ENH: Convert TODO: to INFO: for old code review comments.

Very old TODO's are clouding the usefulness of these comments as
flags in the IDE development.  Lower them to INFO comments rather
than TODO items.'

.travis_build_script.sh

@@ -32,7 +32,7 @@ cmake \
     -DUSE_ReferenceAtlas:BOOL=OFF \
      ${SOURCE_DIR}
 
-#make -j 2 # BUILD EVERYTHING: TODO: BUILD_SUPPORT_SEPARATE.
+#make -j 2 # BUILD EVERYTHING: INFO: BUILD_SUPPORT_SEPARATE.
 make -j 2
 
 cd ${BUILD_DIR}/BRAINSTools-build/

ARCHIVE/BRAINSCut/BRAINSCutApplyModel.cxx

@@ -34,7 +34,7 @@
 #include <itkMultiplyImageFilter.h>
 #include "itkNumberToString.h"
 
-// TODO: consider using itk::LabelMap Hole filling process in ITK4
+// INFO: consider using itk::LabelMap Hole filling process in ITK4
 BRAINSCutApplyModel ::BRAINSCutApplyModel()
   : m_myDataHandler( nullptr )
   , m_applyDataSetList()

ARCHIVE/BRAINSCut/BRAINSCutGenerateRegistrations.cxx

@@ -177,9 +177,9 @@ BRAINSCutGenerateRegistrations ::CreateTransformFile( const std::string & Moving
 
   // Set Histogram Matching Options
   // BSplineRegistrationHelper->SetNumberOfHistogramBins(250);
-  // TODO: decide what to do here too much freedom?
+  // INFO: decide what to do here too much freedom?
   // BSplineRegistrationHelper->SetNumberOfMatchPoints(10);
-  // TODO:: HISTOGRAMMATCHING OPTION is now Disabled!
+  // INFO:: HISTOGRAMMATCHING OPTION is now Disabled!
   BSplineRegistrationHelper->SetHistogramMatch( false );
 
   // Set Fixed Volume
@@ -271,7 +271,7 @@ BRAINSCutGenerateRegistrations ::CreateTransformFile( const std::string & Moving
 
   //  Start Registration
 
-  // TODO: is this line really print before start registration????
+  // INFO: is this line really print before start registration????
 
   if ( verbose == true )
   {

ARCHIVE/BRAINSCut/BRAINSCutTrainModel.h

@@ -69,7 +69,7 @@ class BRAINSCutTrainModel
   void
   FillANNLayerStructureArray3D( int * const layer ) const;
 
-  // TODO: REGINA all "Get" functions should be const
+  // INFO: REGINA all "Get" functions should be const
   /** setting function with net configuration */
   std::string
   GetModelBasename();
@@ -164,7 +164,7 @@ class BRAINSCutTrainModel
   appendToFile( std::string filename, std::string line );
 
 private:
-  // TODO:  REGINA:  These all need to be called with "m_" prefix
+  // INFO:  REGINA:  These all need to be called with "m_" prefix
   BRAINSCutDataHandler m_myDataHandler;
 
   unsigned int m_trainIteration;

ARCHIVE/BRAINSCut/BRAINSCutUtilities.h

@@ -94,7 +94,7 @@ using WorkingIndexType = WorkingImageType::IndexType;
 using InputVectorType = std::vector< WorkingPixelType >;
 using OutputVectorType = std::vector< WorkingPixelType >;
 
-// HACK TODO:  Regina int below should be unsigned int to avoid negative index numbers
+// HACK INFO:  Regina int below should be unsigned int to avoid negative index numbers
 using InputVectorMapType = std::map< int, InputVectorType >; // < index ,feature vector > pair
 using OutputVectorMapType = std::map< int, OutputVectorType >;
 using PredictValueMapType = std::map< int, scalarType >;

ARCHIVE/BRAINSCut/BRAINSCutVectorTrainingSet.h

@@ -105,7 +105,7 @@ class BRAINSCutVectorTrainingSet
   void
   SetNumberOfSubSet( const unsigned int count = 1 );
 
-  // TODO: REGINA  All "Get" functions should be const
+  // INFO: REGINA  All "Get" functions should be const
   unsigned int
   GetNumberOfSubSet();
 
@@ -115,7 +115,7 @@ class BRAINSCutVectorTrainingSet
   SaveCurrentSubSet( std::string filename );
 
 private:
-  // TODO: REGINA these all need to have "m_" prefix
+  // INFO: REGINA these all need to have "m_" prefix
   /** file names */
   std::string trainingVectorFilename;
   std::string trainingHeaderFilename;

ARCHIVE/BRAINSCut/CMakeLists.txt

@@ -68,8 +68,8 @@ set(BRAINSCutCOMMONLIB_SRCS
   ${BRAINSCut_HDRS}
   )
 
-#TODO: DELETE CreateVectors.cxx
-#TODO:  Rename BRAINSCutDataHandler to something more meaningful
+#INFO: DELETE CreateVectors.cxx
+#INFO:  Rename BRAINSCutDataHandler to something more meaningful
 
 ## Build BRAINSCutCOMMONLIB library
 ##
@@ -100,7 +100,7 @@ endif()
 ##
 set(ALL_PROGS_LIST
   BRAINSCut
-  ShuffleVectorsModule  ## TODO: Make into SEM program
+  ShuffleVectorsModule  ## INFO: Make into SEM program
   SimilarityIndex
   )
 foreach( prog ${ALL_PROGS_LIST} )

ARCHIVE/BRAINSCut/ImageFeatureExtractor.cpp

@@ -18,10 +18,10 @@
 //#include "BRAINSCutApplyModel.h"
 #include "cnpy/cnpy.h"
 
-// TODO: Write VTK lines for visualization in Slicer3D
-// TODO: Fix command-line interface to use SlicerExecutionModel
-// TODO: Remove hard-coded elements of this file
-// TODO: Fix Gradient Magnitude mode to use "MaxGradient" of N Input feature images (or other strategy)
+// INFO: Write VTK lines for visualization in Slicer3D
+// INFO: Fix command-line interface to use SlicerExecutionModel
+// INFO: Remove hard-coded elements of this file
+// INFO: Fix Gradient Magnitude mode to use "MaxGradient" of N Input feature images (or other strategy)
 
 
 int

ARCHIVE/BRAINSCut/Nipype/WorkupT1T2BRAINSCut.py

@@ -286,7 +286,7 @@ def create_brains_cut_workflow(
     cutWF.connect(
         atlasObject, "r_globus_ProbabilityMap", RF12BC, "probabilityMapsRightGlobus"
     )
-    # TODO:
+    # INFO:
     cutWF.connect(
         atlasObject,
         "RandomForestAllSubcorticalsBalancedModel_txtD0060NT0060_gz",

ARCHIVE/BRAINSCut/Nipype/XMLConfigurationGenerator.py

@@ -217,7 +217,7 @@ def xml_generator(
 
     #####################################################################################
     # ANN Parameters
-    # TODO: Simplify!!!
+    # INFO: Simplify!!!
     #
     outStream.write('   <ANNParameters Iterations             = "5"\n')
     outStream.write('                     MaximumVectorsPerEpoch = "700000"\n')

ARCHIVE/BRAINSCut/Reliability/GenerateXMLConfigurationFileFromList.sh

@@ -138,7 +138,7 @@ do
 
   #
   # Add Image
-  # TODO::deal with type of apply
+  # INFO::deal with type of apply
 
   ANNOutputDirectory="${ModelDirectory}/${currentSubject}_${ANNHN}/"
 

ARCHIVE/BRAINSCut/TestSuite/NetConfigurations/BRAINSCutTest.xml.in

@@ -17,7 +17,7 @@
 
   <!-- ==========================================================================
         Registration Description
-        TODO:: Change BRAINSCut Registration Script to Python
+        INFO:: Change BRAINSCut Registration Script to Python
        ========================================================================== -->
   <RegistrationConfiguration
     ImageTypeToUse="T1"

ARCHIVE/BRAINSCut/TrainModel.cxx

@@ -292,18 +292,18 @@ ANNTrain( // NetConfiguration & prob,
 
   int           lastSubSetNumber = -1;
   std::ifstream testfilestr;
-  // TODO: DELETE neural_data_set_type *TestSetPtr = 0;
-  // TODO: DELETE int                   test_InputVectorSize = 0;
-  // TODO: DELETE int                   test_OutputVectorSize = 0;
-  // TODO: DELETE int                   test_NumberTrainingVectorsFromFile = 0;
+  // INFO: DELETE neural_data_set_type *TestSetPtr = 0;
+  // INFO: DELETE int                   test_InputVectorSize = 0;
+  // INFO: DELETE int                   test_OutputVectorSize = 0;
+  // INFO: DELETE int                   test_NumberTrainingVectorsFromFile = 0;
   testfilestr.close();
   // To trace minimum traininig point
   double TrainSet_MinimumMSE = 100.0;
   int    TrainSet_MinimumMSEPoint = 0;
 
   // To trace minimum traininig point
-  // TODO: DELETE double TestSet_MinimumMSE = 100.0;
-  // TODO: DELETE int TestSet_MinimumMSEPoint = 0;
+  // INFO: DELETE double TestSet_MinimumMSE = 100.0;
+  // INFO: DELETE int TestSet_MinimumMSEPoint = 0;
   // OPENCV Training Model Creation
   int                layer[] = { InputVectorSize, HiddenVectorSize, OutputVectorSize };
   neural_vector_type layerStructure = cvCreateMat( 1, 3, CV_32SC1 );
@@ -464,7 +464,7 @@ ANNTrain( // NetConfiguration & prob,
     }
   }
   // Printing out minimum training error
-  // TODO: Should I add this to the Header file??!!!! KEY
+  // INFO: Should I add this to the Header file??!!!! KEY
   if ( TrainSet_MinimumMSEPoint != 0 ) // if training has been proceeeded
   {
     std::cout << "###################################################\n"

ARCHIVE/BRAINSCut/XMLConfigurationFileParser.cxx

@@ -336,7 +336,7 @@ XMLConfigurationFileParser::ValidateDataSets()
   // return true;
 
   /*
-   * TODO:: change validation part to check the simple file existance checking
+   * INFO:: change validation part to check the simple file existance checking
    *
    *
   for( std::list<DataSet *>::iterator it = dataSets.begin();

ARCHIVE/BRAINSRefacer/BRAINSRefacer.cxx

@@ -189,7 +189,7 @@ main( int argc, char ** argv )
   ThresholdFilterType::Pointer distanceThreshold = ThresholdFilterType::New();
   distanceThreshold->SetInput( distanceMapFilter->GetOutput() );
   distanceThreshold->SetLower( 0.0 );
-  distanceThreshold->SetUpper( 4096 ); // TODO: This should be changed to the max pixel value for the image type??? or
+  distanceThreshold->SetUpper( 4096 ); // INFO: This should be changed to the max pixel value for the image type??? or
                                        // will we always be using double for calculations??
   distanceThreshold->SetOutsideValue( 0.0 );
 

ARCHIVE/BRAINSRefacer/TestSuite/BRAINSRefacerBrainDataTest.cxx

@@ -1,7 +1,7 @@
 
 // Author: Jeffrey Obadal
 /*
- * TODO: Refactor code into new paths
+ * INFO: Refactor code into new paths
  * Path 1: check brain data -- use labelmap as reference, do safety check that no brain data has changed
  * Path 2: (new file?) check deformation -- subpath1: labelmap - similar to path 1, but check non-brain data has changed
  *                                          subpath2: landmark - use landmark mask and check face area has changed

ARCHIVE/BRAINSRefacer/TestSuite/BRAINSRefacerCheckPixelType.cxx

@@ -23,7 +23,7 @@ main( int argc, char * argv[] )
   itk::ImageIOBase::Pointer inputImageIO =
     itk::ImageIOFactory::CreateImageIO( inputImageName.c_str(), itk::ImageIOFactory::ReadMode );
 
-  // TODO: add better error checking: file exists, read permissions...etc
+  // INFO: add better error checking: file exists, read permissions...etc
 
   if ( !inputImageIO )
   {

ARCHIVE/BRAINSRefacer/TestSuite/CMakeLists.txt

@@ -322,8 +322,8 @@ foreach(PIXELTYPE ${PIXEL_LIST_BRAINSREFACER} )
     )
   set_property(TEST ${RefacerTestName} APPEND PROPERTY DEPENDS ${PARENT_TEST})
 
-# #TODO: Test that the output pixel type is the same as the input
+# #INFO: Test that the output pixel type is the same as the input
 
-# #TODO: Test that the deformation field is symmetrical
+# #INFO: Test that the deformation field is symmetrical
 
 endforeach()

ARCHIVE/BRAINSSurfaceTools/BRAINSSurfaceRegister/LabelMaps/itkNaryRelabelImageFilter.hxx

@@ -87,7 +87,7 @@ NaryRelabelImageFilter< TInputImage, TOutputImage >::GenerateData()
         translator[i][v] = label;
 
         // increment the label for the next to translate
-        // TODO: throw an exception if the maximum number of labels is exceeded
+        // INFO: throw an exception if the maximum number of labels is exceeded
         label++;
       }
       progress.CompletedPixel();

ARCHIVE/BRAINSSurfaceTools/GenusZeroImageFilter/GenusZeroImageFilter.cxx

@@ -254,7 +254,7 @@ main( int argc, char * argv[] )
   }
   transformer->Update();
 
-  // TODO: add progress
+  // INFO: add progress
   // (transformer->GetOutput())->ReleaseDataFlagOn();
 
   // but for now we're just going to write it out
@@ -265,7 +265,7 @@ main( int argc, char * argv[] )
   if ( computeSurface )
   {
     writer->SetFileName( vtkOutput.c_str() );
-    // TODO: add progress
+    // INFO: add progress
     writer->Write();
   }
 

ARCHIVE/BRAINSSurfaceTools/vtkITK/vtkITKArchetypeImageSeriesReader.h

@@ -702,7 +702,7 @@ class VTK_ITK_EXPORT vtkITKArchetypeImageSeriesReader : public vtkImageAlgorithm
   }
 
   /// insert unique item into array. Duplicate code for TCL wrapping.
-  /// TODO: need to clean up
+  /// INFO: need to clean up
   int
   InsertSeriesInstanceUIDs( const char * aUID )
   {

ARCHIVE/BRAINSSurfaceTools/vtkITK/vtkITKIslandMath.h

@@ -40,7 +40,7 @@ class VTK_ITK_EXPORT vtkITKIslandMath : public vtkSimpleImageToImageFilter
   vtkSetMacro( MaximumSize, vtkIdType );
 
   ///
-  /// TODO: Not yet implemented
+  /// INFO: Not yet implemented
   /// If zero, islands are defined by 3D connectivity
   /// If non-zero, islands are evaluated in a sequence of 2D planes
   /// (IJ=3, IK=2, JK=1)

ARCHIVE/DicomSignature/DicomSignature.cxx

@@ -243,7 +243,7 @@ main( int argc, char * argv[] )
     EVP_DigestUpdate( &mdctx, mySpacingInfo.str().c_str(), mySpacingInfo.str().size() );
     EVP_DigestUpdate( &mdctx, myOriginInfo.str().c_str(), myOriginInfo.str().size() );
     EVP_DigestUpdate( &mdctx, myDirectionInfo.str().c_str(), myDirectionInfo.str().size() );
-    // TODO:  Add EVP_DigestUpdate for gdcm strings for
+    // INFO:  Add EVP_DigestUpdate for gdcm strings for
     // <element tag="0008,0021" vr="DA" vm="1" len="8"
     // name="SeriesDate">20090430</element>
     const std::string SeriesDateKey( "0008|0021" );

ARCHIVE/ICCDEF/ApplyWarp.cxx

@@ -18,7 +18,7 @@
  *=========================================================================*/
 /*==================================================================
 
-TODO:  NEED TO COMMENT WHAT THIS PROGRAM IS TO BE USED FOR
+INFO:  NEED TO COMMENT WHAT THIS PROGRAM IS TO BE USED FOR
 
 ==================================================================*/
 

ARCHIVE/ICCDEF/AverageBrainGenerator.cxx

@@ -18,7 +18,7 @@
  *=========================================================================*/
 /*==================================================================
 
-TODO:  NEED TO COMMENT WHAT THIS PROGRAM IS TO BE USED FOR
+INFO:  NEED TO COMMENT WHAT THIS PROGRAM IS TO BE USED FOR
 
 2009.08
 Zhao,Yongqiang

ARCHIVE/ICCDEF/iccdefRegistration_New.cxx

@@ -347,7 +347,7 @@ ThirionFunction( const struct ICCDEFWarpAppParameters & command )
   if ( command.outputDebug )
   {
     bool debug = true;
-    app->SetOutDebug( debug ); // TODO:  SetOutDebug should be a boolean not a
+    app->SetOutDebug( debug ); // INFO:  SetOutDebug should be a boolean not a
                                // string.
   }
 

ARCHIVE/ICCDEF/itkVectorFFTWRealToHalfHermitianForwardFFTImageFilter.hxx

@@ -36,7 +36,7 @@
 
 namespace itk
 {
-/** TODO:  There should be compile time type checks so that
+/** INFO:  There should be compile time type checks so that
            if only ITK_USE_FFTWF is defined, then only floats are valid.
            and if ITK_USE_FFTWD is defined, then only doubles are valid.
 */

AutoWorkup/BAW/AutoWorkup.py

@@ -110,7 +110,7 @@ def setup_environment(argv):
         )
         print(
             "FREESURFER needs to check for sane environment here!"
-        )  # TODO: raise warning, write method, what???
+        )  # INFO: raise warning, write method, what???
     for key, value in list(environment["env"].items()):
         if key in ["PATH", "PYTHONPATH"] + misc.FS_VARS:
             pass

AutoWorkup/BAW/BAWantsRegistrationBuildTemplate.py

@@ -351,12 +351,12 @@ def baw_ants_registration_template_build_single_iteration_wf(
         run_without_submitting=True,
         name="inputspec",
     )
-    ## HACK: TODO: We need to have the AVG_AIR.nii.gz be warped with a default voxel value of 1.0
-    ## HACK: TODO: Need to move all local functions to a common untility file, or at the top of the file so that
+    ## HACK: INFO: We need to have the AVG_AIR.nii.gz be warped with a default voxel value of 1.0
+    ## HACK: INFO: Need to move all local functions to a common untility file, or at the top of the file so that
     ##             they do not change due to re-indenting.  Otherwise re-indenting for flow control will trigger
     ##             their hash to change.
-    ## HACK: TODO: REMOVE 'transforms_list' it is not used.  That will change all the hashes
-    ## HACK: TODO: Need to run all python files through the code beutifiers.  It has gotten pretty ugly.
+    ## HACK: INFO: REMOVE 'transforms_list' it is not used.  That will change all the hashes
+    ## HACK: INFO: Need to run all python files through the code beutifiers.  It has gotten pretty ugly.
     outputSpec = pe.Node(
         interface=util.IdentityInterface(
             fields=["template", "transforms_list", "passive_deformed_templates"]
@@ -499,7 +499,7 @@ def baw_ants_registration_template_build_single_iteration_wf(
     )
 
     ## Now average the images together
-    ## TODO:  For now GradientStep is set to 0.25 as a hard coded default value.
+    ## INFO:  For now GradientStep is set to 0.25 as a hard coded default value.
     GradientStep = 0.25
     GradientStepWarpImage = pe.Node(
         interface=MultiplyImages(), name="GradientStepWarpImage"
@@ -674,7 +674,7 @@ def baw_ants_registration_template_build_single_iteration_wf(
         "transforms",
     )
     ## FlattenTransformAndImagesListNode.inputs.invert_transform_flags = [False,False,False,False,False,False]
-    ## TODO: Please check of invert_transform_flags has a fixed number.
+    ## INFO: Please check of invert_transform_flags has a fixed number.
     ## PREVIOUS TemplateBuildSingleIterationWF.connect(BeginANTS, 'forward_invert_flags', FlattenTransformAndImagesListNode, 'invert_transform_flags')
     wimtPassivedeformed = pe.MapNode(
         interface=ApplyTransforms(),
@@ -775,7 +775,7 @@ def baw_ants_registration_template_build_single_iteration_wf(
         "output_average_image",
     )
 
-    ## -- TODO:  Now neeed to reshape all the passive images as well
+    ## -- INFO:  Now neeed to reshape all the passive images as well
     ReshapeAveragePassiveImageWithShapeUpdate = pe.MapNode(
         interface=ApplyTransforms(),
         iterfield=["input_image", "reference_image", "output_image", "interpolation"],