File: GenericImageData.cxx

package info (click to toggle)
itksnap 3.6.0-5
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 22,132 kB
  • sloc: cpp: 91,089; ansic: 1,994; sh: 327; makefile: 16
file content (672 lines) | stat: -rw-r--r-- 18,142 bytes parent folder | download | duplicates (2)
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
/*=========================================================================

  Program:   ITK-SNAP
  Module:    $RCSfile: GenericImageData.cxx,v $
  Language:  C++
  Date:      $Date: 2010/06/28 18:45:08 $
  Version:   $Revision: 1.14 $
  Copyright (c) 2007 Paul A. Yushkevich
  
  This file is part of ITK-SNAP 

  ITK-SNAP is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation, either version 3 of the License, or
  (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
 
  You should have received a copy of the GNU General Public License
  along with this program.  If not, see <http://www.gnu.org/licenses/>.

  -----

  Copyright (c) 2003 Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

  This software is distributed WITHOUT ANY WARRANTY; without even
  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  PURPOSE.  See the above copyright notices for more information. 

=========================================================================*/
// ITK Includes
#include "itkImage.h"
#include "itkImageIterator.h"
#include "RLEImageRegionIterator.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkMinimumMaximumImageCalculator.h"
#include "itkUnaryFunctorImageFilter.h"
#include "itkRGBAPixel.h"
#include "IRISSlicer.h"
#include "IRISException.h"
#include "IRISApplication.h"
#include <algorithm>
#include <list>
#include <map>
#include <iostream>
#include "SNAPEventListenerCallbacks.h"
#include "GenericImageData.h"
#include "Rebroadcaster.h"
#include "LayerIterator.h"
#include "GuidedNativeImageIO.h"
#include "ImageAnnotationData.h"

// System includes
#include <fstream>
#include <iostream>
#include <iomanip>


void 
GenericImageData
::SetSegmentationVoxel(const Vector3ui &index, LabelType value)
{
  // Make sure that the main image data and the segmentation data exist
  assert(IsSegmentationLoaded());

  // Store the voxel
  m_LabelWrapper->SetVoxel(index, value);

  // Mark the image as modified
  m_LabelWrapper->GetImage()->Modified();
}

GenericImageData
::GenericImageData()
  : m_UndoManager(4,200000)
{
  // Make main image wrapper point to grey wrapper initially
  m_MainImageWrapper = NULL;

  // Pass the label table from the parent to the label wrapper
  m_LabelWrapper = NULL;
  
  // Add to the relevant lists
  m_Wrappers[MAIN_ROLE].push_back(m_MainImageWrapper);
  m_Wrappers[LABEL_ROLE].push_back(m_LabelWrapper.GetPointer());

  // Create empty annotations
  m_Annotations = ImageAnnotationData::New();

  // Initialize the display viewport geometry objects
  m_DisplayViewportGeometry[0] = ImageBaseType::New();
  m_DisplayViewportGeometry[1] = ImageBaseType::New();
  m_DisplayViewportGeometry[2] = ImageBaseType::New();
}

GenericImageData
::~GenericImageData()
{
  UnloadMainImage();
}

Vector3d 
GenericImageData
::GetImageSpacing() 
{
  assert(m_MainImageWrapper->IsInitialized());
  return m_MainImageWrapper->GetImageBase()->GetSpacing().GetVnlVector();
}

Vector3d 
GenericImageData
::GetImageOrigin() 
{
  assert(m_MainImageWrapper->IsInitialized());
  return m_MainImageWrapper->GetImageBase()->GetOrigin().GetVnlVector();
}


void
GenericImageData
::SetMainImageInternal(ImageWrapperBase *wrapper)
{
  // Set properties
  wrapper->SetDefaultNickname("Main Image");

  // Make the wrapper the main image
  SetSingleImageWrapper(MAIN_ROLE, wrapper);
  m_MainImageWrapper = wrapper;

  // Reset the segmentation image
  ResetSegmentationImage();

  // Set opaque
  m_MainImageWrapper->SetAlpha(255);
}

#include "itkIdentityTransform.h"

SmartPtr<ImageWrapperBase>
GenericImageData::CreateAnatomicWrapper(GuidedNativeImageIO *io, ITKTransformType *transform)
{
  // The output wrapper
  SmartPtr<ImageWrapperBase> out_wrapper;

  // If the transform is not NULL, the reference space must be specified
  ImageBaseType *refSpace = (transform) ? this->GetMain()->GetImageBase() : NULL;

  // Split depending on whether the image is scalar or vector
  if(io->GetNumberOfComponentsInNativeImage() > 1)
    {
    // The image will be cast to a vector anatomic image
    typedef AnatomicImageWrapper::ImageType AnatomicImageType;

    // Rescale the image to desired number of bits
    RescaleNativeImageToIntegralType<AnatomicImageType> rescaler;
    AnatomicImageType::Pointer image = rescaler(io);

    // Create a mapper to native intensity
    LinearInternalToNativeIntensityMapping mapper(
          rescaler.GetNativeScale(), rescaler.GetNativeShift());

    // Create a main wrapper of fixed type.
    SmartPtr<AnatomicImageWrapper> wrapper = AnatomicImageWrapper::New();

    // Set properties
    wrapper->SetDisplayGeometry(m_DisplayGeometry);
    wrapper->SetImage(image, refSpace, transform);
    wrapper->SetNativeMapping(mapper);
    for(int i = 0; i < 3; i++)
      wrapper->SetDisplayViewportGeometry(i, m_DisplayViewportGeometry[i]);

    out_wrapper = wrapper.GetPointer();
    }

  else
    {
    // Rescale the image to desired number of bits
    typedef AnatomicScalarImageWrapper::ImageType AnatomicImageType;

    // Rescale the image to desired number of bits
    RescaleNativeImageToIntegralType<AnatomicImageType> rescaler;
    AnatomicImageType::Pointer image = rescaler(io);

    // Create a mapper to native intensity
    LinearInternalToNativeIntensityMapping mapper(
          rescaler.GetNativeScale(), rescaler.GetNativeShift());

    // Create a main wrapper of fixed type.
    SmartPtr<AnatomicScalarImageWrapper> wrapper = AnatomicScalarImageWrapper::New();

    // Set properties
    wrapper->SetDisplayGeometry(m_DisplayGeometry);
    wrapper->SetImage(image, refSpace, transform);
    wrapper->SetNativeMapping(mapper);

    for(int i = 0; i < 3; i++)
      wrapper->SetDisplayViewportGeometry(i, m_DisplayViewportGeometry[i]);

    out_wrapper = wrapper.GetPointer();
    }

  // Create an image coordinate geometry object
  return out_wrapper;
}

void GenericImageData::SetMainImage(GuidedNativeImageIO *io)
{
  // Create the wrapper from the Native IO (the wrapper will either be a scalar
  // or a vector-valued image, depending on the number of components)
  SmartPtr<ImageWrapperBase> wrapper = this->CreateAnatomicWrapper(io, NULL);

  // Assign this wrapper to the main image
  this->SetMainImageInternal(wrapper);
}

void
GenericImageData
::ResetSegmentationImage()
{
  // Initialize the segmentation data to zeros
  m_LabelWrapper = LabelImageWrapper::New();
  m_LabelWrapper->InitializeToWrapper(m_MainImageWrapper, (LabelType) 0);
  m_LabelWrapper->SetDefaultNickname("Segmentation Image");

  m_LabelWrapper->GetDisplayMapping()->SetLabelColorTable(m_Parent->GetColorLabelTable());
  SetSingleImageWrapper(LABEL_ROLE, m_LabelWrapper.GetPointer());

  // Reset the undo manager
  m_UndoManager.Clear();
}

void
GenericImageData
::UnloadMainImage()
{
  // First unload the overlays if exist
  UnloadOverlays();

  // Clear the main image wrappers
  RemoveSingleImageWrapper(MAIN_ROLE);
  m_MainImageWrapper = NULL;

  // Reset the label wrapper
  RemoveSingleImageWrapper(LABEL_ROLE);
  m_LabelWrapper = NULL;

  // Clear the annotations
  m_Annotations->Reset();
}

void
GenericImageData
::AddOverlay(GuidedNativeImageIO *io)
{
  // Create the wrapper from the Native IO (the wrapper will either be a scalar
  // or a vector-valued image, depending on the number of components)
  SmartPtr<ImageWrapperBase> wrapper = this->CreateAnatomicWrapper(io, NULL);

  // Assign this wrapper to the main image
  this->AddOverlayInternal(wrapper);
}

void
GenericImageData
::AddCoregOverlay(GuidedNativeImageIO *io, ITKTransformType *transform)
{
  // Create the wrapper from the Native IO (the wrapper will either be a scalar
  // or a vector-valued image, depending on the number of components)
  SmartPtr<ImageWrapperBase> wrapper = this->CreateAnatomicWrapper(io, transform);

  // Assign this wrapper to the main image
  this->AddOverlayInternal(wrapper, false);
}

void
GenericImageData
::AddOverlayInternal(ImageWrapperBase *overlay, bool checkSpace)
{
  // Check that the image matches the size of the main image
  if(checkSpace && m_MainImageWrapper->GetBufferedRegion() != overlay->GetBufferedRegion())
    {
    throw IRISException("Main and overlay data sizes are different");
    }

  // Pass the image to a Grey image wrapper
  overlay->SetAlpha(0.5);
  overlay->SetDefaultNickname("Additional Image");

  // Sync up spacing between the main and overlay image
  if(checkSpace)
    overlay->CopyImageCoordinateTransform(m_MainImageWrapper);

  // Add to the overlay wrapper list
  PushBackImageWrapper(OVERLAY_ROLE, overlay);
}

void
GenericImageData
::UnloadOverlays()
{
  while (m_Wrappers[OVERLAY_ROLE].size() > 0)
    UnloadOverlayLast();
}

void
GenericImageData
::UnloadOverlayLast()
{
  // Make sure at least one grey overlay is loaded
  if (!IsOverlayLoaded())
    return;

  // Release the data associated with the last overlay
  PopBackImageWrapper(OVERLAY_ROLE);
}

void GenericImageData
::UnloadOverlay(ImageWrapperBase *overlay)
{
  // Erase the overlay
  WrapperList &overlays = m_Wrappers[OVERLAY_ROLE];
  WrapperIterator it =
      std::find(overlays.begin(), overlays.end(), overlay);
  if(it != overlays.end())
    overlays.erase(it);
}

void
GenericImageData
::SetSegmentationImage(LabelImageType *newLabelImage) 
{
  // Check that the image matches the size of the grey image
  assert(m_MainImageWrapper->IsInitialized() &&
    m_MainImageWrapper->GetBufferedRegion() == 
         newLabelImage->GetBufferedRegion());

  // Pass the image to the segmentation wrapper (why this and not create a
  // new label wrapper? Why should a wrapper have longer lifetime than an
  // image that it wraps around
  m_LabelWrapper->SetImage(newLabelImage);

  // Sync up spacing between the main and label image
  m_LabelWrapper->CopyImageCoordinateTransform(m_MainImageWrapper);

  // Reset the undo manager
  m_UndoManager.Clear();
}

GenericImageData::UndoManagerType::Delta *
GenericImageData
::CompressLabelImage()
{
  UndoManagerType::Delta *new_cumulative = new UndoManagerType::Delta();
  LabelImageType *seg = this->GetSegmentation()->GetImage();

  itk::ImageRegionConstIterator<LabelImageType> it(seg, seg->GetLargestPossibleRegion());
  for (; !it.IsAtEnd(); ++it)
    {
    new_cumulative->Encode(it.Get());
    }

  new_cumulative->FinishEncoding();
  return new_cumulative;
}

bool
GenericImageData
::IsOverlayLoaded()
{
  return (m_Wrappers[OVERLAY_ROLE].size() > 0);
}

bool
GenericImageData
::IsSegmentationLoaded()
{
  return m_LabelWrapper && m_LabelWrapper->IsInitialized();
}

void
GenericImageData
::SetCrosshairs(const Vector3ui &crosshairs)
{
  // Set crosshairs in all wrappers
  for(LayerIterator lit(this); !lit.IsAtEnd(); ++lit)
    if(lit.GetLayer() && lit.GetLayer()->IsInitialized())
      lit.GetLayer()->SetSliceIndex(crosshairs);
}

void GenericImageData::SetDisplayGeometry(const IRISDisplayGeometry &dispGeom)
{
  for(LayerIterator lit(this); !lit.IsAtEnd(); ++lit)
    if(lit.GetLayer())
      {
      // Set the direction matrix in the image
      lit.GetLayer()->SetDisplayGeometry(m_Parent->GetDisplayGeometry());
      }
}

GenericImageData::ImageBaseType *GenericImageData::GetDisplayViewportGeometry(int index)
{
  return m_DisplayViewportGeometry[index];
}

void GenericImageData::SetDirectionMatrix(const vnl_matrix<double> &direction)
{
  for(LayerIterator lit(this); !lit.IsAtEnd(); ++lit)
    if(lit.GetLayer())
      {
      // Set the direction matrix in the image
      lit.GetLayer()->SetDirectionMatrix(direction);
      }
}

const ImageCoordinateGeometry &GenericImageData::GetImageGeometry() const
{
  assert(m_MainImageWrapper->IsInitialized());
  return m_MainImageWrapper->GetImageGeometry();
}

void GenericImageData::StoreIntermediateUndoDelta(UndoManagerDelta *delta)
{
  m_UndoManager.AddDeltaToStaging(delta);
}

void GenericImageData::StoreUndoPoint(const char *text, UndoManagerDelta *delta)
{
  // If there is a delta, add it to staging
  if(delta)
    m_UndoManager.AddDeltaToStaging(delta);

  // Commit the deltas
  m_UndoManager.CommitStaging(text);
}

void GenericImageData::ClearUndoPoints()
{
  m_UndoManager.Clear();
}

bool
GenericImageData
::IsUndoPossible()
{
  return m_UndoManager.IsUndoPossible();
}

void
GenericImageData
::Undo()
{
  // Get the commit for the undo
  const UndoManagerType::Commit &commit = m_UndoManager.GetCommitForUndo();

  // The label image that will undergo undo
  typedef itk::ImageRegionIterator<LabelImageType> IteratorType;
  LabelImageType *imSeg = this->GetSegmentation()->GetImage();

  // Iterate over all the deltas in reverse order
  UndoManagerType::DList::const_reverse_iterator dit = commit.GetDeltas().rbegin();
  for(; dit != commit.GetDeltas().rend(); ++dit)
    {
    // Apply the changes in the current delta
    UndoManagerType::Delta *delta = *dit;

    // Iterator for the relevant region in the label image
    IteratorType lit(imSeg, delta->GetRegion());

    // Iterate over the rles in the delta
    for(size_t i = 0; i < delta->GetNumberOfRLEs(); i++)
      {
      size_t n = delta->GetRLELength(i);
      LabelType d = delta->GetRLEValue(i);
      for(size_t j = 0; j < n; j++)
        {
        if(d != 0)
          lit.Set(lit.Get() - d);
        ++lit;
        }
      }
    }

  // Set modified flags
  imSeg->Modified();
  InvokeEvent(SegmentationChangeEvent());
}

bool
GenericImageData
::IsRedoPossible()
{
  return m_UndoManager.IsRedoPossible();
}

void
GenericImageData
::Redo()
{
  // Get the commit for the redo
  const UndoManagerType::Commit &commit = m_UndoManager.GetCommitForRedo();

  // The label image that will undergo redo
  typedef itk::ImageRegionIterator<LabelImageType> IteratorType;
  LabelImageType *imSeg = this->GetSegmentation()->GetImage();

  // Iterate over all the deltas in reverse order
  UndoManagerType::DList::const_iterator dit = commit.GetDeltas().begin();
  for(; dit != commit.GetDeltas().end(); ++dit)
    {
    // Apply the changes in the current delta
    UndoManagerType::Delta *delta = *dit;

    // Iterator for the relevant region in the label image
    IteratorType lit(imSeg, delta->GetRegion());

    // Iterate over the rles in the delta
    for(size_t i = 0; i < delta->GetNumberOfRLEs(); i++)
      {
      size_t n = delta->GetRLELength(i);
      LabelType d = delta->GetRLEValue(i);
      for(size_t j = 0; j < n; j++)
        {
        if(d != 0)
          lit.Set(lit.Get() + d);
        ++lit;
        }
      }
    }

  // Set modified flags
  imSeg->Modified();
  InvokeEvent(SegmentationChangeEvent());
}

GenericImageData::RegionType
GenericImageData
::GetImageRegion() const
{
  assert(m_MainImageWrapper->IsInitialized());
  return m_MainImageWrapper->GetBufferedRegion();
}


unsigned int GenericImageData::GetNumberOfLayers(int role_filter)
{
  unsigned int n = 0;

  LayerIterator it = this->GetLayers(role_filter);
  while(!it.IsAtEnd())
    {
    n++; ++it;
    }

  return n;
}

ImageWrapperBase *
GenericImageData
::FindLayer(unsigned long unique_id, bool search_derived, int role_filter)
{
  for(LayerIterator it = this->GetLayers(role_filter); !it.IsAtEnd(); ++it)
    {
    if(it.GetLayer()->GetUniqueId() == unique_id)
      {
      return it.GetLayer();
      }
    else if(search_derived)
      {
      VectorImageWrapperBase *vec = it.GetLayerAsVector();
      if(vec)
        {
        for(int j = SCALAR_REP_COMPONENT; j < NUMBER_OF_SCALAR_REPS; j++)
          {
          int n = (j == SCALAR_REP_COMPONENT) ? vec->GetNumberOfComponents() : 1;
          for(int k = 0; k < n; k++)
            {
            ImageWrapperBase *w = vec->GetScalarRepresentation((ScalarRepresentation) j, k);
            if(w && w->GetUniqueId() == unique_id)
              return w;
            }
          }
        }
      }
    }

  return NULL;
}

int GenericImageData::GetNumberOfOverlays()
{
  return m_Wrappers[OVERLAY_ROLE].size();
}

ImageWrapperBase *GenericImageData::GetLastOverlay()
{
    return m_Wrappers[OVERLAY_ROLE].back();
}


void GenericImageData::PushBackImageWrapper(LayerRole role,
                                            ImageWrapperBase *wrapper)
{
  // Append the wrapper
  m_Wrappers[role].push_back(wrapper);

  // Rebroadcast the wrapper-related events as our own events
  Rebroadcaster::RebroadcastAsSourceEvent(wrapper, WrapperChangeEvent(), this);
}


void GenericImageData::PopBackImageWrapper(LayerRole role)
{
  m_Wrappers[role].pop_back();
}

void GenericImageData::MoveLayer(ImageWrapperBase *layer, int direction)
{
  // Find the layer
  LayerIterator it(this);
  it.Find(layer);
  if(!it.IsAtEnd())
    {
    WrapperList &wl = m_Wrappers[it.GetRole()];
    int k = it.GetPositionInRole();

    // Make sure the operation is legal!
    assert(k + direction >= 0 && k + direction < wl.size());

    // Do the swap
    std::swap(wl[k], wl[k+direction]);
    }
}

void GenericImageData::RemoveImageWrapper(LayerRole role,
                                          ImageWrapperBase *wrapper)
{
  m_Wrappers[role].erase(
        std::find(m_Wrappers[role].begin(), m_Wrappers[role].end(), wrapper));
}

void GenericImageData::SetSingleImageWrapper(LayerRole role,
                                             ImageWrapperBase *wrapper)
{
  assert(m_Wrappers[role].size() == 1);
  m_Wrappers[role].front() = wrapper;

  // Rebroadcast the wrapper-related events as our own events
  Rebroadcaster::RebroadcastAsSourceEvent(wrapper, WrapperChangeEvent(), this);
}

void GenericImageData::RemoveSingleImageWrapper(LayerRole role)
{
  assert(m_Wrappers[role].size() == 1);
  m_Wrappers[role].front() = NULL;
}








void GenericImageData::AddOverlay(ImageWrapperBase *new_layer)
{
  this->AddOverlayInternal(new_layer, true);
}