRepetitions * enc_step
scan_time_step = int(ds_temp.RepetitionTime * enc_step) # in ms
vect4 = []
scan_time=0
step = int(nframes/NRepetitions)
for t in range(0,NRepetitions):
scan_time = scan_time + scan_time_step
for kk in range(0,step):
vect4.append(scan_time)
ds_temp.TriggerTime = np.array(vect4)[iteration]
# DWI acquisition
elif "diffusion" in ds_temp.ProtocolName or "EPI" in ds_temp.ProtocolName:
string = str(method_parameters.get("PVM_DwBvalEach"))
b_values = re.findall("[0-9]+", string)
#b_values.pop(0)
b_values.insert(0, "0")
bvalues = []
for elem in b_values:
bvalues.append(float(elem))
vect3 = []
step = int(nframes / len(b_values))
for t in range(0, len(b_values)):
for kk in range(0, step):
vect3.append(bvalues[t])
ds_temp.DiffusionBValue = np.array(vect3)[iteration]
# CEST acquisition
elif "cest" in ds_temp.ProtocolName and method_parameters.get("PVM_SatTransOnOff") == 'On':
ds_temp.Creator = method_parameters.get("OWNER")
ds_temp.ChemicalExchangeSaturationType = method_parameters.get("Method")
ds_temp.SaturationType = method_parameters.get("PVM_SatTransType")
ds_temp.PulseShape = method_parameters.get("PVM_SatTransPulseEnum")
ds_temp.PulseLength = method_parameters.get("PVM_SatTransPulse")[0]
ds_temp.B1Saturation = method_parameters.get("PVM_SatTransPulseAmpl_uT")
ds_temp.PulseNumber = method_parameters.get("PVM_SatTransNPulses")
# train module needs to be checked
if 'train' in method_parameters.get("Method"):
tau_p = float(method_parameters.get("PVM_SatTransPulse")[0])
tau_d = float(method_parameters.get("PVM_SatTransInterPulseDelay"))
n = int(method_parameters.get("PVM_SatTransNPulses"))
#method_parameters.get("PVM_SatTransModuleTime") #the result of this two lines should be the same
#magtransmoduletime = (tau_p + tau_d) * n
ds_temp.InterpulseDelay = tau_d
ds_temp.DutyCycle = tau_p/(tau_p + tau_d) * 100
ds_temp.SaturationLength = method_parameters.get("PVM_SatTransModuleTime")
else:
ds_temp.DutyCycle = '100'
ds_temp.SaturationLength = ds_temp.PulseLength * ds_temp.PulseNumber
NSatFreq = method_parameters.get('PVM_NSatFreq')
if NSatFreq != None:
f_step = int(nframes/NSatFreq)
ds_temp.MeasurementNumber = NSatFreq
ds_temp.RecoveryTime = int(ds_temp.RepetitionTime) - int(ds_temp.PulseLength)
freq_list = method_parameters.get('PVM_SatTransFreqValues') # frequency list is formatted differently for CEST Off and On, need to distinguish both cases
freq_list_temp = []
# p = '[-+]?\d*\.\d+|[-+]?\d+'
if re.search('[-+]?\d*\.\d+|[-+]?\d+',freq_list[0]) is not None:
for catch in re.finditer('[-+]?\d*\.\d+|[-+]?\d+', freq_list[0]):
freq_list_temp.append(catch[0])
freq_list = freq_list_temp
if "OFF" not in parameters.get("VisuAcquisitionProtocol") and len(freq_list) > 2:
############## CEST ON ################
if method_parameters.get("PVM_SatTransFreqUnit") == 'unit_ppm':
sat_freq_ppm = np.array(freq_list, dtype=float)
if NSatFreq > 1 and NSatFreq == nframes:
ds_temp.SaturationOffsetPpm = sat_freq_ppm[iteration]
ds_temp.SaturationOffsetHz = sat_freq_ppm[iteration] * ds_temp.ImagingFrequency
elif NSatFreq > 1 and NSatFreq != nframes:
SatFreqPpm = []
for t in range(0, NSatFreq):
for kk in range(0, f_step):
SatFreqPpm.append(sat_freq_ppm[t])
ds_temp.SaturationOffsetPpm = str(np.array(SatFreqPpm,dtype=float)[iteration])
sat_freq_hz = SatFreqPpm[iteration] * ds_temp.ImagingFrequency
ds_temp.SaturationOffsetHz = sat_freq_hz
### Tags for CEST ON only
ds_temp.PulseLength2 = method_parameters.get("PVM_SatTransPulseLength2")
ds_temp.ReadoutTime = (ds_temp.RepetitionTime - ds_temp.PulseLength - (ds_temp.PulseLength2 * (f_step - 1))) / f_step
elif method_parameters.get("PVM_SatTransFreqUnit") == 'unit_hz':
sat_freq_hz = np.array(freq_list, dtype=float)
if NSatFreq > 1 and NSatFreq == nframes:
ds_temp.SaturationOffsetHz = sat_freq_hz[iteration]
ds_temp.SaturationOffsetPpm = sat_freq_hz[iteration] * ds_temp.ImagingFrequency
elif NSatFreq > 1 and NSatFreq != nframes:
SatFreqHz = []
for t in range(0, NSatFreq):
for kk in range(0, f_step):
SatFreqHz.append(sat_freq_hz[t])
ds_temp.SaturationOffsetHz = str(np.array(SatFreqHz,dtype=float)[iteration])
sat_freq_ppm = SatFreqHz[iteration] * ds_temp.ImagingFrequency
ds_temp.SaturationOffsetPpm = sat_freq_ppm
### Tags for CEST ON only
ds_temp.PulseLength2 = method_parameters.get("PVM_SatTransPulseLength2")
ds_temp.ReadoutTime = (ds_temp.RepetitionTime - ds_temp.PulseLength - (ds_temp.PulseLength2 * (f_step - 1))) / f_step
else:
############## CEST OFF ################
if method_parameters.get("PVM_SatTransFreqUnit") == 'unit_ppm':
sat_freq_ppm = np.array(freq_list, dtype=float)
SatFreqPpm = []
for t in range(0, NSatFreq):
for kk in range(0, f_step):
SatFreqPpm.append(sat_freq_ppm[t])
ds_temp.SaturationOffsetPpm = str(np.array(SatFreqPpm,dtype=float)[iteration])
sat_freq_hz = SatFreqPpm[iteration] * ds_temp.ImagingFrequency
ds_temp.SaturationOffsetHz = sat_freq_hz
### Not tested
elif method_parameters.get("PVM_SatTransFreqUnit") == 'unit_hz':
sat_freq_hz = np.array(freq_list, dtype=float)
SatFreqHz= []
for t in range(0, NSatFreq):
for kk in range(0, f_step):
SatFreqHz.append(sat_freq_hz[t])
ds_temp.SaturationOffsetHz = str(np.array(SatFreqHz,dtype=float)[iteration])
sat_freq_ppm = SatFreqHz[iteration] * ds_temp.ImagingFrequency
ds_temp.SaturationOffsetPpm = sat_freq_ppm
elif NSatFreq == None and method_parameters.get("PVM_SatTransFreqUnit") == 'unit_ppm':
freq_list = method_parameters.get('PVM_SatTransFreqValues') # frequency list is formatted differently for CEST Off and On, need to distinguish both cases
freq_list = freq_list[0].split(" ")
while '' in freq_list:
freq_list.remove('')
[elem.strip(' ') for elem in freq_list]
sat_freq_ppm = np.array(freq_list, dtype=float)
ds_temp.SaturationOffsetPpm = sat_freq_ppm[iteration]
ds_temp.SaturationOffsetHz = sat_freq_ppm[iteration] * ds_temp.ImagingFrequency
elif NSatFreq == None and method_parameters.get("PVM_SatTransFreqUnit") == 'unit_hz':
freq_list = method_parameters.get('PVM_SatTransFreqValues') # frequency list is formatted differently for CEST Off and On, need to distinguish both cases
freq_list = freq_list[0].split(" ")
while '' in freq_list:
freq_list.remove('')
[elem.strip(' ') for elem in freq_list]
sat_freq_hz = np.array(freq_list, dtype=float)
ds_temp.SaturationOffsetHz = sat_freq_hz[iteration]
ds_temp.SaturationOffsetPpm = sat_freq_hz[iteration] * ds_temp.ImagingFrequency
# Image pixel module with the tags starting with 0028.
# This group is responsible for describing how to read the pixels
ds_temp.SamplesPerPixel = 1
ds_temp.PhotometricInterpretation = "MONOCHROME2"
ds_temp.PixelRepresentation = 0
ds_temp.BitsAllocated = 16
ds_temp.BitsStored = 16
ds_temp.HighBit = 15
ds_temp.WindowCenterWidthExplanation = "MinMax"
ds_temp.PixelData = layer
ds_temp[0x7FE0, 0x0010].VR = "OW"
ds_temp.WindowWidth = int(np.amax(img) + 1)
ds_temp.WindowCenter = int((np.amax(img) + 1) / 2)
ds_temp[0x0028, 0x1050].VR = "DS"
ds_temp[0x0028, 0x1051].VR = "DS"
ds_temp.SmallestImagePixelValue = int(np.amin(layer))
ds_temp.LargestImagePixelValue = int(np.amax(layer))
ds_temp[0x0028, 0x0106].VR = "US"
ds_temp[0x0028, 0x0107].VR = "US"
ds_temp.RescaleSlope = factor
for j in range(0, nframes - 1):
ds_temp.RescaleIntercept = str(parameters.get("VisuCoreDataOffs")[j])
# Set creation date/time
dt = datetime.datetime.now()
ds_temp.InstanceCreationDate = dt.strftime("%Y%m%d")
timeStr = dt.strftime("%H%M%S")
ds_temp.InstanceCreationTime = timeStr
ds_temp.NumberOfSlices = acqp_parameters.get("NSLICES")
string2 = str(reco_parameters.get("RECO_fov"))
vect2 = re.findall("[0-9]+", string2)
vect2.pop(0)
vect3 = []
for elem in vect2:
vect3.append(float(elem))
ds_temp.ReconstructionFieldOfView = vect3
outfile = "%s%s.dcm" % (filename_little_endian, str(iteration + 1))
# Save DICOM files in separate slices
os.chdir(dst_path)
ds_temp.is_little_endian = True
ds_temp.is_implicit_VR = False
ds_temp.save_as(outfile)
elif os.path.isfile(current_path):
if 'Custom' in current_path:
shutil.copy(current_path, dst_folder)
else:
if master.results_flag == 1:
current_path = os.path.join(folder_to_convert, path).replace('\\', '/')
res = current_path
rel_path = os.path.relpath(res, folder_to_convert)
dst_path = os.path.join(dst_folder, 'MR', 'resources', rel_path).replace('\\', '/')
shutil.copytree(current_path, dst_path)
# if master.conv_flag == 1:
yield i, len(list_path)
if parameters:
pass
else:
messagebox.showerror(
"Error!",
"Bruker files have not been found in the chosen folder/subfolders!",
)
master.root.config(cursor="arrow")
master.convert_btn['state'] = tk.NORMAL
master.info_btn['state'] = tk.NORMAL
master.upload_btn['state'] = tk.NORMAL
master.process_btn['state'] = tk.NORMAL
# sys.exit(1)
# Inserire folder nella lista delle directory non convertite
end_time = time.time()
print('Elapsed time for conversion: ' + str(end_time - start_time) + ' s')
return