added the "-fill" argument to filter_mrc, and debugged the "-mask-rec…

…t", "-mask-sphere", "-mask-rect-subtract", and "-mask-sphere-subtract" arguments.

bin/filter_mrc/settings.cpp

@@ -159,6 +159,7 @@ Settings::Settings() {
   in_threshold_10_a = 0.0;
   in_threshold_10_b = 0.0;
   out_thresh2_use_clipping = false;
+  out_thresh2_use_clipping_sigma = true;
   out_thresh_a_value = 0.0;
   out_thresh_b_value = 1.0;
   rescale_min_max_in = false;
@@ -391,7 +392,7 @@ Settings::ParseArgs(vector<string>& vArgs)
     else if (vArgs[i] == "-mask-sphere")
     {
       try {
-        if ((i+6 >= vArgs.size()) ||
+        if ((i+4 >= vArgs.size()) ||
             (vArgs[i+1] == "") ||
             (vArgs[i+2] == "") ||
             (vArgs[i+3] == "") ||
@@ -418,7 +419,7 @@ Settings::ParseArgs(vector<string>& vArgs)
     else if (vArgs[i] == "-mask-sphere-subtract")
     {
       try {
-        if ((i+6 >= vArgs.size()) ||
+        if ((i+4 >= vArgs.size()) ||
             (vArgs[i+1] == "") ||
             (vArgs[i+2] == "") ||
             (vArgs[i+3] == "") ||
@@ -531,7 +532,7 @@ Settings::ParseArgs(vector<string>& vArgs)
       try {
         if ((i+1 >= vArgs.size()) || (vArgs[i+1] == ""))
           throw invalid_argument("");
-        blur_distance = -stof(vArgs[i+1]);
+        blur_distance = stof(vArgs[i+1]);
       }
       catch (invalid_argument& exc) {
         throw InputErr("Error: The " + vArgs[i] +
@@ -547,6 +548,8 @@ Settings::ParseArgs(vector<string>& vArgs)
         in_threshold_01_a = 0.9213503964748575;  // ≈ (1+erf(1))/2
 
       in_threshold_01_b = in_threshold_01_a;
+      use_intensity_map = true;
+
       num_arguments_deleted = 2;
     } // if ((vArgs[i] == "-blur-contract") || (vArgs[i] == "-blur-expand"))
 
@@ -1452,6 +1455,24 @@ Settings::ParseArgs(vector<string>& vArgs)
     } // if (vArgs[i] == "-rescale")
 
 
+    else if (vArgs[i] == "-fill")
+    {
+      try {
+        if ((i+1 >= vArgs.size()) || (vArgs[i+1] == ""))
+          throw invalid_argument("");
+        use_intensity_map = true;
+        use_rescale_multiply = true;
+        out_rescale_multiply = 0.0;
+        out_rescale_offset = stof(vArgs[i+1]);
+      }
+      catch (invalid_argument& exc) {
+        throw InputErr("Error: The " + vArgs[i] +
+                       " argument must be followed by a number.");
+      }
+      num_arguments_deleted = 2;
+    } // if (vArgs[i] == "-rescale")
+
+
     else if ((vArgs[i] == "-thresh-range") ||
              (vArgs[i] == "-thresh-range-out"))
     {

doc/doc_filter_mrc.md

@@ -1567,6 +1567,7 @@ to read with other programs (such as ChimeraX and IMOD).
 
 
 
+
 ### -rescale m b
 
 Rescale the voxel intensities (multiply the brightnesses by *m*)
@@ -2411,7 +2412,8 @@ This command can be issued *multiple times*, along with the
 [-mask-sphere](#--mask-sphere-x0-y0-z0-r), and
 [-mask-sphere-subtract](#--mask-sphere-subtract-x0-y0-z0-r)
 commands to define complex regions in space.
-***WARNING: This feature has not yet been tested. -Andrew 2021-7-05***
+The resulting mask region can be visualized using the
+[-fill](#--fill-brightness) argument.
 
 *Note:*
 By default, the *xmin*, *xmax*, *ymin*, *ymax*, *zmin*, and *zmax*
@@ -2430,7 +2432,6 @@ Note: If you are using IMOD to locate voxel coordinates,
 
 
 ### -mask-rect-subtract xmin xmax ymin ymax zmin zmax
-***WARNING: This feature has not yet been tested. -Andrew 2021-7-05***
 
 This command can be used to *remove* the voxels in a existing mask
 which belong to a rectangular region bounded by the 6 numeric arguments: 
@@ -2441,12 +2442,12 @@ This command can be issued multiple times as part of an ordered chain of
 [-mask-sphere](#--mask-sphere-x0-y0-z0-r), and
 [-mask-sphere-subtract](#--mask-sphere-subtract-x0-y0-z0-r)
 commands which collectively define complex regions in space.
+The resulting mask region can be visualized using the
+[-fill](#--fill-brightness) argument.
 
 
 
 ### -mask-sphere x0 y0 z0 r
-### -mask-sphere-subtract x0 y0 z0 r
-***WARNING: This feature has not yet been tested. -Andrew 2021-7-05***
 
 You can can use the "**-mask-sphere**" argument to define one or more spherical
 regions in space that will be used as a *mask* in later operations.
@@ -2463,6 +2464,8 @@ This command can be issued *multiple times*, along with the
 [-mask-rect](#--mask-rect-xmin-xmax-ymin-ymax-zmin-zmax),
 [-mask-rect-subtract](#--mask-rect-subtract-xmin-xmax-ymin-ymax-zmin-zmax),
 commands to define complex regions in space.
+The resulting mask region can be visualized using the
+[-fill](#--fill-brightness) argument.
 
 *Note:*
 By default, the *x0*, *y0*, *z0*, and *r*
@@ -2473,8 +2476,7 @@ the "**-mask-crds-units distance**" (where **distance** is the word "distance",
 not a number).
 
 
-### -mask-rect-subtract xmin xmax ymin ymax zmin zmax
-***WARNING: This feature has not yet been tested. -Andrew 2021-7-05***
+### -mask-sphere-subtract x0 y0 z0 r
 
 This command can be used to *remove* the voxels in a existing mask which
 belong to a spherical region centered at *x0*, *y0*, *z0*, with radius *r*.
@@ -2484,6 +2486,18 @@ This command can be issued multiple times as part of an ordered chain of
 [-mask-rect](#--mask-rect-xmin-xmax-ymin-ymax-zmin-zmax),
 [-mask-rect-subtract](#--mask-rect-subtract-xmin-xmax-ymin-ymax-zmin-zmax),
 commands which collectively define complex regions in space.
+The resulting mask region can be visualized using the
+[-fill](#--fill-brightness) argument.
+
+
+### -fill brightness
+
+Replace all of the voxel brightnesses with *brightness*.
+If masks are used, then voxels outside the mask will be omitted.
+When using the *-mask-rect* and *-mask-sphere* arguments,
+using "**-fill 1**" will generate a 3-D image
+(which you can view in IMOD, for example)
+This provides a way to see where the mask region is located.
 
 
 

lib/visfd/draw.hpp

@@ -126,10 +126,9 @@ DrawRegions(int const image_size[3], //!< image size
                 continue;
 
               // now decide what to do with this voxel
-              if (negative_means_subtract) {
-                // then interpret negative voxel values as set exclusion
-                //if ((value == -1) && (aaafDest[iz+jz][iy+jy][ix+jx] == 1))
-                if ((value < 0) && (aaafDest[iz+jz][iy+jy][ix+jx] > 0))
+              if (value < 0) {
+                if (negative_means_subtract &&
+                    (aaafDest[iz+jz][iy+jy][ix+jx] > 0))
                   // then exclude this voxel from the existing set of voxels
                   aaafDest[iz+jz][iy+jy][ix+jx] = 0.0; // 0=excluded, 1=included
               }
@@ -152,22 +151,21 @@ DrawRegions(int const image_size[3], //!< image size
         Scalar izmin = floor(vRegions[i].data.rect.zmin + 0.5);
         Scalar izmax = floor(vRegions[i].data.rect.zmax + 0.5);
 
-        for (int iz=std::min<float>(izmin, 0);
-             iz < std::max<float>(izmax, image_size[2]);
+        for (int iz=std::max<float>(izmin, 0);
+             iz < std::min<float>(izmax, image_size[2]);
              iz++) {
-          for (int iy=std::min<float>(iymin, 0);
-               iy < std::max<float>(iymax, image_size[1]);
+          for (int iy=std::max<float>(iymin, 0);
+               iy < std::min<float>(iymax, image_size[1]);
                iy++) {
-            for (int ix=std::min<float>(ixmin, 0);
-                 ix < std::max<float>(ixmax, image_size[0]);
+            for (int ix=std::max<float>(ixmin, 0);
+                 ix < std::min<float>(ixmax, image_size[0]);
                  ix++) {
               if (aaafMask && (aaafMask[iz][iy][ix] == 0.0))
                 continue;
               // now decide what to do with this voxel
-              if (negative_means_subtract) {
-                // then interpret negative voxel values as set exclusion
-                //if ((value == -1) && (aaafDest[iz][iy][ix] == 1))
-                if ((value < 0) && (aaafDest[iz][iy][ix] > 0))
+              if (value < 0) {
+                if (negative_means_subtract &&
+                    (aaafDest[iz][iy][ix] > 0))
                   // then exclude this voxel from the existing set of voxels
                   aaafDest[iz][iy][ix] = 0.0; // 0=excluded, 1=included
               }

lib/visfd/filter3d.hpp

@@ -1142,6 +1142,13 @@ ApplyGauss(int const image_size[3], //!< image size in x,y,z directions
 {
   assert(aaafSource);
   assert(aaafDest);
+  assert(sigma[0] >= 0.0);
+  assert(sigma[1] >= 0.0);
+  assert(sigma[2] >= 0.0);
+  assert(truncate_halfwidth[0] > 0);
+  assert(truncate_halfwidth[1] > 0);
+  assert(truncate_halfwidth[2] > 0);
+
   //assert(aaafMask);
   //Allocate filters in all 3 directions.  (Later apply them sequentially.)
   Filter1D<Scalar, int> aFilter[3];