Merge remote-tracking branch 'github/master' into dev

bin/population_template

@@ -994,7 +994,7 @@ def execute(): #pylint: disable=unused-variable
     if use_masks:
       progress = app.ProgressBar('Reslicing input masks to average header', len(ins))
       for inp in ins:
-        run.command('mrtransform ' + inp.ims_path[cid] + ' ' + inp.msk_transformed + ' ' +
+        run.command('mrtransform ' + inp.msk_path + ' ' + inp.msk_transformed + ' ' +
                     '-interp nearest -template ' + cns.templates[0] + ' ' +
                     datatype_option)
         progress.increment()

build

@@ -146,11 +146,13 @@ targets = []
 
 
 todo, headers, object_deps, file_flags = {}, {}, {}, {}
+formatstr=''
 lock = threading.Lock()
 print_lock = threading.Lock()
+index_lock = threading.Lock()
 stop = False
 error_stream = None
-main_cindex = 0
+todo_index = 0
 
 logfile = open ('build.log', 'wb') #pylint: disable=consider-using-with
 timingfile = None
@@ -687,6 +689,14 @@ for filepath in list_unexpected_bin_files(exe_suffix):
 class TargetException (Exception):
   pass
 
+
+def next_index ():
+  global todo_index
+  with index_lock:
+    todo_index+=1
+    return todo_index
+
+
 class Entry:
   def __init__ (self, name):
     name = os.path.normpath (name)
@@ -725,7 +735,8 @@ class Entry:
 
 
 
-  def execute (self, cindex, formatstr):
+  def execute (self):
+    global formatstr
     folder = os.path.dirname (self.name)
     try:
       os.makedirs (folder)
@@ -742,7 +753,7 @@ class Entry:
             fd.write ('<file>' + entry + '</file>\n')
         fd.write ('</qresource>\n</RCC>\n')
     if self.cmd:
-      return execute (formatstr.format (cindex, self.action, self.name), self.cmd)
+      return execute (formatstr.format (next_index(), self.action, self.name), self.cmd)
     return None
 
 
@@ -1079,25 +1090,21 @@ def list_lib_deps ():
 
 
 def build_next ():
-  global stop, main_cindex
-  total_count = len(todo)
-  cindex = 0
-  formatstr = '({:>'+str(len(str(total_count)))+'}/'+str(total_count)+') [{}] {}'
+  global stop, formatstr
+  formatstr = '({:>'+str(len(str(initial_num_todo)))+'}/'+str(initial_num_todo)+') [{}] {}'
 
   try:
     while not stop:
       current = None
       with lock:
         if todo:
-          for label, item in todo.items():
-            if item.currently_being_processed:
+          for name,entry in todo.items():
+            if entry.currently_being_processed:
               continue
-            unsatisfied_deps = set(item.deps).intersection (todo.keys())
+            unsatisfied_deps = set(entry.deps).intersection (todo.keys())
             if not unsatisfied_deps:
-              item.currently_being_processed = True
-              current = label
-              main_cindex+=1
-              cindex = main_cindex
+              entry.currently_being_processed = True
+              current = name
               break
         else:
           stop = max (stop, 1)
@@ -1109,15 +1116,16 @@ def build_next ():
         continue
 
       target = todo[current]
-      if target.execute(cindex, formatstr):
+      if target.execute():
         target.currently_being_processed = False
         stop = 2
         return
 
       with lock:
         del todo[current]
 
-  except Exception:
+  except Exception as excp:
+    disp (str(excp))
     stop = 2
     return
 
@@ -1408,19 +1416,8 @@ except TargetException as excp: # pylint: disable=unused-variable
 
 # for nogui config, remove GUI elements from targets and todo list:
 if nogui:
-  nogui_targets = []
-  for entry in targets:
-    if not is_GUI_target (entry):
-      nogui_targets.append (entry)
-  targets = nogui_targets
-
-  nogui_todo = {}
-  for label, item in todo.items():
-    if not is_GUI_target (item.name):
-      nogui_todo[label] = item
-  todo = nogui_todo
-
-
+  targets = [ entry for entry in targets if not is_GUI_target (entry) ]
+  todo = { name:entry for name, entry in todo.items() if not is_GUI_target (name) }
 
 
 
@@ -1444,11 +1441,9 @@ Printing dependencies for all files:
     entry.display()
   sys.exit (0)
 
-todo_tmp = {}
-for label, item in todo.items():
-  if item.action != '--' and item.need_rebuild():
-    todo_tmp[label] = item
-todo = todo_tmp
+
+# remove todo items that don't need rebuild:
+todo = { name:entry for name, entry in todo.items() if entry.action != '--' and entry.need_rebuild() }
 
 log ('TODO list contains ' + str(len(todo)) + ''' items
 
@@ -1464,18 +1459,19 @@ except (KeyError, ValueError):
     num_processors = os.sysconf('SC_NPROCESSORS_ONLN')
   except ValueError:
     num_processors = 1
+log ('''
 
-while todo:
+Build will use ''' + str(num_processors) + ''' threads
 
-  stop = False
-  main_cindex = 0
-  num_todo_previous = len(todo)
+''')
 
-  log ('''
 
-  launching ''' + str(num_processors) + ''' threads
+while todo:
 
-  ''')
+  stop = False
+  num_todo_previous = len(todo)
+  initial_num_todo = len(todo)
+  todo_index = 0
 
   threads = []
   for i in range (1, num_processors): # pylint: disable=unused-variable

cmd/connectomestats.cpp

@@ -271,7 +271,7 @@ void run()
       ++progress;
     }
   }
-  const bool nans_in_data = data.allFinite();
+  const bool nans_in_data = !data.allFinite();
 
   // Only add contrast matrix row number to image outputs if there's more than one hypothesis
   auto postfix = [&] (const size_t i) { return (num_hypotheses > 1) ? ("_" + hypotheses[i].name()) : ""; };
@@ -293,24 +293,24 @@ void run()
     }
     for (size_t i = 0; i != num_hypotheses; ++i) {
       if (!hypotheses[i].is_F()) {
-        save_matrix (mat2vec.V2M (abs_effect_size.col(i)), "abs_effect" + postfix(i) + ".csv");
+        save_matrix (mat2vec.V2M (abs_effect_size.col(i)), output_prefix + "abs_effect" + postfix(i) + ".csv");
         ++progress;
         if (num_vgs == 1)
-          save_matrix (mat2vec.V2M (std_effect_size.col(i)), "std_effect" + postfix(i) + ".csv");
+          save_matrix (mat2vec.V2M (std_effect_size.col(i)), output_prefix + "std_effect" + postfix(i) + ".csv");
       } else {
         ++progress;
       }
       ++progress;
     }
     if (nans_in_data || extra_columns.size()) {
-      save_matrix (mat2vec.V2M (cond), "cond.csv");
+      save_matrix (mat2vec.V2M (cond), output_prefix + "cond.csv");
       ++progress;
     }
     if (num_vgs == 1) {
-      save_matrix (mat2vec.V2M (stdev.row(0)), "std_dev.csv");
+      save_matrix (mat2vec.V2M (stdev.row(0)), output_prefix + "std_dev.csv");
     } else {
       for (size_t i = 0; i != num_vgs; ++i) {
-        save_matrix (mat2vec.V2M (stdev.row(i)), "std_dev" + str(i) + ".csv");
+        save_matrix (mat2vec.V2M (stdev.row(i)), output_prefix + "std_dev" + str(i) + ".csv");
         ++progress;
       }
     }

cmd/mrclusterstats.cpp

@@ -320,7 +320,7 @@ void run() {
       write_output (stdev.row(0), *v2v, prefix + "std_dev.mif", output_header);
     } else {
       for (size_t i = 0; i != num_vgs; ++i) {
-        write_output (stdev.row(i), *v2v, prefix + "std_dev.mif", output_header);
+        write_output (stdev.row(i), *v2v, prefix + "std_dev" + str(i) + ".mif", output_header);
         ++progress;
       }
     }

cmd/mrtransform.cpp

@@ -614,6 +614,8 @@ void run ()
     if (modulate_jac)
       apply_linear_jacobian (output, linear_transform);
 
+    DWI::export_grad_commandline (output);
+
   } else if (warp.valid()) {
 
     if (replace)