Merge branch 'CA6.0beta'

src/CurveAlign_CT-FIRE/Cellanalysis/StarDistPrediction.py

@@ -24,9 +24,9 @@ def prediction(images, index):
     labels, details = model.predict_instances(img, prob_thresh=0.2, nms_thresh=0.5)
 
     im = Image.fromarray(labels)
-    im.save('mask.tif')
+    im.save('mask_sd.tif')
 
-    sio.savemat('labels.mat', {'labels':labels})
-    sio.savemat('details.mat', {'details':details})
+    sio.savemat('labels_sd.mat', {'labels':labels})
+    sio.savemat('details_sd.mat', {'details':details})
 
     return labels, details

src/CurveAlign_CT-FIRE/Cellanalysis/TumorRegionAnnotationGUI_exported.m

@@ -4,7 +4,7 @@
     properties (Access = public)
         TumorRegionDetectionoptionsUIFigure  matlab.ui.Figure
         SliderDensityParameter          matlab.ui.control.Slider
-        SliderGrideRow                  matlab.ui.control.Slider
+        SliderGridRow                   matlab.ui.control.Slider
         SliderGridCol                   matlab.ui.control.Slider
         GridRowsEditField               matlab.ui.control.NumericEditField
         GridRowsEditFieldLabel          matlab.ui.control.Label
@@ -39,8 +39,8 @@
         % Code that executes after component creation
         function startupFcn(app, mainApp)
             app.CallingApp = mainApp;
-            app.parameterOptions.imagePath = pwd;%mainApp.CAPannotations.imagePath;
-            app.parameterOptions.imageName = mainApp.CAPannotations.imageName;
+            app.parameterOptions.imagePath = mainApp.imagePath;
+            app.parameterOptions.imageName = mainApp.imageName;
             app.PathtoimageEditField.Value = fullfile(app.parameterOptions.imagePath,...
                app.parameterOptions.imageName);
 
@@ -59,8 +59,118 @@ function CancelButtonPushed(app, event)
 
         % Button pushed function: OKButton
         function OKButtonPushed(app, event)
+            %         parameterOptions = struct('imagePath','','imageName','','imageType','HE bright field',...
+            %             'method','ranking', 'gridColumn', 50,'gridRow', 50,'parameter_threshold',5,...
+            %             'defaultParameters',1,'sendtoROImanager',1);
+            if ~strcmp(app.parameterOptions.imageType,'HE bright field')
+                disp('Only available for HE bright field images so far')
+                return
+            end
+%              parameterOptions = struct('imagePath','','imageName','','imageType','HE bright field',...
+%             'method','ranking', 'gridColumn', 50,'gridRow', 50,'parameter_threshold',5,... 
+%             'defaultParameters',1,'sendtoROImanager',1);
+            gridCols = app.parameterOptions.gridColumn;
+            gridRows = app.parameterOptions.gridRow;
+            thresholdP = app.parameterOptions.parameter_threshold;
+            % three options
+            % 1-Ranking
+            % 2-Area threshold (in Pixels)
+            % 3-Distance Based
+            if strcmp(app.AnnotationMethodsDropDown.Value,'Ranking')
+               % thresholdValue = app.ParametersEditField.Value;
+                turmorDetected = imageCardTumor(app.CallingApp.imageName,'Rank',...
+                    [gridCols gridRows],thresholdP);
+            elseif strcmp(app.AnnotationMethodsDropDown.Value,'Area threshold (in Pixels)')
+               % thresholdValue = app.ParametersEditField.Value;
+                turmorDetected = imageCardTumor(app.CallingApp.imageName,'Thres',...
+                    [gridCols gridRows],thresholdP);
+            elseif strcmp(app.AnnotationMethodsDropDown.Value,'Distance Based')
+                % thresholdValue = app.ParametersEditField.Value;
+                turmorDetected = imageCardTumor(app.CallingApp.imageName,'Radius',...
+                    [gridCols gridRows],nan,thresholdP);
+            else
+                fprintf('This tumor annotation method-%s is not available \ n',app.AnnotationMethodsDropDown.Value)
+                return
+            end
+            % add more annotation properties in the main program
+            app.CallingApp.CAPannotations.tumorAnnotations.tumorArray = turmorDetected.tumorArray;
+            annotationNumber = size (app.CallingApp.CAPannotations.tumorAnnotations.tumorArray,2);
+            % statsArray = cell(1,annotationNumber); % struct('Mask','','Centroid','','Area','','Perimeter','')
+            % nrow = app.CallingApp.CAPimage.imageInfo.Height;
+            % ncol = app.CallingApp.CAPimage.imageInfo.Width;
+            % for i = 1: annotationNumber
+            %     tumorData = app.CallingApp.CAPannotations.tumorAnnotations.tumorArray(1,i);
+            %     tumorBoundaryCol = tumorData.boundary(:,2);
+            %     tumorBoundaryRow = tumorData.boundary(:,1);    
+            %     tumorMask = poly2mask(tumorBoundaryCol,tumorBoundaryRow,nrow,ncol);
+            %     stats = regionprops(tumorMask,'Centroid','Area','Perimeter','Orientation');
+            %     statsArray{1,i}.Mask = tumorMask;
+            %     statsArray{1,i}.Centroid = stats.Centroid;
+            %     statsArray{1,i}.Area = stats.Area;
+            %     statsArray{1,i}.Perimeter = stats.Perimeter;
+            %     statsArray{1,i}.Orientation = stats.Orientation;
+            % end
+            % app.CallingApp.CAPannotations.tumorAnnotations.statsArray = statsArray;
+            app.CallingApp.annotationView.Type = repmat({'tumor'},annotationNumber,1);
+            app.CallingApp.annotationType = 'tumor';
+            app.CallingApp.figureOptions.plotImage =0;
+            app.CallingApp.figureOptions.plotObjects =0;
             app.CallingApp.figureOptions.plotAnnotations = 1;
+            % delete fibers if exist
+            if ~isempty (app.CallingApp.fibersView.fiberH1)
+                fiberNumber =  size(app.CallingApp.fibersView.fiberH1,1);
+                for i= 1: fiberNumber
+                    delete(app.CallingApp.fibersView.fiberH1{i,1});
+                end
+            end
             app.CallingApp.plotImage_public;
+            app.CallingApp.TabGroup.SelectedTab = app.CallingApp.ROImanagerTab;
+
+        end
+
+        % Value changed function: SliderDensityParameter
+        function SliderDensityParameterValueChanged(app, event)
+            value = app.SliderDensityParameter.Value;
+            app.SliderDensityParameter.Value = round(value);
+            app.parameterOptions.parameter_threshold =  app.SliderDensityParameter.Value;
+            app.ParametersEditField.Value = app.SliderDensityParameter.Value;
+        end
+
+        % Value changed function: SliderGridCol
+        function SliderGridColValueChanged(app, event)
+            value = app.SliderGridCol.Value;                      
+            app.SliderGridCol.Value = round(value);
+            app.parameterOptions.gridColumn =  app.SliderGridCol.Value;
+            app.GridColumnsEditField.Value = app.SliderGridCol.Value;
+        end
+
+        % Value changed function: SliderGridRow
+        function SliderGridRowValueChanged(app, event)
+            value = app.SliderGridRow.Value;
+            app.SliderGridRow.Value = round(value);
+            app.parameterOptions.gridRow =  app.SliderGridRow.Value;
+            app.GridRowsEditField.Value = app.SliderGridRow.Value;
+        end
+
+        % Value changed function: GridRowsEditField
+        function GridRowsEditFieldValueChanged(app, event)
+            value = app.GridRowsEditField.Value;
+            app.SliderGridRow.Value = value; 
+            app.parameterOptions.gridRow =  app.SliderGridRow.Value;
+        end
+
+        % Value changed function: GridColumnsEditField
+        function GridColumnsEditFieldValueChanged(app, event)
+            value = app.GridColumnsEditField.Value;
+            app.SliderGridCol.Value = value;
+            app.parameterOptions.gridColumn =  app.SliderGridCol.Value;
+        end
+
+        % Value changed function: ParametersEditField
+        function ParametersEditFieldValueChanged(app, event)
+            value = app.ParametersEditField.Value;
+            app.SliderDensityParameter.Value = value;
+            app.parameterOptions.parameter_threshold =  app.SliderDensityParameter.Value;
         end
     end
 
@@ -95,11 +205,11 @@ function createComponents(app)
 
             % Create ImagetypeDropDown
             app.ImagetypeDropDown = uidropdown(app.TumorRegionDetectionoptionsUIFigure);
-            app.ImagetypeDropDown.Items = {'H&E', 'Single channel', 'Two-channel', 'Others'};
+            app.ImagetypeDropDown.Items = {'HE bright field', 'Fluorescence_1-Channel', 'Fluorescence_2-Channel', 'Two-channel', 'Phase contrast', 'Gray scale'};
             app.ImagetypeDropDown.DropDownOpeningFcn = createCallbackFcn(app, @ImagetypeDropDownValueChanged, true);
             app.ImagetypeDropDown.ValueChangedFcn = createCallbackFcn(app, @ImagetypeDropDownValueChanged, true);
             app.ImagetypeDropDown.Position = [210 335 173 22];
-            app.ImagetypeDropDown.Value = 'H&E';
+            app.ImagetypeDropDown.Value = 'HE bright field';
 
             % Create DefaultparametersCheckBox
             app.DefaultparametersCheckBox = uicheckbox(app.TumorRegionDetectionoptionsUIFigure);
@@ -144,6 +254,7 @@ function createComponents(app)
 
             % Create GridColumnsEditField
             app.GridColumnsEditField = uieditfield(app.TumorRegionDetectionoptionsUIFigure, 'numeric');
+            app.GridColumnsEditField.ValueChangedFcn = createCallbackFcn(app, @GridColumnsEditFieldValueChanged, true);
             app.GridColumnsEditField.Position = [176 253 35 22];
             app.GridColumnsEditField.Value = 50;
 
@@ -155,6 +266,7 @@ function createComponents(app)
 
             % Create ParametersEditField
             app.ParametersEditField = uieditfield(app.TumorRegionDetectionoptionsUIFigure, 'numeric');
+            app.ParametersEditField.ValueChangedFcn = createCallbackFcn(app, @ParametersEditFieldValueChanged, true);
             app.ParametersEditField.Position = [178 173 33 22];
             app.ParametersEditField.Value = 5;
 
@@ -166,26 +278,30 @@ function createComponents(app)
 
             % Create GridRowsEditField
             app.GridRowsEditField = uieditfield(app.TumorRegionDetectionoptionsUIFigure, 'numeric');
+            app.GridRowsEditField.ValueChangedFcn = createCallbackFcn(app, @GridRowsEditFieldValueChanged, true);
             app.GridRowsEditField.Position = [178 212 36 22];
             app.GridRowsEditField.Value = 50;
 
             % Create SliderGridCol
             app.SliderGridCol = uislider(app.TumorRegionDetectionoptionsUIFigure);
-            app.SliderGridCol.Position = [235 271 170 3];
+            app.SliderGridCol.ValueChangedFcn = createCallbackFcn(app, @SliderGridColValueChanged, true);
+            app.SliderGridCol.Position = [235 271 245 3];
             app.SliderGridCol.Value = 50;
 
-            % Create SliderGrideRow
-            app.SliderGrideRow = uislider(app.TumorRegionDetectionoptionsUIFigure);
-            app.SliderGrideRow.Position = [235 222 170 3];
-            app.SliderGrideRow.Value = 50;
+            % Create SliderGridRow
+            app.SliderGridRow = uislider(app.TumorRegionDetectionoptionsUIFigure);
+            app.SliderGridRow.ValueChangedFcn = createCallbackFcn(app, @SliderGridRowValueChanged, true);
+            app.SliderGridRow.Position = [235 222 245 3];
+            app.SliderGridRow.Value = 50;
 
             % Create SliderDensityParameter
             app.SliderDensityParameter = uislider(app.TumorRegionDetectionoptionsUIFigure);
-            app.SliderDensityParameter.Limits = [0 10];
-            app.SliderDensityParameter.MajorTicks = [0 2 4 6 8 10];
-            app.SliderDensityParameter.MajorTickLabels = {'0', '2', '4', '6', '8', '10'};
-            app.SliderDensityParameter.MinorTicks = [1 2 3 4 5 6 7 8 9 10];
-            app.SliderDensityParameter.Position = [235 183 170 3];
+            app.SliderDensityParameter.Limits = [0 20];
+            app.SliderDensityParameter.MajorTicks = [0 5 10 15 20];
+            app.SliderDensityParameter.MajorTickLabels = {'0', '5', '10', '15', '20'};
+            app.SliderDensityParameter.ValueChangedFcn = createCallbackFcn(app, @SliderDensityParameterValueChanged, true);
+            app.SliderDensityParameter.MinorTicks = [0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20];
+            app.SliderDensityParameter.Position = [235 183 245 3];
             app.SliderDensityParameter.Value = 5;
 
             % Show the figure after all components are created

src/CurveAlign_CT-FIRE/Cellanalysis/WholeCell/cellpose_seg.py

@@ -5,5 +5,5 @@ def cyto_seg(img_path,chan=[0,0]):
     img = io.imread(img_path)
     model = models.Cellpose(gpu=False, model_type='cyto')
     mask, flows, styles, diams = model.eval(img, diameter=None, channels=chan)
-    sio.savemat('mask.mat', {'mask':mask})
+    sio.savemat('mask4cells.mat', {'mask4cells':mask})
     return mask

src/CurveAlign_CT-FIRE/Cellanalysis/WholeCell/deepcell_seg.py

@@ -10,5 +10,5 @@ def cyto_seg(img_path):
     #print(im.shape)
     app = CytoplasmSegmentation()
     mask = app.predict(im)
-    sio.savemat('mask.mat', {'mask':mask})
+    sio.savemat('mask4cells.mat', {'mask4cells':mask})
     return mask

src/CurveAlign_CT-FIRE/Cellanalysis/WholeCell/imgCardWholeCell.m

@@ -25,13 +25,32 @@
             else
                 image = imageName;
             end
-            pymatlabflag = 0; % didnot go through in matlab, pyenv terminated unexpectedly
+            if strcmp(model,'Cellpose') || strcmp(model,'DeepCell')
+                pymatlabflag = 1; % didnot go through in matlab, pyenv terminated unexpectedly
+            elseif strcmp(model,'FromMask-others')
+                pymatlabflag = 0;
+            end
             if pymatlabflag ==1
-                wholeCellLink(image,model)
+                disp('running whole cell segmenation')
+                mask4cells = wholeCellLink(image,model);
             else
-                fprintf('run the whole cell analysis outside the MATLAB environent \n')
+                [fileGet, pathGet]=uigetfile({'*.tif;*.mat','Tiff or MAT Files';'*.*','All Files'},...
+                    'Select Cell mask file(s) from StarDist output',pwd,'MultiSelect','off');
+                if ischar(fileGet)
+                    [~,~,fileType] = fileparts(fileGet);
+                    if strcmp(fileType,'.mat')
+                        load(fullfile(pathGet,fileGet),'mask4cells');
+                    elseif strcmp(fileType,'.tif')
+                        mask4cells = imread(fullfile(pathGet,fileGet));
+                    else
+                        error('This file %s is not a valid mask file \n', fullfile(pathGet,fileGet))
+                    end
+                else
+                    error('Previous segmented whole cell file is NOT loaded')
+                end
+
             end
-            load('mask.mat','mask');
+            mask = mask4cells;
             obj.cellArray = wholeCellCreation(imageName,mask,obj);
         end
     end

src/CurveAlign_CT-FIRE/Cellanalysis/WholeCell/wholeCellLink.m

@@ -1,22 +1,29 @@
-function wholeCellLink(image,model)
+function mask4cells = wholeCellLink(image,model)
 % This function links deep learning models written in Python to MATLAB.
 % image - the image that needs to be segmented
 % model - two models available: 'Cellpose' and 'DeepCell'
 
 %pe = pyenv;
-pathToStardist = fileparts(which('cellpose_seg.py'));
-if count(py.sys.path,pathToStardist) == 0
-    insert(py.sys.path,int32(0),pathToStardist);
-end
+% pathToStardist = fileparts(which('cellpose_seg.py'));
+% if count(py.sys.path,pathToStardist) == 0
+%     insert(py.sys.path,int32(0),pathToStardist);
+% end
 
 if strcmp(model,'Cellpose')
     % terminate(pyenv)
     % pyenv('Version','C:\Users\liu372\.conda\envs\CApy311\python.exe', 'ExecutionMode', 'OutOfProcess')
-    py.cellpose_seg.cyto_seg(image);
+    py.importlib.import_module('cellpose_seg');
+    mask4cells= uint32(py.cellpose_seg.cyto_seg(image));
+
 elseif strcmp(model,'DeepCell') 
 %     terminate(pyenv)
 %     pyenv('Version','/Users/ympro/opt/anaconda3/envs/deepcell/bin/python')
-    py.deepcell_seg.cyto_seg(image);
-end
+    py.importlib.import_module('deepcell_seg')
+    mask4cells = uint32(py.deepcell_seg.cyto_seg(image));
+elseif strcmp(model,'FromMask') 
+   cellobj = imgCardWholeCell(model,imageName,imagePath);
+   mask4cells = cellobj.cellArray.mask;
 
+end
+
 end

src/CurveAlign_CT-FIRE/Cellanalysis/cellDensity.m

@@ -1,6 +1,6 @@
 function [numCellsArray, minDistanceArray, numPixelsArray] = cellDensity(radius, stats) 
 
-load('details.mat','details')
+load('details_sd.mat','details')
 center = details.points;
 numCellsTotal = length(center);