fixed a bug in "-find-minima" and "-find-maxima" which only occurs wh…

…en also used with the "-out" argument. (The bug was in the "_FindExtrema()" function in "morphology_implementation.hpp")

bin/filter_mrc/filter_mrc.cpp

@@ -1,8 +1,8 @@
 /// @brief
 /// This program allows the user to run one filter operation on an image file.
 /// This file contains main() as well as many functions named "Handle...()".
-/// Depending on which filter was selected, a different "Handle()" function
-/// will be invoked.
+/// After reading the image files, depending on which filter was selected,
+/// a different "Handle()" function will be invoked.
 /// Each of these "Handle...()" functions will collect the parameters supplied
 /// by the user and invoke an corresponding function from the visfd library.
 
@@ -29,7 +29,7 @@ using namespace std;
 
 
 string g_program_name("filter_mrc");
-string g_version_string("0.29.10");
+string g_version_string("0.29.11");
 string g_date_string("2021-7-26");
 
 

bin/filter_mrc/handlers.cpp

@@ -1043,21 +1043,24 @@ HandleExtrema(const Settings &settings,
   }
 
   // Note: _FindExtrema() is defind in "morphology_implementation.hpp"
-  _FindExtrema(tomo_in.header.nvoxels,
-               tomo_in.aaafI,
-               mask.aaafI,
-               pv_minima_crds_voxels,
-               pv_maxima_crds_voxels,
-               pv_minima_scores,
-               pv_maxima_scores,
-               pv_minima_nvoxels,
-               pv_maxima_nvoxels,
-               minima_threshold,
-               maxima_threshold,
-               settings.neighbor_connectivity,
-               settings.extrema_on_boundary,
-               tomo_out.aaafI, //<--an image showing where the minima are?
-               &cerr);
+  size_t num_extrema =
+    _FindExtrema(tomo_in.header.nvoxels,
+                 tomo_in.aaafI,
+                 mask.aaafI,
+                 pv_minima_crds_voxels,
+                 pv_maxima_crds_voxels,
+                 pv_minima_scores,
+                 pv_maxima_scores,
+                 pv_minima_nvoxels,
+                 pv_maxima_nvoxels,
+                 minima_threshold,
+                 maxima_threshold,
+                 settings.neighbor_connectivity,
+                 settings.extrema_on_boundary,
+                 tomo_out.aaafI, //<--an image showing where the minima are?
+                 &cerr);
+
+  cerr << "Found " << num_extrema << " extrema" << endl;
 
   // non-max suppression
   // discards minima or maxima which lie too close together.

bin/filter_mrc/settings.cpp

@@ -2107,6 +2107,7 @@ Settings::ParseArgs(vector<string>& vArgs)
 
 
     else if (vArgs[i] == "-find-minima") {
+      filter_type = FIND_EXTREMA;
       try {
         if (i+1 >= vArgs.size())
           throw invalid_argument("");
@@ -2122,6 +2123,7 @@ Settings::ParseArgs(vector<string>& vArgs)
 
 
     else if (vArgs[i] == "-find-maxima") {
+      filter_type = FIND_EXTREMA;
       try {
         if (i+1 >= vArgs.size())
           throw invalid_argument("");

lib/visfd/morphology_implementation.hpp

@@ -493,14 +493,14 @@ _FindExtrema(int const image_size[3],          //!< size of the image in x,y,z d
         for (int ix = 0; ix < image_size[0]; ix++) {
           if (aaafMask && (aaafMask[iz][iy][ix] == 0.0))
             continue; // don't modify voxels outside the mask
-          aaaiDest[iz][iy][ix] = aaaiExtrema[iz][iy][ix];
           // Until now, minima in the image are represented by negative integers
           // and maxima are represented by positive integers.
           if (((! find_minima) || (! find_maxima)) &&
               (aaaiExtrema[iz][iy][ix] < 0))
             // If we only asked for minima OR maxima (not both)
             // then just use positive integers only.
             aaaiExtrema[iz][iy][ix] = -aaaiExtrema[iz][iy][ix];
+          aaaiDest[iz][iy][ix] = aaaiExtrema[iz][iy][ix];
         }
       }
     }
@@ -726,6 +726,7 @@ _FindExtrema(int const image_size[3],          //!< size of the image in x,y,z d
 ///         or maxima, but not both.  (If you want both, use the other version.
 ///         That version is faster than invoking this function twice.)
 ///         See the description of that version for details.
+/// @note   THIS FUNCTION WAS NOT INTENDED FOR PUBLIC USE
 
 template<typename Scalar, typename Coordinate, typename IntegerIndex, typename Label>
 size_t
@@ -744,7 +745,7 @@ _FindExtrema(int const image_size[3],            //!< size of input image array
 {
   // NOTE:
   // C++ will not allow us to supply nullptr to a function that expects a pointer 
-  // to a template expression: Template argument deduction/substitution fails.
+  // to a template expression: "Template argument deduction/substitution fails."
   // We need to re-cast "nullptr" as a pointer with the correct type.
   // One way to do that is to define these new versions of nullptr:
   vector<array<Coordinate, 3> > *null_vai3 = nullptr;