minor fixes

Yemini-Lab · Aug 8, 2024 · c443dbc · c443dbc
1 parent b47a923
commit c443dbc
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Showing 9 changed files with 38 additions and 13 deletions.
diff --git a/+Methods/ChunkyMethods.m b/+Methods/ChunkyMethods.m
@@ -152,7 +152,8 @@ function apply_colormap(app, actions, progress)
                 if exist('progress', 'var')
                     progress.Value = a/length(actions);
                 end
-
+
+                processed_vol = zeros(new_dims);
                 processed_vol = Methods.ChunkyMethods.apply_vol(app, actions{a}, processed_vol);
             end
 
@@ -221,17 +222,18 @@ function spectral_unmix(app, ctx)
 
             % Grab parent app & lock image processing tab.
             channel = ctx.Source.Tag;
-            app.proc_lock('lock');
+            Program.GUIHandling.gui_lock(app, 'lock', 'processing_tab');
 
             % Check if we've saved unmixing parameters. If not, initialize.
             if ~exist('app.spectral_cache', 'var')
-                app.spectral_cache = struct('ch_db', [], 'ch_px', {}, 'ch_val', {}, 'bg_px', [], 'bg_val', [], 'blurred_img', []);
+                app.spectral_cache = struct('ch_db', [0], 'ch_px', {}, 'ch_val', {}, 'bg_px', [], 'bg_val', [], 'blurred_img', []);
             end
 
             % Grab channel indices.
-            ch_idx = [app.RDropDown.Value, app.GDropDown.Value, app.BDropDown.Value, app.WDropDown.Value];
+            ch_idx = [str2num(app.ProcRDropDown.Value), str2num(app.ProcGDropDown.Value), str2num(app.ProcBDropDown.Value)];
 
-            check = uiconfirm(app.UIFigure,sprintf('Click on the pixel on this slice that best represents %s.', channel),'Confirmation','Options',{'OK', 'Select different slice'},'DefaultOption','OK');
+            check = uiconfirm(app.CELL_ID,sprintf('Click on the pixel on this slice that best represents %s.', channel),'Confirmation','Options',{'OK', 'Select different slice'},'DefaultOption','OK');
+            image_data = app.proc_image.data(:, :, :, :);
 
             switch check
                 case 'OK'
@@ -241,9 +243,9 @@ function spectral_unmix(app, ctx)
 
                     pixels = [pos(1), pos(2), round(app.proc_zSlider.Value)];
 
-                    r = impixel(app.image_data(:,:,app.proc_zSlider.Value, ch_idx(1)), pos(1), pos(2));
-                    g = impixel(app.image_data(:,:,app.proc_zSlider.Value, ch_idx(2)), pos(1), pos(2));
-                    b = impixel(app.image_data(:,:,app.proc_zSlider.Value, ch_idx(3)), pos(1), pos(2));
+                    r = impixel(image_data(:,:,app.proc_zSlider.Value, ch_idx(1)), pos(1), pos(2));
+                    g = impixel(image_data(:,:,app.proc_zSlider.Value, ch_idx(2)), pos(1), pos(2));
+                    b = impixel(image_data(:,:,app.proc_zSlider.Value, ch_idx(3)), pos(1), pos(2));
 
                     switch channel
                         case 'r'
@@ -265,22 +267,26 @@ function spectral_unmix(app, ctx)
                             % TBD
                     end
 
-                    if ~ismember(channel, app.spectral_cache.ch_db)
-                        app.spectral_cache.ch_db = [app.spectral_cache.ch_db, t_idx];
+                    if app.spectral_cache.ch_db ~= [0]
+                        if ~ismember(channel, app.spectral_cache.ch_db)
+                            app.spectral_cache.ch_db = [app.spectral_cache.ch_db, t_idx];
+                        end
+                    else
+                        app.spectral_cache.ch_db = [t_idx];
                     end
 
                     app.spectral_cache.ch_px{t_idx} = pixels;
 
                 case 'Select different slice'
-                    app.proc_lock('unlock');
+                    Program.GUIHandling.gui_lock(app, 'unlock', 'processing_tab');
                     return
             end
 
             % If necessary, grab background.
             if ~isempty(app.spectral_cache.bg_px)
                 bg_pixels = app.spectral_cache.bg_px;
             else
-                uiconfirm(app.UIFigure,'Click on the pixel on this slice that best represents background.','Confirmation','Options',{'OK'},'DefaultOption','OK');
+                uiconfirm(app.CELL_ID,'Click on the pixel on this slice that best represents background.','Confirmation','Options',{'OK'},'DefaultOption','OK');
                 color_roi = drawpoint(app.proc_xyAxes);
                 pos = round(color_roi.Position);
                 delete(color_roi);

diff --git a/+Wrapper/__pycache__/build_pdists.cpython-310.pyc b/+Wrapper/__pycache__/build_pdists.cpython-310.pyc
diff --git a/+Wrapper/__pycache__/build_tree.cpython-310.pyc b/+Wrapper/__pycache__/build_tree.cpython-310.pyc
diff --git a/+Wrapper/__pycache__/getters.cpython-310.pyc b/+Wrapper/__pycache__/getters.cpython-310.pyc
diff --git a/+Wrapper/__pycache__/n_io.cpython-310.pyc b/+Wrapper/__pycache__/n_io.cpython-310.pyc
diff --git a/+Wrapper/__pycache__/track_all.cpython-310.pyc b/+Wrapper/__pycache__/track_all.cpython-310.pyc
diff --git a/.gitignore b/.gitignore
@@ -188,3 +188,12 @@ External_Dependencies/matnwb/doc/matlabicon.gif
 External_Dependencies/matnwb/doc/simulinkicon.gif
 .idea/.name
 *.pyc
+*.pyc
+*.toc
+*.pyc
+*.pyz
++Wrapper/build/main/warn-main.txt
+*.html
++Wrapper/main.spec
+.idea/.name
+*.pkg
diff --git a/visualize_light.mlapp b/visualize_light.mlapp
diff --git a/win_visualize.prj b/win_visualize.prj
@@ -1,5 +1,5 @@
 <deployment-project plugin="plugin.ezdeploy" plugin-version="1.0">
-  <configuration build-checksum="145520311" file="C:\Users\sep27\Documents\GitHub\NeuroPAL_ID\win_visualize.prj" location="C:\Users\sep27\Documents\GitHub\NeuroPAL_ID" name="win_visualize" preferred-package-location="C:\Users\sep27\Documents\GitHub\NeuroPAL_ID\win_visualize\for_redistribution" preferred-package-type="package.type.exe" target="target.ezdeploy.standalone" target-name="Application Compiler">
+  <configuration build-checksum="3362907317" file="C:\Users\sep27\Documents\GitHub\NeuroPAL_ID\win_visualize.prj" location="C:\Users\sep27\Documents\GitHub\NeuroPAL_ID" name="win_visualize" preferred-package-location="C:\Users\sep27\Documents\GitHub\NeuroPAL_ID\win_visualize\for_redistribution" preferred-package-type="package.type.exe" target="target.ezdeploy.standalone" target-name="Application Compiler">
     <param.appname>NeuroPAL_ID</param.appname>
     <param.icon>${PROJECT_ROOT}\win_visualize_resources\icon.ico</param.icon>
     <param.icons>
@@ -117,6 +117,7 @@ Please add it to your desktop so you can easily find it.
       <file>${PROJECT_ROOT}\Data\Documents\Instructions.pdf</file>
     </fileset.package>
     <fileset.depfun>
+      <file>C:\Users\sep27\AppData\Roaming\MathWorks\MATLAB Add-Ons\Collections\Microscopy Image Browser 2 (MIB2)\ImportExportTools\HDF5\xml2struct.m</file>
       <file>C:\Users\sep27\AppData\Roaming\MathWorks\MATLAB Add-Ons\Collections\NeurodataWithoutBorders_matnwb(2)\+contrib\+blackrock\AddNEVFile.m</file>
       <file>C:\Users\sep27\AppData\Roaming\MathWorks\MATLAB Add-Ons\Collections\NeurodataWithoutBorders_matnwb(2)\+contrib\+blackrock\AddNSFile.m</file>
       <file>C:\Users\sep27\AppData\Roaming\MathWorks\MATLAB Add-Ons\Collections\NeurodataWithoutBorders_matnwb(2)\+contrib\+blackrock\get_channel_info.m</file>
@@ -744,8 +745,14 @@ Please add it to your desktop so you can easily find it.
       <file>${PROJECT_ROOT}\+DataHandling\imreadND2.m</file>
       <file>${PROJECT_ROOT}\+DataHandling\imreadVlab.m</file>
       <file>${PROJECT_ROOT}\+DataHandling\NeuroPALImage.m</file>
+      <file>${PROJECT_ROOT}\+DataHandling\readAnnoH5.m</file>
+      <file>${PROJECT_ROOT}\+DataHandling\readStimFile.m</file>
+      <file>${PROJECT_ROOT}\+DataHandling\readTrackmate.m</file>
+      <file>${PROJECT_ROOT}\+DataHandling\writeNWB.m</file>
+      <file>${PROJECT_ROOT}\+DataHandling\writeTrackMate.m</file>
       <file>${PROJECT_ROOT}\+Methods\AutoDetect.m</file>
       <file>${PROJECT_ROOT}\+Methods\AutoId.m</file>
+      <file>${PROJECT_ROOT}\+Methods\ChunkyMethods.m</file>
       <file>${PROJECT_ROOT}\+Methods\find_outlier.m</file>
       <file>${PROJECT_ROOT}\+Methods\logsumexp.m</file>
       <file>${PROJECT_ROOT}\+Methods\MatchHist.m</file>
@@ -762,10 +769,13 @@ Please add it to your desktop so you can easily find it.
       <file>${PROJECT_ROOT}\+Neurons\NeuronBirth.m</file>
       <file>${PROJECT_ROOT}\+Output\Illustration.m</file>
       <file>${PROJECT_ROOT}\+Output\ImageAnalysis.m</file>
+      <file>${PROJECT_ROOT}\+Program\GUIHandling.m</file>
       <file>${PROJECT_ROOT}\+Program\GUIPreferences.m</file>
       <file>${PROJECT_ROOT}\+Program\ProgramInfo.m</file>
+      <file>${PROJECT_ROOT}\+Program\ProgramTests.m</file>
       <file>${PROJECT_ROOT}\autoseg_window.mlapp</file>
       <file>${PROJECT_ROOT}\channel_selector.mlapp</file>
+      <file>${PROJECT_ROOT}\Data\Images\loading.gif</file>
       <file>${PROJECT_ROOT}\Data\Images\ZephIR_Logo.png</file>
       <file>${PROJECT_ROOT}\Data\Models\avg_hist.mat</file>
       <file>${PROJECT_ROOT}\Data\NeuroPAL\herm_data.mat</file>