Merge pull request #376 from clEsperanto/rename_parameters

rename parameters in add_images_weighted
clEsperanto · Oct 17, 2024 · a599c24 · a599c24
2 parents d61a5a0 + 1750e2d
commit a599c24
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Showing 15 changed files with 134 additions and 109 deletions.
diff --git a/clic/include/tier1.hpp b/clic/include/tier1.hpp
@@ -35,8 +35,8 @@ absolute_func(const Device::Pointer & device, const Array::Pointer & src, Array:
  * @param src0 The first input image to added. [const Array::Pointer &]
  * @param src1 The second image to be added. [const Array::Pointer &]
  * @param dst The output image where results are written into. [Array::Pointer ( = None )]
- * @param factor0 Multiplication factor of each pixel of src0 before adding it. [float ( = 1 )]
- * @param factor1 Multiplication factor of each pixel of src1 before adding it. [float ( = 1 )]
+ * @param factor1 Multiplication factor of each pixel of src0 before adding it. [float ( = 1 )]
+ * @param factor2 Multiplication factor of each pixel of src1 before adding it. [float ( = 1 )]
  * @return Array::Pointer
  *
  * @note 'combine', 'in assistant'
@@ -47,8 +47,8 @@ add_images_weighted_func(const Device::Pointer & device,
                          const Array::Pointer &  src0,
                          const Array::Pointer &  src1,
                          Array::Pointer          dst,
-                         float                   factor0,
-                         float                   factor1) -> Array::Pointer;
+                         float                   factor1,
+                         float                   factor2) -> Array::Pointer;
 
 
 /**
@@ -282,58 +282,62 @@ copy_func(const Device::Pointer & device, const Array::Pointer & src, Array::Poi
 
 /**
  * @name copy_slice
- * @brief This method has two purposes: It copies a 2D image to a given slice z position in a 3D image stack or It
- * copies a given slice at position z in an image stack to a 2D image. The first case is only available via ImageJ
+ * @brief This method has two purposes: It copies a 2D image to a given slice_index z position in a 3D image stack or It
+ * copies a given slice_index at position z in an image stack to a 2D image. The first case is only available via ImageJ
  * macro. If you are using it, it is recommended that the target 3D image already preexists in GPU memory before calling
  * this method. Otherwise, CLIJ create the image stack with z planes.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Input image to copy from. [const Array::Pointer &]
- * @param dst Output copy image slice. [Array::Pointer ( = None )]
- * @param slice [int ( = 0 )]
+ * @param dst Output copy image slice_index. [Array::Pointer ( = None )]
+ * @param slice_index [int ( = 0 )]
  * @return Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_copySlice
  *
  */
 auto
-copy_slice_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int slice)
+copy_slice_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int slice_index)
   -> Array::Pointer;
 
 
 /**
  * @name copy_horizontal_slice
- * @brief This method has two purposes: It copies a 2D image to a given slice y position in a 3D image stack or It
- * copies a given slice at position y in an image stack to a 2D image.
+ * @brief This method has two purposes: It copies a 2D image to a given slice_index y position in a 3D image stack or It
+ * copies a given slice_index at position y in an image stack to a 2D image.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Input image to copy from. [const Array::Pointer &]
- * @param dst Output copy image slice. [Array::Pointer ( = None )]
- * @param slice [int ( = 0 )]
+ * @param dst Output copy image slice_index. [Array::Pointer ( = None )]
+ * @param slice_index [int ( = 0 )]
  * @return Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_copySlice
  *
  */
 auto
-copy_horizontal_slice_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int slice)
-  -> Array::Pointer;
+copy_horizontal_slice_func(const Device::Pointer & device,
+                           const Array::Pointer &  src,
+                           Array::Pointer          dst,
+                           int                     slice_index) -> Array::Pointer;
 
 
 /**
  * @name copy_vertical_slice
- * @brief This method has two purposes: It copies a 2D image to a given slice x position in a 3D image stack or It
- * copies a given slice at position x in an image stack to a 2D image.
+ * @brief This method has two purposes: It copies a 2D image to a given slice_index x position in a 3D image stack or It
+ * copies a given slice_index at position x in an image stack to a 2D image.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Input image to copy from. [const Array::Pointer &]
- * @param dst Output copy image slice. [Array::Pointer ( = None )]
- * @param slice [int ( = 0 )]
+ * @param dst Output copy image slice_index. [Array::Pointer ( = None )]
+ * @param slice_index [int ( = 0 )]
  * @return Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_copySlice
  *
  */
 auto
-copy_vertical_slice_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int slice)
-  -> Array::Pointer;
+copy_vertical_slice_func(const Device::Pointer & device,
+                         const Array::Pointer &  src,
+                         Array::Pointer          dst,
+                         int                     slice_index) -> Array::Pointer;
 
 
 /**
@@ -1836,9 +1840,9 @@ not_equal_constant_func(const Device::Pointer & device, const Array::Pointer & s
  * @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 index_x Origin pixel coodinate in x to paste. [int ( = 0 )]
- * @param index_y Origin pixel coodinate in y to paste. [int ( = 0 )]
- * @param index_z Origin pixel coodinate in z to paste. [int ( = 0 )]
+ * @param destination_x Origin pixel coodinate in x to paste. [int ( = 0 )]
+ * @param destination_y Origin pixel coodinate in y to paste. [int ( = 0 )]
+ * @param destination_z Origin pixel coodinate in z to paste. [int ( = 0 )]
  * @return Array::Pointer
  *
  * @note 'combine', 'in assistant'
@@ -1848,9 +1852,9 @@ auto
 paste_func(const Device::Pointer & device,
            const Array::Pointer &  src,
            Array::Pointer          dst,
-           int                     index_x,
-           int                     index_y,
-           int                     index_z) -> Array::Pointer;
+           int                     destination_x,
+           int                     destination_y,
+           int                     destination_z) -> Array::Pointer;
 
 
 /**
@@ -2031,8 +2035,8 @@ replace_values_func(const Device::Pointer & device,
  * @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 scalar0 Old value. [float ( = 0 )]
- * @param scalar1 New value. [float ( = 1 )]
+ * @param value_to_replace Old value. [float ( = 0 )]
+ * @param value_replacement New value. [float ( = 1 )]
  * @return Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_replaceIntensity
  *
@@ -2041,8 +2045,8 @@ auto
 replace_value_func(const Device::Pointer & device,
                    const Array::Pointer &  src,
                    Array::Pointer          dst,
-                   float                   scalar0,
-                   float                   scalar1) -> Array::Pointer;
+                   float                   value_to_replace,
+                   float                   value_replacement) -> Array::Pointer;
 
 /**
  * @name replace_intensity
@@ -2051,8 +2055,8 @@ replace_value_func(const Device::Pointer & device,
  * @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 scalar0 Old value. [float ( = 0 )]
- * @param scalar1 New value. [float ( = 1 )]
+ * @param value_to_replace Old value. [float ( = 0 )]
+ * @param value_replacement New value. [float ( = 1 )]
  * @return Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_replaceIntensity
  * @deprecated This function is deprecated. Consider using replace_value() instead.
@@ -2061,8 +2065,8 @@ auto
 replace_intensity_func(const Device::Pointer & device,
                        const Array::Pointer &  src,
                        Array::Pointer          dst,
-                       float                   scalar0,
-                       float                   scalar1) -> Array::Pointer;
+                       float                   value_to_replace,
+                       float                   value_replacement) -> Array::Pointer;
 
 /**
  * @name replace_intensities
@@ -2193,14 +2197,15 @@ set_func(const Device::Pointer & device, const Array::Pointer & src, float scala
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Input image to process. [const Array::Pointer &]
- * @param column Column index. [int ( = 0 )]
+ * @param column_index Column index. [int ( = 0 )]
  * @param value Value to set. [float ( = 0 )]
  * @return Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_setColumn
  *
  */
 auto
-set_column_func(const Device::Pointer & device, const Array::Pointer & src, int column, float value) -> Array::Pointer;
+set_column_func(const Device::Pointer & device, const Array::Pointer & src, int column_index, float value)
+  -> Array::Pointer;
 
 
 /**
@@ -2224,14 +2229,15 @@ set_image_borders_func(const Device::Pointer & device, const Array::Pointer & sr
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Input image to process. [const Array::Pointer &]
- * @param plane Plane index. [int ( = 0 )]
+ * @param plane_index Plane index. [int ( = 0 )]
  * @param value Value to set. [float ( = 0 )]
  * @return Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_setPlane
  *
  */
 auto
-set_plane_func(const Device::Pointer & device, const Array::Pointer & src, int plane, float value) -> Array::Pointer;
+set_plane_func(const Device::Pointer & device, const Array::Pointer & src, int plane_index, float value)
+  -> Array::Pointer;
 
 
 /**
@@ -2282,14 +2288,14 @@ set_ramp_z_func(const Device::Pointer & device, const Array::Pointer & src) -> A
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Input image to process. [const Array::Pointer &]
- * @param row [int ( = 0 )]
+ * @param row_index [int ( = 0 )]
  * @param value [float ( = 0 )]
  * @return Array::Pointer
  * @see https://clij.github.io/clij2-docs/reference_setRow
  *
  */
 auto
-set_row_func(const Device::Pointer & device, const Array::Pointer & src, int row, float value) -> Array::Pointer;
+set_row_func(const Device::Pointer & device, const Array::Pointer & src, int row_index, float value) -> Array::Pointer;
 
 
 /**

diff --git a/clic/include/tier3.hpp b/clic/include/tier3.hpp
@@ -236,9 +236,9 @@ generate_touch_matrix_func(const Device::Pointer & device, const Array::Pointer
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src [const Array::Pointer &]
  * @param dst [Array::Pointer ( = None )]
- * @param nbins [int ( = 256 )]
- * @param min [float ( = None )]
- * @param max [float ( = None )]
+ * @param num_bins [int ( = 256 )]
+ * @param minimum_intensity [float ( = None )]
+ * @param maximum_intensity [float ( = None )]
  * @return Array::Pointer
  *
  * @see https://clij.github.io/clij2-docs/reference_histogram
@@ -248,9 +248,9 @@ auto
 histogram_func(const Device::Pointer & device,
                const Array::Pointer &  src,
                Array::Pointer          dst,
-               int                     nbins,
-               float                   min = NaN,
-               float                   max = NaN) -> Array::Pointer;
+               int                     num_bins,
+               float                   minimum_intensity = NaN,
+               float                   maximum_intensity = NaN) -> Array::Pointer;
 
 
 /**

diff --git a/clic/include/tier4.hpp b/clic/include/tier4.hpp
@@ -146,14 +146,16 @@ label_pixel_count_map_func(const Device::Pointer & device, const Array::Pointer
  * @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 withBG Determines if the background label should be included. [bool ( = False )]
+ * @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, bool withBG)
-  -> Array::Pointer;
+centroids_of_labels_func(const Device::Pointer & device,
+                         const Array::Pointer &  src,
+                         Array::Pointer          dst,
+                         bool                    include_background) -> Array::Pointer;
 
 
 /**
@@ -213,8 +215,8 @@ remove_labels_with_map_values_within_range_func(const Device::Pointer & device,
  * @param values_map Vector of values associated with the labels. [const Array::Pointer &]
  * @param label_map_input Input image where labels will be filtered. [const Array::Pointer &]
  * @param dst Output image where labels will be written to. [Array::Pointer ( = None )]
- * @param min_value_range Minimum value to keep. [float ( = 0 )]
- * @param max_value_range Maximum value to keep. [float ( = 100 )]
+ * @param minimum_value_range Minimum value to keep. [float ( = 0 )]
+ * @param maximum_value_range Maximum value to keep. [float ( = 100 )]
  * @return Array::Pointer
  *
  * @note 'label processing', 'combine'
@@ -226,8 +228,8 @@ exclude_labels_with_map_values_out_of_range_func(const Device::Pointer & device,
                                                  const Array::Pointer &  values_map,
                                                  const Array::Pointer &  label_map_input,
                                                  Array::Pointer          dst,
-                                                 float                   min_value_range,
-                                                 float                   max_value_range) -> Array::Pointer;
+                                                 float                   minimum_value_range,
+                                                 float                   maximum_value_range) -> Array::Pointer;
 
 /**
  * @name exclude_labels_with_map_values_within_range
@@ -238,8 +240,8 @@ exclude_labels_with_map_values_out_of_range_func(const Device::Pointer & device,
  * @param values_map Vector of values associated with the labels. [const Array::Pointer &]
  * @param label_map_input Input image where labels will be filtered. [const Array::Pointer &]
  * @param dst Output image where labels will be written to. [Array::Pointer ( = None )]
- * @param min_value_range Minimum value to keep. [float ( = 0 )]
- * @param max_value_range Maximum value to keep. [float ( = 100 )]
+ * @param minimum_value_range Minimum value to keep. [float ( = 0 )]
+ * @param maximum_value_range Maximum value to keep. [float ( = 100 )]
  * @return Array::Pointer
  *
  * @note 'label processing', 'combine'
@@ -251,8 +253,8 @@ exclude_labels_with_map_values_within_range_func(const Device::Pointer & device,
                                                  const Array::Pointer &  values_map,
                                                  const Array::Pointer &  label_map_input,
                                                  Array::Pointer          dst,
-                                                 float                   min_value_range,
-                                                 float                   max_value_range) -> Array::Pointer;
+                                                 float                   minimum_value_range,
+                                                 float                   maximum_value_range) -> Array::Pointer;
 
 /**
  * @name extension_ratio_map

diff --git a/clic/src/tier1/add_images_weighted.cpp b/clic/src/tier1/add_images_weighted.cpp
@@ -13,13 +13,13 @@ add_images_weighted_func(const Device::Pointer & device,
                          const Array::Pointer &  src0,
                          const Array::Pointer &  src1,
                          Array::Pointer          dst,
-                         float                   factor0,
-                         float                   factor1) -> Array::Pointer
+                         float                   factor1,
+                         float                   factor2) -> Array::Pointer
 {
   tier0::create_like(src0, dst, dType::FLOAT);
   const KernelInfo    kernel = { "add_images_weighted", kernel::add_images_weighted };
   const ParameterList params = {
-    { "src0", src0 }, { "src1", src1 }, { "dst", dst }, { "scalar0", factor0 }, { "scalar1", factor1 }
+    { "src0", src0 }, { "src1", src1 }, { "dst", dst }, { "scalar0", factor1 }, { "scalar1", factor2 }
   };
   const RangeArray range = { dst->width(), dst->height(), dst->depth() };
   execute(device, kernel, params, range);

diff --git a/clic/src/tier1/copy_horizontal_slice.cpp b/clic/src/tier1/copy_horizontal_slice.cpp
@@ -10,11 +10,13 @@ namespace cle::tier1
 {
 
 auto
-copy_horizontal_slice_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int slice)
-  -> Array::Pointer
+copy_horizontal_slice_func(const Device::Pointer & device,
+                           const Array::Pointer &  src,
+                           Array::Pointer          dst,
+                           int                     slice_index) -> Array::Pointer
 {
   tier0::create_like(src, dst);
-  const ParameterList params = { { "src", src }, { "dst", dst }, { "index", slice } };
+  const ParameterList params = { { "src", src }, { "dst", dst }, { "index", slice_index } };
   KernelInfo          kernel;
   RangeArray          range;
   if (dst->depth() > 1)

diff --git a/clic/src/tier1/copy_slice.cpp b/clic/src/tier1/copy_slice.cpp
@@ -10,11 +10,11 @@ namespace cle::tier1
 {
 
 auto
-copy_slice_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int slice)
+copy_slice_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int slice_index)
   -> Array::Pointer
 {
   tier0::create_like(src, dst);
-  const ParameterList params = { { "src", src }, { "dst", dst }, { "index", slice } };
+  const ParameterList params = { { "src", src }, { "dst", dst }, { "index", slice_index } };
   KernelInfo          kernel;
   RangeArray          range;
   if (dst->depth() > 1)

diff --git a/clic/src/tier1/copy_vertical_slice.cpp b/clic/src/tier1/copy_vertical_slice.cpp
@@ -10,11 +10,13 @@ namespace cle::tier1
 {
 
 auto
-copy_vertical_slice_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int slice)
-  -> Array::Pointer
+copy_vertical_slice_func(const Device::Pointer & device,
+                         const Array::Pointer &  src,
+                         Array::Pointer          dst,
+                         int                     slice_index) -> Array::Pointer
 {
   tier0::create_like(src, dst);
-  const ParameterList params = { { "src", src }, { "dst", dst }, { "index", slice } };
+  const ParameterList params = { { "src", src }, { "dst", dst }, { "index", slice_index } };
   KernelInfo          kernel;
   RangeArray          range;
   if (dst->depth() > 1)