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update some parameter name to fit better prototype #414

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update some parameter name to fit better prototype #414

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b6ee5c5
update some parameter name to fit better prototype
StRigaud Jan 16, 2025
f4bfc8f
style(pre-commit.ci): auto fixes
pre-commit-ci[bot] Jan 16, 2025
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122 changes: 61 additions & 61 deletions clic/include/tier1.hpp
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39 changes: 20 additions & 19 deletions clic/include/tier3.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -50,8 +50,8 @@ 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 Input label image [const Array::Pointer &]
* @param list Vector of 0 and 1 flagging labels to remove [const Array::Pointer &]
* @param input_labels Input label image [const Array::Pointer &]
* @param label_list Vector of 0 and 1 flagging labels to remove [const Array::Pointer &]
* @param dst Output label image [Array::Pointer ( = None )]
* @return Array::Pointer
*
Expand All @@ -60,8 +60,8 @@ center_of_mass_func(const Device::Pointer & device, const Array::Pointer & src)
*/
auto
remove_labels_func(const Device::Pointer & device,
const Array::Pointer & src,
const Array::Pointer & list,
const Array::Pointer & input_labels,
const Array::Pointer & label_list,
Array::Pointer dst) -> Array::Pointer;

/**
Expand All @@ -72,18 +72,18 @@ 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 Input label image [const Array::Pointer &]
* @param list Vector of 0 and 1 flagging labels to remove [const Array::Pointer &]
* @param input_labels Input label image [const Array::Pointer &]
* @param label_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
*
* @deprecated This function is deprecated. Use remove_labels() instead.
*/
auto
exclude_labels_func(const Device::Pointer & device,
const Array::Pointer & src,
const Array::Pointer & list,
const Array::Pointer & input_labels,
const Array::Pointer & label_list,
Array::Pointer dst) -> Array::Pointer;

/**
Expand Down Expand Up @@ -200,14 +200,14 @@ generate_binary_overlap_matrix_func(const Device::Pointer & device,
* adjacency graph
*
* @param device Device to perform the operation on. [const Device::Pointer &]
* @param src Input label image [const Array::Pointer &]
* @param input_labels 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
*/
auto
generate_touch_matrix_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst)
generate_touch_matrix_func(const Device::Pointer & device, const Array::Pointer & input_labels, Array::Pointer dst)
-> Array::Pointer;


Expand Down Expand Up @@ -279,16 +279,16 @@ 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 label Input label image [const Array::Pointer &]
* @param input_labels Input label image [const Array::Pointer &]
* @param pointlist Output coordinate list [Array::Pointer ( = None )]
* @return Array::Pointer
*
* @see https://clij.github.io/clij2-docs/reference_labelledSpotsToPointList
*/
auto
labelled_spots_to_pointlist_func(const Device::Pointer & device,
const Array::Pointer & label,
Array::Pointer dspointlistt) -> Array::Pointer;
const Array::Pointer & input_labels,
Array::Pointer pointlist) -> Array::Pointer;


/**
Expand Down Expand Up @@ -366,14 +366,15 @@ morphological_chan_vese_func(const Device::Pointer & device,
*
* @param device Device to perform the operation on. [const Device::Pointer &]
* @param intensity Intensity image. [Array::Pointer ( = None )]
* @param label Label image to compute the statistics. [Array::Pointer ( = None )]]
* @param input_labels Label image to compute the statistics. [Array::Pointer ( = None )]]
* @return StatisticsMap
*
* @see https://clij.github.io/clij2-docs/reference_statisticsOfLabelledPixels
*/
auto
statistics_of_labelled_pixels_func(const Device::Pointer & device, Array::Pointer intensity, Array::Pointer label)
-> StatisticsMap;
statistics_of_labelled_pixels_func(const Device::Pointer & device,
Array::Pointer intensity,
Array::Pointer input_labels) -> StatisticsMap;

/**
* @name statistics_of_background_and_labelled_pixels
Expand All @@ -386,15 +387,15 @@ statistics_of_labelled_pixels_func(const Device::Pointer & device, Array::Pointe
*
* @param device Device to perform the operation on. [const Device::Pointer &]
* @param intensity Intensity image. [Array::Pointer ( = None )]
* @param label Label image to compute the statistics. [Array::Pointer ( = None )]]
* @param input_labels Label image to compute the statistics. [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,
Array::Pointer intensity,
Array::Pointer label) -> StatisticsMap;
Array::Pointer input_labels) -> StatisticsMap;

} // namespace cle::tier3

Expand Down
52 changes: 26 additions & 26 deletions clic/include/tier4.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ threshold_otsu_func(const Device::Pointer & device, const Array::Pointer & src,
*
* @param device Device to perform the operation on. [const Device::Pointer &]
* @param src intensity image [const Array::Pointer &]
* @param labels label image [const Array::Pointer &]
* @param input_labels label image [const Array::Pointer &]
* @param dst Parametric image computed[Array::Pointer ( = None )]
* @return Array::Pointer
*
Expand All @@ -121,7 +121,7 @@ threshold_otsu_func(const Device::Pointer & device, const Array::Pointer & src,
auto
mean_intensity_map_func(const Device::Pointer & device,
const Array::Pointer & src,
const Array::Pointer & labels,
const Array::Pointer & input_labels,
Array::Pointer dst) -> Array::Pointer;


Expand All @@ -131,23 +131,24 @@ mean_intensity_map_func(const Device::Pointer & device,
* 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 input_labels 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
pixel_count_map_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst) -> Array::Pointer;
pixel_count_map_func(const Device::Pointer & device, const Array::Pointer & input_labels, Array::Pointer dst)
-> Array::Pointer;

/**
* @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 input_labels Label image to measure [const Array::Pointer &]
* @param dst Parametric image computed[Array::Pointer ( = None )]
* @return Array::Pointer
*
Expand All @@ -156,7 +157,7 @@ pixel_count_map_func(const Device::Pointer & device, const Array::Pointer & src,
* @deprecated This function is deprecated. Use pixel_count_map_func instead.
*/
auto
label_pixel_count_map_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst)
label_pixel_count_map_func(const Device::Pointer & device, const Array::Pointer & input_labels, Array::Pointer dst)
-> Array::Pointer;


Expand All @@ -167,17 +168,16 @@ 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 label_image Label image where the centroids will be determined from. [const Array::Pointer &]
* @param centroids_coordinates Output list of coordinates where the centroids will be written to. [Array::Pointer ( =
* None )]
* @param input_labels Label image where the centroids will be determined from. [const Array::Pointer &]
* @param centroids_coordinates Output list of coordinates of centroids. [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 & label_image,
const Array::Pointer & input_labels,
Array::Pointer centroids_coordinates,
bool include_background) -> Array::Pointer;

Expand All @@ -188,7 +188,7 @@ centroids_of_labels_func(const Device::Pointer & device,
* 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 input_labels 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 )]
Expand All @@ -200,7 +200,7 @@ centroids_of_labels_func(const Device::Pointer & device,
*/
auto
remove_labels_with_map_values_out_of_range_func(const Device::Pointer & device,
const Array::Pointer & src,
const Array::Pointer & input_labels,
const Array::Pointer & values,
Array::Pointer dst,
float min_value,
Expand All @@ -212,7 +212,7 @@ remove_labels_with_map_values_out_of_range_func(const Device::Pointer & device,
* 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 input_labels 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 )]
Expand All @@ -224,7 +224,7 @@ remove_labels_with_map_values_out_of_range_func(const Device::Pointer & device,
*/
auto
remove_labels_with_map_values_within_range_func(const Device::Pointer & device,
const Array::Pointer & src,
const Array::Pointer & input_labels,
const Array::Pointer & values,
Array::Pointer dst,
float min_value,
Expand Down Expand Up @@ -289,15 +289,15 @@ exclude_labels_with_map_values_within_range_func(const Device::Pointer & device,
* 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 input_labels Input label image. [const Array::Pointer &]
* @param dst Output parametric image. [Array::Pointer ( = None )]
* @return Array::Pointer
*
* @note 'label processing', 'in assistant', 'map'
* @see https://clij.github.io/clij2-docs/reference_extensionRatioMap
*/
auto
extension_ratio_map_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst)
extension_ratio_map_func(const Device::Pointer & device, const Array::Pointer & input_labels, Array::Pointer dst)
-> Array::Pointer;

/**
Expand All @@ -309,15 +309,15 @@ extension_ratio_map_func(const Device::Pointer & device, const Array::Pointer &
* 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 input_labels Input label image. [const Array::Pointer &]
* @param dst Output parametric image. [Array::Pointer ( = None )]
* @return Array::Pointer
*
* @note 'label processing', 'in assistant', 'map'
* @see https://clij.github.io/clij2-docs/reference_meanExtensionMap
*/
auto
mean_extension_map_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst)
mean_extension_map_func(const Device::Pointer & device, const Array::Pointer & input_labels, Array::Pointer dst)
-> Array::Pointer;

/**
Expand All @@ -329,15 +329,15 @@ mean_extension_map_func(const Device::Pointer & device, const Array::Pointer & s
* 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 input_labels Input label image. [const Array::Pointer &]
* @param dst Output parametric image. [Array::Pointer ( = None )]
* @return Array::Pointer
*
* @note 'label processing', 'in assistant', 'map'
* @see https://clij.github.io/clij2-docs/reference_meanExtensionMap
*/
auto
maximum_extension_map_func(const Device::Pointer & device, const Array::Pointer & src, Array::Pointer dst)
maximum_extension_map_func(const Device::Pointer & device, const Array::Pointer & input_labels, Array::Pointer dst)
-> Array::Pointer;

/**
Expand All @@ -349,7 +349,7 @@ maximum_extension_map_func(const Device::Pointer & device, const Array::Pointer
*
* @param device Device to perform the operation on. [const Device::Pointer &]
* @param src intensity image [const Array::Pointer &]
* @param labels label image [const Array::Pointer &]
* @param input_labels label image [const Array::Pointer &]
* @param dst Parametric image computed[Array::Pointer ( = None )]
* @return Array::Pointer
*
Expand All @@ -359,7 +359,7 @@ maximum_extension_map_func(const Device::Pointer & device, const Array::Pointer
auto
minimum_intensity_map_func(const Device::Pointer & device,
const Array::Pointer & src,
const Array::Pointer & labels,
const Array::Pointer & input_labels,
Array::Pointer dst) -> Array::Pointer;


Expand All @@ -372,7 +372,7 @@ minimum_intensity_map_func(const Device::Pointer & device,
*
* @param device Device to perform the operation on. [const Device::Pointer &]
* @param src intensity image [const Array::Pointer &]
* @param labels label image [const Array::Pointer &]
* @param input_labels label image [const Array::Pointer &]
* @param dst Parametric image computed[Array::Pointer ( = None )]
* @return Array::Pointer
*
Expand All @@ -382,7 +382,7 @@ minimum_intensity_map_func(const Device::Pointer & device,
auto
maximum_intensity_map_func(const Device::Pointer & device,
const Array::Pointer & src,
const Array::Pointer & labels,
const Array::Pointer & input_labels,
Array::Pointer dst) -> Array::Pointer;


Expand All @@ -395,7 +395,7 @@ maximum_intensity_map_func(const Device::Pointer & device,
*
* @param device Device to perform the operation on. [const Device::Pointer &]
* @param src intensity image [const Array::Pointer &]
* @param labels label image [const Array::Pointer &]
* @param input_labels label image [const Array::Pointer &]
* @param dst Parametric image computed[Array::Pointer ( = None )]
* @return Array::Pointer
*
Expand All @@ -405,7 +405,7 @@ maximum_intensity_map_func(const Device::Pointer & device,
auto
standard_deviation_intensity_map_func(const Device::Pointer & device,
const Array::Pointer & src,
const Array::Pointer & labels,
const Array::Pointer & input_labels,
Array::Pointer dst) -> Array::Pointer;


Expand Down
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