fixed a minor bug in the -save-progress and -load-progress arguments.…

… Updated some documentation.

bin/filter_mrc/filter_mrc.cpp

@@ -29,8 +29,8 @@ using namespace std;
 
 
 string g_program_name("filter_mrc");
-string g_version_string("0.29.17");
-string g_date_string("2021-9-10");
+string g_version_string("0.29.18");
+string g_date_string("2021-9-11");
 
 
 

bin/filter_mrc/handlers.cpp

@@ -1711,7 +1711,7 @@ HandleTV(const Settings &settings,
           }
         }
       }
-      cerr << " -- sorting ALL voxels by ridge saliency --\n" << endl;
+      cerr << " -- sorting all voxels by ridge saliency --\n" << endl;
       vector<float> saliencies(n_voxels);
       size_t i = 0;
       for (int iz=0; iz < image_size[2]; iz++) {

bin/filter_mrc/settings.cpp

@@ -280,6 +280,9 @@ Settings::ParseArgs(vector<string>& vArgs)
         // Now save all the current command line arguments into the INFO file.
         fstream f;
         f.open(save_intermediate_fname_info, ios::out);
+        if (! f)
+          throw VisfdErr("Error: Unable to open \"" +
+                         save_intermediate_fname_info +"\" for writing.\n");
         for (int j = 1; j < vArgs.size(); j++) {
           if ((j == i) || (j == i+1))
             continue;  // omit the "-save-progress filename" arguments
@@ -324,6 +327,9 @@ Settings::ParseArgs(vector<string>& vArgs)
         // Now load the arguments that were in the INFO file.
         fstream f;
         f.open(load_intermediate_fname_info, ios::in);
+        if (! f)
+          throw VisfdErr("Error: Unable to open \"" +
+                         load_intermediate_fname_info +"\" for reading.\n");
         vector<string> new_args;
         string line;
         while (getline(f, line, '\n'))

doc/doc_filter_mrc.md

@@ -195,16 +195,45 @@ filter_mrc -in tomogram.rec \
   -connect 1.0e+09 -connect-angle 15 \
   -select-cluster 1 -normals-file largest_membrane_pointcloud.ply
 ```
-Note:
+This will generate a new file ("largest_membrane_pointcloud.ply")
+containing a list of points located on the largest surface.
+You can use
+[*SSDRecon*](https://github.com/mkazhdan/PoissonRecon)
+to load this file and close the holes in the surface.  (See below.)
+
+**Note:**
 Here I assumed that the user has already followed the instructions in
 [example 1](#Example-1).  (Consequently, to save time, we used the
 ["-load-progress"](#-load-progress-FILENAME)
 to argument to skip over the time consuming
 process of detecting the membrane again.)
-This will generate a new file ("largest_membrane_pointcloud.ply")
-containing a list of points located on the largest surface. You can use
-[*SSDRecon*](https://github.com/mkazhdan/PoissonRecon)
-to load this file and close the holes in the surface:
+
+**Note:**
+All of these parameters make reasonably good
+defaults for membrane detection except the
+["**-connect**"](#-connect-threshold)
+parameter ("1.0e+09" in the example).
+It must be chosen carefully because it will vary from image to image.
+Strategies for choosing this parameter are discussed
+[below](#determining-the--connect-threshold-parameter).
+Repeat the step above with different parameters until the resulting
+"membranes_clusters.rec" shows that the different surface fragments
+have merged into larger surfaces correctly.
+(Verify this by opening the file in 3dmod, clicking on different portions
+of the dark surface that you care about, pressing the "F" key each time,
+and checking that the resulting ID numbers match.)
+If a suitable parameter can not be found that merges the membrane
+fragments togethe, you can also use the
+["**-must-link**"](#-must-link-FILE)
+argument to manually force connections between
+disconnected surface fragments. (See below.)
+You can also *modify* the image to erase or mask problematic regions (using the
+[-draw-spheres](#-draw-spheres-filename), or
+[-mask-rect-subtract](#-mask-rect-subtract-xmin-xmax-ymin-ymax-zmin-zmax), and
+[-mask-sphere-subtract](#-mask-sphere-subtract-x0-y0-z0-r) arguments).
+
+Now use [*SSDRecon*](https://github.com/mkazhdan/PoissonRecon)
+to load the PLY file we just created and close the holes in the surface:
 ```
 SSDRecon --in largest_membrane_pointcloud.ply \
   --out largest_membrane.ply --depth 12 --scale 2.0
@@ -251,26 +280,6 @@ filter_mrc -i segmented.rec -o segmented_interior.rec -erosion 50.0
 to see what works best.)
 
 
-
-**Note:**
-All of these parameters make reasonably good
-defaults for membrane detection except the
-["**-connect**"](#-connect-threshold)
-parameter ("1.0e+09" in the example).
-It must be chosen carefully because it will vary from image to image.
-Use the "-load-progress FILENAME" argument to save time
-while experimenting with different thresholds.
-Strategies for choosing this parameter are discussed
-[below](#determining-the--connect-threshold-parameter).
-If a suitable parameter can not be found, you can also use the
-["**-must-link**"](#-must-link-FILE)
-argument to manually force connections between
-disconnected regions. (See below.)
-You can also *modify* the image to erase or mask problematic regions (using the
-[-draw-spheres](#-draw-spheres-filename), or
-[-mask-rect-subtract](#-mask-rect-subtract-xmin-xmax-ymin-ymax-zmin-zmax), and
-[-mask-sphere-subtract](#-mask-sphere-subtract-x0-y0-z0-r) arguments).
-
 Note:
 If the resulting surface is *not closed*,
 then try increasing the "--scale" parameter.

lib/mrc_simple/mrc_simple.cpp

@@ -182,7 +182,7 @@ void MrcSimple::Read(string in_file_name,
   fstream mrc_file;
   mrc_file.open(in_file_name, ios::binary | ios::in);
   if (! mrc_file) 
-    throw MrcfileErr("Error: unable to open \""+ in_file_name +"\" for reading.\n");
+    throw MrcfileErr("Error: Unable to open \""+ in_file_name +"\" for reading.\n");
   // Try to infer signed-vs-unsigned integers from the file name:
   //http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-June/005245.html
   if ((len_in_file_name > 4)
@@ -354,7 +354,7 @@ void MrcSimple::Write(string out_file_name) {
   fstream mrc_file;
   mrc_file.open(out_file_name, ios::binary | ios::out);
   if (! mrc_file) 
-    throw MrcfileErr("Error: unable to open \""+ out_file_name+"\" for writing.\n");
+    throw MrcfileErr("Error: Unable to open \""+ out_file_name+"\" for writing.\n");
   Write(mrc_file);  // You can also use "mrc_file << tomo;"
   mrc_file.close();
 }