diff --git a/dictionary_clesperanto.md b/dictionary_clesperanto.md index 78e857ea..3c9d5542 100644 --- a/dictionary_clesperanto.md +++ b/dictionary_clesperanto.md @@ -6126,7 +6126,7 @@ This list contains the dictionary to translate between clij2, clijx, clEsperanto * Ext.CLIJx_readImageFromDisc(Image destination, String filename) ## read_intensities_from_map -(experimental) +(deprecated) **CLIJx** * boolean readIntensitiesFromMap(ClearCLImageInterface labels, ClearCLImageInterface map_image, ClearCLImageInterface values_destination) @@ -6154,6 +6154,30 @@ This list contains the dictionary to translate between clij2, clijx, clEsperanto **Macro** * Ext.CLIJx_readRawImageFromDisc(Image destination, String filename, Number width, Number height, Number depth, Number bitsPerPixel) +## read_values_from_map +(experimental) + +**CLIJx** +* boolean readValuesFromMap(ClearCLImageInterface labels, ClearCLImageInterface map_image, ClearCLImageInterface values_destination) + +**clEsperantoJ** +* ClearCLImageInterface read_values_from_map(ClearCLImageInterface labels, ClearCLImageInterface map_image, ClearCLImageInterface values_destination) + +**Macro** +* Ext.CLIJx_readValuesFromMap(Image labels, Image map_image, ByRef Image values_destination) + +## read_values_from_positions +(experimental) + +**CLIJx** +* boolean readValuesFromPositions(ClearCLImageInterface pointlist, ClearCLImageInterface map_image, ClearCLImageInterface values_destination) + +**clEsperantoJ** +* ClearCLImageInterface read_values_from_positions(ClearCLImageInterface pointlist, ClearCLImageInterface map_image, ClearCLImageInterface values_destination) + +**Macro** +* Ext.CLIJx_readValuesFromPositions(Image pointlist, Image map_image, ByRef Image values_destination) + ## read_intensities_from_positions (experimental) @@ -8516,4 +8540,4 @@ This list contains the dictionary to translate between clij2, clijx, clEsperanto -591 methods listed. \ No newline at end of file +593 methods listed. \ No newline at end of file diff --git a/reference.md b/reference.md index 58c1a2b3..c1b83027 100644 --- a/reference.md +++ b/reference.md @@ -991,7 +991,7 @@ Multiplies all pixels value x in a given image X with a constant scalar s. Multiplies all pixels value x in a given image X with a constant scalar s from a list of scalars. ### multiplyImages -Multiplies all pairs of pixel values x and y from two image X and Y. +Multiplies all pairs of pixel values x and y from two images X and Y. ### multiplyMatrix Multiplies two matrices with each other. @@ -1177,6 +1177,12 @@ Takes a label image and an parametric image and reads parametric values from the ### readRawImageFromDisc (Experimental) Reads a raw file from disc and pushes it immediately to the GPU. +### readValuesFromMap (Experimental) +Takes a label image and an parametric image and reads parametric values from the labels positions. + +### readValuesFromPositions (Experimental) +Takes a pointlist and a parametric image and reads parametric values from the positions. + ### reduceLabelsToLabelEdges (Experimental) Takes a label map and reduces all labels to their edges. Label IDs stay the same and background will be zero. @@ -1427,7 +1433,7 @@ Subtracts one image X from a scalar s pixel wise. Subtracts one image X from another image Y pixel wise. ### sumImageSliceBySlice -Sums all pixels slice by slice and returns them in an array. +Sums all pixels slice by slice and returns the sums in a vector. ### sumOfAllPixels Determines the sum of all pixels in a given image. @@ -1628,4 +1634,4 @@ Project a defined Z-slice of a 3D stack into a 2D image. ### zPositionRangeProjection (Experimental) Project multiple Z-slices of a 3D stack into a new 3D stack. -558 methods listed. +560 methods listed. diff --git a/reference__graph.md b/reference__graph.md index fedfa493..2c69a2c9 100644 --- a/reference__graph.md +++ b/reference__graph.md @@ -233,6 +233,9 @@ Takes a list of point indices to generate a touch matrix (a.k.a. adjacency graph ### readIntensitiesFromMap (Experimental) Takes a label image and an parametric image and reads parametric values from the labels positions. +### readValuesFromMap (Experimental) +Takes a label image and an parametric image and reads parametric values from the labels positions. + ## S @@ -263,4 +266,4 @@ Takes a pointlist with dimensions n*d with n point coordinates in d dimensions a ### touchingNeighborCountMap (Experimental) Takes a label map, determines which labels touch and replaces every label with the number of touching neighboring labels. -73 methods listed. +74 methods listed. diff --git a/reference__label.md b/reference__label.md index 9f5ddebb..a3415f5b 100644 --- a/reference__label.md +++ b/reference__label.md @@ -335,6 +335,9 @@ Pulls all labels in a label map as ROIs to the ROI manager. ### readIntensitiesFromMap (Experimental) Takes a label image and an parametric image and reads parametric values from the labels positions. +### readValuesFromMap (Experimental) +Takes a label image and an parametric image and reads parametric values from the labels positions. + ### reduceLabelsToLabelEdges (Experimental) Takes a label map and reduces all labels to their edges. Label IDs stay the same and background will be zero. @@ -401,4 +404,4 @@ Applies a pre-trained CLIJx-Weka model to an image and a corresponding label map ### wekaRegionalLabelClassifier (Experimental) Applies a pre-trained CLIJx-Weka model to an image and a corresponding label map to classify labeled objects. -113 methods listed. +114 methods listed. diff --git a/reference__math.md b/reference__math.md index 890c6be9..01a2ae7b 100644 --- a/reference__math.md +++ b/reference__math.md @@ -153,7 +153,7 @@ Multiplies all pixels value x in a given image X with a constant scalar s. Multiplies all pixels value x in a given image X with a constant scalar s from a list of scalars. ### multiplyImages -Multiplies all pairs of pixel values x and y from two image X and Y. +Multiplies all pairs of pixel values x and y from two images X and Y. ### multiplyMatrix Multiplies two matrices with each other. diff --git a/reference__measurement.md b/reference__measurement.md index 01c72ce3..d9fb7522 100644 --- a/reference__measurement.md +++ b/reference__measurement.md @@ -395,6 +395,12 @@ Converts an image into a table. ### readIntensitiesFromMap (Experimental) Takes a label image and an parametric image and reads parametric values from the labels positions. +### readValuesFromMap (Experimental) +Takes a label image and an parametric image and reads parametric values from the labels positions. + +### readValuesFromPositions (Experimental) +Takes a pointlist and a parametric image and reads parametric values from the positions. + ## S @@ -435,7 +441,7 @@ Determines image size (bounding box), area (in pixels/voxels), min, max and mean 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. ### sumImageSliceBySlice -Sums all pixels slice by slice and returns them in an array. +Sums all pixels slice by slice and returns the sums in a vector. ### sumOfAllPixels Determines the sum of all pixels in a given image. @@ -455,4 +461,4 @@ Determines the variance of all pixels in an image. ### varianceOfMaskedPixels Determines the variance in an image, but only in pixels which have non-zero values in another binary mask image. -132 methods listed. +134 methods listed. diff --git a/reference__pyclesperanto.md b/reference__pyclesperanto.md index 947a78b4..4fc608ad 100644 --- a/reference__pyclesperanto.md +++ b/reference__pyclesperanto.md @@ -543,7 +543,7 @@ Multiplies all pixel intensities with the x, y or z coordinate, depending on spe Multiplies all pixels value x in a given image X with a constant scalar s. ### multiplyImages -Multiplies all pairs of pixel values x and y from two image X and Y. +Multiplies all pairs of pixel values x and y from two images X and Y. ### multiplyMatrix Multiplies two matrices with each other. diff --git a/reference_clear.md b/reference_clear.md index a2ecd840..46f1376f 100644 --- a/reference_clear.md +++ b/reference_clear.md @@ -68,6 +68,7 @@ Ext.CLIJ2_clear(); [boundingBoxes.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/boundingBoxes.ijm) [center_of_mass.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/center_of_mass.ijm) [centroid_visualisation.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/centroid_visualisation.ijm) + [check_if_positions_are_in_roi.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/check_if_positions_are_in_roi.ijm) [clij1_clij2_combination.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/clij1_clij2_combination.ijm) [compare_workflows.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/compare_workflows.ijm) [convert.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/convert.ijm) diff --git a/reference_create2D.md b/reference_create2D.md index 7cdbea36..828251fa 100644 --- a/reference_create2D.md +++ b/reference_create2D.md @@ -53,6 +53,7 @@ Ext.CLIJ2_create2D(Image destination, Number width, Number height, Number bitDep ### Example scripts [allocateBig2DImages.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/allocateBig2DImages.ijm) [centroid_visualisation.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/centroid_visualisation.ijm) + [check_if_positions_are_in_roi.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/check_if_positions_are_in_roi.ijm) [createImages.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/createImages.ijm) [crop_and_paste.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/crop_and_paste.ijm) [customOperation.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/customOperation.ijm) diff --git a/reference_generateLabelFeatureImage.md b/reference_generateLabelFeatureImage.md index 5586f0f8..51c0ed54 100644 --- a/reference_generateLabelFeatureImage.md +++ b/reference_generateLabelFeatureImage.md @@ -25,18 +25,10 @@ Use this terminology to specify which features should be generated: * SUM_INTENSITY * STANDARD_DEVIATION_INTENSITY * PIXEL_COUNT -* local_mean_average_distance_of_touching_neighbors -* local_maximum_average_distance_of_touching_neighbors * count_touching_neighbors -* local_minimum_average_distance_of_touching_neighbors * average_touch_pixel_count -* local_minimum_count_touching_neighbors * average_distance_of_touching_neighbors -* local_mean_count_touching_neighbors * MEAN_OF_LAPLACIAN -* local_standard_deviation_average_distance_of_touching_neighbors -* local_maximum_count_touching_neighbors -* local_standard_deviation_count_touching_neighbors Example: "MEAN_INTENSITY count_touching_neighbors" diff --git a/reference_multiplyImages.md b/reference_multiplyImages.md index a2688b62..cf94cce0 100644 --- a/reference_multiplyImages.md +++ b/reference_multiplyImages.md @@ -1,7 +1,7 @@ ## multiplyImages -Multiplies all pairs of pixel values x and y from two image X and Y. +Multiplies all pairs of pixel values x and y from two images X and Y.
f(x, y) = x * ydiff --git a/reference_pull.md b/reference_pull.md index fe4eb31e..a27cd786 100644 --- a/reference_pull.md +++ b/reference_pull.md @@ -71,6 +71,7 @@ Ext.CLIJ2_pull(String image); [bitdepthConversion.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/bitdepthConversion.ijm) [blur.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/blur.ijm) [centroid_visualisation.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/centroid_visualisation.ijm) + [check_if_positions_are_in_roi.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/check_if_positions_are_in_roi.ijm) [clij1_clij2_combination.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/clij1_clij2_combination.ijm) [compare_workflows.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/compare_workflows.ijm) [convert.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/convert.ijm) diff --git a/reference_pullToResultsTable.md b/reference_pullToResultsTable.md index a71feeac..c397d657 100644 --- a/reference_pullToResultsTable.md +++ b/reference_pullToResultsTable.md @@ -11,6 +11,12 @@ Ext.CLIJ2_pullToResultsTable(Image source); ``` + + +### Example scripts + [check_if_positions_are_in_roi.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/check_if_positions_are_in_roi.ijm) + + [Back to CLIJ2 reference](https://clij.github.io/clij2-docs/reference) [Back to CLIJ2 documentation](https://clij.github.io/clij2-docs) diff --git a/reference_push.md b/reference_push.md index 010234cc..139a5cab 100644 --- a/reference_push.md +++ b/reference_push.md @@ -99,6 +99,7 @@ Ext.CLIJ2_push(String image); [boundingBoxes.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/boundingBoxes.ijm) [center_of_mass.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/center_of_mass.ijm) [centroid_visualisation.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/centroid_visualisation.ijm) + [check_if_positions_are_in_roi.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/check_if_positions_are_in_roi.ijm) [clij1_clij2_combination.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/clij1_clij2_combination.ijm) [compare_workflows.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/compare_workflows.ijm) [convert.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/convert.ijm) diff --git a/reference_pushResultsTable.md b/reference_pushResultsTable.md index 756d2a0f..f94ab228 100644 --- a/reference_pushResultsTable.md +++ b/reference_pushResultsTable.md @@ -5,6 +5,10 @@ Converts a table to an image. Rows stay rows, columns stay columns. +### pushResultsTable is often followed by +* release (1) + + ### Usage in ImageJ macro ``` Ext.CLIJ2_pushResultsTable(Image destination); @@ -22,6 +26,7 @@ Ext.CLIJ2_pushResultsTable(Image destination); ### Example scripts + [check_if_positions_are_in_roi.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/check_if_positions_are_in_roi.ijm) [excludeLabelsWithinRange.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/excludeLabelsWithinRange.ijm) [filter_label_maps.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/filter_label_maps.ijm) [neighbors_of_neighbors.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/neighbors_of_neighbors.ijm) diff --git a/reference_readIntensitiesFromMap.md b/reference_readIntensitiesFromMap.md index 27b2cd7a..c1fc8aa1 100644 --- a/reference_readIntensitiesFromMap.md +++ b/reference_readIntensitiesFromMap.md @@ -7,11 +7,7 @@ The read intensity valus are stored in a new vector. Note: This will only work if all labels have number of voxels == 1 or if all pixels in each label have the same value. -### Parameters - -labels -map_image -values_destination +DEPRECATED: Use ReadValuesFromMap instead Categories: [Labels](https://clij.github.io/clij2-docs/reference__label), [Measurements](https://clij.github.io/clij2-docs/reference__measurement), [Graphs](https://clij.github.io/clij2-docs/reference__graph) @@ -21,96 +17,6 @@ Ext.CLIJx_readIntensitiesFromMap(Image labels, Image map_image, Image values_des ``` -### Usage in object oriented programming languages - - - -
// init CLIJ and GPU -import net.haesleinhuepf.clijx.CLIJx; -import net.haesleinhuepf.clij.clearcl.ClearCLBuffer; -CLIJx clijx = CLIJx.getInstance(); - -// get input parameters -ClearCLBuffer labels = clijx.push(labelsImagePlus); -ClearCLBuffer map_image = clijx.push(map_imageImagePlus); -values_destination = clijx.create(labels); -- -
-// Execute operation on GPU -clijx.readIntensitiesFromMap(labels, map_image, values_destination); -- -
-// show result -values_destinationImagePlus = clijx.pull(values_destination); -values_destinationImagePlus.show(); - -// cleanup memory on GPU -clijx.release(labels); -clijx.release(map_image); -clijx.release(values_destination); -- -
% init CLIJ and GPU -clijx = init_clatlabx(); - -% get input parameters -labels = clijx.pushMat(labels_matrix); -map_image = clijx.pushMat(map_image_matrix); -values_destination = clijx.create(labels); -- -
-% Execute operation on GPU -clijx.readIntensitiesFromMap(labels, map_image, values_destination); -- -
-% show result -values_destination = clijx.pullMat(values_destination) - -% cleanup memory on GPU -clijx.release(labels); -clijx.release(map_image); -clijx.release(values_destination); -- -
import pyclesperanto_prototype as cle - -cle.read_intensities_from_map(labels, map_image, values_destination) - -- - - -
// init CLIJ and GPU +import net.haesleinhuepf.clijx.CLIJx; +import net.haesleinhuepf.clij.clearcl.ClearCLBuffer; +CLIJx clijx = CLIJx.getInstance(); + +// get input parameters +ClearCLBuffer labels = clijx.push(labelsImagePlus); +ClearCLBuffer map_image = clijx.push(map_imageImagePlus); +values_destination = clijx.create(labels); ++ +
+// Execute operation on GPU +clijx.readValuesFromMap(labels, map_image, values_destination); ++ +
+// show result +values_destinationImagePlus = clijx.pull(values_destination); +values_destinationImagePlus.show(); + +// cleanup memory on GPU +clijx.release(labels); +clijx.release(map_image); +clijx.release(values_destination); ++ +
% init CLIJ and GPU +clijx = init_clatlabx(); + +% get input parameters +labels = clijx.pushMat(labels_matrix); +map_image = clijx.pushMat(map_image_matrix); +values_destination = clijx.create(labels); ++ +
+% Execute operation on GPU +clijx.readValuesFromMap(labels, map_image, values_destination); ++ +
+% show result +values_destination = clijx.pullMat(values_destination) + +% cleanup memory on GPU +clijx.release(labels); +clijx.release(map_image); +clijx.release(values_destination); ++ +
// init CLIJ and GPU +import net.haesleinhuepf.clijx.CLIJx; +import net.haesleinhuepf.clij.clearcl.ClearCLBuffer; +CLIJx clijx = CLIJx.getInstance(); + +// get input parameters +ClearCLBuffer pointlist = clijx.push(pointlistImagePlus); +ClearCLBuffer map_image = clijx.push(map_imageImagePlus); +values_destination = clijx.create(pointlist); ++ +
+// Execute operation on GPU +clijx.readValuesFromPositions(pointlist, map_image, values_destination); ++ +
+// show result +values_destinationImagePlus = clijx.pull(values_destination); +values_destinationImagePlus.show(); + +// cleanup memory on GPU +clijx.release(pointlist); +clijx.release(map_image); +clijx.release(values_destination); ++ +
% init CLIJ and GPU +clijx = init_clatlabx(); + +% get input parameters +pointlist = clijx.pushMat(pointlist_matrix); +map_image = clijx.pushMat(map_image_matrix); +values_destination = clijx.create(pointlist); ++ +
+% Execute operation on GPU +clijx.readValuesFromPositions(pointlist, map_image, values_destination); ++ +
+% show result +values_destination = clijx.pullMat(values_destination) + +% cleanup memory on GPU +clijx.release(pointlist); +clijx.release(map_image); +clijx.release(values_destination); ++ +