Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ENH: Expose gradient filter option for metrics. #1351

Merged
merged 1 commit into from
May 4, 2022
Merged

ENH: Expose gradient filter option for metrics. #1351

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
30 changes: 21 additions & 9 deletions Examples/antsMotionCorr.cxx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1056,6 +1056,12 @@ ants_motion(itk::ants::CommandLineParser * parser)
metricSamplingStrategy = AffineRegistrationType::MetricSamplingStrategyEnum::REGULAR;
}

bool useGradientFilter = false;
if (metricOption->GetFunction(0)->GetNumberOfParameters() > 6)
{
useGradientFilter = parser->Convert<bool>(metricOption->GetFunction(currentStage)->GetParameter(6));
}

if (std::strcmp(whichMetric.c_str(), "cc") == 0)
{
auto radiusOption = parser->Convert<unsigned int>(metricOption->GetFunction(currentStage)->GetParameter(3));
Expand All @@ -1071,8 +1077,8 @@ ants_motion(itk::ants::CommandLineParser * parser)
typename CorrelationMetricType::RadiusType radius;
radius.Fill(radiusOption);
correlationMetric->SetRadius(radius);
correlationMetric->SetUseMovingImageGradientFilter(false);
correlationMetric->SetUseFixedImageGradientFilter(false);
correlationMetric->SetUseMovingImageGradientFilter(useGradientFilter);
correlationMetric->SetUseFixedImageGradientFilter(useGradientFilter);

metric = correlationMetric;
}
Expand All @@ -1090,8 +1096,8 @@ ants_motion(itk::ants::CommandLineParser * parser)
typename MutualInformationMetricType::Pointer mutualInformationMetric = MutualInformationMetricType::New();
// mutualInformationMetric = mutualInformationMetric;
mutualInformationMetric->SetNumberOfHistogramBins(binOption);
mutualInformationMetric->SetUseMovingImageGradientFilter(false);
mutualInformationMetric->SetUseFixedImageGradientFilter(false);
mutualInformationMetric->SetUseMovingImageGradientFilter(useGradientFilter);
mutualInformationMetric->SetUseFixedImageGradientFilter(useGradientFilter);
metric = mutualInformationMetric;
}
else if (std::strcmp(whichMetric.c_str(), "demons") == 0)
Expand All @@ -1103,6 +1109,8 @@ ants_motion(itk::ants::CommandLineParser * parser)
}
using DemonsMetricType = itk::MeanSquaresImageToImageMetricv4<FixedImageType, FixedImageType>;
typename DemonsMetricType::Pointer demonsMetric = DemonsMetricType::New();
demonsMetric->SetUseMovingImageGradientFilter(useGradientFilter);
demonsMetric->SetUseFixedImageGradientFilter(useGradientFilter);
// demonsMetric = demonsMetric;
metric = demonsMetric;
}
Expand All @@ -1115,6 +1123,8 @@ ants_motion(itk::ants::CommandLineParser * parser)
}
using corrMetricType = itk::CorrelationImageToImageMetricv4<FixedImageType, FixedImageType>;
typename corrMetricType::Pointer corrMetric = corrMetricType::New();
corrMetric->SetUseMovingImageGradientFilter(useGradientFilter);
corrMetric->SetUseFixedImageGradientFilter(useGradientFilter);
metric = corrMetric;
if (verbose)
std::cout << " global corr metric set " << std::endl;
Expand Down Expand Up @@ -1835,24 +1845,26 @@ antsMotionCorrInitializeCommandLineOptions(itk::ants::CommandLineParser * parser
std::string("The fixed image should be a single time point (eg the average of the time series). ") +
std::string(
"By default, this image is not used, the fixed image for correction of each volume is the preceding volume ") +
std::string("in the time series. See below for the option to use a fixed reference image for all volumes. ");
std::string("in the time series. See below for the option to use a fixed reference image for all volumes. ") +
std::string("useGradientFilter specifies whether a smoothing") +
std::string("filter is applied when estimating the metric gradient.");

OptionType::Pointer option = OptionType::New();
option->SetLongName("metric");
option->SetShortName('m');
option->SetUsageOption(
0,
"CC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]");
"CC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>,<useGradientFilter=false>]");
option->SetUsageOption(1,
"MI[fixedImage,movingImage,metricWeight,numberOfBins,<samplingStrategy={Regular,Random}>,<"
"samplingPercentage=[0,1]>]");
"samplingPercentage=[0,1]>,<useGradientFilter=false>]");
option->SetUsageOption(2,

"Demons[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<"
"samplingPercentage=[0,1]>]");
"samplingPercentage=[0,1]>,<useGradientFilter=false>]");
option->SetUsageOption(
3,
"GC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]");
"GC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>,<useGradientFilter=false>]");
option->SetDescription(description);
parser->AddOption(option);
}
Expand Down