From dcb3b729c9e35bbb3d05692d3c910a71483b8e13 Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 11:46:56 +1000
Subject: [PATCH 01/13] GUI: rework the load_shapefile argument parsing

---
 lib/Biodiverse/GUI/Grid.pm | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/lib/Biodiverse/GUI/Grid.pm b/lib/Biodiverse/GUI/Grid.pm
index aabe68071..efd955339 100644
--- a/lib/Biodiverse/GUI/Grid.pm
+++ b/lib/Biodiverse/GUI/Grid.pm
@@ -627,8 +627,11 @@ sub set_overlay {
     }
     
     if ($shapefile) {
-        my @args = @{ $self->{dataset_info} };
-        $self->load_shapefile(@args, $shapefile, $colour);
+        $self->load_shapefile(
+            dataset_info => $self->{dataset_info},
+            file   => $shapefile,
+            colour => $colour,
+        );
     }
 
     return;
@@ -649,7 +652,12 @@ EOL
 }
 
 sub load_shapefile {
-    my ($self, $min_x, $min_y, $max_x, $max_y, $cell_x, $cell_y, $shapefile, $colour) = @_;
+    my ($self, %args) = @_;
+    # my ($self, $min_x, $min_y, $max_x, $max_y, $cell_x, $cell_y, $shapefile, $colour) = @_;
+    my $info = $args{info} // $self->{dataset_info};
+    my ($min_x, $min_y, $max_x, $max_y, $cell_x, $cell_y) = @$info;
+    my $shapefile = $args{file};
+    my $colour    = $args{colour};
 
     my @rect = (
         $min_x - $cell_x,
@@ -692,6 +700,7 @@ sub load_shapefile {
     );
 
     $shapefile_group->raise_to_top();
+    # $shapefile_group->lower_to_bottom();
     $self->{shapefile_group} = $shapefile_group;
 
     # Add all shapes
@@ -736,6 +745,7 @@ sub load_shapefile {
                 my $poly = Gnome2::Canvas::Item->new (
                     $shapefile_group,
                     'Gnome2::Canvas::Line',
+                    # 'Gnome2::Canvas::Polygon',
                     points          => \@plot_points,
                     fill_color_gdk  => $colour,
                 );

From cd2db2f1df81cd3a5552d17689da5591d6824cd6 Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 11:47:36 +1000
Subject: [PATCH 02/13] GUI: soften language when missing shapefiles removed
 from project

"Deleted" might make some users believe the files are deleted.
---
 lib/Biodiverse/GUI/Project.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/Biodiverse/GUI/Project.pm b/lib/Biodiverse/GUI/Project.pm
index 898ac4607..63a8eae3b 100644
--- a/lib/Biodiverse/GUI/Project.pm
+++ b/lib/Biodiverse/GUI/Project.pm
@@ -1551,7 +1551,7 @@ sub init_overlay_hash {
     # Tell user if any missing
     if ( scalar @missing_overlays > 0 ) {
         my $text =
-"The following overlays are missing and have been deleted from the project:\n";
+"The following overlays are missing and have been removed from the project:\n";
         foreach my $name (@missing_overlays) {
             $text .= "  $name\n";
         }

From 507f6cfe0754f1a434492daddbc5f7ff15c443a6 Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 12:12:21 +1000
Subject: [PATCH 03/13] GUI overlay selector: don't expand colour buttons

Previously these became larger as the window was made taller.
---
 bin/ui/wndOverlays.ui | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/ui/wndOverlays.ui b/bin/ui/wndOverlays.ui
index c40e0363e..c90b5d0ab 100644
--- a/bin/ui/wndOverlays.ui
+++ b/bin/ui/wndOverlays.ui
@@ -90,7 +90,7 @@
             </child>
           </object>
           <packing>
-            <property name="expand">True</property>
+            <property name="expand">False</property>
             <property name="fill">True</property>
             <property name="position">2</property>
           </packing>

From 4e1ea1b86df6921e6b691ab52c8d41361cd14866 Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 13:17:45 +1000
Subject: [PATCH 04/13] GUI: Support plotting of shapefiles as polygon

Currently defaults to being under the grid cells.
---
 lib/Biodiverse/GUI/Grid.pm     | 31 +++++++++-------
 lib/Biodiverse/GUI/Overlays.pm | 65 +++++++++++++++++++++++++++-------
 2 files changed, 72 insertions(+), 24 deletions(-)

diff --git a/lib/Biodiverse/GUI/Grid.pm b/lib/Biodiverse/GUI/Grid.pm
index efd955339..f15cf7d8f 100644
--- a/lib/Biodiverse/GUI/Grid.pm
+++ b/lib/Biodiverse/GUI/Grid.pm
@@ -616,9 +616,8 @@ sub get_base_struct {
 
 # Draws a polygonal shapefile
 sub set_overlay {
-    my $self      = shift;
-    my $shapefile = shift;
-    my $colour    = shift || OVERLAY_COLOUR;
+    my ($self, %args) = @_;
+
 
     # Delete any existing
     if ($self->{shapefile_group}) {
@@ -626,11 +625,11 @@ sub set_overlay {
         delete $self->{shapefile_group};
     }
     
-    if ($shapefile) {
+    if (defined $args{shapefile}) {
         $self->load_shapefile(
+            colour       => OVERLAY_COLOUR,  #  default
             dataset_info => $self->{dataset_info},
-            file   => $shapefile,
-            colour => $colour,
+            %args,
         );
     }
 
@@ -653,11 +652,12 @@ EOL
 
 sub load_shapefile {
     my ($self, %args) = @_;
-    # my ($self, $min_x, $min_y, $max_x, $max_y, $cell_x, $cell_y, $shapefile, $colour) = @_;
+
     my $info = $args{info} // $self->{dataset_info};
     my ($min_x, $min_y, $max_x, $max_y, $cell_x, $cell_y) = @$info;
-    my $shapefile = $args{file};
+    my $shapefile = $args{shapefile};
     my $colour    = $args{colour};
+    my $plot_as_poly = $args{plot_as_poly};
 
     my @rect = (
         $min_x - $cell_x,
@@ -699,8 +699,16 @@ sub load_shapefile {
         y => 0,
     );
 
-    $shapefile_group->raise_to_top();
-    # $shapefile_group->lower_to_bottom();
+    my $is_polygon = $shapefile->shape_type_text =~ m/polygon/i;
+
+    my $canvas_shape_type = 'Gnome2::Canvas::Line';
+    if ($is_polygon && $plot_as_poly) {
+        $canvas_shape_type = 'Gnome2::Canvas::Polygon';
+        $shapefile_group->lower_to_bottom();
+    }
+    else {
+        $shapefile_group->raise_to_top();
+    }
     $self->{shapefile_group} = $shapefile_group;
 
     # Add all shapes
@@ -744,8 +752,7 @@ sub load_shapefile {
             if (@plot_points > 2) { # must have more than one point (two coords)
                 my $poly = Gnome2::Canvas::Item->new (
                     $shapefile_group,
-                    'Gnome2::Canvas::Line',
-                    # 'Gnome2::Canvas::Polygon',
+                    $canvas_shape_type,
                     points          => \@plot_points,
                     fill_color_gdk  => $colour,
                 );
diff --git a/lib/Biodiverse/GUI/Overlays.pm b/lib/Biodiverse/GUI/Overlays.pm
index 1046d2c5a..224260c3a 100644
--- a/lib/Biodiverse/GUI/Overlays.pm
+++ b/lib/Biodiverse/GUI/Overlays.pm
@@ -14,6 +14,9 @@ use Biodiverse::GUI::Project;
 my $default_colour       = Gtk2::Gdk::Color->parse('#001169');
 my $last_selected_colour = $default_colour;
 
+use constant COL_FNAME     => 0;
+use constant COL_PLOT_POLY => 1;
+
 sub show_dialog {
     my $grid = shift;
 
@@ -70,12 +73,22 @@ sub init_overlay_list {
     my $tree = $dlgxml->get_object('treeOverlays');
 
     my $col_name = Gtk2::TreeViewColumn->new();
-    my $name_renderer = Gtk2::CellRendererText->new();
-    $col_name->set_title('Filename');
+    my $name_renderer = Gtk2::CellRendererText->new ();
+    $col_name->set_title('File name');
     $col_name->pack_start($name_renderer, 1);
     $col_name->add_attribute($name_renderer,  text => 0);
     $tree->insert_column($col_name, -1);
 
+    my $col_plot_poly = Gtk2::TreeViewColumn->new();
+    $col_plot_poly->set_title('Plot as polygon');
+    my $poly_renderer = Gtk2::CellRendererToggle->new();
+    $col_plot_poly->pack_start($poly_renderer, 0);
+    $poly_renderer->signal_connect('toggled' => \&_plot_poly_toggled, $model);
+    $col_plot_poly->set_attributes($poly_renderer,
+        'active' => 1,
+    );
+    $tree->insert_column($col_plot_poly, -1);
+
     #  fiddling around with colour selection
     #my $colColour = Gtk2::TreeViewColumn->new();
     #my $colour_button = Gtk2::CellRendererPixbuf->new();
@@ -84,25 +97,39 @@ sub init_overlay_list {
     #$colColour->add_attribute($colour_button, text => 0);
     #$tree->insert_column($colColour, -1);
 
-    $tree->set_headers_visible(0);
+    $tree->set_headers_visible(1);
     $tree->set_model($model);
 
     return $tree;
 }
 
+sub _plot_poly_toggled {
+    my ($cell, $path_str, $model) = @_;
+
+    my $path = Gtk2::TreePath->new_from_string ($path_str);
+
+    # get toggled iter
+    my $iter = $model->get_iter ($path);
+    my ($bool) = $model->get ($iter, COL_PLOT_POLY);
+
+    # toggle the value
+    $model->set ($iter, COL_PLOT_POLY, !$bool);
+}
+
 # Make the object tree that appears on the left
 sub make_overlay_model {
+    my $project = shift;
+
     my $model = Gtk2::ListStore->new(
         'Glib::String',
-        #'Glib::Boolean',  #  fiddling around with colour selection
+        'Glib::Boolean',
     );
-    my $project = shift;
 
     my $overlays = $project->get_overlay_list();
 
     foreach my $name (@{$overlays}) {
         my $iter = $model->append;
-        $model->set($iter, 0, $name);
+        $model->set($iter, 0, $name, 1, 1);
     }
 
 
@@ -120,9 +147,10 @@ sub get_selection {
     return if not $path;
 
     my $iter = $model->get_iter($path);
-    my $name = $model->get($iter, 0);
+    my $name = $model->get($iter, COL_FNAME);
+    my $plot_as_poly = $model->get($iter, COL_PLOT_POLY);
 
-    return wantarray ? ($name, $iter) : $name;
+    return wantarray ? ($iter, $name, $plot_as_poly) : $name;
 }
 
 
@@ -164,7 +192,7 @@ sub on_add {
 
     if (!_shp_type_is_point($filename)) {
         my $iter = $list->get_model->append;
-        $list->get_model->set($iter, 0, $filename);
+        $list->get_model->set($iter, COL_FNAME, $filename);
         my $sel = $list->get_selection;
         $sel->select_iter($iter);
 
@@ -193,12 +221,21 @@ sub _shp_type_is_point {
     return $type =~/point/i;
 }
 
+sub _shp_type_is_polygon {
+    my $name = shift;
+
+    my $shpfile = Geo::ShapeFile->new ($name);
+    my $type = $shpfile->shape_type_text;
+
+    return $type =~/polygon/i;
+}
+
 sub on_delete {
     my $button = shift;
     my $args = shift;
     my ($list, $project) = @$args;
 
-    my ($filename, $iter) = get_selection($list);
+    my ($iter, $filename) = get_selection($list);
     return if not $filename;
     $project->delete_overlay($filename);
     $list->get_model->remove($iter);
@@ -223,7 +260,7 @@ sub on_set {
     my $args = shift;
     my ($list, $project, $grid, $dlg, $colour_button) = @$args;
 
-    my $filename = get_selection($list);
+    my ($iter, $filename, $plot_as_poly) = get_selection($list);
 
     my $colour = $colour_button->get_color;
 
@@ -232,7 +269,11 @@ sub on_set {
     return if not $filename;
 
     print "[Overlay] Setting overlay to $filename\n";
-    $grid->set_overlay( $project->get_overlay($filename), $colour );
+    $grid->set_overlay(
+        shapefile    => $project->get_overlay($filename),
+        colour       => $colour,
+        plot_as_poly => $plot_as_poly,
+    );
     #$dlg->destroy();
 
     $last_selected_colour = $colour;

From 2889a4cc0001f6d51fcf9ef6a11951b0b5b2987a Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 13:57:17 +1000
Subject: [PATCH 05/13] GUI overlays: name button Remove instead of Delete

"Deleted" might make some users believe the files are deleted.

Similar to a previous change.
---
 bin/ui/wndOverlays.ui | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/ui/wndOverlays.ui b/bin/ui/wndOverlays.ui
index c90b5d0ab..d0b10fb42 100644
--- a/bin/ui/wndOverlays.ui
+++ b/bin/ui/wndOverlays.ui
@@ -121,13 +121,13 @@
             </child>
             <child>
               <object class="GtkButton" id="btnDelete">
-                <property name="label">gtk-delete</property>
+                <property name="label">Remove</property>
                 <property name="visible">True</property>
                 <property name="can_focus">True</property>
                 <property name="can_default">True</property>
                 <property name="receives_default">True</property>
                 <property name="has_tooltip">True</property>
-                <property name="tooltip-text" translatable="yes">Delete selected file from the list</property>
+                <property name="tooltip-text" translatable="yes">Remove selected entry from the list</property>
                 <property name="use_stock">True</property>
               </object>
               <packing>

From e050dbe05728582595867a98109b7623654e0565 Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 13:59:23 +1000
Subject: [PATCH 06/13] GUI: more refined removal of overlays

Previously we were deleting objects that were still needed.
This could occur when a file was loaded more than once.

The system simply reloaded in such cases but this avoids
doing that extra work.
---
 lib/Biodiverse/GUI/Overlays.pm | 10 ++++++----
 lib/Biodiverse/GUI/Project.pm  | 21 ++++++++++++---------
 2 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/lib/Biodiverse/GUI/Overlays.pm b/lib/Biodiverse/GUI/Overlays.pm
index 224260c3a..b86e30f0a 100644
--- a/lib/Biodiverse/GUI/Overlays.pm
+++ b/lib/Biodiverse/GUI/Overlays.pm
@@ -16,6 +16,7 @@ my $last_selected_colour = $default_colour;
 
 use constant COL_FNAME     => 0;
 use constant COL_PLOT_POLY => 1;
+use constant COL_COLOUR    => 1;
 
 sub show_dialog {
     my $grid = shift;
@@ -149,8 +150,9 @@ sub get_selection {
     my $iter = $model->get_iter($path);
     my $name = $model->get($iter, COL_FNAME);
     my $plot_as_poly = $model->get($iter, COL_PLOT_POLY);
+    my $array_iter = $path->to_string;  #  only works for a simple tree
 
-    return wantarray ? ($iter, $name, $plot_as_poly) : $name;
+    return wantarray ? ($iter, $name, $plot_as_poly, $array_iter) : $name;
 }
 
 
@@ -235,9 +237,9 @@ sub on_delete {
     my $args = shift;
     my ($list, $project) = @$args;
 
-    my ($iter, $filename) = get_selection($list);
-    return if not $filename;
-    $project->delete_overlay($filename);
+    my ($iter, $filename, undef, $array_iter) = get_selection($list);
+    return if not defined $filename;
+    $project->delete_overlay($filename, $array_iter);
     $list->get_model->remove($iter);
 
     return;
diff --git a/lib/Biodiverse/GUI/Project.pm b/lib/Biodiverse/GUI/Project.pm
index 63a8eae3b..8d7041152 100644
--- a/lib/Biodiverse/GUI/Project.pm
+++ b/lib/Biodiverse/GUI/Project.pm
@@ -1499,17 +1499,20 @@ sub get_overlay {
 sub delete_overlay {
     my $self = shift;
     my $name = shift;
+    my $array_iter = shift;
 
-    # Remove from list
-    foreach my $i ( 0 .. $#{ $self->{OVERLAYS} } ) {
-        if ( $self->{OVERLAYS}[$i] eq $name ) {
-            splice( @{ $self->{OVERLAYS} }, $i, 1 );
-            last;
-        }
-    }
+    my $overlays = $self->{OVERLAYS};
 
-    # remove from hash
-    delete $self->{overlay_objects}{$name};
+    # Remove from list unless not found or possible
+    $array_iter //= List::Util::first {$_ eq $name} @$overlays;
+    return if $array_iter < 0 || $array_iter > $#$overlays;
+
+    splice( @$overlays, $array_iter, 1 );
+
+    # remove from hash if no longer needed
+    if (!grep {$_ eq $name} @$overlays) {
+        delete $self->{overlay_objects}{$name};
+    }
 
     return;
 }

From e0a78e469ce79a9eee9c80000ecc0de3861ff425 Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 14:18:18 +1000
Subject: [PATCH 07/13] GUI overlays: rename some methods for clarity

---
 lib/Biodiverse/GUI/Overlays.pm | 6 +++---
 lib/Biodiverse/GUI/Project.pm  | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/Biodiverse/GUI/Overlays.pm b/lib/Biodiverse/GUI/Overlays.pm
index b86e30f0a..62886ee56 100644
--- a/lib/Biodiverse/GUI/Overlays.pm
+++ b/lib/Biodiverse/GUI/Overlays.pm
@@ -16,7 +16,7 @@ my $last_selected_colour = $default_colour;
 
 use constant COL_FNAME     => 0;
 use constant COL_PLOT_POLY => 1;
-use constant COL_COLOUR    => 1;
+# use constant COL_COLOUR    => 2;
 
 sub show_dialog {
     my $grid = shift;
@@ -130,7 +130,7 @@ sub make_overlay_model {
 
     foreach my $name (@{$overlays}) {
         my $iter = $model->append;
-        $model->set($iter, 0, $name, 1, 1);
+        $model->set($iter, COL_FNAME, $name, COL_PLOT_POLY, 0);
     }
 
 
@@ -272,7 +272,7 @@ sub on_set {
 
     print "[Overlay] Setting overlay to $filename\n";
     $grid->set_overlay(
-        shapefile    => $project->get_overlay($filename),
+        shapefile    => $project->get_overlay_shape_object($filename),
         colour       => $colour,
         plot_as_poly => $plot_as_poly,
     );
diff --git a/lib/Biodiverse/GUI/Project.pm b/lib/Biodiverse/GUI/Project.pm
index 8d7041152..7be976542 100644
--- a/lib/Biodiverse/GUI/Project.pm
+++ b/lib/Biodiverse/GUI/Project.pm
@@ -1477,7 +1477,7 @@ sub get_overlay_list {
     return $self->{OVERLAYS};
 }
 
-sub get_overlay {
+sub get_overlay_shape_object {
     my $self = shift;
     my $name = shift;
 

From 0a42cecdaa064ea38b1a3d2e4554a1c0ccc834a3 Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 15:11:45 +1000
Subject: [PATCH 08/13] GUI: show/hide the overlay dialog instead of rebuilding
 each time

This simplifies the attribute handing.
---
 lib/Biodiverse/GUI/GUIManager.pm |  1 +
 lib/Biodiverse/GUI/Overlays.pm   | 43 +++++++++++++++++++++++++-------
 2 files changed, 35 insertions(+), 9 deletions(-)

diff --git a/lib/Biodiverse/GUI/GUIManager.pm b/lib/Biodiverse/GUI/GUIManager.pm
index 872fa67ad..944086737 100644
--- a/lib/Biodiverse/GUI/GUIManager.pm
+++ b/lib/Biodiverse/GUI/GUIManager.pm
@@ -61,6 +61,7 @@ BEGIN {
         gladexml => undef,    # Main window widgets
         tabs => [],    # Stores refs to Tabs objects. In order of page index.
         progress_bars => undef,
+        overlay_components => undef,
         test_val      => ''
     };
     bless $singleton, 'Biodiverse::GUI::GUIManager';
diff --git a/lib/Biodiverse/GUI/Overlays.pm b/lib/Biodiverse/GUI/Overlays.pm
index 62886ee56..03be20faf 100644
--- a/lib/Biodiverse/GUI/Overlays.pm
+++ b/lib/Biodiverse/GUI/Overlays.pm
@@ -5,6 +5,7 @@ use warnings;
 use Gtk2;
 #use Data::Dumper;
 use Geo::ShapeFile;
+use Ref::Util qw/is_hashref/;
 
 our $VERSION = '4.99_002';
 
@@ -23,11 +24,26 @@ sub show_dialog {
 
     # Create dialog
     my $gui = Biodiverse::GUI::GUIManager->instance;
+    my $overlay_components = $gui->{overlay_components};
+
+    if ($overlay_components) {
+        my $dlg = $overlay_components->{dialog};
+        my $colour_button = $overlay_components->{colour_button};
+        $colour_button->set_color($last_selected_colour);
+        $dlg->show_all;
+        return;
+    }
+
     my $dlgxml = Gtk2::Builder->new();
     $dlgxml->add_from_file($gui->get_gtk_ui_file('wndOverlays.ui'));
     my $dlg = $dlgxml->get_object('wndOverlays');
     my $colour_button = $dlgxml->get_object('colorbutton_overlays');
-    $dlg->set_transient_for( $gui->get_object('wndMain') );
+    $dlg->set_transient_for($gui->get_object('wndMain'));
+
+    $gui->{overlay_components} = {
+        dialog        => $dlg, 
+        colour_button => $colour_button,
+    };
 
     $colour_button->set_color($last_selected_colour);
 
@@ -128,12 +144,21 @@ sub make_overlay_model {
 
     my $overlays = $project->get_overlay_list();
 
-    foreach my $name (@{$overlays}) {
+    foreach my $entry (@{$overlays}) {
         my $iter = $model->append;
-        $model->set($iter, COL_FNAME, $name, COL_PLOT_POLY, 0);
+        if (!is_hashref $entry) {  # previous versions did not store these
+            $entry = {
+                name         => $entry,
+                plot_as_poly => 0,
+            };
+        }
+        $model->set(
+            $iter,
+            COL_FNAME,     $entry->{name},
+            COL_PLOT_POLY, $entry->{plot_as_poly}
+        );
     }
 
-
     return $model;
 }
 
@@ -194,11 +219,11 @@ sub on_add {
 
     if (!_shp_type_is_point($filename)) {
         my $iter = $list->get_model->append;
-        $list->get_model->set($iter, COL_FNAME, $filename);
+        $list->get_model->set($iter, COL_FNAME, $filename, COL_PLOT_POLY, 0);
         my $sel = $list->get_selection;
         $sel->select_iter($iter);
 
-        $project->add_overlay($filename);
+        $project->add_overlay({name => $filename});
     }
     else {  #  warn about points - one day we will fix this
         my $error = "Selected shapefile is a point type.";
@@ -252,7 +277,7 @@ sub on_clear {
     my ($list, $project, $grid, $dlg) = @$args;
 
     $grid->set_overlay(undef);
-    $dlg->destroy();
+    $dlg->hide();
 
     return;
 }
@@ -266,7 +291,7 @@ sub on_set {
 
     my $colour = $colour_button->get_color;
 
-    $dlg->destroy;
+    $dlg->hide;
 
     return if not $filename;
 
@@ -287,7 +312,7 @@ sub on_cancel {
     my $button = shift;
     my $dlg    = shift;
 
-    $dlg->destroy;
+    $dlg->hide;
 
     return;
 }

From f1345f032ec7125f6366a5707ff87948c9cc696d Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 15:30:47 +1000
Subject: [PATCH 09/13] GUI overlays: handle new hash structure

---
 lib/Biodiverse/GUI/Project.pm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/lib/Biodiverse/GUI/Project.pm b/lib/Biodiverse/GUI/Project.pm
index 7be976542..124563862 100644
--- a/lib/Biodiverse/GUI/Project.pm
+++ b/lib/Biodiverse/GUI/Project.pm
@@ -1519,10 +1519,10 @@ sub delete_overlay {
 
 sub add_overlay {
     my $self = shift;
-    my $name = shift;
+    my $entry = shift;
 
-    $self->{overlay_objects}{$name} = undef;
-    push @{ $self->{OVERLAYS} }, $name;
+    $self->{overlay_objects}{$entry->{name}} = undef;
+    push @{ $self->{OVERLAYS} }, $entry;
 
     return;
 }
@@ -1534,13 +1534,14 @@ sub init_overlay_hash {
     my $existing_overlays = [];
     my @missing_overlays;
 
-    foreach my $name ( @{ $self->{OVERLAYS} } ) {
+    foreach my $entry ( @{ $self->{OVERLAYS} } ) {
+        my $name = is_hashref $entry ? $entry->{name} : $entry;
 
         if ( Biodiverse::Common->file_is_readable (file_name => $name) ) {
 
             # Set hash entry to undef - will load on demand
             $self->{overlay_objects}{$name} = undef;
-            push @$existing_overlays, $name;
+            push @$existing_overlays, $entry;
         }
         else {
             print "[Project] Missing overlay: $name\n";

From 2ba6777be9b99f47bbd87f41c32c95793bbab032 Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 15:31:36 +1000
Subject: [PATCH 10/13] GUI overlays: use methods to access components

---
 lib/Biodiverse/GUI/GUIManager.pm | 10 ++++++++++
 lib/Biodiverse/GUI/Overlays.pm   |  8 ++++----
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/lib/Biodiverse/GUI/GUIManager.pm b/lib/Biodiverse/GUI/GUIManager.pm
index 944086737..e393ec6b5 100644
--- a/lib/Biodiverse/GUI/GUIManager.pm
+++ b/lib/Biodiverse/GUI/GUIManager.pm
@@ -332,6 +332,16 @@ sub show_progress {
     }
 }
 
+sub get_overlay_components {
+    my ($self) = @_;
+    return $self->{overlay_components};
+}
+
+sub set_overlay_components {
+    my ($self, $components) = @_;
+    $self->{overlay_components} = $components;
+}
+
 ##########################################################
 # Initialisation
 ##########################################################
diff --git a/lib/Biodiverse/GUI/Overlays.pm b/lib/Biodiverse/GUI/Overlays.pm
index 03be20faf..c30eea366 100644
--- a/lib/Biodiverse/GUI/Overlays.pm
+++ b/lib/Biodiverse/GUI/Overlays.pm
@@ -24,7 +24,7 @@ sub show_dialog {
 
     # Create dialog
     my $gui = Biodiverse::GUI::GUIManager->instance;
-    my $overlay_components = $gui->{overlay_components};
+    my $overlay_components = $gui->get_overlay_components;
 
     if ($overlay_components) {
         my $dlg = $overlay_components->{dialog};
@@ -40,10 +40,10 @@ sub show_dialog {
     my $colour_button = $dlgxml->get_object('colorbutton_overlays');
     $dlg->set_transient_for($gui->get_object('wndMain'));
 
-    $gui->{overlay_components} = {
+    $gui->set_overlay_components ({
         dialog        => $dlg, 
         colour_button => $colour_button,
-    };
+    });
 
     $colour_button->set_color($last_selected_colour);
 
@@ -276,7 +276,7 @@ sub on_clear {
     my $args = shift;
     my ($list, $project, $grid, $dlg) = @$args;
 
-    $grid->set_overlay(undef);
+    $grid->set_overlay();
     $dlg->hide();
 
     return;

From 17ce982c7d64f09d3bd58f728de61d58486f53b7 Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Mon, 3 Jun 2024 16:08:11 +1000
Subject: [PATCH 11/13] GUI overlays: get_selection returns a hash in list
 context

This simplifies later expansion of returned values.
---
 lib/Biodiverse/GUI/Overlays.pm | 28 +++++++++++++++++++++++++---
 1 file changed, 25 insertions(+), 3 deletions(-)

diff --git a/lib/Biodiverse/GUI/Overlays.pm b/lib/Biodiverse/GUI/Overlays.pm
index c30eea366..5c1972ade 100644
--- a/lib/Biodiverse/GUI/Overlays.pm
+++ b/lib/Biodiverse/GUI/Overlays.pm
@@ -1,5 +1,6 @@
 package Biodiverse::GUI::Overlays;
 
+use 5.010;
 use strict;
 use warnings;
 use Gtk2;
@@ -91,6 +92,7 @@ sub init_overlay_list {
 
     my $col_name = Gtk2::TreeViewColumn->new();
     my $name_renderer = Gtk2::CellRendererText->new ();
+    #$name_renderer->signal_connect('toggled' => \&_update_colour_for_selection, $model);
     $col_name->set_title('File name');
     $col_name->pack_start($name_renderer, 1);
     $col_name->add_attribute($name_renderer,  text => 0);
@@ -133,6 +135,19 @@ sub _plot_poly_toggled {
     $model->set ($iter, COL_PLOT_POLY, !$bool);
 }
 
+# sub _update_colour_for_selection {
+#     my ($cell, $path_str, $model) = @_;
+#
+#     my $path = Gtk2::TreePath->new_from_string ($path_str);
+#
+#     # get toggled iter
+#     my $iter = $model->get_iter ($path);
+#     my $colour = $model->get ($iter, COL_PLOT_COLOUR);
+#
+#     # toggle the value
+#     $model->set ($iter, COL_PLOT_POLY, !$bool);
+# }
+
 # Make the object tree that appears on the left
 sub make_overlay_model {
     my $project = shift;
@@ -177,7 +192,9 @@ sub get_selection {
     my $plot_as_poly = $model->get($iter, COL_PLOT_POLY);
     my $array_iter = $path->to_string;  #  only works for a simple tree
 
-    return wantarray ? ($iter, $name, $plot_as_poly, $array_iter) : $name;
+    return wantarray
+        ? (iter => $iter, filename => $name, plot_as_poly => $plot_as_poly, array_iter => $array_iter)
+        : $name;
 }
 
 
@@ -262,7 +279,9 @@ sub on_delete {
     my $args = shift;
     my ($list, $project) = @$args;
 
-    my ($iter, $filename, undef, $array_iter) = get_selection($list);
+    # my ($iter, $filename, undef, $array_iter) = get_selection($list);
+    my %results = get_selection($list);
+    my ($iter, $filename, $array_iter) = @results{qw/iter filename array_iter/};
     return if not defined $filename;
     $project->delete_overlay($filename, $array_iter);
     $list->get_model->remove($iter);
@@ -287,7 +306,10 @@ sub on_set {
     my $args = shift;
     my ($list, $project, $grid, $dlg, $colour_button) = @$args;
 
-    my ($iter, $filename, $plot_as_poly) = get_selection($list);
+    # my ($iter, $filename, $plot_as_poly, $array_iter) = get_selection($list);
+    my %results = get_selection($list);
+    my ($iter, $filename, $plot_as_poly, $array_iter)
+        = @results{qw /iter filename plot_as_poly array_iter/};
 
     my $colour = $colour_button->get_color;
 

From 18b3413d7d74f12c4ceec9455b55a766251e373e Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Tue, 4 Jun 2024 09:40:20 +1000
Subject: [PATCH 12/13] GUI overlays: attempt at per-layer colours, currently
 disabled

---
 lib/Biodiverse/GUI/Overlays.pm | 97 +++++++++++++++++++++++++---------
 1 file changed, 72 insertions(+), 25 deletions(-)

diff --git a/lib/Biodiverse/GUI/Overlays.pm b/lib/Biodiverse/GUI/Overlays.pm
index 5c1972ade..d383217eb 100644
--- a/lib/Biodiverse/GUI/Overlays.pm
+++ b/lib/Biodiverse/GUI/Overlays.pm
@@ -16,9 +16,10 @@ use Biodiverse::GUI::Project;
 my $default_colour       = Gtk2::Gdk::Color->parse('#001169');
 my $last_selected_colour = $default_colour;
 
-use constant COL_FNAME     => 0;
-use constant COL_PLOT_POLY => 1;
-# use constant COL_COLOUR    => 2;
+use constant COL_FNAME       => 0;
+use constant COL_PLOT_POLY   => 1;
+use constant COL_PLOT_COLOUR => 2;
+use constant COL_PLOT_COLOUR_BK => 3;
 
 sub show_dialog {
     my $grid = shift;
@@ -95,7 +96,7 @@ sub init_overlay_list {
     #$name_renderer->signal_connect('toggled' => \&_update_colour_for_selection, $model);
     $col_name->set_title('File name');
     $col_name->pack_start($name_renderer, 1);
-    $col_name->add_attribute($name_renderer,  text => 0);
+    $col_name->add_attribute($name_renderer,  text => COL_FNAME);
     $tree->insert_column($col_name, -1);
 
     my $col_plot_poly = Gtk2::TreeViewColumn->new();
@@ -108,13 +109,24 @@ sub init_overlay_list {
     );
     $tree->insert_column($col_plot_poly, -1);
 
-    #  fiddling around with colour selection
-    #my $colColour = Gtk2::TreeViewColumn->new();
-    #my $colour_button = Gtk2::CellRendererPixbuf->new();
-    #$colColour->set_title('Colour');
-    #$colColour->pack_start($colour_button, 1);
-    #$colColour->add_attribute($colour_button, text => 0);
-    #$tree->insert_column($colColour, -1);
+    # my $col_colour = Gtk2::TreeViewColumn->new();
+    # my $colour_renderer_toggle = Gtk2::CellRendererToggle->new();
+    # my $colour_renderer_text   = Gtk2::CellRendererText->new();
+    # $col_colour->set_title('Colour');
+    # $col_colour->pack_start($colour_renderer_toggle, 0);
+    # $col_colour->pack_start($colour_renderer_text, 0);
+    # $col_colour->add_attribute($colour_renderer_toggle, active => COL_PLOT_COLOUR);
+    # $col_colour->set_attributes($colour_renderer_toggle, active => 1);
+    # $col_colour->add_attribute($colour_renderer_text,
+    #     'cell-background' => COL_PLOT_COLOUR_BK,
+    # );
+    # $col_colour->set_attributes($colour_renderer_text,
+    #     'cell-background' => COL_PLOT_COLOUR_BK,
+    # );
+    # $colour_renderer_toggle->signal_connect(
+    #     'toggled' => \&_update_colour_for_selection, $model
+    # );
+    # $tree->insert_column($col_colour, -1);
 
     $tree->set_headers_visible(1);
     $tree->set_model($model);
@@ -135,18 +147,45 @@ sub _plot_poly_toggled {
     $model->set ($iter, COL_PLOT_POLY, !$bool);
 }
 
-# sub _update_colour_for_selection {
-#     my ($cell, $path_str, $model) = @_;
-#
-#     my $path = Gtk2::TreePath->new_from_string ($path_str);
-#
-#     # get toggled iter
-#     my $iter = $model->get_iter ($path);
-#     my $colour = $model->get ($iter, COL_PLOT_COLOUR);
-#
-#     # toggle the value
-#     $model->set ($iter, COL_PLOT_POLY, !$bool);
-# }
+sub _update_colour_for_selection {
+    my ($cell, $path_str, $model) = @_;
+
+    my $path = Gtk2::TreePath->new_from_string ($path_str);
+
+    # get toggled iter
+    my $iter = $model->get_iter ($path);
+    my ($bool) = $model->get ($iter, COL_PLOT_COLOUR);
+
+    my $gui = Biodiverse::GUI::GUIManager->instance;
+    my $overlay_components = $gui->get_overlay_components;
+    my $colour_button = $overlay_components->{colour_button};
+
+    my $colour = $model->get ($iter, COL_PLOT_COLOUR_BK);
+    if (!defined $colour or $colour eq 'undef') {
+        $colour = $colour_button->get_colour; #$self->get_last_colour;
+    }
+
+    if (!Scalar::Util::blessed $colour) {
+        $colour = Gtk2::Gdk::Color->parse($colour);
+    }
+    $colour_button->set_color($colour);
+
+    $colour_button->clicked;
+    $colour = $colour_button->get_color;
+
+    say STDERR $bool, ' ', $colour->to_string;
+
+    # toggle the value
+    $model->set ($iter,
+        COL_PLOT_COLOUR, !$bool,
+    );
+    $model->set ($iter,
+        COL_PLOT_COLOUR_BK, $colour->to_string,
+        # 'cell-background' => $colour->to_string,
+    );
+    say '--- ' .  $model->get ($iter, COL_PLOT_COLOUR);
+    say '--- ' .  $model->get ($iter, COL_PLOT_COLOUR_BK);
+}
 
 # Make the object tree that appears on the left
 sub make_overlay_model {
@@ -155,6 +194,8 @@ sub make_overlay_model {
     my $model = Gtk2::ListStore->new(
         'Glib::String',
         'Glib::Boolean',
+        # 'Glib::Boolean',  #  next two are colour stuff
+        # 'Glib::String',
     );
 
     my $overlays = $project->get_overlay_list();
@@ -165,12 +206,18 @@ sub make_overlay_model {
             $entry = {
                 name         => $entry,
                 plot_as_poly => 0,
+                # has_colour   => undef,
+                # colour       => undef,
             };
         }
+        # use DDP;
+        # p $entry;
         $model->set(
             $iter,
-            COL_FNAME,     $entry->{name},
-            COL_PLOT_POLY, $entry->{plot_as_poly}
+            COL_FNAME,       $entry->{name},
+            COL_PLOT_POLY,   $entry->{plot_as_poly},
+            # COL_PLOT_COLOUR, !!$entry->{colour},
+            # COL_PLOT_COLOUR_BK, ($entry->{colour} // 'white'),
         );
     }
 

From a68f4887daba75dc59c1fb6acbd0888c74fc7383 Mon Sep 17 00:00:00 2001
From: shawnlaffan <shawnlaffan@gmail.com>
Date: Tue, 4 Jun 2024 12:10:18 +1000
Subject: [PATCH 13/13] GUI overlays: ensure the overlay dialogue only links to
 the current grid

Otherwise we trigger replots across all open tabs,
which currently is not what we want.
---
 lib/Biodiverse/GUI/Overlays.pm | 88 ++++++++++++++++++++++++----------
 1 file changed, 64 insertions(+), 24 deletions(-)

diff --git a/lib/Biodiverse/GUI/Overlays.pm b/lib/Biodiverse/GUI/Overlays.pm
index d383217eb..4f592405d 100644
--- a/lib/Biodiverse/GUI/Overlays.pm
+++ b/lib/Biodiverse/GUI/Overlays.pm
@@ -27,11 +27,19 @@ sub show_dialog {
     # Create dialog
     my $gui = Biodiverse::GUI::GUIManager->instance;
     my $overlay_components = $gui->get_overlay_components;
+    my $project = $gui->get_project;
 
     if ($overlay_components) {
-        my $dlg = $overlay_components->{dialog};
+        my $dlg           = $overlay_components->{dialog};
         my $colour_button = $overlay_components->{colour_button};
         $colour_button->set_color($last_selected_colour);
+
+        set_button_actions (
+            project => $project,
+            grid    => $grid,
+            %$overlay_components,
+        );
+
         $dlg->show_all;
         return;
     }
@@ -42,48 +50,80 @@ sub show_dialog {
     my $colour_button = $dlgxml->get_object('colorbutton_overlays');
     $dlg->set_transient_for($gui->get_object('wndMain'));
 
-    $gui->set_overlay_components ({
-        dialog        => $dlg, 
-        colour_button => $colour_button,
-    });
-
     $colour_button->set_color($last_selected_colour);
 
-    my $project = $gui->get_project;
     my $model = make_overlay_model($project);
     my $list = init_overlay_list($dlgxml, $model);
 
+    my %buttons = map {$_ => $dlgxml->get_object($_)}
+        (qw /btnAdd btnDelete btnClear btnSet btnOverlayCancel btn_overlay_set_default_colour/);
+    my %components = (
+        dialog        => $dlg,
+        colour_button => $colour_button,
+        list          => $list,
+        buttons       => \%buttons,
+    );
+
+    my $signals = set_button_actions (
+        %components,
+        project       => $project,
+        grid          => $grid,
+    );
+
+    #  store some but not all components we set actions for
+    $gui->set_overlay_components ({
+        %components,
+        signals       => $signals,
+    });
+
+    $dlg->set_modal(1);
+    $dlg->show_all();
+
+    return;
+}
+
+sub set_button_actions {
+    my %args = @_;
+    my ($list, $project, $grid, $dlg, $colour_button)
+        = @args{qw /list project grid dialog colour_button/};
+
+    my $buttons = $args{buttons};
+    my $signals = $args{signals} // {};
     # Connect buttons
-    $dlgxml->get_object('btnAdd')->signal_connect(
+
+    #  these are always the same
+    $signals->{btnAdd} //= $buttons->{btnAdd}->signal_connect(
         clicked => \&on_add,
         [$list, $project],
     );
-    $dlgxml->get_object('btnDelete')->signal_connect(
+    $signals->{btnDelete} //= $buttons->{btnDelete}->signal_connect(
         clicked => \&on_delete,
         [$list, $project],
     );
-    $dlgxml->get_object('btnClear')->signal_connect(
-        clicked => \&on_clear,
-        [$list, $project, $grid, $dlg],
-    );
-    $dlgxml->get_object('btnSet')->signal_connect(
-        clicked => \&on_set,
-        [$list, $project, $grid, $dlg, $colour_button],
-    );
-    $dlgxml->get_object('btnOverlayCancel')->signal_connect(
+    $signals->{btnOverlayCancel} //= $buttons->{btnOverlayCancel}->signal_connect(
         clicked => \&on_cancel,
         $dlg,
     );
-    $dlgxml->get_object('btn_overlay_set_default_colour')->signal_connect(
+    $signals->{btn_overlay_set_default_colour}
+        //= $buttons->{btn_overlay_set_default_colour}->signal_connect(
         clicked => \&on_set_default_colour,
         $colour_button,
     );
 
-
-    $dlg->set_modal(1);
-    $dlg->show_all();
-
-    return;
+    #  these vary by grid so need to be disconnected first or we mess up other plots
+    foreach my $btn (qw/btnClear btnSet/) {
+        my $id = $signals->{$btn} // next;
+        $buttons->{$btn}->signal_handler_disconnect($id);
+    }
+    $signals->{btnClear} = $buttons->{btnClear}->signal_connect(
+        clicked => \&on_clear,
+        [$list, $project, $grid, $dlg],
+    );
+    $signals->{btnSet} = $buttons->{btnSet}->signal_connect(
+        clicked => \&on_set,
+        [$list, $project, $grid, $dlg, $colour_button],
+    );
+    return $signals;
 }
 
 sub init_overlay_list {