From b054849d208375cb40c70b0b6fefdc3ab2714aa7 Mon Sep 17 00:00:00 2001 From: haesleinhuepf Date: Mon, 13 Apr 2020 20:44:58 +0200 Subject: [PATCH] regenerated ops --- .../net/haesleinhuepf/clij2/CLIJ2Ops.java | 274 +++++++++--------- 1 file changed, 137 insertions(+), 137 deletions(-) diff --git a/src/main/java/net/haesleinhuepf/clij2/CLIJ2Ops.java b/src/main/java/net/haesleinhuepf/clij2/CLIJ2Ops.java index 0e834fd9..a3861f21 100644 --- a/src/main/java/net/haesleinhuepf/clij2/CLIJ2Ops.java +++ b/src/main/java/net/haesleinhuepf/clij2/CLIJ2Ops.java @@ -406,15 +406,15 @@ default boolean maskLabel(ClearCLBuffer arg1, ClearCLBuffer arg2, ClearCLBuffer /** * Takes two binary images A and B with marked spots and determines for each spot in image A the closest spot in image B. Afterwards, it saves the average shortest distances from image A to image B as 'mean_closest_spot_distance_A_B' and from image B to image A as 'mean_closest_spot_distance_B_A' to the results table. The distance between B and A is only determined if the `bidirectional` checkbox is checked. */ - default double meanClosestSpotDistance(ClearCLBuffer arg1, ClearCLBuffer arg2) { - return MeanClosestSpotDistance.meanClosestSpotDistance(getCLIJ2(), arg1, arg2); + default double[] meanClosestSpotDistance(ClearCLBuffer arg1, ClearCLBuffer arg2, boolean arg3) { + return MeanClosestSpotDistance.meanClosestSpotDistance(getCLIJ2(), arg1, arg2, arg3); } /** * Takes two binary images A and B with marked spots and determines for each spot in image A the closest spot in image B. Afterwards, it saves the average shortest distances from image A to image B as 'mean_closest_spot_distance_A_B' and from image B to image A as 'mean_closest_spot_distance_B_A' to the results table. The distance between B and A is only determined if the `bidirectional` checkbox is checked. */ - default double[] meanClosestSpotDistance(ClearCLBuffer arg1, ClearCLBuffer arg2, boolean arg3) { - return MeanClosestSpotDistance.meanClosestSpotDistance(getCLIJ2(), arg1, arg2, arg3); + default double meanClosestSpotDistance(ClearCLBuffer arg1, ClearCLBuffer arg2) { + return MeanClosestSpotDistance.meanClosestSpotDistance(getCLIJ2(), arg1, arg2); } @@ -478,15 +478,15 @@ default boolean paste(ClearCLImageInterface arg1, ClearCLImageInterface arg2, do /** * Pastes an image into another image at a given position. */ - default boolean paste(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { - return Paste3D.paste(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue(), new Double (arg5).intValue()); + default boolean paste3D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { + return Paste3D.paste3D(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue(), new Double (arg5).intValue()); } /** * Pastes an image into another image at a given position. */ - default boolean paste3D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { - return Paste3D.paste3D(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue(), new Double (arg5).intValue()); + default boolean paste(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { + return Paste3D.paste(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue(), new Double (arg5).intValue()); } @@ -873,15 +873,15 @@ default boolean notEqualConstant(ClearCLBuffer arg1, ClearCLBuffer arg2, double /** * Draws a box at a given start point with given size. All pixels other than in the box are untouched. Consider using clij.op.set(buffer, 0); in advance. */ - default boolean drawBox(ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8) { - return DrawBox.drawBox(getCLIJ2(), arg1, new Double (arg2).floatValue(), new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), new Double (arg6).floatValue(), new Double (arg7).floatValue(), new Double (arg8).floatValue()); + default boolean drawBox(ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5) { + return DrawBox.drawBox(getCLIJ2(), arg1, new Double (arg2).floatValue(), new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue()); } /** * Draws a box at a given start point with given size. All pixels other than in the box are untouched. Consider using clij.op.set(buffer, 0); in advance. */ - default boolean drawBox(ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5) { - return DrawBox.drawBox(getCLIJ2(), arg1, new Double (arg2).floatValue(), new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue()); + default boolean drawBox(ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8) { + return DrawBox.drawBox(getCLIJ2(), arg1, new Double (arg2).floatValue(), new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), new Double (arg6).floatValue(), new Double (arg7).floatValue(), new Double (arg8).floatValue()); } /** @@ -914,8 +914,8 @@ default boolean drawLine(ClearCLImageInterface arg1, double arg2, double arg3, d /** * Draws a sphere around a given point with given radii in x, y and z (if 3D). All pixels other than in the sphere are untouched. Consider using clij.op.set(buffer, 0); in advance. */ - default boolean drawSphere(ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8) { - return DrawSphere.drawSphere(getCLIJ2(), arg1, new Double (arg2).floatValue(), new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), new Double (arg6).floatValue(), new Double (arg7).floatValue(), new Double (arg8).floatValue()); + default boolean drawSphere(ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5) { + return DrawSphere.drawSphere(getCLIJ2(), arg1, new Double (arg2).floatValue(), new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue()); } /** @@ -928,8 +928,8 @@ default boolean drawSphere(ClearCLImageInterface arg1, double arg2, double arg3, /** * Draws a sphere around a given point with given radii in x, y and z (if 3D). All pixels other than in the sphere are untouched. Consider using clij.op.set(buffer, 0); in advance. */ - default boolean drawSphere(ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5) { - return DrawSphere.drawSphere(getCLIJ2(), arg1, new Double (arg2).floatValue(), new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue()); + default boolean drawSphere(ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8) { + return DrawSphere.drawSphere(getCLIJ2(), arg1, new Double (arg2).floatValue(), new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), new Double (arg6).floatValue(), new Double (arg7).floatValue(), new Double (arg8).floatValue()); } /** @@ -1017,29 +1017,29 @@ default boolean nClosestPoints(ClearCLBuffer arg1, ClearCLBuffer arg2) { /** * Determines bounding box, area (in pixels/voxels), min, max and mean intensity of labelled objects in a label map and corresponding pixels in the original image.Instead of a label map, you can also use a binary image as a binary image is a label map with just one label. */ - default ResultsTable statisticsOfLabelledPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, ResultsTable arg3) { - return StatisticsOfLabelledPixels.statisticsOfLabelledPixels(getCLIJ2(), arg1, arg2, arg3); + default double[][] statisticsOfLabelledPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, int arg3, int arg4) { + return StatisticsOfLabelledPixels.statisticsOfLabelledPixels(getCLIJ2(), arg1, arg2, arg3, arg4); } /** * Determines bounding box, area (in pixels/voxels), min, max and mean intensity of labelled objects in a label map and corresponding pixels in the original image.Instead of a label map, you can also use a binary image as a binary image is a label map with just one label. */ - default double[] statisticsOfLabelledPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, int arg3) { + default ResultsTable statisticsOfLabelledPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, ResultsTable arg3) { return StatisticsOfLabelledPixels.statisticsOfLabelledPixels(getCLIJ2(), arg1, arg2, arg3); } /** * Determines bounding box, area (in pixels/voxels), min, max and mean intensity of labelled objects in a label map and corresponding pixels in the original image.Instead of a label map, you can also use a binary image as a binary image is a label map with just one label. */ - default double[][] statisticsOfLabelledPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, int arg3, int arg4) { - return StatisticsOfLabelledPixels.statisticsOfLabelledPixels(getCLIJ2(), arg1, arg2, arg3, arg4); + default double[][] statisticsOfLabelledPixels(ClearCLBuffer input, ClearCLBuffer labelmap) { + return StatisticsOfLabelledPixels.statisticsOfLabelledPixels(getCLIJ2(), input, labelmap); } /** * Determines bounding box, area (in pixels/voxels), min, max and mean intensity of labelled objects in a label map and corresponding pixels in the original image.Instead of a label map, you can also use a binary image as a binary image is a label map with just one label. */ - default double[][] statisticsOfLabelledPixels(ClearCLBuffer input, ClearCLBuffer labelmap) { - return StatisticsOfLabelledPixels.statisticsOfLabelledPixels(getCLIJ2(), input, labelmap); + default double[] statisticsOfLabelledPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, int arg3) { + return StatisticsOfLabelledPixels.statisticsOfLabelledPixels(getCLIJ2(), arg1, arg2, arg3); } @@ -1049,16 +1049,16 @@ default double[][] statisticsOfLabelledPixels(ClearCLBuffer input, ClearCLBuffer * Determines the variance of all pixels in an image. The value will be stored in a new row of ImageJs * Results table in the column 'Variance'. */ - default double varianceOfAllPixels(ClearCLBuffer source) { - return VarianceOfAllPixels.varianceOfAllPixels(getCLIJ2(), source); + default double varianceOfAllPixels(ClearCLImageInterface arg1, double arg2) { + return VarianceOfAllPixels.varianceOfAllPixels(getCLIJ2(), arg1, new Double (arg2).floatValue()); } /** * Determines the variance of all pixels in an image. The value will be stored in a new row of ImageJs * Results table in the column 'Variance'. */ - default double varianceOfAllPixels(ClearCLImageInterface arg1, double arg2) { - return VarianceOfAllPixels.varianceOfAllPixels(getCLIJ2(), arg1, new Double (arg2).floatValue()); + default double varianceOfAllPixels(ClearCLBuffer source) { + return VarianceOfAllPixels.varianceOfAllPixels(getCLIJ2(), source); } @@ -1068,16 +1068,16 @@ default double varianceOfAllPixels(ClearCLImageInterface arg1, double arg2) { * Determines the standard deviation of all pixels in an image. The value will be stored in a new row of ImageJs * Results table in the column 'Standard_deviation'. */ - default double standardDeviationOfAllPixels(ClearCLImageInterface source) { - return StandardDeviationOfAllPixels.standardDeviationOfAllPixels(getCLIJ2(), source); + default double standardDeviationOfAllPixels(ClearCLImageInterface arg1, double arg2) { + return StandardDeviationOfAllPixels.standardDeviationOfAllPixels(getCLIJ2(), arg1, new Double (arg2).floatValue()); } /** * Determines the standard deviation of all pixels in an image. The value will be stored in a new row of ImageJs * Results table in the column 'Standard_deviation'. */ - default double standardDeviationOfAllPixels(ClearCLImageInterface arg1, double arg2) { - return StandardDeviationOfAllPixels.standardDeviationOfAllPixels(getCLIJ2(), arg1, new Double (arg2).floatValue()); + default double standardDeviationOfAllPixels(ClearCLImageInterface source) { + return StandardDeviationOfAllPixels.standardDeviationOfAllPixels(getCLIJ2(), source); } @@ -1086,15 +1086,15 @@ default double standardDeviationOfAllPixels(ClearCLImageInterface arg1, double a /** * Determines the variance in an image, but only in pixels which have non-zero values in another binary mask image. The result is put in the results table as new column named 'Masked_variance'. */ - default double varianceOfMaskedPixels(ClearCLBuffer source, ClearCLBuffer mask) { - return VarianceOfMaskedPixels.varianceOfMaskedPixels(getCLIJ2(), source, mask); + default double varianceOfMaskedPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { + return VarianceOfMaskedPixels.varianceOfMaskedPixels(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue()); } /** * Determines the variance in an image, but only in pixels which have non-zero values in another binary mask image. The result is put in the results table as new column named 'Masked_variance'. */ - default double varianceOfMaskedPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { - return VarianceOfMaskedPixels.varianceOfMaskedPixels(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue()); + default double varianceOfMaskedPixels(ClearCLBuffer source, ClearCLBuffer mask) { + return VarianceOfMaskedPixels.varianceOfMaskedPixels(getCLIJ2(), source, mask); } @@ -1104,16 +1104,16 @@ default double varianceOfMaskedPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, do * Determines the standard deviation of all pixels in an image which have non-zero value in a corresponding mask image. The value will be stored in a new row of ImageJs * Results table in the column 'Masked_standard_deviation'. */ - default double standardDeviationOfMaskedPixels(ClearCLBuffer source, ClearCLBuffer mask) { - return StandardDeviationOfMaskedPixels.standardDeviationOfMaskedPixels(getCLIJ2(), source, mask); + default double standardDeviationOfMaskedPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { + return StandardDeviationOfMaskedPixels.standardDeviationOfMaskedPixels(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue()); } /** * Determines the standard deviation of all pixels in an image which have non-zero value in a corresponding mask image. The value will be stored in a new row of ImageJs * Results table in the column 'Masked_standard_deviation'. */ - default double standardDeviationOfMaskedPixels(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { - return StandardDeviationOfMaskedPixels.standardDeviationOfMaskedPixels(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue()); + default double standardDeviationOfMaskedPixels(ClearCLBuffer source, ClearCLBuffer mask) { + return StandardDeviationOfMaskedPixels.standardDeviationOfMaskedPixels(getCLIJ2(), source, mask); } @@ -1282,14 +1282,6 @@ default boolean replaceIntensities(ClearCLImageInterface arg1, ClearCLImageInter // net.haesleinhuepf.clij2.plugins.AverageDistanceOfNClosestPoints //---------------------------------------------------- - /** - * Determine the n point indices with shortest distance for all points in a distance matrix. - * This corresponds to the n row indices with minimum values for each column of the distance matrix. - */ - default boolean averageDistanceOfNClosestPoints(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { - return AverageDistanceOfNClosestPoints.averageDistanceOfNClosestPoints(getCLIJ2(), arg1, arg2, new Double (arg3).intValue()); - } - /** * */ @@ -1298,6 +1290,14 @@ default boolean averageDistanceOfClosestPoints(ClearCLBuffer arg1, ClearCLBuffer return AverageDistanceOfNClosestPoints.averageDistanceOfClosestPoints(getCLIJ2(), arg1, arg2, new Double (arg3).intValue()); } + /** + * Determine the n point indices with shortest distance for all points in a distance matrix. + * This corresponds to the n row indices with minimum values for each column of the distance matrix. + */ + default boolean averageDistanceOfNClosestPoints(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { + return AverageDistanceOfNClosestPoints.averageDistanceOfNClosestPoints(getCLIJ2(), arg1, arg2, new Double (arg3).intValue()); + } + // net.haesleinhuepf.clij2.plugins.TouchMatrixToMesh //---------------------------------------------------- @@ -1312,18 +1312,18 @@ default boolean touchMatrixToMesh(ClearCLBuffer arg1, ClearCLBuffer arg2, ClearC // net.haesleinhuepf.clij2.plugins.Resample //---------------------------------------------------- /** - * Resamples an image with given size factors using an affine transform. + * */ - @Deprecated - default boolean resample(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5, boolean arg6) { - return Resample.resample(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), arg6); + default boolean resample3D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5, boolean arg6) { + return Resample.resample3D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), arg6); } /** - * + * Resamples an image with given size factors using an affine transform. */ - default boolean resample3D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5, boolean arg6) { - return Resample.resample3D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), arg6); + @Deprecated + default boolean resample(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5, boolean arg6) { + return Resample.resample(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), arg6); } /** @@ -1359,8 +1359,8 @@ default boolean radialProjection(ClearCLBuffer arg1, ClearCLBuffer arg2, double * Computes a radial projection of an image stack. Starting point for the line is the center in any * X/Y-plane of a given input image stack. This operation is similar to ImageJs 'Radial Reslice' method but offers less flexibility. */ - default boolean resliceRadial(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8) { - return ResliceRadial.resliceRadial(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), new Double (arg6).floatValue(), new Double (arg7).floatValue(), new Double (arg8).floatValue()); + default boolean resliceRadial(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { + return ResliceRadial.resliceRadial(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue()); } /** @@ -1375,8 +1375,8 @@ default boolean resliceRadial(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg * Computes a radial projection of an image stack. Starting point for the line is the center in any * X/Y-plane of a given input image stack. This operation is similar to ImageJs 'Radial Reslice' method but offers less flexibility. */ - default boolean resliceRadial(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { - return ResliceRadial.resliceRadial(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue()); + default boolean resliceRadial(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8) { + return ResliceRadial.resliceRadial(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), new Double (arg6).floatValue(), new Double (arg7).floatValue(), new Double (arg8).floatValue()); } @@ -1608,18 +1608,18 @@ default ClearCLKernel minimumBox(ClearCLImageInterface arg1, ClearCLImageInterfa } /** - * + * Applies a minimum filter with kernel size 3x3 n times to an image iteratively. Odd iterations are done with box neighborhood, even iterations with a diamond. Thus, with n > 2, the filter shape is an octagon. The given number of iterations makes the filter result very similar to minimum sphere. Approximately:radius = iterations - 2 */ - @Deprecated - default ClearCLKernel minimumDiamond(ClearCLImageInterface arg1, ClearCLImageInterface arg2, ClearCLKernel arg3) { - return MinimumOctagon.minimumDiamond(getCLIJ2(), arg1, arg2, arg3); + default boolean minimumOctagon(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { + return MinimumOctagon.minimumOctagon(getCLIJ2(), arg1, arg2, new Double (arg3).intValue()); } /** - * Applies a minimum filter with kernel size 3x3 n times to an image iteratively. Odd iterations are done with box neighborhood, even iterations with a diamond. Thus, with n > 2, the filter shape is an octagon. The given number of iterations makes the filter result very similar to minimum sphere. Approximately:radius = iterations - 2 + * */ - default boolean minimumOctagon(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { - return MinimumOctagon.minimumOctagon(getCLIJ2(), arg1, arg2, new Double (arg3).intValue()); + @Deprecated + default ClearCLKernel minimumDiamond(ClearCLImageInterface arg1, ClearCLImageInterface arg2, ClearCLKernel arg3) { + return MinimumOctagon.minimumDiamond(getCLIJ2(), arg1, arg2, arg3); } @@ -1634,13 +1634,6 @@ default ClearCLKernel maximumBox(ClearCLImageInterface arg1, ClearCLImageInterfa return MaximumOctagon.maximumBox(getCLIJ2(), arg1, arg2, arg3); } - /** - * Applies a maximum filter with kernel size 3x3 n times to an image iteratively. Odd iterations are done with box neighborhood, even iterations with a diamond. Thus, with n > 2, the filter shape is an octagon. The given number of iterations makes the filter result very similar to minimum sphere. Approximately:radius = iterations - 2 - */ - default boolean maximumOctagon(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { - return MaximumOctagon.maximumOctagon(getCLIJ2(), arg1, arg2, new Double (arg3).intValue()); - } - /** * */ @@ -1649,6 +1642,13 @@ default ClearCLKernel maximumDiamond(ClearCLImageInterface arg1, ClearCLImageInt return MaximumOctagon.maximumDiamond(getCLIJ2(), arg1, arg2, arg3); } + /** + * Applies a maximum filter with kernel size 3x3 n times to an image iteratively. Odd iterations are done with box neighborhood, even iterations with a diamond. Thus, with n > 2, the filter shape is an octagon. The given number of iterations makes the filter result very similar to minimum sphere. Approximately:radius = iterations - 2 + */ + default boolean maximumOctagon(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { + return MaximumOctagon.maximumOctagon(getCLIJ2(), arg1, arg2, new Double (arg3).intValue()); + } + // net.haesleinhuepf.clij2.plugins.AddImages //---------------------------------------------------- @@ -1681,9 +1681,8 @@ default boolean addImagesWeighted(ClearCLImageInterface arg1, ClearCLImageInterf * * 
f(x, y) = x - y
*/ - @Deprecated - default boolean subtract(ClearCLImageInterface subtrahend, ClearCLImageInterface minuend, ClearCLImageInterface destination) { - return SubtractImages.subtract(getCLIJ2(), subtrahend, minuend, destination); + default boolean subtractImages(ClearCLImageInterface subtrahend, ClearCLImageInterface minuend, ClearCLImageInterface destination) { + return SubtractImages.subtractImages(getCLIJ2(), subtrahend, minuend, destination); } /** @@ -1691,8 +1690,9 @@ default boolean subtract(ClearCLImageInterface subtrahend, ClearCLImageInterface * * 
f(x, y) = x - y
*/ - default boolean subtractImages(ClearCLImageInterface subtrahend, ClearCLImageInterface minuend, ClearCLImageInterface destination) { - return SubtractImages.subtractImages(getCLIJ2(), subtrahend, minuend, destination); + @Deprecated + default boolean subtract(ClearCLImageInterface subtrahend, ClearCLImageInterface minuend, ClearCLImageInterface destination) { + return SubtractImages.subtract(getCLIJ2(), subtrahend, minuend, destination); } @@ -1736,8 +1736,8 @@ default boolean affineTransform2D(ClearCLImage arg1, ClearCLImageInterface arg2, * Example transform: * transform = "center scale=2 rotate=45 -center"; */ - default boolean affineTransform2D(ClearCLBuffer source, ClearCLImageInterface destination, String transform) { - return AffineTransform2D.affineTransform2D(getCLIJ2(), source, destination, transform); + default boolean affineTransform2D(ClearCLImage arg1, ClearCLImageInterface arg2, float[] arg3) { + return AffineTransform2D.affineTransform2D(getCLIJ2(), arg1, arg2, arg3); } /** @@ -1757,8 +1757,8 @@ default boolean affineTransform2D(ClearCLBuffer source, ClearCLImageInterface de * Example transform: * transform = "center scale=2 rotate=45 -center"; */ - default boolean affineTransform2D(ClearCLImage arg1, ClearCLImageInterface arg2, float[] arg3) { - return AffineTransform2D.affineTransform2D(getCLIJ2(), arg1, arg2, arg3); + default boolean affineTransform2D(ClearCLBuffer source, ClearCLImageInterface destination, String transform) { + return AffineTransform2D.affineTransform2D(getCLIJ2(), source, destination, transform); } /** @@ -1778,7 +1778,7 @@ default boolean affineTransform2D(ClearCLImage arg1, ClearCLImageInterface arg2, * Example transform: * transform = "center scale=2 rotate=45 -center"; */ - default boolean affineTransform2D(ClearCLBuffer arg1, ClearCLImageInterface arg2, net.imglib2.realtransform.AffineTransform2D arg3) { + default boolean affineTransform2D(ClearCLBuffer arg1, ClearCLImageInterface arg2, float[] arg3) { return AffineTransform2D.affineTransform2D(getCLIJ2(), arg1, arg2, arg3); } @@ -1799,7 +1799,7 @@ default boolean affineTransform2D(ClearCLBuffer arg1, ClearCLImageInterface arg2 * Example transform: * transform = "center scale=2 rotate=45 -center"; */ - default boolean affineTransform2D(ClearCLBuffer arg1, ClearCLImageInterface arg2, float[] arg3) { + default boolean affineTransform2D(ClearCLBuffer arg1, ClearCLImageInterface arg2, net.imglib2.realtransform.AffineTransform2D arg3) { return AffineTransform2D.affineTransform2D(getCLIJ2(), arg1, arg2, arg3); } @@ -1864,8 +1864,8 @@ default boolean affineTransform3D(ClearCLImage arg1, ClearCLImageInterface arg2, * Example transform: * transform = "center scale=2 rotate=45 -center"; */ - default boolean affineTransform3D(ClearCLBuffer source, ClearCLImageInterface destination, String transform) { - return AffineTransform3D.affineTransform3D(getCLIJ2(), source, destination, transform); + default boolean affineTransform3D(ClearCLImage arg1, ClearCLImageInterface arg2, float[] arg3) { + return AffineTransform3D.affineTransform3D(getCLIJ2(), arg1, arg2, arg3); } /** @@ -1895,8 +1895,8 @@ default boolean affineTransform3D(ClearCLBuffer source, ClearCLImageInterface de * Example transform: * transform = "center scale=2 rotate=45 -center"; */ - default boolean affineTransform3D(ClearCLImage arg1, ClearCLImageInterface arg2, float[] arg3) { - return AffineTransform3D.affineTransform3D(getCLIJ2(), arg1, arg2, arg3); + default boolean affineTransform3D(ClearCLBuffer source, ClearCLImageInterface destination, String transform) { + return AffineTransform3D.affineTransform3D(getCLIJ2(), source, destination, transform); } /** @@ -1926,7 +1926,7 @@ default boolean affineTransform3D(ClearCLImage arg1, ClearCLImageInterface arg2, * Example transform: * transform = "center scale=2 rotate=45 -center"; */ - default boolean affineTransform3D(ClearCLBuffer arg1, ClearCLImageInterface arg2, net.imglib2.realtransform.AffineTransform3D arg3) { + default boolean affineTransform3D(ClearCLBuffer arg1, ClearCLImageInterface arg2, float[] arg3) { return AffineTransform3D.affineTransform3D(getCLIJ2(), arg1, arg2, arg3); } @@ -1957,7 +1957,7 @@ default boolean affineTransform3D(ClearCLBuffer arg1, ClearCLImageInterface arg2 * Example transform: * transform = "center scale=2 rotate=45 -center"; */ - default boolean affineTransform3D(ClearCLBuffer arg1, ClearCLImageInterface arg2, float[] arg3) { + default boolean affineTransform3D(ClearCLBuffer arg1, ClearCLImageInterface arg2, net.imglib2.realtransform.AffineTransform3D arg3) { return AffineTransform3D.affineTransform3D(getCLIJ2(), arg1, arg2, arg3); } @@ -1967,32 +1967,32 @@ default boolean affineTransform3D(ClearCLBuffer arg1, ClearCLImageInterface arg2 /** * Deforms an image according to distances provided in the given vector images. It is recommended to use 32-bit images for input, output and vector images. */ - default boolean applyVectorField(ClearCLImageInterface source, ClearCLImageInterface vectorX, ClearCLImageInterface vectorY, ClearCLImageInterface destination) { - return ApplyVectorField2D.applyVectorField(getCLIJ2(), source, vectorX, vectorY, destination); + default boolean applyVectorField2D(ClearCLImageInterface source, ClearCLImageInterface vectorX, ClearCLImageInterface vectorY, ClearCLImageInterface destination) { + return ApplyVectorField2D.applyVectorField2D(getCLIJ2(), source, vectorX, vectorY, destination); } /** * Deforms an image according to distances provided in the given vector images. It is recommended to use 32-bit images for input, output and vector images. */ - default boolean applyVectorField2D(ClearCLImageInterface source, ClearCLImageInterface vectorX, ClearCLImageInterface vectorY, ClearCLImageInterface destination) { - return ApplyVectorField2D.applyVectorField2D(getCLIJ2(), source, vectorX, vectorY, destination); + default boolean applyVectorField(ClearCLImageInterface source, ClearCLImageInterface vectorX, ClearCLImageInterface vectorY, ClearCLImageInterface destination) { + return ApplyVectorField2D.applyVectorField(getCLIJ2(), source, vectorX, vectorY, destination); } // net.haesleinhuepf.clij2.plugins.ApplyVectorField3D //---------------------------------------------------- /** - * Deforms an image according to distances provided in the given vector images. It is recommended to use 32-bit images for input, output and vector images. + * Deforms an image stack according to distances provided in the given vector image stacks. It is recommended to use 32-bit image stacks for input, output and vector image stacks. */ - default boolean applyVectorField(ClearCLImageInterface arg1, ClearCLImageInterface arg2, ClearCLImageInterface arg3, ClearCLImageInterface arg4, ClearCLImageInterface arg5) { - return ApplyVectorField3D.applyVectorField(getCLIJ2(), arg1, arg2, arg3, arg4, arg5); + default boolean applyVectorField3D(ClearCLImageInterface source, ClearCLImageInterface vectorX, ClearCLImageInterface vectorY, ClearCLImageInterface vectorZ, ClearCLImageInterface destination) { + return ApplyVectorField3D.applyVectorField3D(getCLIJ2(), source, vectorX, vectorY, vectorZ, destination); } /** - * Deforms an image stack according to distances provided in the given vector image stacks. It is recommended to use 32-bit image stacks for input, output and vector image stacks. + * Deforms an image according to distances provided in the given vector images. It is recommended to use 32-bit images for input, output and vector images. */ - default boolean applyVectorField3D(ClearCLImageInterface source, ClearCLImageInterface vectorX, ClearCLImageInterface vectorY, ClearCLImageInterface vectorZ, ClearCLImageInterface destination) { - return ApplyVectorField3D.applyVectorField3D(getCLIJ2(), source, vectorX, vectorY, vectorZ, destination); + default boolean applyVectorField(ClearCLImageInterface arg1, ClearCLImageInterface arg2, ClearCLImageInterface arg3, ClearCLImageInterface arg4, ClearCLImageInterface arg5) { + return ApplyVectorField3D.applyVectorField(getCLIJ2(), arg1, arg2, arg3, arg4, arg5); } @@ -2026,22 +2026,22 @@ default boolean histogram(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, d /** * Determines the histogram of a given image. */ - default ClearCLBuffer histogram(ClearCLBuffer arg1) { - return Histogram.histogram(getCLIJ2(), arg1); + default float[] histogram(ClearCLBuffer arg1, double arg2, double arg3, double arg4) { + return Histogram.histogram(getCLIJ2(), arg1, new Double (arg2).floatValue(), new Double (arg3).floatValue(), new Double (arg4).intValue()); } /** * Determines the histogram of a given image. */ - default boolean histogram(ClearCLBuffer arg1, ClearCLBuffer arg2) { - return Histogram.histogram(getCLIJ2(), arg1, arg2); + default ClearCLBuffer histogram(ClearCLBuffer arg1) { + return Histogram.histogram(getCLIJ2(), arg1); } /** * Determines the histogram of a given image. */ - default float[] histogram(ClearCLBuffer arg1, double arg2, double arg3, double arg4) { - return Histogram.histogram(getCLIJ2(), arg1, new Double (arg2).floatValue(), new Double (arg3).floatValue(), new Double (arg4).intValue()); + default boolean histogram(ClearCLBuffer arg1, ClearCLBuffer arg2) { + return Histogram.histogram(getCLIJ2(), arg1, arg2); } /** @@ -2296,8 +2296,8 @@ default boolean copySlice(ClearCLImageInterface arg1, ClearCLImageInterface arg2 * * Note: If the destination image pre-exists already, it will be overwritten and keep it's dimensions. */ - default boolean crop2D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4) { - return Crop2D.crop2D(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue()); + default boolean crop(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4) { + return Crop2D.crop(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue()); } /** @@ -2305,29 +2305,29 @@ default boolean crop2D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, d * * Note: If the destination image pre-exists already, it will be overwritten and keep it's dimensions. */ - default boolean crop(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4) { - return Crop2D.crop(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue()); + default boolean crop2D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4) { + return Crop2D.crop2D(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue()); } // net.haesleinhuepf.clij2.plugins.Crop3D //---------------------------------------------------- /** - * Crops a given sub-stack out of a given image stack. + * Crops a given rectangle out of a given image. * * Note: If the destination image pre-exists already, it will be overwritten and keep it's dimensions. */ - default boolean crop3D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { - return Crop3D.crop3D(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue(), new Double (arg5).intValue()); + default boolean crop(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { + return Crop3D.crop(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue(), new Double (arg5).intValue()); } /** - * Crops a given rectangle out of a given image. + * Crops a given sub-stack out of a given image stack. * * Note: If the destination image pre-exists already, it will be overwritten and keep it's dimensions. */ - default boolean crop(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { - return Crop3D.crop(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue(), new Double (arg5).intValue()); + default boolean crop3D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { + return Crop3D.crop3D(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue(), new Double (arg5).intValue()); } @@ -2597,18 +2597,18 @@ default boolean countNonZeroPixels2DSphere(ClearCLBuffer arg1, ClearCLBuffer arg // net.haesleinhuepf.clij2.plugins.CountNonZeroPixelsSliceBySliceSphere //---------------------------------------------------- /** - * + * Counts non-zero pixels in a sphere around every pixel slice by slice in a stack and puts the resulting number in the destination image stack. */ - @Deprecated - default boolean countNonZeroPixelsLocallySliceBySlice(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4) { - return CountNonZeroPixelsSliceBySliceSphere.countNonZeroPixelsLocallySliceBySlice(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue()); + default boolean countNonZeroPixelsSliceBySliceSphere(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4) { + return CountNonZeroPixelsSliceBySliceSphere.countNonZeroPixelsSliceBySliceSphere(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue()); } /** - * Counts non-zero pixels in a sphere around every pixel slice by slice in a stack and puts the resulting number in the destination image stack. + * */ - default boolean countNonZeroPixelsSliceBySliceSphere(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4) { - return CountNonZeroPixelsSliceBySliceSphere.countNonZeroPixelsSliceBySliceSphere(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue()); + @Deprecated + default boolean countNonZeroPixelsLocallySliceBySlice(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4) { + return CountNonZeroPixelsSliceBySliceSphere.countNonZeroPixelsLocallySliceBySlice(getCLIJ2(), arg1, arg2, new Double (arg3).intValue(), new Double (arg4).intValue()); } @@ -3171,22 +3171,22 @@ default boolean gaussianBlur3D(ClearCLImageInterface arg1, ClearCLImageInterface } /** - * Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape. + * Computes the Gaussian blurred image of an image given two sigma values in X, Y and Z. Thus, the filterkernel can have non-isotropic shape. * * The implementation is done separable. In case a sigma equals zero, the direction is not blurred. */ - default boolean gaussianBlur(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { - return GaussianBlur3D.gaussianBlur(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue()); + @Deprecated + default boolean blur3D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { + return GaussianBlur3D.blur3D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue()); } /** - * Computes the Gaussian blurred image of an image given two sigma values in X, Y and Z. Thus, the filterkernel can have non-isotropic shape. + * Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape. * * The implementation is done separable. In case a sigma equals zero, the direction is not blurred. */ - @Deprecated - default boolean blur3D(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { - return GaussianBlur3D.blur3D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue()); + default boolean gaussianBlur(ClearCLImageInterface arg1, ClearCLImageInterface arg2, double arg3, double arg4, double arg5) { + return GaussianBlur3D.gaussianBlur(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue()); } @@ -3279,15 +3279,15 @@ default boolean scale(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3) { /** * Scales an image with a given factor. */ - default boolean scale2D(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4) { - return Scale2D.scale2D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue()); + default boolean scale2D(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4, boolean arg5) { + return Scale2D.scale2D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), arg5); } /** * Scales an image with a given factor. */ - default boolean scale2D(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4, boolean arg5) { - return Scale2D.scale2D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), arg5); + default boolean scale2D(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4) { + return Scale2D.scale2D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue()); } @@ -3296,15 +3296,15 @@ default boolean scale2D(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, dou /** * Scales an image with a given factor. */ - default boolean scale3D(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4, double arg5) { - return Scale3D.scale3D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue()); + default boolean scale3D(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4, double arg5, boolean arg6) { + return Scale3D.scale3D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), arg6); } /** * Scales an image with a given factor. */ - default boolean scale3D(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4, double arg5, boolean arg6) { - return Scale3D.scale3D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue(), arg6); + default boolean scale3D(ClearCLBuffer arg1, ClearCLBuffer arg2, double arg3, double arg4, double arg5) { + return Scale3D.scale3D(getCLIJ2(), arg1, arg2, new Double (arg3).floatValue(), new Double (arg4).floatValue(), new Double (arg5).floatValue()); }