Add new filters and operations

clic/include/statistics.hpp

@@ -14,8 +14,7 @@ using StatisticsMap = std::unordered_map<std::string, std::vector<float>>;
 auto
 compute_statistics_per_labels(const Device::Pointer & device,
                               const Array::Pointer &  label,
-                              const Array::Pointer &  intensity,
-                              size_t                  offset) -> StatisticsMap;
+                              const Array::Pointer &  intensity) -> StatisticsMap;
 
 auto
 _statistics_per_label(const Device::Pointer & device,

clic/include/tier1.hpp

@@ -2059,6 +2059,47 @@ replace_value_func(const Device::Pointer & device,
                    float                   scalar0,
                    float                   scalar1) -> Array::Pointer;
 
+/**
+ * @name replace_intensity
+ * @brief Replaces a specific intensity in an image with a given new value.
+ *
+ * @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 )]
+ * @return Array::Pointer
+ * @see https://clij.github.io/clij2-docs/reference_replaceIntensity
+ * @deprecated This function is deprecated. Consider using replace_value() instead.
+ */
+auto
+replace_intensity_func(const Device::Pointer & device,
+                       const Array::Pointer &  src,
+                       Array::Pointer          dst,
+                       float                   scalar0,
+                       float                   scalar1) -> Array::Pointer;
+
+/**
+ * @name replace_intensities
+ * @brief Replaces integer intensities specified in a vector image. The values are passed as a vector of values.
+ * The vector index represents the old intensity and the value at that position represents the new intensity.s
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src0 Input image to process. [const Array::Pointer &]
+ * @param src1 List of intensities to replace, as a vector of values. [const Array::Pointer &]
+ * @param dst Output result image. [Array::Pointer ( = None )]
+ * @return Array::Pointer
+ *
+ * @note 'bia-bob-suggestion'
+ * @see https://clij.github.io/clij2-docs/reference_replaceIntensities
+ * @deprecated This function is deprecated. Consider using replace_values() instead.
+ */
+auto
+replace_intensities_func(const Device::Pointer & device,
+                         const Array::Pointer &  src0,
+                         const Array::Pointer &  src1,
+                         Array::Pointer          dst) -> Array::Pointer;
+
 /**
  * @name maximum_sphere
  * @brief Computes the local maximum of a pixels spherical neighborhood. The spheres size is specified by its halfwidth,

clic/include/tier2.hpp

@@ -895,6 +895,46 @@ subtract_images_func(const Device::Pointer & device,
                      const Array::Pointer &  src1,
                      Array::Pointer          dst) -> Array::Pointer;
 
+/**
+ * @name sub_stack
+ * @brief Crop a volume into a new volume, along the z-axis.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Input image. [const Array::Pointer &]
+ * @param dst Output image. [Array::Pointer ( = None )]
+ * @param start_z Start z coordinate of the crop. [int ( = 0 )]
+ * @param end_z End z coordinate of the crop. [int ( = 0 )]
+ * @return Array::Pointer
+ *
+ * @note 'transform', 'in assistant'
+ * @see https://clij.github.io/clij2-docs/reference_subStack
+ */
+auto
+sub_stack_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst, int start_z, int end_z)
+  -> Array::Pointer;
+
+/**
+ * @name reduce_stack
+ * @brief Reduces the number of z-slices in a stack by a given factor. With the offset you have control which slices
+ * stays: with a factor 3 and offset 0, slices 0,3,6, etc. are kept. with a factor 4 and offset 1, slices 1,5,9, etc.
+ * are kept.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Input image. [const Array::Pointer &]
+ * @param dst Output image. [Array::Pointer ( = None )]
+ * @param reduction_factor Reduction factor. [int ( = 2 )]
+ * @param offset Offset. [int ( = 0 )]
+ * @return Array::Pointer
+ *
+ * @note 'transform', 'in assistant'
+ * @see https://clij.github.io/clij2-docs/reference_reduceStack
+ */
+auto
+reduce_stack_func(const Device::Pointer & device,
+                  const Array::Pointer &  src,
+                  Array::Pointer          dst,
+                  int                     reduction_factor,
+                  int                     offset) -> Array::Pointer;
 
 /**
  * @name sum_of_all_pixels

clic/include/tier3.hpp

@@ -368,16 +368,36 @@ morphological_chan_vese_func(const Device::Pointer & device,
  * The intensity image is optional and set to 0 if not provided.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
- * @param src Label image to compute the statistics. [const Array::Pointer &]]
+ * @param label Label image to compute the statistics. [const Array::Pointer &]]
  * @param intensity Intensity image. [Array::Pointer ( = None )]
- * @param withBG Include the background label in the statistics. [bool ( = False )]
  * @return StatisticsMap
+ *
+ * @see https://clij.github.io/clij2-docs/reference_statisticsOfLabelledPixels
  */
 auto
 statistics_of_labelled_pixels_func(const Device::Pointer & device,
-                                   const Array::Pointer &  src,
-                                   Array::Pointer          intensity,
-                                   bool                    withBG) -> StatisticsMap;
+                                   const Array::Pointer &  label,
+                                   Array::Pointer          intensity) -> StatisticsMap;
+
+/**
+ * @name statistics_of_background_and_labelled_pixels
+ * @brief Compute, for the background and labels, the bounding box, area (in pixels/voxels), minimum intensity,
+ * maximum intensity, average intensity, standard deviation of the intensity, and some shape descriptors of
+ * labelled objects in a label image and its corresponding intensity image.
+ *
+ * The intensity image is optional and set to 0 if not provided.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param label Label image to compute the statistics. [const Array::Pointer &]]
+ * @param intensity Intensity image. [Array::Pointer ( = None )]
+ * @return StatisticsMap
+ *
+ * @see https://clij.github.io/clij2-docs/reference_statisticsOfBackgroundAndLabelledPixels
+ */
+auto
+statistics_of_background_and_labelled_pixels_func(const Device::Pointer & device,
+                                                  const Array::Pointer &  label,
+                                                  const Array::Pointer &  intensity) -> StatisticsMap;
 
 } // namespace cle::tier3
 

clic/include/tier4.hpp

@@ -105,25 +105,162 @@ threshold_otsu_func(const Device::Pointer & device, const Array::Pointer & src,
 
 
 /**
- * @name filter_label_by_size
- * @brief Filter labelled objects outside of the min/max size range value.
+ * @name label_pixel_count_map
+ * @brief Takes a label map, determines the number of pixels per label and replaces every label with the that number.
+ * This results in a parametric image expressing area or volume.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Label image to measure [const Array::Pointer &]
+ * @param dst Parametric image computed[Array::Pointer ( = None )]
+ * @return Array::Pointer
+ *
+ * @note 'label measurement', 'map', 'in assistant'
+ * @see https://clij.github.io/clij2-docs/reference_pixelCountMap
+ */
+auto
+label_pixel_count_map_func(const Device::Pointer & device,
+                           const Array::Pointer &  src,
+                           Array::Pointer          dst) -> Array::Pointer;
+
+
+/**
+ * @name centroids_of_labels
+ * @brief Determines the centroids of all labels in a label image or image stack.
+ * It writes the resulting coordinates in point list image of dimensions n * d
+ * 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 withBG Determines if the background label should be included. [bool ( = False )]
+ * @return Array::Pointer
+ *
+ * @note 'bia-bob-suggestion'
+ * @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;
+
+
+/**
+ * @name remove_labels_with_values_out_of_range
+ * @brief Remove labels with values outside a given value range based on a vector of values
+ * associated with the labels.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Input image where labels will be filtered. [const Array::Pointer &]
+ * @param values Vector of values associated with the labels. [const Array::Pointer &]
+ * @param dst Output image where labels will be written to. [Array::Pointer ( = None )]
+ * @param min_value Minimum value to keep. [float ( = 0 )]
+ * @param max_value Maximum value to keep. [float ( = 100 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'combine'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsWithValuesOutOfRange
+ */
+auto
+remove_labels_with_values_out_of_range_func(const Device::Pointer & device,
+                                            const Array::Pointer &  src,
+                                            const Array::Pointer &  values,
+                                            Array::Pointer          dst,
+                                            float                   min_value,
+                                            float                   max_value) -> Array::Pointer;
+
+/**
+ * @name remove_labels_with_values_within_range
+ * @brief Remove labels with values inside a given value range based on a vector of values
+ * associated with the labels.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Input image where labels will be filtered. [const Array::Pointer &]
+ * @param values Vector of values associated with the labels. [const Array::Pointer &]
+ * @param dst Output image where labels will be written to. [Array::Pointer ( = None )]
+ * @param min_value Minimum value to keep. [float ( = 0 )]
+ * @param max_value Maximum value to keep. [float ( = 100 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'combine'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsWithValuesWithinRange
+ */
+auto
+remove_labels_with_values_within_range_func(const Device::Pointer & device,
+                                            const Array::Pointer &  src,
+                                            const Array::Pointer &  values,
+                                            Array::Pointer          dst,
+                                            float                   min_value,
+                                            float                   max_value) -> Array::Pointer;
+
+/**
+ * @name exclude_labels_with_values_out_of_range
+ * @brief Exclude labels with values outside a given value range based on a vector of values
+ * associated with the labels.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Input image where labels will be filtered. [const Array::Pointer &]
+ * @param values Vector of values associated with the labels. [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 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'combine'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsWithValuesOutOfRange
+ * @deprecated This function is deprecated. Use remove_labels_with_values_out_of_range_func instead.
+ */
+auto
+exclude_labels_with_values_out_of_range_func(const Device::Pointer & device,
+                                             const Array::Pointer &  src,
+                                             const Array::Pointer &  values,
+                                             Array::Pointer          dst,
+                                             float                   min_value_range,
+                                             float                   max_value_range) -> Array::Pointer;
+
+/**
+ * @name exclude_labels_with_values_within_range
+ * @brief Exclude labels with values inside a given value range based on a vector of values
+ * associated with the labels.
+ *
+ * @param device Device to perform the operation on. [const Device::Pointer &]
+ * @param src Input image where labels will be filtered. [const Array::Pointer &]
+ * @param values Vector of values associated with the labels. [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 )]
+ * @return Array::Pointer
+ *
+ * @note 'label processing', 'combine'
+ * @see https://clij.github.io/clij2-docs/reference_excludeLabelsWithValuesWithinRange
+ * @deprecated This function is deprecated. Use remove_labels_with_values_within_range_func instead.
+ */
+auto
+exclude_labels_with_values_within_range_func(const Device::Pointer & device,
+                                             const Array::Pointer &  src,
+                                             const Array::Pointer &  values,
+                                             Array::Pointer          dst,
+                                             float                   min_value_range,
+                                             float                   max_value_range) -> Array::Pointer;
+
+/**
+ * @name extension_ratio_map
+ * @brief Determines the ratio of the extension for every label in a label map and returns it as
+ * a parametric map.
+ *
+ * The extension ration is defined as the maximum distance of any pixel in the label to the label's centroid divided by
+ * the average distance of all pixels in the label to the centroid.
  *
  * @param device Device to perform the operation on. [const Device::Pointer &]
  * @param src Input label image. [const Array::Pointer &]
- * @param dst Output label image. [Array::Pointer ( = None )]
- * @param min_size Minimum size of labels to keep. [float ( = 0 )]
- * @param max_size Maximum size of labels to keep. [float ( = 100 )]
+ * @param dst Output parametric image. [Array::Pointer ( = None )]
  * @return Array::Pointer
  *
- * @note 'label processing', 'in assistant'
- * @see https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
+ * @note 'label processing', 'in assistant', 'map'
+ * @see https://clij.github.io/clij2-docs/reference_extensionRatioMap
  */
 auto
-filter_label_by_size_func(const Device::Pointer & device,
-                          const Array::Pointer &  src,
-                          Array::Pointer          dst,
-                          float                   min_size,
-                          float                   max_size) -> Array::Pointer;
+extension_ratio_map_func(const Device::Pointer & device,
+                         const Array::Pointer &  src,
+                         Array::Pointer          dst) -> Array::Pointer;
 
 
 } // namespace cle::tier4