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EditSequenceFile.cxx
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/*=Plus=header=begin======================================================
Program: Plus
Copyright (c) Laboratory for Percutaneous Surgery. All rights reserved.
See License.txt for details.
=========================================================Plus=header=end*/
// Local includes
#include "PlusConfigure.h"
#include "PlusMath.h"
#include "igsioTrackedFrame.h"
#include "vtkPlusSequenceIO.h"
#include "vtkIGSIOTrackedFrameList.h"
#include "vtkIGSIOTransformRepository.h"
// VTK includes
#include <vtkImageData.h>
#include <vtkMatrix4x4.h>
#include <vtkSmartPointer.h>
#include <vtkTransform.h>
#include <vtkXMLDataElement.h>
#include <vtkXMLUtilities.h>
#include <vtksys/CommandLineArguments.hxx>
#include <vtksys/RegularExpression.hxx>
enum OperationType
{
UPDATE_FRAME_FIELD_NAME,
UPDATE_FRAME_FIELD_VALUE,
DELETE_FRAME_FIELD,
UPDATE_FIELD_NAME,
UPDATE_FIELD_VALUE,
DELETE_FIELD,
ADD_TRANSFORM,
TRIM,
APPEND,
MIX,
FILL_IMAGE_RECTANGLE,
CROP,
REMOVE_IMAGE_DATA,
DECIMATE,
NO_OPERATION
};
class FrameFieldUpdate
{
public:
FrameFieldUpdate()
{
TrackedFrameList = NULL;
FrameScalarStart = 0;
FrameScalarIncrement = 0;
FrameScalarDecimalDigits = 5;
FrameTransformStart = NULL;
FrameTransformIncrement = NULL;
}
std::string FieldName;
std::string UpdatedFieldName;
std::string UpdatedFieldValue;
vtkIGSIOTrackedFrameList* TrackedFrameList;
double FrameScalarStart;
double FrameScalarIncrement;
int FrameScalarDecimalDigits;
vtkMatrix4x4* FrameTransformStart;
vtkMatrix4x4* FrameTransformIncrement;
std::string FrameTransformIndexFieldName;
};
PlusStatus TrimSequenceFile(vtkIGSIOTrackedFrameList* trackedFrameList, unsigned int firstFrameIndex, unsigned int lastFrameIndex);
PlusStatus DecimateSequenceFile(vtkIGSIOTrackedFrameList* trackedFrameList, unsigned int decimationFactor);
PlusStatus UpdateFrameFieldValue(FrameFieldUpdate& fieldUpdate);
PlusStatus DeleteFrameField(vtkIGSIOTrackedFrameList* trackedFrameList, std::string fieldName);
PlusStatus ConvertStringToMatrix(std::string& strMatrix, vtkMatrix4x4* matrix);
PlusStatus AddTransform(vtkIGSIOTrackedFrameList* trackedFrameList, std::vector<std::string> transformNamesToAdd, std::string deviceSetConfigurationFileName);
PlusStatus FillRectangle(vtkIGSIOTrackedFrameList* trackedFrameList, const std::vector<unsigned int>& fillRectOrigin, const std::vector<unsigned int>& fillRectSize, int fillGrayLevel);
PlusStatus CropRectangle(vtkIGSIOTrackedFrameList* trackedFrameList, igsioVideoFrame::FlipInfoType& flipInfo, const std::vector<int>& cropRectOrigin, const std::vector<int>& cropRectSize);
namespace
{
const std::string FIELD_VALUE_FRAME_SCALAR = "{frame-scalar}";
const std::string FIELD_VALUE_FRAME_TRANSFORM = "{frame-transform}";
}
// Fuse all fields in sequence files into the first sequence
//----------------------------------------------------------------------------
PlusStatus MixTrackedFrameLists(vtkIGSIOTrackedFrameList* trackedFrameList, std::vector<std::string> inputFileNames)
{
if (inputFileNames.size() == 0)
{
LOG_ERROR("No --source-seq-files specified");
return PLUS_FAIL;
}
LOG_INFO("Read master sequence file: " << inputFileNames[0]);
if (vtkPlusSequenceIO::Read(inputFileNames[0], trackedFrameList) != PLUS_SUCCESS)
{
LOG_ERROR("Couldn't read sequence file: " << inputFileNames[0]);
return PLUS_FAIL;
}
if (trackedFrameList->GetNumberOfTrackedFrames() == 0)
{
LOG_ERROR("No frames in sequence file: " << inputFileNames[0]);
return PLUS_FAIL;
}
for (unsigned int i = 1; i < inputFileNames.size(); i++)
{
LOG_INFO("Read input sequence file: " << inputFileNames[i]);
vtkSmartPointer<vtkIGSIOTrackedFrameList> additionalTrackedFrameList = vtkSmartPointer<vtkIGSIOTrackedFrameList>::New();
if (vtkPlusSequenceIO::Read(inputFileNames[i], additionalTrackedFrameList) != PLUS_SUCCESS)
{
LOG_ERROR("Couldn't read sequence file: " << inputFileNames[0]);
return PLUS_FAIL;
}
if (additionalTrackedFrameList->GetNumberOfTrackedFrames() == 0)
{
continue;
}
unsigned int additionalFrameIndex = 0;
double maxTimestampValueForCurrentAdditionalFrame = additionalTrackedFrameList->GetTrackedFrame(0)->GetTimestamp();
if (additionalTrackedFrameList->GetNumberOfTrackedFrames() >= 2)
{
maxTimestampValueForCurrentAdditionalFrame = (additionalTrackedFrameList->GetTrackedFrame(additionalFrameIndex + 1)->GetTimestamp() + additionalTrackedFrameList->GetTrackedFrame(additionalFrameIndex)->GetTimestamp()) / 2.0;
}
for (unsigned int f = 0; f < trackedFrameList->GetNumberOfTrackedFrames(); ++f)
{
igsioTrackedFrame* masterTrackedFrame = trackedFrameList->GetTrackedFrame(f);
// Determine which additional frame belongs to this master frame
while (masterTrackedFrame->GetTimestamp() > maxTimestampValueForCurrentAdditionalFrame
&& additionalFrameIndex + 1 < additionalTrackedFrameList->GetNumberOfTrackedFrames())
{
if (additionalFrameIndex == additionalTrackedFrameList->GetNumberOfTrackedFrames() - 1)
{
// last frame, all remaining frames are assigned to it
break;
}
additionalFrameIndex++;
// use this frame index until timestamp is closest to this frame's timestamp
maxTimestampValueForCurrentAdditionalFrame = (additionalTrackedFrameList->GetTrackedFrame(additionalFrameIndex)->GetTimestamp() +
additionalTrackedFrameList->GetTrackedFrame(additionalFrameIndex + 1)->GetTimestamp()) / 2.0;
}
// Copy frame fields
igsioTrackedFrame* additionalFrame = additionalTrackedFrameList->GetTrackedFrame(additionalFrameIndex);
auto customFrameFields = additionalFrame->GetCustomFields();
for (auto fieldIter = customFrameFields.begin(); fieldIter != customFrameFields.end(); ++fieldIter)
{
if (!fieldIter->first.compare("FrameNumber") ||
!fieldIter->first.compare("Timestamp") ||
!fieldIter->first.compare("UnfilteredTimestamp") ||
!fieldIter->first.compare("ImageStatus"))
{
// Timing and image information is taken from the first sequence
continue;
}
masterTrackedFrame->SetFrameField(fieldIter->first, fieldIter->second.second, fieldIter->second.first);
}
}
}
return PLUS_SUCCESS;
}
//----------------------------------------------------------------------------
// Append tracked frame list (one after the other)
PlusStatus AppendTrackedFrameLists(vtkIGSIOTrackedFrameList* trackedFrameList, std::vector<std::string> inputFileNames, bool incrementTimestamps, std::vector<std::string> customHeaderFields)
{
double lastTimestamp = 0;
for (unsigned int i = 0; i < inputFileNames.size(); i++)
{
LOG_INFO("Read input sequence file: " << inputFileNames[i]);
vtkSmartPointer<vtkIGSIOTrackedFrameList> timestampFrameList = vtkSmartPointer<vtkIGSIOTrackedFrameList>::New();
if (vtkPlusSequenceIO::Read(inputFileNames[i], timestampFrameList) != PLUS_SUCCESS)
{
LOG_ERROR("Couldn't read sequence file: " << inputFileNames[0]);
return PLUS_FAIL;
}
if (incrementTimestamps)
{
vtkIGSIOTrackedFrameList* tfList = timestampFrameList;
for (unsigned int f = 0; f < tfList->GetNumberOfTrackedFrames(); ++f)
{
igsioTrackedFrame* tf = tfList->GetTrackedFrame(f);
tf->SetTimestamp(lastTimestamp + tf->GetTimestamp());
}
lastTimestamp = tfList->GetTrackedFrame(tfList->GetNumberOfTrackedFrames() - 1)->GetTimestamp();
}
if (!customHeaderFields.empty())
{
std::string fieldValue;
for (unsigned int i = 0; i < customHeaderFields.size(); ++i)
{
fieldValue = timestampFrameList->GetCustomString(customHeaderFields[i]);
trackedFrameList->SetCustomString(customHeaderFields[i], fieldValue);
}
}
if (trackedFrameList->AddTrackedFrameList(timestampFrameList) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to append tracked frame list!");
return PLUS_FAIL;
}
}
return PLUS_SUCCESS;
}
//----------------------------------------------------------------------------
int main(int argc, char** argv)
{
// Parse command-line arguments
bool printHelp = false;
int verboseLevel(vtkPlusLogger::LOG_LEVEL_UNDEFINED);
vtksys::CommandLineArguments args;
std::string inputFileName; // Sequence file name with path to edit
std::vector<std::string> inputFileNames; // Sequence file name list with path to edit
std::string outputFileName; // Sequence file name with path to save the result
std::string strOperation;
OperationType operation;
bool useCompression = false;
bool incrementTimestamps = false;
int firstFrameIndex = -1; // First frame index used for trimming the sequence file.
int lastFrameIndex = -1; // Last frame index used for trimming the sequence file.
std::string fieldName; // Field name to edit
std::string updatedFieldName; // Updated field name after edit
std::string updatedFieldValue; // Updated field value after edit
std::vector<std::string> customHeaderFieldsToMaintain; // Custom header field list to maintain from input to output
int frameScalarDecimalDigits = 5; // Number of digits saved for frame field value into sequence file (Default: 5)
double frameScalarStart = 0.0; // Frame scalar field value starting index (Default: 0.0)
double frameScalarIncrement = 1.0; // Frame scalar field value increment (Default: 1.0)
int decimationFactor = 2; // Keep every 2nd frame by default
std::string strFrameTransformStart; // Frame transform field starting 4x4 transform matrix (Default: identity)
vtkSmartPointer<vtkMatrix4x4> frameTransformStart = vtkSmartPointer<vtkMatrix4x4>::New(); // Frame transform field starting 4x4 transform matrix (Default: identity)
std::string strFrameTransformIncrement; // Frame transform increment 4x4 transform matrix
vtkSmartPointer<vtkMatrix4x4> frameTransformIncrement = vtkSmartPointer<vtkMatrix4x4>::New(); // Frame transform increment 4x4 transform matrix
std::string strFrameTransformIndexFieldName;
std::string strUpdatedReferenceTransformName;
std::string transformNamesToAdd; // Name of the transform to add to each frame
std::string deviceSetConfigurationFileName; // Used device set configuration file path and name
std::vector<int> rectOriginPix; // Fill/crop rectangle top-left corner position in MF coordinate frame, in pixels
std::vector<int> rectSizePix; // Fill/crop rectangle size in MF coordinate frame, in pixels
int fillGrayLevel = 0; // Rectangle fill color
bool flipX(false);
bool flipY(false);
bool flipZ(false);
args.Initialize(argc, argv);
args.AddArgument("--help", vtksys::CommandLineArguments::NO_ARGUMENT, &printHelp, "Print this help.");
args.AddArgument("--verbose", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &verboseLevel, "Verbose level (1=error only, 2=warning, 3=info, 4=debug, 5=trace)");
args.AddArgument("--source-seq-file", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &inputFileName, "Input sequence file name with path to edit");
args.AddArgument("--source-seq-files", vtksys::CommandLineArguments::MULTI_ARGUMENT, &inputFileNames, "Input sequence file name list with path to edit");
args.AddArgument("--output-seq-file", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &outputFileName, "Output sequence file name with path to save the result");
args.AddArgument("--operation", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &strOperation, "Operation to modify sequence file. See available operations below.");
// Trimming parameters
args.AddArgument("--first-frame-index", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &firstFrameIndex, "First frame index used for trimming the sequence file. Index of the first frame of the sequence is 0.");
args.AddArgument("--last-frame-index", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &lastFrameIndex, "Last frame index used for trimming the sequence file.");
// Decimation parameters
args.AddArgument("--decimation-factor", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &decimationFactor, "Used for DECIMATE operation, where every N-th frame is kept. This parameter specifies N (Default: 2)");
args.AddArgument("--field-name", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &fieldName, "Field name to edit");
args.AddArgument("--updated-field-name", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &updatedFieldName, "Updated field name after edit");
args.AddArgument("--updated-field-value", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &updatedFieldValue, "Updated field value after edit");
args.AddArgument("--maintain-custom-headers", vtksys::CommandLineArguments::MULTI_ARGUMENT, &customHeaderFieldsToMaintain, "List of custom header fields to pass through to output file.");
args.AddArgument("--frame-scalar-start", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &frameScalarStart, "Frame scalar field value starting index (Default: 0.0)");
args.AddArgument("--frame-scalar-increment", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &frameScalarIncrement, "Frame scalar field value increment (Default: 1.0)");
args.AddArgument("--frame-scalar-decimal-digits", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &frameScalarDecimalDigits, "Number of digits saved for frame scalar field value into sequence file (Default: 5)");
args.AddArgument("--frame-transform-start", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &strFrameTransformStart, "Frame transform field starting 4x4 transform matrix (Default: identity)");
args.AddArgument("--frame-transform-increment", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &strFrameTransformIncrement, "Frame transform increment 4x4 transform matrix (Default: identity)");
args.AddArgument("--frame-transform-index-field-name", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &strFrameTransformIndexFieldName, "If specified then increment is applied as many times as the value of this field");
args.AddArgument("--update-reference-transform", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &strUpdatedReferenceTransformName, "Set the reference transform name to update old files by changing all ToolToReference transforms to ToolToTracker transform.");
args.AddArgument("--use-compression", vtksys::CommandLineArguments::NO_ARGUMENT, &useCompression, "Compress sequence file images.");
args.AddArgument("--increment-timestamps", vtksys::CommandLineArguments::NO_ARGUMENT, &incrementTimestamps, "Increment timestamps in the order of the input-file-names");
args.AddArgument("--add-transform", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &transformNamesToAdd, "Name of the transform to add to each frame (e.g., StylusTipToTracker); multiple transforms can be added separated by a comma (e.g., StylusTipToReference,ProbeToReference)");
args.AddArgument("--config-file", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &deviceSetConfigurationFileName, "Used device set configuration file path and name");
// Clip and transform arguments
args.AddArgument("--rect-origin", vtksys::CommandLineArguments::MULTI_ARGUMENT, &rectOriginPix, "Fill or crop rectangle top-left corner position in MF coordinate frame, in pixels, separated by space (e.g., --rect-origin 12 34).");
args.AddArgument("--rect-size", vtksys::CommandLineArguments::MULTI_ARGUMENT, &rectSizePix, "Fill or crop rectangle size in MF coordinate frame, in pixels, separated by space (e.g., --rect-size 56 78).");
args.AddArgument("--flipX", vtksys::CommandLineArguments::NO_ARGUMENT, &flipX, "Flip image along X axis.");
args.AddArgument("--flipY", vtksys::CommandLineArguments::NO_ARGUMENT, &flipY, "Flip image along Y axis.");
args.AddArgument("--flipZ", vtksys::CommandLineArguments::NO_ARGUMENT, &flipZ, "Flip image along Z axis.");
args.AddArgument("--fill-gray-level", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &fillGrayLevel, "Rectangle fill gray level. 0 = black, 255 = white. (Default: 0)");
if (!args.Parse())
{
std::cerr << "Problem parsing arguments" << std::endl;
std::cout << "Help: " << args.GetHelp() << std::endl;
exit(EXIT_FAILURE);
}
///////////////////////////////////////////////////////////////////
if (argc == 1 || printHelp)
{
std::cout << args.GetHelp() << std::endl;
std::cout << std::endl << "Operations: " << std::endl << std::endl;
std::cout << "- UPDATE_FRAME_FIELD_NAME: update per-frame field names for each frame. If field does not exist then it is added." << std::endl;
std::cout << " Requires --field-name and --updated-field-name." << std::endl;
std::cout << "- UPDATE_FRAME_FIELD_VALUE: update per-frame field values for each frame, if not exists add it." << std::endl;
std::cout << " Uses --field-name, --updated-field-name, --updated-field-value, --frame-scalar-*, --frame-transform-*" << std::endl;
std::cout << "- DELETE_FRAME_FIELD: delete per-frame field (field values specified for each frame)." << std::endl;
std::cout << " Requires --field-name." << std::endl;
std::cout << "- UPDATE_FIELD_NAME: update field name, if not exists add it." << std::endl;
std::cout << " Requires --field-name and --updated-field-name." << std::endl;
std::cout << "- UPDATE_FIELD_VALUE: update field value, if not exists add it." << std::endl;
std::cout << " Requires --field-name and --updated-field-value." << std::endl;
std::cout << "- DELETE_FIELD: delete field with name specified." << std::endl;
std::cout << " Requires --field-name." << std::endl;
std::cout << "- ADD_TRANSFORM: add specified transform." << std::endl;
std::cout << " Requires --add-transform." << std::endl;
std::cout << "- TRIM: Trim sequence file." << std::endl;
std::cout << " Requires --first-frame-index and --last-frame-index." << std::endl;
std::cout << "- DECIMATE: Keep every N-th frame of the sequence file." << std::endl;
std::cout << " Requires --decimation-factor." << std::endl;
std::cout << "- APPEND: Append multiple sequence files (one after the other)." << std::endl;
std::cout << " Set input files with the --source-seq-files parameter." << std::endl;
std::cout << "- MIX: Merge fields stored in multiple sequence files." << std::endl;
std::cout << " Timepoints are defined by the first sequence. Image data is taken from the first sequence." << std::endl;
std::cout << " No interpolation is performed, fields are copied from the frame with the closest timestamp." << std::endl;
std::cout << " Set input files with the --source-seq-files parameter." << std::endl;
std::cout << "- FILL_IMAGE_RECTANGLE: Fill a rectangle in the image (useful for removing patient data from sequences)." << std::endl;
std::cout << " Requires --rect-origin, --rect-size, and --fill-gray-level. E.g., --rect-origin 12 34 --rect-size 56 78)" << std::endl;
std::cout << "- CROP: Crop a rectangle in the image (useful for cropping b-mode image from the data obtained via frame-grabber)." << std::endl;
std::cout << " Requires --rect-origin and --rect-size. (e.g., --rect-size 56 78). Optional: --flip*." << std::endl;
std::cout << "- REMOVE_IMAGE_DATA: Remove image data from a meta file that has both image and tracker data, and keep only the tracker data." << std::endl;
return EXIT_SUCCESS;
}
vtkPlusLogger::Instance()->SetLogLevel(verboseLevel);
// Check command line arguments
if (inputFileName.empty() && inputFileNames.empty())
{
LOG_ERROR("At least one input file name is mandantory!");
return EXIT_FAILURE;
}
if (outputFileName.empty())
{
LOG_ERROR("Please set output file name!");
return EXIT_FAILURE;
}
std::string fileExtension = vtksys::SystemTools::GetFilenameLastExtension(inputFileName);
bool headerOnlyUpdatePossible = (inputFileName == outputFileName) // file overwrite requested
&& (igsioCommon::IsEqualInsensitive(fileExtension, ".mhd") || igsioCommon::IsEqualInsensitive(fileExtension, ".nhdr"))
&& !useCompression; // hard to carry over compressed data size
bool headerOnlyOperation = false; // false by default
// Set operation
if (strOperation.empty())
{
operation = NO_OPERATION;
LOG_INFO("No modification operation has been specified (specify --operation parameter to change the input sequence).");
headerOnlyOperation = true;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "UPDATE_FRAME_FIELD_NAME"))
{
operation = UPDATE_FRAME_FIELD_NAME;
headerOnlyOperation = true;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "UPDATE_FRAME_FIELD_VALUE"))
{
operation = UPDATE_FRAME_FIELD_VALUE;
headerOnlyOperation = true;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "DELETE_FRAME_FIELD"))
{
operation = DELETE_FRAME_FIELD;
headerOnlyOperation = true;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "UPDATE_FIELD_NAME"))
{
operation = UPDATE_FIELD_NAME;
headerOnlyOperation = true;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "UPDATE_FIELD_VALUE"))
{
operation = UPDATE_FIELD_VALUE;
headerOnlyOperation = true;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "DELETE_FIELD"))
{
operation = DELETE_FIELD;
headerOnlyOperation = true;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "ADD_TRANSFORM"))
{
operation = ADD_TRANSFORM;
headerOnlyOperation = true;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "TRIM"))
{
operation = TRIM;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "DECIMATE"))
{
operation = DECIMATE;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "APPEND"))
{
operation = APPEND;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "MERGE"))
{
LOG_WARNING("MERGE operation name is deprecated. Use APPEND instead.")
operation = APPEND;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "MIX"))
{
operation = MIX;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "FILL_IMAGE_RECTANGLE"))
{
operation = FILL_IMAGE_RECTANGLE;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "CROP"))
{
if (rectOriginPix.size() != 2 && rectOriginPix.size() != 3 &&
rectSizePix.size() != 2 && rectSizePix.size() != 3)
{
LOG_ERROR("--rect-origin and --rect-size must be of the form --rect-origin X Y <Z> and --rect-size I J <K>")
return EXIT_FAILURE;
}
operation = CROP;
}
else if (igsioCommon::IsEqualInsensitive(strOperation, "REMOVE_IMAGE_DATA"))
{
operation = REMOVE_IMAGE_DATA;
}
else
{
LOG_ERROR("Invalid operation selected: " << strOperation);
return EXIT_FAILURE;
}
// Convert strings transforms to vtkMatrix
if (ConvertStringToMatrix(strFrameTransformStart, frameTransformStart) != PLUS_SUCCESS)
{
LOG_ERROR("String to matrix conversion failed for transform start matrix!");
return EXIT_FAILURE;
}
if (ConvertStringToMatrix(strFrameTransformIncrement, frameTransformIncrement) != PLUS_SUCCESS)
{
LOG_ERROR("String to matrix conversion failed for transform increment matrix!");
return EXIT_FAILURE;
}
///////////////////////////////////////////////////////////////////
// Read input files
vtkSmartPointer<vtkIGSIOTrackedFrameList> trackedFrameList = vtkSmartPointer<vtkIGSIOTrackedFrameList>::New();
if (!inputFileName.empty())
{
// Insert file name to the beginning of the list
inputFileNames.insert(inputFileNames.begin(), inputFileName);
}
// Multiple input files are appended unless sequences are mixed
PlusStatus status = PLUS_SUCCESS;
if (operation == MIX)
{
status = MixTrackedFrameLists(trackedFrameList, inputFileNames);
}
else
{
status = AppendTrackedFrameLists(trackedFrameList, inputFileNames, incrementTimestamps, customHeaderFieldsToMaintain);
}
if (status == PLUS_FAIL)
{
return EXIT_FAILURE;
}
///////////////////////////////////////////////////////////////////
// Make the operation
switch (operation)
{
case NO_OPERATION:
case APPEND:
case MIX:
{
// No need to do anything just save into output file
}
break;
case TRIM:
{
if (firstFrameIndex < 0)
{
firstFrameIndex = 0;
}
if (lastFrameIndex < 0)
{
lastFrameIndex = 0;
}
unsigned int firstFrameIndexUint = static_cast<unsigned int>(firstFrameIndex);
unsigned int lastFrameIndexUint = static_cast<unsigned int>(lastFrameIndex);
if (TrimSequenceFile(trackedFrameList, firstFrameIndexUint, lastFrameIndexUint) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to trim sequence file");
return EXIT_FAILURE;
}
}
break;
case DECIMATE:
{
if (DecimateSequenceFile(trackedFrameList, decimationFactor) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to decimate sequence file");
return EXIT_FAILURE;
}
}
break;
case UPDATE_FRAME_FIELD_NAME:
{
FrameFieldUpdate fieldUpdate;
fieldUpdate.TrackedFrameList = trackedFrameList;
fieldUpdate.FieldName = fieldName;
fieldUpdate.UpdatedFieldName = updatedFieldName;
if (UpdateFrameFieldValue(fieldUpdate) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to update frame field name '" << fieldName << "' to '" << updatedFieldName << "'");
return EXIT_FAILURE;
}
}
break;
case UPDATE_FRAME_FIELD_VALUE:
{
FrameFieldUpdate fieldUpdate;
fieldUpdate.TrackedFrameList = trackedFrameList;
fieldUpdate.FieldName = fieldName;
fieldUpdate.UpdatedFieldName = updatedFieldName;
fieldUpdate.UpdatedFieldValue = updatedFieldValue;
fieldUpdate.FrameScalarDecimalDigits = frameScalarDecimalDigits;
fieldUpdate.FrameScalarIncrement = frameScalarIncrement;
fieldUpdate.FrameScalarStart = frameScalarStart;
fieldUpdate.FrameTransformStart = frameTransformStart;
fieldUpdate.FrameTransformIncrement = frameTransformIncrement;
fieldUpdate.FrameTransformIndexFieldName = strFrameTransformIndexFieldName;
if (UpdateFrameFieldValue(fieldUpdate) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to update frame field value");
return EXIT_FAILURE;
}
}
break;
case DELETE_FRAME_FIELD:
{
if (DeleteFrameField(trackedFrameList, fieldName) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to delete frame field");
return EXIT_FAILURE;
}
}
break;
case DELETE_FIELD:
{
// Delete field
LOG_INFO("Delete field: " << fieldName);
if (trackedFrameList->SetCustomString(fieldName.c_str(), NULL) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to delete field: " << fieldName);
return EXIT_FAILURE;
}
}
break;
case UPDATE_FIELD_NAME:
{
// Update field name
LOG_INFO("Update field name '" << fieldName << "' to '" << updatedFieldName << "'");
const char* fieldValue = trackedFrameList->GetCustomString(fieldName.c_str());
if (fieldValue != NULL)
{
// Delete field
if (trackedFrameList->SetCustomString(fieldName.c_str(), NULL) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to delete field: " << fieldName);
return EXIT_FAILURE;
}
// Add new field
if (trackedFrameList->SetCustomString(updatedFieldName.c_str(), fieldValue) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to update field '" << updatedFieldName << "' with value '" << fieldValue << "'");
return EXIT_FAILURE;
}
}
}
break;
case UPDATE_FIELD_VALUE:
{
// Update field value
LOG_INFO("Update field '" << fieldName << "' with value '" << updatedFieldValue << "'");
if (trackedFrameList->SetCustomString(fieldName.c_str(), updatedFieldValue.c_str()) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to update field '" << fieldName << "' with value '" << updatedFieldValue << "'");
return EXIT_FAILURE;
}
}
break;
case ADD_TRANSFORM:
{
// Add transform
LOG_INFO("Add transform '" << transformNamesToAdd << "' using device set configuration file '" << deviceSetConfigurationFileName << "'");
std::vector<std::string> transformNamesList;
igsioCommon::SplitStringIntoTokens(transformNamesToAdd, ',', transformNamesList);
if (AddTransform(trackedFrameList, transformNamesList, deviceSetConfigurationFileName) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to add transform '" << transformNamesToAdd << "' using device set configuration file '" << deviceSetConfigurationFileName << "'");
return EXIT_FAILURE;
}
}
break;
case FILL_IMAGE_RECTANGLE:
{
if (rectOriginPix.size() != 2 || rectSizePix.size() != 2)
{
LOG_ERROR("Incorrect size of vector for rectangle origin or size. Aborting.");
return PLUS_FAIL;
}
if (rectOriginPix[0] < 0 || rectOriginPix[1] < 0 || rectSizePix[0] < 0 || rectSizePix[1] < 0)
{
LOG_ERROR("Negative value for rectangle origin or size entered. Aborting.");
return PLUS_FAIL;
}
std::vector<unsigned int> rectOriginPixUint(rectOriginPix.begin(), rectOriginPix.end());
std::vector<unsigned int> rectSizePixUint(rectSizePix.begin(), rectSizePix.end());
// Fill a rectangular region in the image with a solid color
if (FillRectangle(trackedFrameList, rectOriginPixUint, rectSizePixUint, fillGrayLevel) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to fill rectangle");
return EXIT_FAILURE;
}
}
break;
case CROP:
{
// Crop a rectangular region from the image
igsioVideoFrame::FlipInfoType flipInfo;
flipInfo.hFlip = flipX;
flipInfo.vFlip = flipY;
flipInfo.eFlip = flipZ;
if (CropRectangle(trackedFrameList, flipInfo, rectOriginPix, rectSizePix) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to fill rectangle");
return EXIT_FAILURE;
}
}
break;
case REMOVE_IMAGE_DATA:
// No processing is needed, image data is removed when writing the output
break;
default:
{
LOG_WARNING("Unknown operation is specified: " << strOperation);
return EXIT_FAILURE;
}
}
//////////////////////////////////////////////////////////////////
// Convert files to the new file format
if (!strUpdatedReferenceTransformName.empty())
{
igsioTransformName referenceTransformName;
if (referenceTransformName.SetTransformName(strUpdatedReferenceTransformName.c_str()) != PLUS_SUCCESS)
{
LOG_ERROR("Reference transform name is invalid: " << strUpdatedReferenceTransformName);
return EXIT_FAILURE;
}
for (unsigned int i = 0; i < trackedFrameList->GetNumberOfTrackedFrames(); ++i)
{
igsioTrackedFrame* trackedFrame = trackedFrameList->GetTrackedFrame(i);
vtkSmartPointer<vtkMatrix4x4> referenceToTrackerMatrix = vtkSmartPointer<vtkMatrix4x4>::New();
if (trackedFrame->GetFrameTransform(referenceTransformName, referenceToTrackerMatrix) != PLUS_SUCCESS)
{
LOG_WARNING("Couldn't get reference transform with name: " << strUpdatedReferenceTransformName);
continue;
}
std::vector<igsioTransformName> transformNameList;
trackedFrame->GetFrameTransformNameList(transformNameList);
vtkSmartPointer<vtkTransform> toolToTrackerTransform = vtkSmartPointer<vtkTransform>::New();
vtkSmartPointer<vtkMatrix4x4> toolToReferenceMatrix = vtkSmartPointer<vtkMatrix4x4>::New();
for (unsigned int n = 0; n < transformNameList.size(); ++n)
{
// No need to change the reference transform
if (transformNameList[n] == referenceTransformName)
{
continue;
}
ToolStatus status = TOOL_INVALID;
if (trackedFrame->GetFrameTransform(transformNameList[n], toolToReferenceMatrix) != PLUS_SUCCESS)
{
std::string strTransformName;
transformNameList[i].GetTransformName(strTransformName);
LOG_ERROR("Failed to get frame transform: " << strTransformName);
continue;
}
if (trackedFrame->GetFrameTransformStatus(transformNameList[n], status) != PLUS_SUCCESS)
{
std::string strTransformName;
transformNameList[i].GetTransformName(strTransformName);
LOG_ERROR("Failed to get frame transform status: " << strTransformName);
continue;
}
// Compute ToolToTracker transform from ToolToReference
toolToTrackerTransform->Identity();
toolToTrackerTransform->Concatenate(referenceToTrackerMatrix);
toolToTrackerTransform->Concatenate(toolToReferenceMatrix);
// Update the name to ToolToTracker
igsioTransformName toolToTracker(transformNameList[n].From().c_str(), "Tracker");
// Set the new custom transform
if (trackedFrame->SetFrameTransform(toolToTracker, toolToTrackerTransform->GetMatrix()) != PLUS_SUCCESS)
{
std::string strTransformName;
transformNameList[i].GetTransformName(strTransformName);
LOG_ERROR("Failed to set frame transform: " << strTransformName);
continue;
}
// Use the same status as it was before
if (trackedFrame->SetFrameTransformStatus(toolToTracker, status) != PLUS_SUCCESS)
{
std::string strTransformName;
transformNameList[i].GetTransformName(strTransformName);
LOG_ERROR("Failed to set frame transform status: " << strTransformName);
continue;
}
// Delete old transform and status fields
std::string oldTransformName, oldTransformStatus;
transformNameList[n].GetTransformName(oldTransformName);
// Append Transform to the end of the transform name
vtksys::RegularExpression isTransform("Transform$");
if (!isTransform.find(oldTransformName))
{
oldTransformName.append("Transform");
}
oldTransformStatus = oldTransformName;
oldTransformStatus.append("Status");
trackedFrame->DeleteFrameField(oldTransformName.c_str());
trackedFrame->DeleteFrameField(oldTransformStatus.c_str());
}
}
}
///////////////////////////////////////////////////////////////////
// Save output file to file
LOG_INFO("Save output sequence file to: " << outputFileName);
if (vtkPlusSequenceIO::Write(outputFileName, trackedFrameList, trackedFrameList->GetImageOrientation(),
useCompression, operation == REMOVE_IMAGE_DATA, headerOnlyUpdatePossible && headerOnlyOperation) != PLUS_SUCCESS)
{
LOG_ERROR("Couldn't write sequence file: " << outputFileName);
return EXIT_FAILURE;
}
LOG_INFO("Sequence file editing was successful!");
return EXIT_SUCCESS;
}
//-------------------------------------------------------
PlusStatus TrimSequenceFile(vtkIGSIOTrackedFrameList* aTrackedFrameList, unsigned int aFirstFrameIndex, unsigned int aLastFrameIndex)
{
LOG_INFO("Trim sequence file from frame #: " << aFirstFrameIndex << " to frame #" << aLastFrameIndex);
if (aLastFrameIndex >= aTrackedFrameList->GetNumberOfTrackedFrames() || aFirstFrameIndex > aLastFrameIndex)
{
LOG_ERROR("Invalid input range: (" << aFirstFrameIndex << ", " << aLastFrameIndex << ")" << " Permitted range within (0, " << aTrackedFrameList->GetNumberOfTrackedFrames() - 1 << ")");
return PLUS_FAIL;
}
if (aLastFrameIndex != aTrackedFrameList->GetNumberOfTrackedFrames() - 1)
{
aTrackedFrameList->RemoveTrackedFrameRange(aLastFrameIndex + 1, aTrackedFrameList->GetNumberOfTrackedFrames() - 1);
}
if (aFirstFrameIndex != 0)
{
aTrackedFrameList->RemoveTrackedFrameRange(0, aFirstFrameIndex - 1);
}
return PLUS_SUCCESS;
}
//-------------------------------------------------------
PlusStatus DecimateSequenceFile(vtkIGSIOTrackedFrameList* aTrackedFrameList, unsigned int decimationFactor)
{
LOG_INFO("Decimate sequence file: keep 1 frame out of every " << decimationFactor << " frames");
if (decimationFactor < 2)
{
LOG_ERROR("Invalid decimation factor: " << decimationFactor << ". It must be an integer larger or equal than 2.");
return PLUS_FAIL;
}
for (unsigned int i = 0; i < aTrackedFrameList->GetNumberOfTrackedFrames() - 1; i++)
{
unsigned int removeFirstFrameIndex = i + 1;
unsigned int removeLastFrameIndex = i + decimationFactor - 1;
if (removeLastFrameIndex >= aTrackedFrameList->GetNumberOfTrackedFrames())
{
removeLastFrameIndex = aTrackedFrameList->GetNumberOfTrackedFrames() - 1;
if (removeLastFrameIndex < removeFirstFrameIndex)
{
removeLastFrameIndex = removeFirstFrameIndex;
}
}
aTrackedFrameList->RemoveTrackedFrameRange(removeFirstFrameIndex, removeLastFrameIndex);
}
return PLUS_SUCCESS;
}
//-------------------------------------------------------
PlusStatus DeleteFrameField(vtkIGSIOTrackedFrameList* trackedFrameList, std::string fieldName)
{
if (trackedFrameList == NULL)
{
LOG_ERROR("Tracked frame list is NULL!");
return PLUS_FAIL;
}
if (fieldName.empty())
{
LOG_ERROR("Field name is empty!");
return PLUS_FAIL;
}
LOG_INFO("Delete frame field: " << fieldName);
int numberOfErrors(0);
for (unsigned int i = 0; i < trackedFrameList->GetNumberOfTrackedFrames(); ++i)
{
igsioTrackedFrame* trackedFrame = trackedFrameList->GetTrackedFrame(i);
/////////////////////////////////
// Delete field name
std::string fieldValue = trackedFrame->GetFrameField(fieldName);
if (!fieldValue.empty() && trackedFrame->DeleteFrameField(fieldName) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to delete frame field '" << fieldName << "' for frame #" << i);
numberOfErrors++;
}
}
return (numberOfErrors == 0 ? PLUS_SUCCESS : PLUS_FAIL);
}
//-------------------------------------------------------
PlusStatus UpdateFrameFieldValue(FrameFieldUpdate& fieldUpdate)
{
LOG_INFO("Update frame field");
int numberOfErrors(0);
// Set the start scalar value
double scalarVariable = fieldUpdate.FrameScalarStart;
// Set the start transform matrix
vtkSmartPointer<vtkTransform> frameTransform = vtkSmartPointer<vtkTransform>::New();
if (fieldUpdate.FrameTransformStart != NULL)
{
frameTransform->SetMatrix(fieldUpdate.FrameTransformStart);
}
for (unsigned int i = 0; i < fieldUpdate.TrackedFrameList->GetNumberOfTrackedFrames(); ++i)
{
igsioTrackedFrame* trackedFrame = fieldUpdate.TrackedFrameList->GetTrackedFrame(i);
/////////////////////////////////
// Update field name
if (!fieldUpdate.FieldName.empty() && !fieldUpdate.UpdatedFieldName.empty())
{
std::string fieldValue = trackedFrame->GetFrameField(fieldUpdate.FieldName);
if (!fieldValue.empty())
{
std::string copyOfFieldValue(fieldValue);
trackedFrame->DeleteFrameField(fieldUpdate.FieldName);
trackedFrame->SetFrameField(fieldUpdate.UpdatedFieldName, copyOfFieldValue);
}
}
std::string fieldName = fieldUpdate.FieldName;
if (!fieldUpdate.UpdatedFieldName.empty())
{
fieldName = fieldUpdate.UpdatedFieldName;
}
/////////////////////////////////
// Update field value
if (!fieldName.empty() && !fieldUpdate.UpdatedFieldValue.empty())
{
if (igsioCommon::IsEqualInsensitive(fieldUpdate.UpdatedFieldValue, FIELD_VALUE_FRAME_SCALAR))
{
// Update it as a scalar variable
std::ostringstream fieldValue;
fieldValue << std::fixed << std::setprecision(fieldUpdate.FrameScalarDecimalDigits) << scalarVariable;
trackedFrame->SetFrameField(fieldName.c_str(), fieldValue.str().c_str());
scalarVariable += fieldUpdate.FrameScalarIncrement;
}
else if (igsioCommon::IsEqualInsensitive(fieldUpdate.UpdatedFieldValue, FIELD_VALUE_FRAME_TRANSFORM))
{
// Update it as a transform variable
double transformMatrix[16] = { 0 };
if (fieldUpdate.FrameTransformIndexFieldName.empty())
{
vtkMatrix4x4::DeepCopy(transformMatrix, frameTransform->GetMatrix());
}
else
{
std::string frameIndexStr = trackedFrame->GetFrameField(fieldUpdate.FrameTransformIndexFieldName);
int frameIndex = 0;
if (igsioCommon::StringToNumber<int>(frameIndexStr, frameIndex) != PLUS_SUCCESS)
{
LOG_ERROR("Cannot retrieve frame index from value " << frameIndexStr);
}
vtkSmartPointer<vtkMatrix4x4> cumulativeTransform = vtkSmartPointer<vtkMatrix4x4>::New();
cumulativeTransform->DeepCopy(fieldUpdate.FrameTransformStart);
for (int i = 0; i < frameIndex; i++)
{
vtkMatrix4x4::Multiply4x4(fieldUpdate.FrameTransformIncrement, cumulativeTransform, cumulativeTransform);
}
vtkMatrix4x4::DeepCopy(transformMatrix, cumulativeTransform);
}
std::ostringstream strTransform;
strTransform << std::fixed << std::setprecision(fieldUpdate.FrameScalarDecimalDigits)
<< transformMatrix[0] << " " << transformMatrix[1] << " " << transformMatrix[2] << " " << transformMatrix[3] << " "
<< transformMatrix[4] << " " << transformMatrix[5] << " " << transformMatrix[6] << " " << transformMatrix[7] << " "
<< transformMatrix[8] << " " << transformMatrix[9] << " " << transformMatrix[10] << " " << transformMatrix[11] << " "
<< transformMatrix[12] << " " << transformMatrix[13] << " " << transformMatrix[14] << " " << transformMatrix[15] << " ";
trackedFrame->SetFrameField(fieldName.c_str(), strTransform.str().c_str());
if (fieldUpdate.FrameTransformIndexFieldName.empty())
{
frameTransform->Concatenate(fieldUpdate.FrameTransformIncrement);
}
}
else // Update only as a string value
{
trackedFrame->SetFrameField(fieldName.c_str(), fieldUpdate.UpdatedFieldValue.c_str());
}
}
}
return (numberOfErrors == 0 ? PLUS_SUCCESS : PLUS_FAIL);
}
//-------------------------------------------------------
PlusStatus ConvertStringToMatrix(std::string& strMatrix, vtkMatrix4x4* matrix)
{