regenerated docs

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
-<span style="color:green">(experimental)</span>
+<span style="color:orange">(deprecated)</span>
 
 **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
+<span style="color:green">(experimental)</span>
+
+**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
+<span style="color:green">(experimental)</span>
+
+**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
 <span style="color:green">(experimental)</span>
 
@@ -8516,4 +8540,4 @@ This list contains the dictionary to translate between clij2, clijx, clEsperanto
 
 
 
-591 methods listed.
+593 methods listed.

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.
 
 ### <img src="images/mini_clij1_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_multiplyImages">multiplyImages</a>  
-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.
 
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_multiplyMatrix">multiplyMatrix</a>  
 Multiplies two matrices with each other.
@@ -1177,6 +1177,12 @@ Takes a label image and an parametric image and reads parametric values from the
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_readRawImageFromDisc">readRawImageFromDisc (Experimental)</a>  
 Reads a raw file from disc and pushes it immediately to the GPU.
 
+### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_readValuesFromMap">readValuesFromMap (Experimental)</a>  
+Takes a label image and an parametric image and reads parametric values from the labels positions.
+
+### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_readValuesFromPositions">readValuesFromPositions (Experimental)</a>  
+Takes a pointlist and a parametric image and reads parametric values from the positions.
+
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_reduceLabelsToLabelEdges">reduceLabelsToLabelEdges (Experimental)</a>  
 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.
 
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_sumImageSliceBySlice">sumImageSliceBySlice</a>  
-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.
 
 ### <img src="images/mini_clij1_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_sumOfAllPixels">sumOfAllPixels</a>  
 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.
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_zPositionRangeProjection">zPositionRangeProjection (Experimental)</a>  
 Project multiple Z-slices of a 3D stack into a new 3D stack.
 
-558 methods listed.
+560 methods listed.

reference__graph.md

@@ -233,6 +233,9 @@ Takes a list of point indices to generate a touch matrix (a.k.a. adjacency graph
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_readIntensitiesFromMap">readIntensitiesFromMap (Experimental)</a>  
 Takes a label image and an parametric image and reads parametric values from the labels positions.
 
+### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_readValuesFromMap">readValuesFromMap (Experimental)</a>  
+Takes a label image and an parametric image and reads parametric values from the labels positions.
+
 <a name="S"></a>
 
 ## S
@@ -263,4 +266,4 @@ Takes a pointlist with dimensions n*d with n point coordinates in d dimensions a
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_touchingNeighborCountMap">touchingNeighborCountMap (Experimental)</a>  
 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.

reference__label.md

@@ -335,6 +335,9 @@ Pulls all labels in a label map as ROIs to the ROI manager.
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_readIntensitiesFromMap">readIntensitiesFromMap (Experimental)</a>  
 Takes a label image and an parametric image and reads parametric values from the labels positions.
 
+### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_readValuesFromMap">readValuesFromMap (Experimental)</a>  
+Takes a label image and an parametric image and reads parametric values from the labels positions.
+
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_reduceLabelsToLabelEdges">reduceLabelsToLabelEdges (Experimental)</a>  
 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
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_wekaRegionalLabelClassifier">wekaRegionalLabelClassifier (Experimental)</a>  
 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.

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.
 
 ### <img src="images/mini_clij1_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_multiplyImages">multiplyImages</a>  
-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.
 
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_multiplyMatrix">multiplyMatrix</a>  
 Multiplies two matrices with each other.

reference__measurement.md

@@ -395,6 +395,12 @@ Converts an image into a table.
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_readIntensitiesFromMap">readIntensitiesFromMap (Experimental)</a>  
 Takes a label image and an parametric image and reads parametric values from the labels positions.
 
+### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_readValuesFromMap">readValuesFromMap (Experimental)</a>  
+Takes a label image and an parametric image and reads parametric values from the labels positions.
+
+### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_readValuesFromPositions">readValuesFromPositions (Experimental)</a>  
+Takes a pointlist and a parametric image and reads parametric values from the positions.
+
 <a name="S"></a>
 
 ## 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. 
 
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_sumImageSliceBySlice">sumImageSliceBySlice</a>  
-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.
 
 ### <img src="images/mini_clij1_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_sumOfAllPixels">sumOfAllPixels</a>  
 Determines the sum of all pixels in a given image. 
@@ -455,4 +461,4 @@ Determines the variance of all pixels in an image.
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_varianceOfMaskedPixels">varianceOfMaskedPixels</a>  
 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.

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.
 
 ### <img src="images/mini_clij1_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_multiplyImages">multiplyImages</a>  
-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.
 
 ### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><img src="images/mini_cle_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_multiplyMatrix">multiplyMatrix</a>  
 Multiplies two matrices with each other.

reference_clear.md

@@ -68,6 +68,7 @@ Ext.CLIJ2_clear();
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/boundingBoxes.ijm"><img src="images/language_macro.png" height="20"/></a> [boundingBoxes.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/boundingBoxes.ijm)  
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/center_of_mass.ijm"><img src="images/language_macro.png" height="20"/></a> [center_of_mass.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/center_of_mass.ijm)  
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/centroid_visualisation.ijm"><img src="images/language_macro.png" height="20"/></a> [centroid_visualisation.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/centroid_visualisation.ijm)  
+<a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/check_if_positions_are_in_roi.ijm"><img src="images/language_macro.png" height="20"/></a> [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)  
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/clij1_clij2_combination.ijm"><img src="images/language_macro.png" height="20"/></a> [clij1_clij2_combination.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/clij1_clij2_combination.ijm)  
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/compare_workflows.ijm"><img src="images/language_macro.png" height="20"/></a> [compare_workflows.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/compare_workflows.ijm)  
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/convert.ijm"><img src="images/language_macro.png" height="20"/></a> [convert.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/convert.ijm)  

reference_create2D.md

@@ -53,6 +53,7 @@ Ext.CLIJ2_create2D(Image destination, Number width, Number height, Number bitDep
 ### Example scripts
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/allocateBig2DImages.ijm"><img src="images/language_macro.png" height="20"/></a> [allocateBig2DImages.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/allocateBig2DImages.ijm)  
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/centroid_visualisation.ijm"><img src="images/language_macro.png" height="20"/></a> [centroid_visualisation.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/centroid_visualisation.ijm)  
+<a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/check_if_positions_are_in_roi.ijm"><img src="images/language_macro.png" height="20"/></a> [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)  
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/createImages.ijm"><img src="images/language_macro.png" height="20"/></a> [createImages.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/createImages.ijm)  
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/crop_and_paste.ijm"><img src="images/language_macro.png" height="20"/></a> [crop_and_paste.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/crop_and_paste.ijm)  
 <a href="https://github.com/clij/clij2-docs/blob/master/src/main/macro/customOperation.ijm"><img src="images/language_macro.png" height="20"/></a> [customOperation.ijm](https://github.com/clij/clij2-docs/blob/master/src/main/macro/customOperation.ijm)  

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"