renamed "WatershedDirectional()" to "LabelConnected()", and moved thi…

…s function into a file named connect.hpp. Updated the related doxygen comments.
jewettaij · Jul 27, 2021 · 56bc1e9 · 56bc1e9
1 parent 68685e0
commit 56bc1e9
Show file tree

Hide file tree

Showing 9 changed files with 1,473 additions and 1,417 deletions.
diff --git a/bin/filter_mrc/filter_mrc.cpp b/bin/filter_mrc/filter_mrc.cpp
@@ -30,7 +30,7 @@ using namespace std;
 
 string g_program_name("filter_mrc");
 string g_version_string("0.29.10");
-string g_date_string("2021-7-25");
+string g_date_string("2021-7-26");
 
 
 
@@ -540,11 +540,11 @@ int main(int argc, char **argv) {
 
 
 
-    else if (settings.filter_type == Settings::WATERSHED_DIRECTIONAL) {
+    else if (settings.filter_type == Settings::LABEL_CONNECTED) {
 
       // Cluster adjacent nearby voxels with high "saliency" into "islands"
       // neighboring voxels (this is similar to watershed segmentation).
-      HandleWatershedDirectional(settings, tomo_in, tomo_out, mask, voxel_width);
+      HandleLabelConnected(settings, tomo_in, tomo_out, mask, voxel_width);
 
     }
 

diff --git a/bin/filter_mrc/handlers.cpp b/bin/filter_mrc/handlers.cpp
@@ -17,13 +17,14 @@ using namespace std;
 #include <visfd.hpp>
 using namespace visfd;
 
-#include <threshold.hpp>
 #include <mrc_simple.hpp>
 #include <random_gen.h>
 #include <feature.hpp>
 #include <morphology.hpp>
 #include <segmentation.hpp>
+#include <connect.hpp>
 #include <draw.hpp>
+#include <threshold.hpp>
 #include "err.hpp"
 #include "settings.hpp"
 #include "file_io.hpp"
@@ -1296,11 +1297,11 @@ HandleWatershed(const Settings &settings,
 
 
 void
-HandleWatershedDirectional(const Settings &settings,
-                       MrcSimple &tomo_in,
-                       MrcSimple &tomo_out,
-                       MrcSimple &mask,
-                       float voxel_width[3])
+HandleLabelConnected(const Settings &settings,
+                     MrcSimple &tomo_in,
+                     MrcSimple &tomo_out,
+                     MrcSimple &mask,
+                     float voxel_width[3])
 {
   const vector<vector<array<float, 3> > > *pMustLinkConstraints = nullptr;
 
@@ -1330,32 +1331,32 @@ HandleWatershedDirectional(const Settings &settings,
     undefined_voxel_brightness = -1;
 
   size_t num_clusters =
-    WatershedDirectional(tomo_in.header.nvoxels, //image size
-                         tomo_in.aaafI, //<-saliency
-                         aaaiClusterId, //<-which cluster does each voxel belong to?  (results will be stored here)
-                         mask.aaafI,
-                         settings.connect_threshold_saliency,
-                         static_cast<array<float, 3> ***>(nullptr),
-                         -std::numeric_limits<float>::infinity(),
-                         -std::numeric_limits<float>::infinity(),
-                         false, //normal default value for this (ignored) parameter
-                         static_cast<float****>(nullptr),
-                         -std::numeric_limits<float>::infinity(),
-                         -std::numeric_limits<float>::infinity(),
-                         true,  //normal default value for this (ignored) parameter
-                         1,
-                         static_cast<ptrdiff_t>(-1), // an impossible value
-                         &cluster_centers,
-                         &cluster_sizes,
-                         &cluster_saliencies,
-                         RegionSortCriteria::SORT_BY_SIZE,
-                         static_cast<float***>(nullptr),
-                         #ifndef DISABLE_STANDARDIZE_VECTOR_DIRECTION
-                         static_cast<array<float, 3> ***>(nullptr),
-                         #endif
-                         pMustLinkConstraints,
-                         true, //(clusters begin at regions of high saliency)
-                         &cerr);  //!< print progress to the user
+    LabelConnected(tomo_in.header.nvoxels, //image size
+                   tomo_in.aaafI, //<-saliency
+                   aaaiClusterId, //<-which cluster does each voxel belong to?  (results will be stored here)
+                   mask.aaafI,
+                   settings.connect_threshold_saliency,
+                   static_cast<array<float, 3> ***>(nullptr),
+                   -std::numeric_limits<float>::infinity(),
+                   -std::numeric_limits<float>::infinity(),
+                   false, //normal default value for this (ignored) parameter
+                   static_cast<float****>(nullptr),
+                   -std::numeric_limits<float>::infinity(),
+                   -std::numeric_limits<float>::infinity(),
+                   true,  //normal default value for this (ignored) parameter
+                   1,
+                   static_cast<ptrdiff_t>(-1), // an impossible value
+                   &cluster_centers,
+                   &cluster_sizes,
+                   &cluster_saliencies,
+                   RegionSortCriteria::SORT_BY_SIZE,
+                   static_cast<float***>(nullptr),
+                   #ifndef DISABLE_STANDARDIZE_VECTOR_DIRECTION
+                   static_cast<array<float, 3> ***>(nullptr),
+                   #endif
+                   pMustLinkConstraints,
+                   true, //(clusters begin at regions of high saliency)
+                   &cerr);  //!< print progress to the user
 
   ptrdiff_t max_label = aaaiClusterId[0][0][0];
   for (int iz = 0; iz < image_size[2]; ++iz)
@@ -1386,7 +1387,7 @@ HandleWatershedDirectional(const Settings &settings,
 
   Dealloc3D(aaaiClusterId);
 
-} //HandleWatershedDirectional()
+} //HandleLabelConnected()
 
 
 
@@ -1858,32 +1859,32 @@ HandleTV(const Settings &settings,
 
     size_t num_clusters =
 
-      WatershedDirectional(image_size, //image size
-                           aaafSaliency,
-                           aaaiClusterId, //<-which cluster does each voxel belong to?  (results will be stored here)
-                           mask.aaafI,
-                           settings.connect_threshold_saliency,
-                           aaaafDirection,
-                           settings.connect_threshold_vector_saliency,
-                           settings.connect_threshold_vector_neighbor,
-                           false, //eigenvector signs are arbitrary so ignore them
-                           aaaafVoteTensor,
-                           settings.connect_threshold_tensor_saliency,
-                           settings.connect_threshold_tensor_neighbor,
-                           true,  //the tensor should be positive definite near the target
-                           1,
-                           static_cast<ptrdiff_t>(-1), // an impossible value
-                           &cluster_centers,
-                           &cluster_sizes,
-                           &cluster_saliencies,
-                           RegionSortCriteria::SORT_BY_SIZE,
-                           static_cast<float***>(nullptr),
-                           #ifndef DISABLE_STANDARDIZE_VECTOR_DIRECTION
-                           aaaafDirection,
-                           #endif
-                           pMustLinkConstraints,
-                           true, //(clusters begin at regions of high saliency)
-                           &cerr);  //!< print progress to the user
+      LabelConnected(image_size, //image size
+                     aaafSaliency,
+                     aaaiClusterId, //<-which cluster does each voxel belong to?  (results will be stored here)
+                     mask.aaafI,
+                     settings.connect_threshold_saliency,
+                     aaaafDirection,
+                     settings.connect_threshold_vector_saliency,
+                     settings.connect_threshold_vector_neighbor,
+                     false, //eigenvector signs are arbitrary so ignore them
+                     aaaafVoteTensor,
+                     settings.connect_threshold_tensor_saliency,
+                     settings.connect_threshold_tensor_neighbor,
+                     true,  //the tensor should be positive definite near the target
+                     1,
+                     static_cast<ptrdiff_t>(-1), // an impossible value
+                     &cluster_centers,
+                     &cluster_sizes,
+                     &cluster_saliencies,
+                     RegionSortCriteria::SORT_BY_SIZE,
+                     static_cast<float***>(nullptr),
+                     #ifndef DISABLE_STANDARDIZE_VECTOR_DIRECTION
+                     aaaafDirection,
+                     #endif
+                     pMustLinkConstraints,
+                     true, //(clusters begin at regions of high saliency)
+                     &cerr);  //!< print progress to the user
 
     ptrdiff_t max_label = aaaiClusterId[0][0][0];
     for (int iz = 0; iz < image_size[2]; ++iz)
@@ -1926,7 +1927,7 @@ HandleTV(const Settings &settings,
     // where is the lookup table to indicate which cluster a voxel belongs to?
     float ***aaafVoxel2Cluster = nullptr;
     if (settings.cluster_connected_voxels)
-      aaafVoxel2Cluster = tomo_out.aaafI; //tomo_out was filled by WatershedDirectional()
+      aaafVoxel2Cluster = tomo_out.aaafI; //tomo_out was filled by LabelConnected()
 
     for (int iz = 0; iz < image_size[2]; ++iz) {
       for (int iy = 0; iy < image_size[1]; ++iy) {

diff --git a/bin/filter_mrc/handlers.hpp b/bin/filter_mrc/handlers.hpp
@@ -168,11 +168,11 @@ HandleWatershed(const Settings &settings,
 
 
 void
-HandleWatershedDirectional(const Settings &settings,
-                           MrcSimple &tomo_in,
-                           MrcSimple &tomo_out,
-                           MrcSimple &mask,
-                           float voxel_width[3]);
+HandleLabelConnected(const Settings &settings,
+                     MrcSimple &tomo_in,
+                     MrcSimple &tomo_out,
+                     MrcSimple &mask,
+                     float voxel_width[3]);
 
 
 void

diff --git a/bin/filter_mrc/settings.cpp b/bin/filter_mrc/settings.cpp
@@ -3370,7 +3370,7 @@ Settings::ParseArgs(vector<string>& vArgs)
       (filter_type != CURVE))
   {
     assert(connect_threshold_saliency!=std::numeric_limits<float>::infinity());
-    filter_type = WATERSHED_DIRECTIONAL;
+    filter_type = LABEL_CONNECTED;
   }
 
 

diff --git a/bin/filter_mrc/settings.hpp b/bin/filter_mrc/settings.hpp
@@ -50,7 +50,7 @@ class Settings {
     LOG_DOG,         // Approximation to Laplacian-of-Guassian using DOG (fast)
     LOCAL_FLUCTUATIONS, // Report the fluctuation of nearby voxel intensities
     WATERSHED,       // Watershed segmentation
-    WATERSHED_DIRECTIONAL, // Watershed applied to voxels with tensor attributes
+    LABEL_CONNECTED, // Connected component labeling (count islands in a sea)
     BLOB,            // Scale-free blob detection
     CURVE,           // Detect 1D curve-like ridges (a filament detector)
     SURFACE_EDGE,    // Detect the edge of a light-dark boundary (gradient)

diff --git a/lib/visfd/clustering.hpp b/lib/visfd/clustering.hpp