This file is indexed.

/usr/include/ITK-4.5/itkGradientDescentOptimizerv4.hxx is in libinsighttoolkit4-dev 4.5.0-3.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  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
/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef __itkGradientDescentOptimizerv4_hxx
#define __itkGradientDescentOptimizerv4_hxx

#include "itkGradientDescentOptimizerv4.h"

namespace itk
{

/**
* Default constructor
*/
template<typename TInternalComputationValueType>
GradientDescentOptimizerv4Template<TInternalComputationValueType>
::GradientDescentOptimizerv4Template()
{
  this->m_LearningRate = NumericTraits<TInternalComputationValueType>::One;

    // m_MaximumStepSizeInPhysicalUnits is used for automatic learning
    // rate estimation. it may be initialized either by calling
    // SetMaximumStepSizeInPhysicalUnits manually or by using m_ScalesEstimator
    // automatically. and the former has higher priority than the latter.
  this->m_MaximumStepSizeInPhysicalUnits = NumericTraits<TInternalComputationValueType>::Zero;

    // Initialize parameters for the convergence checker
  this->m_MinimumConvergenceValue = 1e-8;//NumericTraits<TInternalComputationValueType>::epsilon();//1e-30;
  this->m_ConvergenceWindowSize = 50;

  this->m_DoEstimateScales = true;
  this->m_DoEstimateLearningRateAtEachIteration = false;
  this->m_DoEstimateLearningRateOnce = true;
  this->m_ReturnBestParametersAndValue = false;
}

/**
* Destructor
*/
template<typename TInternalComputationValueType>
GradientDescentOptimizerv4Template<TInternalComputationValueType>
::~GradientDescentOptimizerv4Template()
{}


/**
*PrintSelf
*/
template<typename TInternalComputationValueType>
void
GradientDescentOptimizerv4Template<TInternalComputationValueType>
::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);
  os << indent << "Learning rate:" << this->m_LearningRate << std::endl;
  os << indent << "MaximumStepSizeInPhysicalUnits: "
  << this->m_MaximumStepSizeInPhysicalUnits << std::endl;
  if( this->m_ScalesEstimator.IsNull() )
    {
    os << indent << "No ScalesEstimator set." << std::endl;
    }
  else
    {
    os << indent << "ScalesEstimator: " << std::endl;
    this->m_ScalesEstimator->Print( os, indent.GetNextIndent() );
    }
  os << indent << "DoEstimateScales: " << this->m_DoEstimateScales << std::endl;
  os << indent << "DoEstimateLearningRateAtEachIteration: "
  << this->m_DoEstimateLearningRateAtEachIteration << std::endl;
  os << indent << "DoEstimateLearningRateOnce: "
  << this->m_DoEstimateLearningRateOnce << std::endl;
}

/**
* Start and run the optimization
*/
template<typename TInternalComputationValueType>
void
GradientDescentOptimizerv4Template<TInternalComputationValueType>
::StartOptimization( bool doOnlyInitialization )
{
  itkDebugMacro("StartOptimization");

  /* Validate some settings */
  if ( this->m_ScalesEstimator.IsNotNull() &&
      this->m_DoEstimateLearningRateOnce &&
      this->m_DoEstimateLearningRateAtEachIteration )
    {
    itkExceptionMacro("Both m_DoEstimateLearningRateOnce and m_DoEstimateLearningRateAtEachIteration are enabled. Not allowed. ");
    }

  /* Estimate the parameter scales if requested. */
  if ( this->m_DoEstimateScales && this->m_ScalesEstimator.IsNotNull() )
    {
    this->m_ScalesEstimator->EstimateScales(this->m_Scales);
    itkDebugMacro( "Estimated scales = " << this->m_Scales );

    /* If user hasn't set this, assign the default. */
    if ( this->m_MaximumStepSizeInPhysicalUnits <=
        NumericTraits<TInternalComputationValueType>::epsilon())
      {
      this->m_MaximumStepSizeInPhysicalUnits = this->m_ScalesEstimator->EstimateMaximumStepSize();
      }
    }

    // Initialize the convergence checker
  this->m_ConvergenceMonitoring = ConvergenceMonitoringType::New();
  this->m_ConvergenceMonitoring->SetWindowSize( this->m_ConvergenceWindowSize );

  /* Must call the superclass version for basic validation and setup */
  Superclass::StartOptimization( doOnlyInitialization );

  if( this->m_ReturnBestParametersAndValue )
    {
    this->m_BestParameters = this->GetCurrentPosition( );
    this->m_CurrentBestValue = NumericTraits< MeasureType >::max();
    }

  this->m_CurrentIteration = 0;

  if( ! doOnlyInitialization )
    {
    this->ResumeOptimization();
    }
}

/**
* StopOptimization
*/
template<typename TInternalComputationValueType>
void
GradientDescentOptimizerv4Template<TInternalComputationValueType>
::StopOptimization(void)
{
  if( this->m_ReturnBestParametersAndValue )
    {
    this->m_Metric->SetParameters( this->m_BestParameters );
    this->m_CurrentMetricValue = this->m_CurrentBestValue;
    }
  Superclass::StopOptimization();
}

/**
* Resume optimization.
*/
template<typename TInternalComputationValueType>
void
GradientDescentOptimizerv4Template<TInternalComputationValueType>
::ResumeOptimization()
{
  this->m_StopConditionDescription.str("");
  this->m_StopConditionDescription << this->GetNameOfClass() << ": ";
  this->InvokeEvent( StartEvent() );

  this->m_Stop = false;
  while( ! this->m_Stop )
    {
    /* Compute metric value/derivative. */
    try
      {
      /* m_Gradient will be sized as needed by metric. If it's already
       * proper size, no new allocation is done. */
      this->m_Metric->GetValueAndDerivative( this->m_CurrentMetricValue, this->m_Gradient );
      }
    catch ( ExceptionObject & err )
      {
      this->m_StopCondition = Superclass::COSTFUNCTION_ERROR;
      this->m_StopConditionDescription << "Metric error during optimization";
      this->StopOptimization();

        // Pass exception to caller
      throw err;
      }

    /* Check if optimization has been stopped externally.
     * (Presumably this could happen from a multi-threaded client app?) */
    if ( this->m_Stop )
      {
      this->m_StopConditionDescription << "StopOptimization() called";
      break;
      }

    /* Check the convergence by WindowConvergenceMonitoringFunction.
     */
    this->m_ConvergenceMonitoring->AddEnergyValue( this->m_CurrentMetricValue );
    try
      {
      this->m_ConvergenceValue = this->m_ConvergenceMonitoring->GetConvergenceValue();
      if (this->m_ConvergenceValue <= this->m_MinimumConvergenceValue)
        {
        this->m_StopConditionDescription << "Convergence checker passed at iteration " << this->m_CurrentIteration << ".";
        this->m_StopCondition = Superclass::CONVERGENCE_CHECKER_PASSED;
        this->StopOptimization();
        break;
        }
      }
    catch(std::exception & e)
      {
      std::cerr << "GetConvergenceValue() failed with exception: " << e.what() << std::endl;
      }

    /* Advance one step along the gradient.
     * This will modify the gradient and update the transform. */
    this->AdvanceOneStep();

    /* Store best value and position */
    if ( this->m_ReturnBestParametersAndValue && this->m_CurrentMetricValue < this->m_CurrentBestValue )
      {
      this->m_CurrentBestValue = this->m_CurrentMetricValue;
      this->m_BestParameters = this->GetCurrentPosition( );
      }

    /* Update and check iteration count */
    this->m_CurrentIteration++;

    if ( this->m_CurrentIteration >= this->m_NumberOfIterations )
      {
      this->m_StopConditionDescription << "Maximum number of iterations (" << this->m_NumberOfIterations << ") exceeded.";
      this->m_StopCondition = Superclass::MAXIMUM_NUMBER_OF_ITERATIONS;
      this->StopOptimization();
      break;
      }
    } //while (!m_Stop)
}

/**
* Advance one Step following the gradient direction
*/
template<typename TInternalComputationValueType>
void
GradientDescentOptimizerv4Template<TInternalComputationValueType>
::AdvanceOneStep()
{
  itkDebugMacro("AdvanceOneStep");

  /* Begin threaded gradient modification.
   * Scale by gradient scales, then estimate the learning
   * rate if options are set to (using the scaled gradient),
   * then modify by learning rate. The m_Gradient variable
   * is modified in-place. */
  this->ModifyGradientByScales();
  this->EstimateLearningRate();
  this->ModifyGradientByLearningRate();

  try
    {
    /* Pass graident to transform and let it do its own updating */
    this->m_Metric->UpdateTransformParameters( this->m_Gradient );
    }
  catch ( ExceptionObject & err )
    {
    this->m_StopCondition = Superclass::UPDATE_PARAMETERS_ERROR;
    this->m_StopConditionDescription << "UpdateTransformParameters error";
    this->StopOptimization();

      // Pass exception to caller
    throw err;
    }

  this->InvokeEvent( IterationEvent() );
}

/**
* Modify the gradient by scales and weights over a given index range.
*/
template<typename TInternalComputationValueType>
void
GradientDescentOptimizerv4Template<TInternalComputationValueType>
::ModifyGradientByScalesOverSubRange( const IndexRangeType& subrange )
{
  const ScalesType& scales = this->GetScales();
  const ScalesType& weights = this->GetWeights();

  ScalesType factor( scales.Size() );

  if( this->GetWeightsAreIdentity() )
    {
    for( SizeValueType i=0; i < factor.Size(); i++ )
      {
      factor[i] = NumericTraits<typename ScalesType::ValueType>::OneValue() / scales[i];
      }
    }
  else
    {
    for( SizeValueType i=0; i < factor.Size(); i++ )
      {
      factor[i] = weights[i] / scales[i];
      }
    }

  /* Loop over the range. It is inclusive. */
  for ( IndexValueType j = subrange[0]; j <= subrange[1]; j++ )
    {
      // scales is checked during StartOptmization for values <=
      // machine epsilon.
      // Take the modulo of the index to handle gradients from transforms
      // with local support. The gradient array stores the gradient of local
      // parameters at each local index with linear packing.
    IndexValueType index = j % scales.Size();
    this->m_Gradient[j] = this->m_Gradient[j] * factor[index];
    }
}

/**
* Modify the gradient by learning rate over a given index range.
*/
template<typename TInternalComputationValueType>
void
GradientDescentOptimizerv4Template<TInternalComputationValueType>
::ModifyGradientByLearningRateOverSubRange( const IndexRangeType& subrange )
{
  /* Loop over the range. It is inclusive. */
  for ( IndexValueType j = subrange[0]; j <= subrange[1]; j++ )
    {
    this->m_Gradient[j] = this->m_Gradient[j] * this->m_LearningRate;
    }
}

/**
* Estimate the learning rate.
*/
template<typename TInternalComputationValueType>
void
GradientDescentOptimizerv4Template<TInternalComputationValueType>
::EstimateLearningRate()
{
  if ( this->m_ScalesEstimator.IsNull() )
    {
    return;
    }
  if ( this->m_DoEstimateLearningRateAtEachIteration ||
      (this->m_DoEstimateLearningRateOnce && this->m_CurrentIteration == 0) )
    {
    TInternalComputationValueType stepScale
    = this->m_ScalesEstimator->EstimateStepScale(this->m_Gradient);

    if (stepScale <= NumericTraits<TInternalComputationValueType>::epsilon())
      {
      this->m_LearningRate = NumericTraits<TInternalComputationValueType>::One;
      }
    else
      {
      this->m_LearningRate = this->m_MaximumStepSizeInPhysicalUnits / stepScale;
      }
    }
}

}//namespace itk

#endif