Regular merge of master hotfixes to dev

.git-blame-ignore-revs

@@ -0,0 +1,99 @@
+# .git-blame-ignore-revs
+# If you want this file to be utilised whener you utilise "git blame" on your local instance of the repository,
+#   run the following command from its root directory:
+# git config blame.ignoreRevsFile .git-blame-ignore-revs
+
+9268f0874fc8b2c3af0a090b8084bd91707a115e
+#Author: Daan Christiaens <[email protected]>
+#Date:   Fri Dec 11 14:41:03 2015 +0100
+#   Update copyright header in all source files, as discussed in #9 and #31.
+
+3024a116078eabd3b1353fc8329a73144632c86c
+#Author: Thijs Dhollander <[email protected]>
+#Date:   Thu Nov 22 17:01:59 2018 +1100
+#    Copyright message update for next release (probably 2019-ish)
+#    Also updated the warranty statement: it appears this was still a formulation left over from the previous GPL license. The new formulation comes directly from the MPL 2.0, but is also more comprehensive; I'm more comfortable with having this more comprehensive.  Furthermore, apart from it apparently being quite important to have a warranty statement at the top of source code files, it's apparently also of little value if it's not either very comprehensive, or it also directly refers to the license where the full text can be found.  Hence, I added that as a sentence.
+#    Finally, also of note (and TODO) would be to add the copyright statement and a copy of the license somewhere on our (mrtrix.org) website. The final link is otherwise relatively useless in the context of the copyright and license statement.
+
+6c6c553ed9e9004ca8495ece436fec4db465d82b
+#Author: Thijs Dhollander <[email protected]>
+#Date:   Wed Dec 13 15:09:37 2017 +1100
+#    Copyright update for upcoming RC which will probably end up around New Year's
+#    Also includes a change of mention of MRtrix to MRtrix3, in line with the phrase MRtrix3 developers, which was already in there/
+#    Also includes removal of 2 .s, because they hindered clickability of the links in certain environments.
+
+654b7281c953f1068142d1f8a152f786862d8876
+#Author: Thijs Dhollander <[email protected]>
+#Date:   Wed Jan 25 17:57:11 2017 +1100
+#    header files
+
+b623e418e36de6884511d9c233b04392ecce89bb
+#Author: Thijs Dhollander <[email protected]>
+#Date:   Wed Jan 25 17:06:35 2017 +1100
+#    Copyright for 2017 in headers
+
+95b144df3d9eb837fae08129cc292c3fb8490eac
+#Author: Robert Smith <[email protected]>
+#Date:   Tue Oct 8 14:33:10 2019 +1100
+#    Add copyright notice to non-CPP files   
+#    Also includes some line ending conversions and indentation changes.
+
+be9a46286a9053fd1c1951fe5394206a95b61bfa
+#Author: MRtrixBot <[email protected]>
+#Date:   Thu May 14 11:30:13 2020 +1000
+#    Initial commit of "update_copyright" changes
+
+5e3112eae6ba4027aba854b3385f032c67dbfedf
+#Author: MRtrixBot <[email protected]>
+#Date:   Mon Feb 7 16:48:14 2022 +0000
+#    update copyright notice and corresponding docs
+
+e8edf6d946822c8ec23d077c2b1e9eef471b2539
+#Author: MRtrixBot <[email protected]>
+#Date:   Tue Jan 3 13:41:40 2023 +0100
+#    Update copyright notice
+
+74ff7cf0b76e2c9595b1341a7e4a49fa5491ce2f
+#Author: MRtrixBot <[email protected]>
+#Date:   Wed Jan 6 12:50:54 2021 +0000
+#    Update copyright notice
+
+65b3ea5e549f3f66a9e3c5d9ebdabb2a9bb462b4
+#Author: Thijs Dhollander <[email protected]>
+#Date:   Thu Nov 22 17:30:36 2018 +1100
+#    Fixed typo in copyright/warranty statement.
+
+729dd6cfc1a773f0f16592b8533c6e9d89d03ac3
+#Author: Thijs Dhollander <[email protected]>
+#Date:   Mon May 15 10:33:05 2017 +1000
+#    copyright update and cleanup
+
+76ad4fbb3ea60ea56ec94e3debfce1b7a35a9535
+#Author: rtabbara <[email protected]>
+#Date:   Thu Feb 18 11:55:53 2016 +1100
+#    User docs: Update commands list with new copyright
+
+6552f6ebe4f9fda441255063230ef9f8d9912591
+#Author: J-Donald Tournier <[email protected]>
+#Date:   Wed Feb 5 12:50:53 2020 +0000
+#    remove carriage returns
+
+811361d3af3ecfec03e20c2ee0f342634810a9c2
+#Author: Thijs Dhollander <[email protected]>
+#Date:   Tue May 9 09:09:51 2017 +1000
+#    docs update
+
+1eb36099870a0fffbc307ac40523dd8b6e35436f
+#Author: Thijs Dhollander <[email protected]>
+#Date:   Thu Feb 2 12:26:20 2017 +1100
+#    standardise number of blank lines between copyright header and the rest of a file (was getting a bit out of hand for some files; now it's 2 blank lines for all)
+
+e8edf6d946822c8ec23d077c2b1e9eef471b2539
+#Author: MRtrixBot <[email protected]>
+#Date:   Tue Jan 3 13:41:40 2023 +0100
+#    Update copyright notice
+
+aad44d847ac48d02bb7f8badf801dbfaa0ccdac0
+#Author: MRtrixBot <[email protected]>
+#Date:   Tue Jan 3 13:42:58 2023 +0100
+#    Update Copyright notice in command docs

.github/workflows/checks.yml

@@ -3,9 +3,11 @@ name: checks
 on:
   pull_request:
     types: [opened, synchronize]
-    branches:
-      - master
-      - dev
+    branches: [ master, dev ]
+  merge_group:
+    types: [checks_requested]
+    branches: [ master ]
+
 
 
 

core/app.cpp

@@ -128,7 +128,7 @@ namespace MR
       inline void get_matches (vector<const Option*>& candidates, const OptionGroup& group, const std::string& stub)
       {
         for (size_t i = 0; i < group.size(); ++i) {
-          if (stub.compare (0, stub.size(), group[i].id, stub.size()) == 0)
+          if (stub.compare (0, stub.size(), std::string(group[i].id), 0, stub.size()) == 0)
             candidates.push_back (&group[i]);
         }
       }

src/dwi/tractography/SIFT2/tckfactor.cpp

@@ -374,19 +374,22 @@ namespace MR {
       {
         if (size_t(coefficients.size()) != contributions.size())
           throw Exception ("Cannot output weighting factors if they have not first been estimated!");
+        decltype(coefficients) weights;
         try {
-          decltype(coefficients) weights (coefficients.size());
-          for (SIFT::track_t i = 0; i != num_tracks(); ++i)
-            weights[i] = (coefficients[i] == min_coeff || !std::isfinite(coefficients[i])) ?
-                         0.0 :
-                         std::exp (coefficients[i]);
-          save_vector (weights, path);
+          weights.resize (coefficients.size());
         } catch (...) {
           WARN ("Unable to assign memory for output factor file: \"" + Path::basename(path) + "\" not created");
+          return;
         }
+        for (SIFT::track_t i = 0; i != num_tracks(); ++i)
+          weights[i] = (coefficients[i] == min_coeff || !std::isfinite(coefficients[i])) ?
+                        0.0 :
+                        std::exp (coefficients[i]);
+        save_vector (weights, path);
       }
 
 
+
       void TckFactor::output_coefficients (const std::string& path) const
       {
         save_vector (coefficients, path);

src/gui/mrview/colourmap_button.cpp

@@ -118,10 +118,10 @@ void ColourMapButton::init_special_colour_menu_items(bool create_shortcuts)
 
 void ColourMapButton::init_customise_state_menu_items()
 {
-    auto show_colour_bar = colourmap_menu->addAction(tr("Show colour bar"), this, SLOT(show_colour_bar_slot(bool)));
-    show_colour_bar->setCheckable(true);
-    show_colour_bar->setChecked(true);
-    addAction(show_colour_bar);
+    show_colour_bar_action = colourmap_menu->addAction(tr("Show colour bar"), this, SLOT(show_colour_bar_slot(bool)));
+    show_colour_bar_action->setCheckable(true);
+    show_colour_bar_action->setChecked(true);
+    addAction(show_colour_bar_action);
 
     invert_scale_action = colourmap_menu->addAction(tr("Invert"), this, SLOT(invert_colourmap_slot(bool)));
     invert_scale_action->setCheckable(true);
@@ -163,12 +163,18 @@ void ColourMapButton::set_colourmap_index(size_t index)
     }
 }
 
-void ColourMapButton::set_scale_inverted(bool yesno)
+void ColourMapButton::set_scale_inverted (bool yesno)
 {
     assert (invert_scale_action != nullptr);
     invert_scale_action->setChecked (yesno);
 }
 
+void ColourMapButton::set_show_colourbar (bool yesno)
+{
+    assert (invert_scale_action != nullptr);
+    show_colour_bar_action->setChecked (yesno);
+}
+
 
 void ColourMapButton::set_fixed_colour()
 {

src/gui/mrview/colourmap_button.h

@@ -34,24 +34,25 @@ class ColourMapButton;
 class ColourMapButtonObserver
 { 
 public:
-    virtual void selected_colourmap(size_t, const ColourMapButton&) {}
-    virtual void selected_custom_colour(const QColor&, const ColourMapButton&) {}
-    virtual void toggle_show_colour_bar(bool, const ColourMapButton&) {}
-    virtual void toggle_invert_colourmap(bool, const ColourMapButton&) {}
-    virtual void reset_colourmap(const ColourMapButton&) {}
+    virtual void selected_colourmap (size_t, const ColourMapButton&) {}
+    virtual void selected_custom_colour (const QColor&, const ColourMapButton&) {}
+    virtual void toggle_show_colour_bar (bool, const ColourMapButton&) {}
+    virtual void toggle_invert_colourmap (bool, const ColourMapButton&) {}
+    virtual void reset_colourmap (const ColourMapButton&) {}
 };
 
 
 class ColourMapButton : public QToolButton
 { 
     Q_OBJECT
 public:
-    ColourMapButton(QWidget* parent, ColourMapButtonObserver& obs,
+    ColourMapButton (QWidget* parent, ColourMapButtonObserver& obs,
                     bool use_shortcuts = false,
                     bool use_special_colourmaps = true,
                     bool use_customise_state_items = true);
-    void set_colourmap_index(size_t index);
-    void set_scale_inverted(bool yesno);
+    void set_colourmap_index (size_t index);
+    void set_scale_inverted (bool yesno);
+    void set_show_colourbar (bool yesno);
     void set_fixed_colour();
     vector<QAction*> colourmap_actions;
     void open_menu (const QPoint& p) { colourmap_menu->exec (p); }
@@ -71,6 +72,7 @@ class ColourMapButton : public QToolButton
     QMenu* colourmap_menu;
     QAction* custom_colour_action;
     QAction* invert_scale_action;
+    QAction* show_colour_bar_action;
 
     size_t fixed_colour_index;
 

src/gui/mrview/displayable.h

@@ -138,10 +138,16 @@ namespace MR
             flags_ = cmap;
           }
 
-          void set_colour (std::array<GLubyte,3> &c) {
+          void set_colour (const std::array<GLubyte,3> &c) {
             colour = c;
           }
 
+          void set_colour (const QColor &c) {
+            colour[0] = c.red();
+            colour[1] = c.green();
+            colour[2] = c.blue();
+          }
+
           void set_use_discard_lower (bool yesno) {
             if (!discard_lower_enabled()) return;
             set_bit (DiscardLower, yesno);

src/gui/mrview/tool/overlay.cpp

@@ -631,7 +631,7 @@ namespace MR
               if (colourmap_index == -2)
                 colourmap_index = overlay->colourmap;
               else
-                colourmap_index = -1;                
+                colourmap_index = -1;
             }
             num_inverted += overlay->scale_inverted();
             rate += overlay->scaling_rate();