Merge pull request #378 from clEsperanto/rename_image_parameter_names

Rename image parameter names
clEsperanto · Oct 18, 2024 · 4e8662d · 4e8662d
2 parents eaaddf2 + 745d875
commit 4e8662d
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Showing 12 changed files with 130 additions and 118 deletions.
diff --git a/clic/include/tier1.hpp b/clic/include/tier1.hpp
@@ -675,18 +675,18 @@ gaussian_blur_func(const Device::Pointer & device,
  * meshes.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 First input image to process. [const Array::Pointer &]
- * @param src1 Second input image to process. [const Array::Pointer &]
+ * @param coordinate_list1 First coordinate list to process. [const Array::Pointer &]
+ * @param coordinate_list2 Second coordinate list to process. [const Array::Pointer &]
  * @param dst Output result image. [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_generateDistanceMatrix
  */
 auto
 generate_distance_matrix_func(const Device::Pointer & device,
-                              const Array::Pointer &  src0,
-                              const Array::Pointer &  src1,
-                              Array::Pointer          dst) -> Array::Pointer;
+                              const Array::Pointer &  coordinate_list1,
+                              const Array::Pointer &  coordinate_list2,
+                              Array::Pointer          distance_matrix_destination) -> Array::Pointer;
 
 
 /**
@@ -2145,18 +2145,18 @@ minimum_sphere_func(const Device::Pointer & device,
  * @brief Multiplies two matrices with each other. Shape of matrix1 should be equal to shape of matrix2 transposed.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 First input image to process. [const Array::Pointer &]
- * @param src1 Second input image to process. [const Array::Pointer &]
- * @param dst Output result image. [Array::Pointer ( = None )]
+ * @param matrix1 First matrix to process. [const Array::Pointer &]
+ * @param matrix2 Second matrix to process. [const Array::Pointer &]
+ * @param matrix_destination Output result matrix. [Array::Pointer ( = None )]
  * @return Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_multiplyMatrix
  *
  */
 auto
 multiply_matrix_func(const Device::Pointer & device,
-                     const Array::Pointer &  src0,
-                     const Array::Pointer &  src1,
-                     Array::Pointer          dst) -> Array::Pointer;
+                     const Array::Pointer &  matrix1,
+                     const Array::Pointer &  matrix2,
+                     Array::Pointer          matrix_destination) -> Array::Pointer;
 
 
 /**

diff --git a/clic/include/tier2.hpp b/clic/include/tier2.hpp
@@ -283,17 +283,17 @@ concatenate_along_z_func(const Device::Pointer & device,
  * matrix where the first column (index = 0) has been set to 0. Use set_column for that.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Input image to process. [const Array::Pointer &]
- * @param dst Output result image. [Array::Pointer ( = None )]
+ * @param touch_matrix Input touch matrix to process. [const Array::Pointer &]
+ * @param touching_neighbors_count_destination Output vector of touch count. [Array::Pointer ( = None )]
  * @param ignore_background [bool ( = True )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_countTouchingNeighbors
  */
 auto
 count_touching_neighbors_func(const Device::Pointer & device,
-                              const Array::Pointer &  src,
-                              Array::Pointer          dst,
+                              const Array::Pointer &  touch_matrix,
+                              Array::Pointer          touching_neighbors_count_destination,
                               bool                    ignore_background) -> Array::Pointer;
 
 

diff --git a/clic/include/tier3.hpp b/clic/include/tier3.hpp
@@ -17,7 +17,7 @@ namespace cle::tier3
  *  an array of 6 values as follows: minX, minY, minZ, maxX, maxY, maxZ.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
+ * @param src Input binary image [const Array::Pointer &]
  * @return std::vector<float>
  *
  * @see https://clij.github.io/clij2-docs/reference_boundingBox
@@ -33,7 +33,7 @@ bounding_box_func(const Device::Pointer & device, const Array::Pointer & src) ->
  * columns MassX, MassY and MassZ.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
+ * @param src Input image [const Array::Pointer &]
  * @return std::vector<float>
  * @see https://clij.github.io/clij2-docs/reference_centerOfMass
  *
@@ -50,9 +50,9 @@ center_of_mass_func(const Device::Pointer & device, const Array::Pointer & src)
  * renumbered to 1 and 2.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param list [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param list Vector of 0 and 1 flagging labels to remove [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_excludeLabels
@@ -72,9 +72,9 @@ remove_labels_func(const Device::Pointer & device,
  * renumbered to 1 and 2.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param list [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param list Vector of 0 and 1 flagging labels to remove [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_excludeLabels
@@ -92,8 +92,8 @@ exclude_labels_func(const Device::Pointer & device,
  * renumbered afterwards.
  *
  * @param device Device to perform the operation on. [const Device::Pointer & ( = None )]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param dst Output label image[Array::Pointer ( = None )]
  * @param exclude_x Exclude labels along min and max x [bool ( = True )]
  * @param exclude_y Exclude labels along min and max y [bool ( = True )]
  * @param exclude_z Exclude labels along min and max z [bool ( = True )]
@@ -116,8 +116,8 @@ remove_labels_on_edges_func(const Device::Pointer & device,
  * renumbered afterwards.
  *
  * @param device Device to perform the operation on. [const Device::Pointer & ( = None )]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @param exclude_x Exclude labels along min and max x [bool ( = True )]
  * @param exclude_y Exclude labels along min and max y [bool ( = True )]
  * @param exclude_z Exclude labels along min and max z [bool ( = True )]
@@ -157,8 +157,8 @@ flag_existing_labels_func(const Device::Pointer & device, const Array::Pointer &
  * gamma g is computed, before normlization is reversed (^ is the power operator):f(x) = (x / max(X)) ^ gamma * max(X)
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input image [const Array::Pointer &]
+ * @param dst Output image [Array::Pointer ( = None )]
  * @param gamma [float ( = 1 )]
  * @return Array::Pointer
  *
@@ -177,9 +177,9 @@ gamma_correction_func(const Device::Pointer & device, const Array::Pointer & src
  * touching then the pixel (3,4) in the matrix will be set to 1.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 [const Array::Pointer &]
- * @param src1 [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src0 First input label image [const Array::Pointer &]
+ * @param src1 Second input label image [const Array::Pointer &]
+ * @param dst Output overlap matrix [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_generateBinaryOverlapMatrix
@@ -200,8 +200,8 @@ generate_binary_overlap_matrix_func(const Device::Pointer & device,
  * adjacency graph
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param dst Output touch matrix [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_generateTouchMatrix
@@ -234,8 +234,8 @@ generate_touch_matrix_func(const Device::Pointer & device, const Array::Pointer
  * http://www.openclprogrammingguide.com
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input image to derive histogram from [const Array::Pointer &]
+ * @param dst Output histogram [Array::Pointer ( = None )]
  * @param num_bins [int ( = 256 )]
  * @param minimum_intensity [float ( = None )]
  * @param maximum_intensity [float ( = None )]
@@ -261,8 +261,8 @@ histogram_func(const Device::Pointer & device,
  * + 1)</pre>
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 [const Array::Pointer &]
- * @param src1 [const Array::Pointer &]
+ * @param src0 First binary image to compare [const Array::Pointer &]
+ * @param src1 Second binary image to compare [const Array::Pointer &]
  * @return float
  *
  * @see https://clij.github.io/clij2-docs/reference_jaccardIndex
@@ -279,8 +279,8 @@ jaccard_index_func(const Device::Pointer & device, const Array::Pointer & src0,
  * contains d pixels (with d = dimensionality of the original image) with the coordinates of the maxima/minima.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param dst Output coordinate list [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_labelledSpotsToPointList

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
@@ -17,8 +17,8 @@ namespace cle::tier4
  *  an array of 6 values as follows: minX, minY, minZ, maxX, maxY, maxZ.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param label_id [int]
+ * @param src Label image [const Array::Pointer &]
+ * @param label_id Identifier of label [int]
  * @return std::vector<float>
  *
  * @see https://clij.github.io/clij2-docs/reference_boundingBox
@@ -33,8 +33,8 @@ label_bounding_box_func(const Device::Pointer & device, const Array::Pointer & s
  * Results table in the column 'MSE'.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 [const Array::Pointer &]
- * @param src1 [const Array::Pointer &]
+ * @param src0 First image to compare [const Array::Pointer &]
+ * @param src1 Second image to compare [const Array::Pointer &]
  * @return float
  *
  * @note 'in assistant', 'combine', 'bia-bob-suggestion'
@@ -51,8 +51,8 @@ mean_squared_error_func(const Device::Pointer & device, const Array::Pointer & s
  * pixels (with d = dimensionality of the original image) with the coordinates of the maxima/minima.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input binary image of spots [const Array::Pointer &]
+ * @param dst Output coordinate list of spots [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_spotsToPointList
@@ -70,7 +70,7 @@ spots_to_pointlist_func(const Device::Pointer & device, const Array::Pointer & s
  * performed on the CPU.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Label image. [const Array::Pointer &]
+ * @param src Input label image. [const Array::Pointer &]
  * @param dst Output label image. [Array::Pointer ( = None )]
  * @param blocksize Renumbering is done in blocks for performance reasons. [int ( = 4096 )]
  * @return Array::Pointer
@@ -144,17 +144,18 @@ label_pixel_count_map_func(const Device::Pointer & device, const Array::Pointer
  * where n is the number of labels and d=3 the dimensionality (x,y,z) of the original image.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Label image where the centroids will be determined from. [const Array::Pointer &]
- * @param dst Output image where the centroids will be written to. [Array::Pointer ( = None )]
+ * @param label_image Label image where the centroids will be determined from. [const Array::Pointer &]
+ * @param coorindate_list_destination Output list of coordinates where the centroids will be written to. [Array::Pointer
+ * ( = None )]
  * @param include_background Determines if the background label should be included. [bool ( = False )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_centroidsOfLabels
  */
 auto
 centroids_of_labels_func(const Device::Pointer & device,
-                         const Array::Pointer &  src,
-                         Array::Pointer          dst,
+                         const Array::Pointer &  label_image,
+                         Array::Pointer          coorindate_list_destination,
                          bool                    include_background) -> Array::Pointer;
 
 

diff --git a/clic/include/tier5.hpp b/clic/include/tier5.hpp
@@ -16,8 +16,8 @@ namespace cle::tier5
  * False. True otherwise This function is supposed to work similarly like its counterpart in numpy [1].
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 [const Array::Pointer &]
- * @param src1 [const Array::Pointer &]
+ * @param src0 First array to compare [const Array::Pointer &]
+ * @param src1 Second array to compare [const Array::Pointer &]
  * @return bool
  *
  * @note 'combine'

diff --git a/clic/include/tier6.hpp b/clic/include/tier6.hpp
@@ -16,8 +16,8 @@ namespace cle::tier6
  * scikitimage [2] and MorpholibJ[3] Notes * This operation assumes input images are isotropic.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src label image to erode [const Array::Pointer &]
- * @param dst result [Array::Pointer ( = None )]
+ * @param src Input label image to erode [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @param radius [int ( = 2 )]
  * @return Array::Pointer
  *
@@ -35,10 +35,10 @@ dilate_labels_func(const Device::Pointer & device, const Array::Pointer & src, A
  * identifier. Notes * This operation assumes input images are isotropic.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src result [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input label image [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @param radius [int ( = 1 )]
- * @param relabel and all label indices exist. [bool ( = False )]
+ * @param relabel Relabel the image, e.g. if object disappear or split. [bool ( = False )]
  * @return Array::Pointer
  *
  * @note 'label processing', 'in assistant'
@@ -60,7 +60,7 @@ erode_labels_func(const Device::Pointer & device,
  *  thresholded binary image is flooded using the Voronoi tesselation approach starting from the found local maxima.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src0 intensity image to add labels [const Array::Pointer &]
+ * @param src0 Intensity image to segment [const Array::Pointer &]
  * @param dst Output label image. [Array::Pointer ( = None )]
  * @param outline_sigma Gaussian blur sigma along all axes [float ( = 0 )]
  * @return Array::Pointer
@@ -82,9 +82,9 @@ gauss_otsu_labeling_func(const Device::Pointer & device,
  * touch. The region growing is limited to a masked area. The resulting label map is written to the output.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param mask [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param src Input binary image [const Array::Pointer &]
+ * @param mask Input mask [const Array::Pointer &]
+ * @param dst Output label image [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @note 'label'
@@ -103,15 +103,16 @@ masked_voronoi_labeling_func(const Device::Pointer & device,
  * touch. The resulting label map is written to the output.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src [const Array::Pointer &]
- * @param dst [Array::Pointer ( = None )]
+ * @param input_binary Input binary image  [const Array::Pointer &]
+ * @param output_labels Output label image [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
  * @note 'label', 'in assistant', 'bia-bob-suggestion'
  * @see https://clij.github.io/clij2-docs/reference_voronoiLabeling
  */
 auto
-voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst) -> Array::Pointer;
+voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & input_binary, Array::Pointer output_labels)
+  -> Array::Pointer;
 
 
 /**
@@ -120,7 +121,7 @@ voronoi_labeling_func(const Device::Pointer & device, const Array::Pointer & src
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Label image to filter. [const Array::Pointer &]
- * @param dst Output label image fitlered. [Array::Pointer ( = None )]
+ * @param dst Output label image filtered. [Array::Pointer ( = None )]
  * @param minimum_size Smallest size object allowed. [float ( = 100 )]
  * @return Array::Pointer
  *
@@ -139,7 +140,7 @@ remove_small_labels_func(const Device::Pointer & device,
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Label image to filter. [const Array::Pointer &]
- * @param dst Output label image fitlered. [Array::Pointer ( = None )]
+ * @param dst Output label image filtered. [Array::Pointer ( = None )]
  * @param maximum_size Largest size object to exclude. [float ( = 100 )]
  * @return Array::Pointer
  *
@@ -154,11 +155,11 @@ exclude_small_labels_func(const Device::Pointer & device,
 
 /**
  * @name remove_large_labels
- * @brief Removes labelled objects bigger than a given size (in pixels) from a label map.
+ * @brief Removes labeled objects bigger than a given size (in pixels) from a label map.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Label image to filter. [const Array::Pointer &]
- * @param dst Output label image fitlered. [Array::Pointer ( = None )]
+ * @param dst Output label image filtered. [Array::Pointer ( = None )]
  * @param maximum_size Biggest size object allowed. [float ( = 100 )]
  * @return Array::Pointer
  *
@@ -177,7 +178,7 @@ remove_large_labels_func(const Device::Pointer & device,
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Label image to filter. [const Array::Pointer &]
- * @param dst Output label image fitlered. [Array::Pointer ( = None )]
+ * @param dst Output label image filtered. [Array::Pointer ( = None )]
  * @param minimum_size Smallest size object to keep. [float ( = 100 )]
  * @return Array::Pointer
  *