Commit before snapshot generation

Author: stegmaierj

Source/aktparawin_livecellminer.m

@@ -1,6 +1,6 @@
 %%
 % LiveCellMiner.
-% Copyright (C) 2020 D. Moreno-Andres, A. Bhattacharyya, W. Antonin, J. Stegmaier
+% Copyright (C) 2021 D. Moreno-Andrés, A. Bhattacharyya, W. Antonin, J. Stegmaier
 %
 % Licensed under the Apache License, Version 2.0 (the "License");
 % you may not use this file except in compliance with the License.

Source/callback_chromatindec_estimate_cell_cycle_stage.m

@@ -1,6 +1,6 @@
 %%
 % LiveCellMiner.
-% Copyright (C) 2020 D. Moreno-Andres, A. Bhattacharyya, W. Antonin, J. Stegmaier
+% Copyright (C) 2021 D. Moreno-Andrés, A. Bhattacharyya, W. Antonin, J. Stegmaier
 %
 % Licensed under the Apache License, Version 2.0 (the "License");
 % you may not use this file except in compliance with the License.
@@ -72,9 +72,9 @@
         definput = {zgf_y_bez(experimentId, associatedExperiments(1)).name};
         combinedName = inputdlg(prompt,dlgtitle,[1 100],definput);
 
-        zgf_y_bez(outputVariableId, i).name = combinedName{1};
+        zgf_y_bez(outputVariableId, i).name = combinedName{1}; %#ok<SAGROW> 
     else
-        zgf_y_bez(outputVariableId, i).name = zgf_y_bez(experimentId, associatedExperiments).name;
+        zgf_y_bez(outputVariableId, i).name = zgf_y_bez(experimentId, associatedExperiments).name; %#ok<SAGROW> 
     end
 end
 

Source/callback_livecellminer_add_combined_experiment_output_variable.m

@@ -1,6 +1,6 @@
 %%
 % LiveCellMiner.
-% Copyright (C) 2020 D. Moreno-Andres, A. Bhattacharyya, W. Antonin, J. Stegmaier
+% Copyright (C) 2021 D. Moreno-Andrés, A. Bhattacharyya, W. Antonin, J. Stegmaier
 %
 % Licensed under the Apache License, Version 2.0 (the "License");
 % you may not use this file except in compliance with the License.
@@ -76,7 +76,7 @@
 
 	%% open the text file and process each line
     fileID = fopen(oligoIdTextFile);
-    currentLine = fgetl(fileID); %% skip the specifiers
+    fgetl(fileID); %% skip the specifiers
     currentLine = fgetl(fileID);
 
 	%% process all lines
@@ -101,7 +101,7 @@
         if (existingID == 0)
             existingID = length(oligoIDs)+1;
             oligoIDs{existingID} = currentOligoID;
-            zgf_y_bez(newOutputVariable,existingID).name = currentOligoID;
+            zgf_y_bez(newOutputVariable,existingID).name = currentOligoID; %#ok<SAGROW> 
         end
 
         %% find positionId in the output variable

Source/callback_livecellminer_add_oligoid_output_variable.m

@@ -1,6 +1,6 @@
 %%
 % LiveCellMiner.
-% Copyright (C) 2020 D. Moreno-Andres, A. Bhattacharyya, W. Antonin, J. Stegmaier
+% Copyright (C) 2021 D. Moreno-Andrés, A. Bhattacharyya, W. Antonin, J. Stegmaier
 %
 % Licensed under the Apache License, Version 2.0 (the "License");
 % you may not use this file except in compliance with the License.

Source/callback_livecellminer_batch_processing.m

@@ -1,6 +1,6 @@
 %%
 % LiveCellMiner.
-% Copyright (C) 2020 D. Moreno-Andres, A. Bhattacharyya, W. Antonin, J. Stegmaier
+% Copyright (C) 2021 D. Moreno-Andrés, A. Bhattacharyya, W. Antonin, J. Stegmaier
 %
 % Licensed under the Apache License, Version 2.0 (the "License");
 % you may not use this file except in compliance with the License.
@@ -97,9 +97,9 @@
                     currentMother(2:3) = [currentMother(3)-timeWindowMother+1, currentMother(3)];
                     currentDaughter1(2:3) = [currentDaughter1(2), currentDaughter1(2) + timeWindowDaughter - 1];
                     currentDaughter2(2:3) = [currentDaughter2(2), currentDaughter2(2) + timeWindowDaughter - 1];                    
-                    motherList = [motherList; currentMother];
-                    daughterList = [daughterList; currentDaughter1; currentDaughter2];
-                    motherDaughterList = [motherDaughterList; motherIndex, daughter1Index, daughter2Index];
+                    motherList = [motherList; currentMother]; %#ok<AGROW> 
+                    daughterList = [daughterList; currentDaughter1; currentDaughter2]; %#ok<AGROW> 
+                    motherDaughterList = [motherDaughterList; motherIndex, daughter1Index, daughter2Index]; %#ok<AGROW> 
                 end
             end
         end

Source/callback_livecellminer_candidate_list_generation.m

@@ -1,6 +1,6 @@
 %%
 % LiveCellMiner.
-% Copyright (C) 2020 D. Moreno-Andres, A. Bhattacharyya, W. Antonin, J. Stegmaier
+% Copyright (C) 2021 D. Moreno-Andrés, A. Bhattacharyya, W. Antonin, J. Stegmaier
 %
 % Licensed under the Apache License, Version 2.0 (the "License");
 % you may not use this file except in compliance with the License.

Source/callback_livecellminer_cell_patch_extraction.m

@@ -1,6 +1,6 @@
 %%
 % LiveCellMiner.
-% Copyright (C) 2020 D. Moreno-Andres, A. Bhattacharyya, W. Antonin, J. Stegmaier
+% Copyright (C) 2021 D. Moreno-Andrés, A. Bhattacharyya, W. Antonin, J. Stegmaier
 %
 % Licensed under the Apache License, Version 2.0 (the "License");
 % you may not use this file except in compliance with the License.
@@ -25,14 +25,14 @@
 %%
 
 function callback_livecellminer_clickEventHandler(~, ~)
-    global parameters;
-    global d_orgs;
+    global parameters; %#ok<GVMIS> 
+    global d_orgs; %#ok<GVMIS> 
 
     %% get the modifier keys
     modifiers = get(gcf,'currentModifier');        %(Use an actual figure number if known)
-    shiftPressed = ismember('shift',modifiers);
-    ctrlPressed = ismember('control',modifiers);
-    altPressed = ismember('alt',modifiers);
+    shiftPressed = ismember('shift',modifiers); %#ok<NASGU> 
+    ctrlPressed = ismember('control',modifiers); %#ok<NASGU> 
+    altPressed = ismember('alt',modifiers); %#ok<NASGU> 
 
     %% identify the click position and the button
     buttonPressed = get(gcf, 'SelectionType');
@@ -71,7 +71,7 @@ function callback_livecellminer_clickEventHandler(~, ~)
            d_orgs(cellPair, 1:frameNumber, parameters.manualStageIndex) = 1;
            d_orgs(cellPair, (frameNumber+1):end, parameters.manualStageIndex) = 0;
         elseif (maxIndex == 1)
-            alreadyLabeledIndices = find(squeeze(d_orgs(cellId, :, parameters.manualStageIndex) == 1));
+            alreadyLabeledIndices = find(squeeze(d_orgs(cellId, :, parameters.manualStageIndex) == 1)); %#ok<MXFND> 
             nextIndex = max(alreadyLabeledIndices)+1;
             d_orgs(cellPair, nextIndex:frameNumber, parameters.manualStageIndex) = 2;
             d_orgs(cellPair, (frameNumber+1):end, parameters.manualStageIndex) = 3;

Source/callback_livecellminer_clickEventHandler.m

@@ -1,6 +1,6 @@
 %%
 % LiveCellMiner.
-% Copyright (C) 2020 D. Moreno-Andres, A. Bhattacharyya, W. Antonin, J. Stegmaier
+% Copyright (C) 2021 D. Moreno-Andrés, A. Bhattacharyya, W. Antonin, J. Stegmaier
 %
 % Licensed under the Apache License, Version 2.0 (the "License");
 % you may not use this file except in compliance with the License.
@@ -132,7 +132,7 @@
        end
 
        %% save the original Ids to retrieve the correct snippets later on
-       originalIds = [originalIds; motherIndex, daughter1Index; motherIndex, daughter2Index];
+       originalIds = [originalIds; motherIndex, daughter1Index; motherIndex, daughter2Index]; %#ok<AGROW> 
 
        %% increment counter by 2 as two lines are added (mother+daughter1 and mother+daughter2)
        currentIndex = currentIndex + 2;

Source/callback_livecellminer_combine_mother_daughter_tracks.m

@@ -1,6 +1,6 @@
 %%
 % LiveCellMiner.
-% Copyright (C) 2020 D. Moreno-Andres, A. Bhattacharyya, W. Antonin, J. Stegmaier
+% Copyright (C) 2021 D. Moreno-Andrés, A. Bhattacharyya, W. Antonin, J. Stegmaier
 %
 % Licensed under the Apache License, Version 2.0 (the "License");
 % you may not use this file except in compliance with the License.