Merge branch 'master' into tiff_image_format

cmd/fixelcrop.cpp

@@ -58,7 +58,7 @@ void run ()
   Fixel::check_fixel_directory (out_fixel_directory, true);
 
   Header out_header = Header (in_index_image);
-  size_t total_nfixels = std::stoul (out_header.keyval ()[Fixel::n_fixels_key]);
+  size_t total_nfixels = Fixel::get_number_of_fixels (in_index_header);
 
   // We need to do a first pass of the mask image to determine the number of cropped fixels
   for (auto l = Loop (0) (mask_image); l; ++l) {

cmd/mrconvert.cpp

@@ -90,16 +90,16 @@ DESCRIPTION
 
   + OptionGroup ("Options to modify generic header entries")
 
-  + Option ("clear_property", 
+  + Option ("clear_property",
             "remove the specified key from the image header altogether.").allow_multiple()
   + Argument ("key").type_text()
 
-  + Option ("set_property", 
+  + Option ("set_property",
             "set the value of the specified key in the image header.").allow_multiple()
   + Argument ("key").type_text()
   + Argument ("value").type_text()
 
-  + Option ("append_property", 
+  + Option ("append_property",
             "append the given value to the specified key in the image header (this adds the value specified as a new line in the header value).").allow_multiple()
   + Argument ("key").type_text()
   + Argument ("value").type_text()
@@ -288,11 +288,11 @@ void run ()
   }
 
   opt = get_options ("set_property");
-  for (size_t n = 0; n < opt.size(); ++n) 
+  for (size_t n = 0; n < opt.size(); ++n)
     header_out.keyval()[opt[n][0].as_text()] = opt[n][1].as_text();
 
   opt = get_options ("append_property");
-  for (size_t n = 0; n < opt.size(); ++n) 
+  for (size_t n = 0; n < opt.size(); ++n)
     add_line (header_out.keyval()[opt[n][0].as_text()], opt[n][1].as_text());
 
 
@@ -342,7 +342,7 @@ void run ()
           }
         } catch (...) {
           WARN ("Phase encoding scheme of input file does not match number of image volumes; omitting information from output image");
-          PhaseEncoding::set_scheme (header_out, pe_scheme);
+          PhaseEncoding::set_scheme (header_out, Eigen::MatrixXd());
         }
       }
     }

cmd/tckconvert.cpp

@@ -29,7 +29,8 @@ void usage ()
 {
   AUTHOR = "Daan Christiaens ([email protected]), "
            "J-Donald Tournier ([email protected]), "
-           "Philip Broser ([email protected]).";
+           "Philip Broser ([email protected]), "
+           "Daniel Blezek ([email protected]).";
 
   SYNOPSIS = "Convert between different track file formats";
 

docs/reference/commands/tckconvert.rst

@@ -80,7 +80,7 @@ Standard options
 
 
 
-**Author:** Daan Christiaens ([email protected]), J-Donald Tournier ([email protected]), Philip Broser ([email protected]).
+**Author:** Daan Christiaens ([email protected]), J-Donald Tournier ([email protected]), Philip Broser ([email protected]), Daniel Blezek ([email protected]).
 
 **Copyright:** Copyright (c) 2008-2017 the MRtrix3 contributors.
 

lib/mrtrix3/app.py

@@ -284,21 +284,24 @@ def debug(text):
   global colourClear, colourDebug
   global _verbosity
   if _verbosity <= 2: return
-  stack = inspect.stack()[1]
-  try:
-    filename = stack.filename
-    fname = stack.function
-  except: # Prior to Version 3.5
-    filename = stack[1]
-    fname = stack[3]
-  funcname = fname + '()'
-  modulename = inspect.getmodulename(filename)
-  if modulename:
-    funcname = modulename + '.' + funcname
-  # If debug() has been called from within some external function (e.g. a library function), it's often to report on the outcome of that function.
-  # In this instance, find the location where that function itself was called from, rather than where debug() was called from.
-  caller = inspect.getframeinfo(inspect.stack()[min(2,len(inspect.stack()))][0])
-  sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + colourDebug + '[DEBUG] ' + funcname + ' (from ' + os.path.basename(caller.filename) + ':' + str(caller.lineno) + '): ' + text + colourClear + '\n')
+  if len(inspect.stack()) == 2: # debug() called directly from script being executed
+    caller = inspect.getframeinfo(inspect.stack()[1][0])
+    origin = '(' + os.path.basename(caller.filename) + ':' + str(caller.lineno) + ')'
+  else: # Some function has called debug(): Get location of both that function, and where that function was invoked
+    stack = inspect.stack()[1]
+    try:
+      filename = stack.filename
+      fname = stack.function
+    except: # Prior to Version 3.5
+      filename = stack[1]
+      fname = stack[3]
+    funcname = fname + '()'
+    modulename = inspect.getmodulename(filename)
+    if modulename:
+      funcname = modulename + '.' + funcname
+    caller = inspect.getframeinfo(inspect.stack()[2][0])
+    origin = funcname + ' (from ' + os.path.basename(caller.filename) + ':' + str(caller.lineno) + ')'
+  sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + colourDebug + '[DEBUG] ' + origin + ': ' + text + colourClear + '\n')
 
 def error(text):
   import os, sys