Package qupath.ext.biop.cellpose
Class OpCreators.ImageNormalizationBuilder
- java.lang.Object
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- qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder
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- Enclosing class:
- OpCreators
public static class OpCreators.ImageNormalizationBuilder extends java.lang.Object
Builder for aOpCreators.TileOpCreator
that can be used for image preprocessing using min/max percentiles or zero-mean-unit-variance normalization.
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Constructor Summary
Constructors Constructor Description ImageNormalizationBuilder()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description OpCreators.TileOpCreator
build()
Build aOpCreators.TileOpCreator
according to the builder's parameters.OpCreators.ImageNormalizationBuilder
downsample(double downsample)
Specify the downsample factor to use when calculating the normalization.OpCreators.ImageNormalizationBuilder
eps(double eps)
Error constant used for numerical stability and avoid dividing by zero.OpCreators.ImageNormalizationBuilder
maxDimension(int maxDimension)
The maximum width or height, which is used to calculate a downsample factor for the image ifdownsample(double)
is not specified.OpCreators.ImageNormalizationBuilder
percentiles(double minPercentile, double maxPercentile)
Specify min and max percentiles to calculate normalization values.OpCreators.ImageNormalizationBuilder
perChannel(boolean perChannel)
Compute the normalization values separately per channel; if false, values are computed jointly across channels.OpCreators.ImageNormalizationBuilder
useMask(boolean useMask)
Optionally use any ROI mask provided for the calculation.OpCreators.ImageNormalizationBuilder
zeroMeanUnitVariance()
Normalize for zero mean and unit variance.OpCreators.ImageNormalizationBuilder
zeroMeanUnitVariance(boolean doZeroMeanUnitVariance)
Optionally normalize for zero mean and unit variance.
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Method Detail
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percentiles
public OpCreators.ImageNormalizationBuilder percentiles(double minPercentile, double maxPercentile)
Specify min and max percentiles to calculate normalization values. SeeImageOps.Normalize.percentile(double, double)
.- Parameters:
minPercentile
-maxPercentile
-- Returns:
- this builder
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eps
public OpCreators.ImageNormalizationBuilder eps(double eps)
Error constant used for numerical stability and avoid dividing by zero. Default is 1e-6;- Parameters:
eps
-- Returns:
- this builder
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perChannel
public OpCreators.ImageNormalizationBuilder perChannel(boolean perChannel)
Compute the normalization values separately per channel; if false, values are computed jointly across channels.- Parameters:
perChannel
-- Returns:
- this builder
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downsample
public OpCreators.ImageNormalizationBuilder downsample(double downsample)
Specify the downsample factor to use when calculating the normalization. If this is not provided, thenmaxDimension(int)
will be used to calculate a downsample value automatically.The downsample should be ≥ 1.0 and high enough to ensure that the entire image can be fit in memory. A downsample of 1.0 for a whole slide image will probably fail due to memory or array size limits.
- Parameters:
downsample
-- Returns:
- this builder
see
maxDimension(int)
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maxDimension
public OpCreators.ImageNormalizationBuilder maxDimension(int maxDimension)
The maximum width or height, which is used to calculate a downsample factor for the image ifdownsample(double)
is not specified.The current default value is 2048;
- Parameters:
maxDimension
-- Returns:
- this builder
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useMask
public OpCreators.ImageNormalizationBuilder useMask(boolean useMask)
Optionally use any ROI mask provided for the calculation. This can restrict the region that is considered.- Parameters:
useMask
-- Returns:
- this builder
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zeroMeanUnitVariance
public OpCreators.ImageNormalizationBuilder zeroMeanUnitVariance()
Normalize for zero mean and unit variance. This is an alternative to usingpercentiles(double, double)
.- Returns:
- this builder
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zeroMeanUnitVariance
public OpCreators.ImageNormalizationBuilder zeroMeanUnitVariance(boolean doZeroMeanUnitVariance)
Optionally normalize for zero mean and unit variance. This is an alternative to usingpercentiles(double, double)
.- Parameters:
doZeroMeanUnitVariance
-- Returns:
- this builder
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build
public OpCreators.TileOpCreator build()
Build aOpCreators.TileOpCreator
according to the builder's parameters.- Returns:
- this builder
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