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GLASS_AI_APP.m
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GLASS_AI_APP.m
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classdef GLASS_AI_APP < matlab.apps.AppBase
% Properties that correspond to app components
properties (Access = public)
GLASSAIUIFigure matlab.ui.Figure
UpdateAvailableButton matlab.ui.control.Button
GLASSAILogo matlab.ui.control.Image
StopAnalysisButton matlab.ui.control.StateButton
MoffittLogo matlab.ui.control.Image
TabGroup matlab.ui.container.TabGroup
GLASSAIParametersTab matlab.ui.container.Tab
AssignmentmethodDropDown matlab.ui.control.DropDown
AssignmentmethodDropDownLabel matlab.ui.control.Label
TumorgradethresholdEditField matlab.ui.control.NumericEditField
TumorgradethresholdEditFieldLabel matlab.ui.control.Label
AssignoverallgradetoeachtumorCheckBox matlab.ui.control.CheckBox
SmoothingSizeSpinner matlab.ui.control.Spinner
SmoothingSizeSpinnerLabel matlab.ui.control.Label
SmoothingMethodDropDown matlab.ui.control.DropDown
SmoothingMethodDropDownLabel matlab.ui.control.Label
PatchtissuethresholdLabel matlab.ui.control.Label
PatchTissueThresholdInput matlab.ui.control.NumericEditField
TumormergeradiusmLabel matlab.ui.control.Label
TumorMergeRadiusInput matlab.ui.control.NumericEditField
TumorsizethresholdsqmLabel matlab.ui.control.Label
TumorSizeThresholdInput matlab.ui.control.NumericEditField
StainNormalizationParametersTab matlab.ui.container.Tab
RemovepurecolorpixelsCheckBox matlab.ui.control.CheckBox
NormMinimumTissuePercent matlab.ui.control.NumericEditField
MinimumTissuePercentEditFieldLabel matlab.ui.control.Label
NormPseudomaxTolerance matlab.ui.control.NumericEditField
PseudomaxToleranceEditFieldLabel matlab.ui.control.Label
NormTransparencyThreshold matlab.ui.control.NumericEditField
TransparencyThresholdEditFieldLabel matlab.ui.control.Label
NormBackgroundIntensity matlab.ui.control.NumericEditField
BackgroundIntensityLabel matlab.ui.control.Label
StainODMatrixPanel matlab.ui.container.Panel
BEditFieldLabel_2 matlab.ui.control.Label
HemSwatch matlab.ui.control.Label
EosSwatch matlab.ui.control.Label
ResetStainParametersButton matlab.ui.control.Button
HemBlueInput matlab.ui.control.NumericEditField
BEditFieldLabel matlab.ui.control.Label
HemGreenInput matlab.ui.control.NumericEditField
GEditFieldLabel matlab.ui.control.Label
HemRedInput matlab.ui.control.NumericEditField
REditFieldLabel matlab.ui.control.Label
EosLabel matlab.ui.control.Label
HemLabel matlab.ui.control.Label
EosBlueInput matlab.ui.control.NumericEditField
EosGreenInput matlab.ui.control.NumericEditField
EosRedInput matlab.ui.control.NumericEditField
GradeMapColorsTab matlab.ui.container.Tab
SkippedPatchColorEditField_B matlab.ui.control.NumericEditField
SkippedPatchColorEditField_G matlab.ui.control.NumericEditField
SkippedPatchColorEditField_R matlab.ui.control.NumericEditField
SkippedPatchColorEditFieldLabel matlab.ui.control.Label
BackgroundColorEditField_B matlab.ui.control.NumericEditField
BackgroundColorEditField_G matlab.ui.control.NumericEditField
BackgroundColorEditField_R matlab.ui.control.NumericEditField
BackgroudColorEditFieldLabel matlab.ui.control.Label
Grade4ColorEditField_B matlab.ui.control.NumericEditField
Grade4ColorEditField_G matlab.ui.control.NumericEditField
Grade4ColorEditField_R matlab.ui.control.NumericEditField
NormalAlveoliColorEditFieldLabel_6 matlab.ui.control.Label
Grade3ColorEditField_B matlab.ui.control.NumericEditField
Grade3ColorEditField_G matlab.ui.control.NumericEditField
Grade3ColorEditField_R matlab.ui.control.NumericEditField
NormalAlveoliColorEditFieldLabel_5 matlab.ui.control.Label
NormalAlveoliColorEditField_B matlab.ui.control.NumericEditField
NormalAlveoliColorEditField_G matlab.ui.control.NumericEditField
NormalAlveoliColorEditField_R matlab.ui.control.NumericEditField
NormalAlveoliColorEditFieldLabel matlab.ui.control.Label
NormalAirwayColorEditField_B matlab.ui.control.NumericEditField
NormalAirwayColorEditField_G matlab.ui.control.NumericEditField
NormalAirwayColorEditField_R matlab.ui.control.NumericEditField
NormalAlveoliColorEditFieldLabel_2 matlab.ui.control.Label
Grade1ColorEditField_B matlab.ui.control.NumericEditField
Grade1ColorEditField_G matlab.ui.control.NumericEditField
Grade1ColorEditField_R matlab.ui.control.NumericEditField
NormalAlveoliColorEditFieldLabel_3 matlab.ui.control.Label
Grade2ColorEditField_B matlab.ui.control.NumericEditField
Grade2ColorEditField_G matlab.ui.control.NumericEditField
Grade2ColorEditField_R matlab.ui.control.NumericEditField
NormalAlveoliColorEditFieldLabel_4 matlab.ui.control.Label
SkippedPatchLamp matlab.ui.control.Lamp
BackgroundLamp matlab.ui.control.Lamp
Grade4Lamp matlab.ui.control.Lamp
Grade3Lamp matlab.ui.control.Lamp
Grade2Lamp matlab.ui.control.Lamp
Grade1Lamp matlab.ui.control.Lamp
NormalAirwayLamp matlab.ui.control.Lamp
NormlaAlveoliLamp matlab.ui.control.Lamp
BLabel matlab.ui.control.Label
GLabel matlab.ui.control.Label
RLabel matlab.ui.control.Label
CLASSLabel matlab.ui.control.Label
OutputImageScalingTab matlab.ui.container.Tab
NormalizedImageOutputCheckBox matlab.ui.control.CheckBox
ConfidenceMapPaletteDropDown matlab.ui.control.DropDown
ConfidenceMappaletteDropDownLabel matlab.ui.control.Label
ConfidenceMapCheckBox matlab.ui.control.CheckBox
ConfidenceMapScalingSlider matlab.ui.control.Slider
ConfidenceMapScalingSliderLabel matlab.ui.control.Label
SegmentationImageCheckBox matlab.ui.control.CheckBox
StainNormalizedImageScalingSlider matlab.ui.control.Slider
StainNormalizedImageScalingLabel matlab.ui.control.Label
SegmentationScalingSlider matlab.ui.control.Slider
SegmentationScalingLabel matlab.ui.control.Label
GradeMapScalingSlider matlab.ui.control.Slider
GradeMapScalingLabel matlab.ui.control.Label
LinksTab matlab.ui.container.Tab
GLASSAIAnnotationEditorGitHubLink matlab.ui.control.Hyperlink
FloresLabLink matlab.ui.control.Hyperlink
GLASSAIManuscriptLink matlab.ui.control.Hyperlink
GLASSAIGitHubLink matlab.ui.control.Hyperlink
CopytobaseButton matlab.ui.control.Button
VersionLabel matlab.ui.control.Label
CopyrightLabel matlab.ui.control.Label
RUOLabel matlab.ui.control.Label
RunCheckLamp matlab.ui.control.Lamp
StatusLabel matlab.ui.control.Label
GLASSAILabel matlab.ui.control.Label
Step2Label matlab.ui.control.Label
Step1Label matlab.ui.control.Label
OutputFolderLamp matlab.ui.control.Lamp
InputFolderLamp matlab.ui.control.Lamp
OutputFolderLocationLabel matlab.ui.control.Label
OutputFolderButton matlab.ui.control.Button
RunButton matlab.ui.control.Button
FileTable matlab.ui.control.Table
InputFolderLocationLabel matlab.ui.control.Label
SelectimagesButton matlab.ui.control.Button
AnalysisOptionsPanel matlab.ui.container.Panel
NormalizestainingSwitch matlab.ui.control.Switch
NormalizestainingSwitchLabel matlab.ui.control.Label
PreviewoutputimagesSwitch matlab.ui.control.Switch
PreviewoutputimagesSwitchLabel matlab.ui.control.Label
OverwriteSlideSummaryInput matlab.ui.control.CheckBox
end
properties (Access = private)
% PROPERTIES %
GLASSAI_APP_VERSION = '2.0.2' % Version of GLASS-AI standalone app
GLASS_AI_NET % Network object for machine learning model
RESOURCE_DIR_PATH %store path to GLASS_AI_resources directory
START_DIR
% RUNTIME_VARS %
LAST_SELECTED_DIR % Path to last selected directory
INPUT_PATH % Path selected using BrowseButton
OUTPUT_PATH % Path selected using OutputFolderButton
SELECTED_FILES % List of files selected for analysis
SELECTED_PATHS % Full path for selected files
IMAGE_BLOCK_SIZE % Store size of blocks to use for image processing
TUMOR_SIZE_THRESHOLD % Store size threshold for individual tumor segmentation
APPEND_SLIDE_SUMMARY %False=append summary outputs of each slide to previous output
IMAGE_RESOLUTION % Store image microns/pixel resolution
TUMOR_MERGE_RADIUS % Store value for smoothing radius in microns
NORMALIZE_STAINS % True = normalize H&E patches before classifying
NORMALIZE_ALPHA % Percent to trim from pseudomin/max for normalization
NORMALIZE_BETA % Minimum OD for stain normalization
NORMALIZE_IO % Background intensity for stain normalization
NORMALIZE_THRESHOLD % Minimum percent opaque pixels for normalization
NORMALIZE_HEREF % Color vectors for hematoxylin and eosin stain
REMOVE_PURE_COLORS % Remove pure colors during stain normalization
OUTPUT_IMAGE_PREVIEW % True = make preview figure of output images
OUTPUT_GRADE_IMAGE_SCALE % scaling applied to grade map output image
MAKE_NORMALIZED_IMAGE % Save normalized H&E image to file
MAKE_SEGMENTATION_IMAGE % Generate labeled tumor segmentation image
OUTPUT_SEGMENTATION_IMAGE_SCALE % scaling applied to segmentation output image
OUTPUT_NORMALIZED_IMAGE_SCALE % scaling applied to stain normalized output image
MAKE_CONFIDENCE_MAP % Output map of maximium activiation weight
OUTPUT_CONFIDENCE_MAP_SCALE % scaling applied to predicted grade confidence map output image
CONFIDENCE_MAP_COLOR % selected color map to use for making confidence map image
PATCH_SIZE = [224, 224, 3]; % size of image patches given to neural network
PATCH_SKIP_THRESHOLD % Patches with less than this amount of tissue will be skipped
SMOOTH_METHOD % Select filter used for classification smoothing
SMOOTH_SIZE =[100 100]% Define filter size in pixels for classificiation smooting
SPLIT_IMAGE % Write image blocks to files to conserve memory
NORMAL_ALVEOLI_COLOR % color of normal alveoli in grade map
NORMAL_AIRWAY_COLOR % color of normal airway in grade map
GRADE_1_COLOR % color of Grade 1 LUAD in grade map
GRADE_2_COLOR % color of Grade 2 LUAD in grade map
GRADE_3_COLOR % color of Grade 3 LUAD in grade map
GRADE_4_COLOR % color of Grade 4 LUAD in grade map
BACKGROUND_COLOR % color background in grade map
SKIPPED_PATCH_COLOR % color of skipped patches in grade map
SYSTEM_MEMORY % Available memory on system
ASSIGN_OVERALL_GRADES % Assign overall grades to each tumor
ASSIGN_GRADES_METHOD % Method to use for overall tumor grade assignment
ASSIGN_GRADES_THRESHOLD % Percentage of tumor area required for grade assignment
% nCounts and iIterators %
nImages % Total number of images selected for analysis
iImage % Current image number (of total) being processed)
% Status Tracking %
analysisStepDescription % Current analysis step
analysisStopWatch % Store time analysis was started
analysisRunTime % Store time elapsed since analysis was started
analysisEndTime % Store time analysis completed
imageStopWatch % Stopwatch for individual image
imageRunTime %Store time elapsed since analysis was started on image
currentFileName % Store file name of the image being analyzed
currentFileExt % Store extension of the image being analyzed
currentFileNameExt % Store file name and extension of the image being analyzed
currentFilePath % Store path to image being analyzed
logFileName % name of log file
logFilePath % location of log file
ErrorAlertAlreadyCreated = false % Flag to store if an error has occured in a defined try block
end % End Properties
methods (Access = private)
function main(app)
% Run GLASS-AI analysis on input images. Performs tumor
% grading and segmentation on the input images using
% the parameters set through the GUI. Outputs overlay
% images and data sheets for further analysis.
% clean up temporary folders on completion or termination
cleanup = onCleanup(@()cleanUpGLASSAI(app));
%% start analysis
net = app.GLASS_AI_NET;
try % catch unexpected errors during any analysis step
while true % stop button function
app.iImage = 0; %initialize image tracking counter to 0
% process each image
%- use currentImage because app properties (i.e., app.iImage)
%- can't be used as iterators in a for loop
for currentImage = 1 : app.nImages
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Breaking from FOR loop over input image files in main().")
break %escape from FOR loop over input images
end
app.iImage = app.iImage + 1;
%% clean leftover temp files
if isfolder(fullfile(app.OUTPUT_PATH,'TempFolder'))
app.StatusLabel.Text = "Cleaning temporary files";
deletetemporaryfiles(app,true)
end
%% start parallel processing pool
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Breaking from FOR loop over input image files in main().")
break %escape from FOR loop over input images
end
% start parallel processing pool if possible/allowed
%- do this for each image because pool may be destroyed
%- if not used for an extended period of time
app.StatusLabel.Text = "Starting parallel processing pool...";
startparpool(app);
%% get image file info
app.currentFilePath = app.SELECTED_PATHS{currentImage};
[~,app.currentFileName,app.currentFileExt] = fileparts(app.currentFilePath);
app.currentFileNameExt = strcat(app.currentFileName,app.currentFileExt);
%% analyze image
%mark the image currently being processed in the FileTable
processingstyle = uistyle("Icon",fullfile(app.RESOURCE_DIR_PATH,"UI files","processing.svg"));
addStyle(app.FileTable,processingstyle,"cell",[app.iImage 3])
scroll(app.FileTable,"row",app.iImage)
runglassai(app,net)
%remove any temporary files
deletetemporaryfiles(app);
%catch stop analysis request after returning from
%runglassai()
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Breaking from FOR loop over input image files in main().")
%mark image that was active when analysis was stopped
stopstyle = uistyle("Icon","warning");
addStyle(app.FileTable,stopstyle,"cell",[app.iImage 3])
break %escape from FOR loop over input images
end
%mark image as completed in file table
finishedstyle = uistyle("Icon","success");
addStyle(app.FileTable,finishedstyle,"cell",[app.iImage 3])
end % End FOR loop over input images
%% Finish Analysis Run
cleanUpGLASSAI(app);
runcheck(app); %recheck options are valid for next run
break %exit while=true loop after last image
end %while loop: stop button function
catch ME % try: catch errors during any analysis step
% write error message to logfile
fprintf("%s - %s %s\n",string(datetime),"[ERROR]: Analysis terminated due to error:", ME.message)
% update status window to alert user to error
app.StatusLabel.Text= sprintf("An error occured. Analysis Terminated.\n Check logfile for more details.");
%rethrow error to stop execution
%- error reporting in RunButtonPushed callback
rethrow(ME)
end % try: catch errors during any analysis step
end % End function: main()
function runglassai(app,net)
% Run GLASS-AI analysis on current image. Performs tumor
% grading and segmentation on the input images using
% the parameters set through the GUI. Outputs overlay
% images and data sheets for further analysis.
%initialize log and stopwatch for current image
fprintf("%s %0.0f %s\n","----- Start image",app.iImage,"-----")
fprintf("%s - %s %s\n",string(datetime),"Beginning analysis of", app.currentFileNameExt)
%start stopwatch for current image
app.imageStopWatch = tic;
try % catch unexpected errors during any analysis step
%% read input image
statusupdate(app,"Loading image");
%check stop button status before proceeding
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
try
fprintf("%s - %s %s\n",string(datetime),"Creating blockedImage from",app.currentFileNameExt)
%read image as blocked image. get index of target
%image resolution.
[wholeImage, imageIndex] = readimage(app,app.currentFilePath);
xImagePixels = wholeImage.Size(imageIndex,2);
yImagePixels = wholeImage.Size(imageIndex,1);
zImagePixels = wholeImage.Size(imageIndex,3);
fprintf("%s - %s %s\n",string(datetime),"Created blockedImage from",app.currentFileNameExt)
catch ME
% alert user that an error occured if not already done
if ~app.ErrorAlertAlreadyCreated
message_text = "An error occured while loading the input image from " + app.currentFileName + "." +...
newline + "[ERROR MESSAGE]" + newline + ME.message;
uialert(app.GLASSAIUIFigure,message_text,"Image loading error");
app.ErrorAlertAlreadyCreated = true;
end
fprintf("%s - %s %s\n",string(datetime),"[ERROR]: An error occured while loading", app.currentFileNameExt)
%rethrow error to stop execution.
rethrow(ME);
end % end TRY: read input image
%% make overview image for stain estimation and tissue masking
statusupdate(app,"Creating overview image");
%check stop button status before proceeding
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
%make low res overview image (1/16 scale).
if prod(wholeImage.Size(1:2)) > 100000000
fprintf("%s - %s %s\n",string(datetime),"Creating overview image of", app.currentFileNameExt)
overviewImage = makeMultiLevel2D(wholeImage,...
Scales=0.125,...
Adapter=images.blocked.PNGBlocks,...
Interpolation="nearest",...
UseParallel = true,...
OutputLocation = fullfile(app.OUTPUT_PATH,'TempFolder','overviewImage'));
%make sure that the overview is at least 1 full block
overviewImage.BlockSize = min(overviewImage.Size,overviewImage.BlockSize);
fprintf("%s - %s %s\n",string(datetime),"Created overview image of", app.currentFileNameExt)
else
fprintf("%s - %s %s %s\n",string(datetime),"Skipping overview image of", app.currentFileNameExt,"due to small image size")
overviewImage = wholeImage;
end
%% mask empty image patchs
statusupdate(app,"Masking out empty patches");
%check stop button status before proceeding
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
%Identify low luminosity pixels (i.e., tissue)
luminosityThreshold = 200;
fprintf("%s - %s %s %s%d\n",string(datetime),"Masking tissue pixels in", app.currentFileNameExt,"with luminosity <",luminosityThreshold)
tissueBlockMask = apply(overviewImage, @(bs)rgb2gray(bs.Data)<luminosityThreshold,...
'UseParallel',true,...,
'OutputLocation',fullfile(app.OUTPUT_PATH,'TempFolder','tissueMask'));
fprintf("%s - %s %s\n",string(datetime),"Masked tissue pixels in", app.currentFileNameExt)
fprintf("%s - %s %s\n",string(datetime),"Gathering tissue mask for", app.currentFileNameExt)
tissueBlockMask = gather(tissueBlockMask);
fprintf("%s - %s %s\n",string(datetime),"Finished gathering tissue mask for", app.currentFileNameExt)
%Clean up tissue mask by morphological closing, removing
%small objects, and including a 50 pixel border around
%remaining objects
tissueBlockMask = imclose(tissueBlockMask,strel('square',10));
fprintf("%s - %s %s\n",string(datetime),"Performed morphological closing on tissue mask for", app.currentFileNameExt)
tissueBlockMask = bwareaopen(tissueBlockMask,1000);
fprintf("%s - %s %s\n",string(datetime),"Removed objects < 1000 pixels in tissue mask for", app.currentFileNameExt)
tissueBlockMask = imdilate(tissueBlockMask,strel('square',50));
fprintf("%s - %s %s\n",string(datetime),"Added 50 pixel border to objects in tissue mask for", app.currentFileNameExt)
%convert mask to blockedImage to make blockLocationSet
tissueBlockMask = blockedImage(tissueBlockMask, BlockSize=[224 224]);
fprintf("%s - %s %s %s\n",string(datetime),"Converted tissue mask for", app.currentFileNameExt,"to blockedImage")
%make spatial referencing the same as input image
tissueBlockMask.WorldEnd = wholeImage.WorldEnd(imageIndex,1:2);
maskedTissueBlockSet = selectBlockLocations(wholeImage,...
'BlockSize',[224 224 3],...
'Levels',imageIndex,...
'Mask', tissueBlockMask,...
'InclusionThreshold', app.PATCH_SKIP_THRESHOLD/100,...
'UseParallel',true);
fprintf("%s - %s %s\n",string(datetime),"Created blockLocationSet using tissue mask for", app.currentFileNameExt)
%% normalize staining
if app.NORMALIZE_STAINS
statusupdate(app,"Estimating stain concentration");
%check stop button status before proceeding
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
%estimate stain from overview image
fprintf("%s - %s %s\n",string(datetime),"Gathering overview image for", app.currentFileNameExt)
gathered_overviewImage = gather(overviewImage);
fprintf("%s - %s %s\n",string(datetime),"Gathered overview image for", app.currentFileNameExt)
[stainMatrix, stainConc] = estimatestaining(app,gathered_overviewImage);
fprintf("%s - %s %s\n",string(datetime),"Estimated staining using overview image for", app.currentFileNameExt)
fprintf("%s\n","Stain Matrix")
fprintf("%0.4f\t%0.4f\n",transpose(stainMatrix(:,1)),transpose(stainMatrix(:,2)))
fprintf("Maximum stain concentrations: %0.4f\t%0.4f\n",stainConc(1),stainConc(2))
clear gathered_overviewImage %dont use for preview in case 1/16 downsampling is too much
%apply stain to wholeImage
statusupdate(app,"Performing stain normalization");
Io = app.NORMALIZE_IO;
HEREF = app.NORMALIZE_HEREF;
fprintf("%s - %s %s\n",string(datetime),"Applying stain normalization to", app.currentFileNameExt)
normalizedImage = apply(wholeImage,@(bim) applystainnormalization(app,bim.Data,stainMatrix,stainConc,Io,HEREF),...
'Adapter',images.blocked.PNGBlocks,...
'Level',imageIndex,...
'UseParallel',true,...
'OutputLocation',fullfile(app.OUTPUT_PATH,'TempFolder','normalized_image'));
fprintf("%s - %s %s\n",string(datetime),"Finished applying stain normalization to", app.currentFileNameExt)
end
%% grade tumors
statusupdate(app,"Performing tumor grading");
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
%perform semantic segmentation
fprintf("%s - %s %s\n",string(datetime),"Starting semantic segmentation on", app.currentFileNameExt)
if app.NORMALIZE_STAINS
fprintf("%s - %s\n",string(datetime),"SEMANTIC SEG: Using stain normalized image for analysis")
[classifications,maxClassProbability,~] = apply(normalizedImage, @(bs) semanticseg(bs.Data, net,OutputType="uint8",ExecutionEnvironment="auto"), ...
'BlockLocationSet', maskedTissueBlockSet,...
'PadPartialBlocks',true,...
'PadMethod','symmetric',...
'Adapter',images.blocked.MATBlocks,...
'UseParallel',true,...
'OutputLocation',fullfile(app.OUTPUT_PATH,'TempFolder','scores'));
else
fprintf("%s - %s\n",string(datetime),"SEMANTIC SEG: Using input image for analysis")
[classifications,maxClassProbability,~] = apply(wholeImage, @(bs) semanticseg(bs.Data, net,OutputType="uint8",ExecutionEnvironment="auto"), ...
'BlockLocationSet', maskedTissueBlockSet,...
'PadPartialBlocks',true,...
'PadMethod','symmetric',...
'Level',imageIndex,...
'Adapter',images.blocked.MATBlocks,...
'UseParallel',true,...
'OutputLocation',fullfile(app.OUTPUT_PATH,'TempFolder','scores'));
end
%Trim any padding added to the image during semanticseg.
classifications = crop(classifications,[1 1],[yImagePixels xImagePixels]);
maxClassProbability = crop(maxClassProbability,[1 1],[yImagePixels xImagePixels]);
fprintf("%s - %s %s\n",string(datetime),"Finished semantic segmentation on", app.currentFileNameExt)
%% process semantic segmentation results
statusupdate(app,"Gathering pixel classifications");
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
%Results need to be gathered to perform smoothing.
%Padding the blockedImage with data from neighboring blocks
%makes this take way too long.
fprintf("%s - %s %s\n",string(datetime),"Gathering classifications from blockedImage for", app.currentFileNameExt)
classifications = gather(classifications);
fprintf("%s - %s %s\n",string(datetime),"Started gathering classifications from blockedImage for", app.currentFileNameExt)
%Smooth classifications using user-selected method and
%window size
if app.SMOOTH_METHOD ~= "none"
%_Status Update_%
statusupdate(app,"Smoothing pixel classifications");
%%%%%%%%%%%%%%%%%
%check stop button status before proceeding
drawnow
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
fprintf("%s - %s %s\n",string(datetime),"Starting pixel classification smoothing on", app.currentFileNameExt)
classifications = smoothclasses(app,classifications);
fprintf("%s - %s %s\n",string(datetime),"Finished pixel classification smoothing on", app.currentFileNameExt)
end
%% save classifications
statusupdate(app,"Saving classifications to file");
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
try
%classifications were already gathered for smoothing
classificationOutputFilePath = fullfile(app.OUTPUT_PATH,strcat(app.currentFileName,'_classes.mat'));
%check for existing file and prompt to replace
overwriteAll = ""; %not yet defined by user, initialize as empty string
[classificationOutputFilePath, overwriteAll] = promptreplacexistingfile(app,classificationOutputFilePath,overwriteAll,".mat","_new.mat");
fprintf("%s - %s %s %s %s\n", string(datetime),"Saving classifications for",app.currentFileNameExt,"to",classificationOutputFilePath)
save(classificationOutputFilePath,'classifications', '-v7.3');
fprintf("%s - %s %s %s %s\n", string(datetime),"Saved raw classifications for",app.currentFileNameExt,"to",classificationOutputFilePath)
catch ME
% alert user that an error occured if not already done
if ~app.ErrorAlertAlreadyCreated
app.ErrorAlertAlreadyCreated = true;
message_text = "GLASS-AI encountered an error while saving image classifications." + ...
newline + "[ERROR MESSAGE]" + newline + ME.message;
uialert(app.GLASSAIUIFigure,message_text,"Analysis error")
end
fprintf("%s - %s %s %s %s\n",string(datetime),"[ERROR]: An error occured during saving of classes for",app.currentFileNameExt,"to",classificationOutputFilePath)
%rethrow error to stop execution
rethrow(ME);
end % End TRY: save the classifications in the output folder in a .mat file
%% segment individual tumors
statusupdate(app,"Segmenting individual tumors");
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
%Find, merge, and filter tumor pixels into objects
segmentedTumorMask = segmentindividualtumors(app, classifications);
%% make tumor ID label mask
statusupdate(app,"Making tumor label mask");
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
%Make a mask with intensities equal to the number of the
%individual tumors ID
tumorIdLabelMask = maketumorlabelmask(app, segmentedTumorMask);
%% Save tumor ID label mask
statusupdate(app,"Saving tumor label mask");
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
try
tumorLabelOutputFilePath=fullfile(app.OUTPUT_PATH, strcat(app.currentFileName,'_tumor_labels.mat'));
[tumorLabelOutputFilePath, overwriteAll] = promptreplacexistingfile(app,tumorLabelOutputFilePath,overwriteAll,".mat","_new.mat");
fprintf("%s - %s %s %s %s\n", string(datetime),"Saving tumor label mask for",app.currentFileNameExt,"to",tumorLabelOutputFilePath)
save(tumorLabelOutputFilePath,'tumorIdLabelMask', '-v7.3');
fprintf("%s - %s %s %s %s\n", string(datetime),"Saved tumor label mask for",app.currentFileNameExt,"to",tumorLabelOutputFilePath)
%Clear after saving since this mask is uint16. It is more
%memory sparing to just refind the connected
%components later.
clear tumorIdLabelMask
catch ME
% alert user that an error occured if not already done
if ~app.ErrorAlertAlreadyCreated
app.ErrorAlertAlreadyCreated = true;
message_text = "GLASS-AI encountered an error while saving tumor label mask." + ...
newline + "[ERROR MESSAGE]" + newline + ME.message;
uialert(app.GLASSAIUIFigure,message_text,"Analysis error")
end
fprintf("%s - %s %s\n",string(datetime),"[ERROR]: An error occured during saving of tumor label mask for",app.currentFileNameExt)
%rethrow error to stop execution
rethrow(ME);
end
%% Analyze individual tumors compositions and areas
statusupdate(app,"Analyzing individual tumors");
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
[individualTumorStats]=individualtumoranalysis(app,classifications,segmentedTumorMask);
%% Generate spreadsheet of individual tumors from each input image
statusupdate(app,"Saving individual tumor stats");
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
individualTumorStatsFilePath = fullfile(app.OUTPUT_PATH,strcat(app.currentFileName, ".xlsx"));
[individualTumorStatsFilePath, overwriteAll] = promptreplacexistingfile(app,individualTumorStatsFilePath,overwriteAll,".xlsx","_new.xlsx");
%get name of the indiviudal tumor stats file to use in the
%image level stats file
[~,imageName,~] = fileparts(individualTumorStatsFilePath);
fprintf("%s - %s %s %s %s\n", string(datetime),"Saving individual tumor stats for",app.currentFileNameExt,"to",individualTumorStatsFilePath)
writetable(individualTumorStats,individualTumorStatsFilePath,'WriteMode','overwrite','Sheet',1);
fprintf("%s - %s %s %s %s\n", string(datetime),"Saved individual tumor stats for",app.currentFileNameExt,"to",individualTumorStatsFilePath)
%% summarize tumors across the image
%_Status Update_%
statusupdate(app,"Summarizing tumors stats");
%check stop button status before proceeding
drawnow
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
%Calculate tumor counts, counts of tumors of each grade,
%total area of tissue of each grade, and percent of tumor
%area of each grade in the whole image
[imageTumorStats]=imageleveltumoranalysis(app,classifications,individualTumorStats,imageName);
%Save summary stats for image
statusupdate(app,"Saving tumor summary to image summary file");
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
% make new file if first image and not appending to old file
doMakeNewFile = (app.iImage==1 && ~app.APPEND_SLIDE_SUMMARY);
fprintf("%s - %s %s %s %s\n", string(datetime),"Saving image-level tumor stats for",imageName,"to","Whole slide summary.xlsx")
if doMakeNewFile
% overwrite existing file
if exist(fullfile(app.OUTPUT_PATH,'Whole slide summary.xlsx'), 'file')
fprintf("%s - %s\n",string(datetime),"[NOTE]: Overwriting existing 'Whole slide summary.xlsx' file")
end
writetable(imageTumorStats,fullfile(app.OUTPUT_PATH,'Whole slide summary.xlsx'),'WriteMode','overwrite','Sheet',1);
fprintf("%s - %s %s %s %s\n", string(datetime),"Saved image-level tumor stats for",imageName,"to","Whole slide summary.xlsx")
else % not first image or appending to old file
% append entries to existing file
writetable(imageTumorStats,fullfile(app.OUTPUT_PATH,'Whole slide summary.xlsx'),'WriteMode','append','Sheet',1);
fprintf("%s - %s %s %s %s\n", string(datetime),"Appended image-level tumor stats for",imageName,"to","Whole slide summary.xlsx")
end
%% create map of pixel grades
statusupdate(app,"Creating pixel-level tumor grade map");
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
try
%Make an RGB image of pixel classifications using the
%colormap defined in the 'Grade Map Colors' tab
%-This could theoretically be done using blockedImages
%-but classifications is already gathered to do the
%-classification smoothing
gradeImage = createtumorgradeimage(app,classifications);
%Resize gradeImage to requested scaling factors
gradeImage = imresize(gradeImage, app.OUTPUT_GRADE_IMAGE_SCALE, 'nearest');
fprintf("%s - %s %.2f%s\n", string(datetime),"Resized tumor grade image to", app.OUTPUT_GRADE_IMAGE_SCALE,"x")
%Save tumor grade image to file
statusupdate(app,"Saving pixel-level tumor grade map");
tumorGradeImageFilePath = fullfile(app.OUTPUT_PATH,strcat(app.currentFileName+"_grades.tif"));
[tumorGradeImageFilePath, overwriteAll] = promptreplacexistingfile(app,tumorGradeImageFilePath,overwriteAll);
if (xImagePixels * yImagePixels) > 40000000 %write as tiled tiff for large images
writetiff(app,gradeImage,tumorGradeImageFilePath);
fprintf("%s - %s %s %s %s %s\n", string(datetime),"Saved tumor grade image for", app.currentFileNameExt, "to",tumorGradeImageFilePath,"using writetiff")
else
imwrite(gradeImage,tumorGradeImageFilePath,'tif','Compression','lzw');
fprintf("%s - %s %s %s %s %s\n", string(datetime),"Saved tumor grade image for", app.currentFileNameExt, "to",tumorGradeImageFilePath,"using imwrite with LZW compression")
end % End IF: write as tiled tiff for large images
%Resize or clear gradeImage to reduce memory load
if app.OUTPUT_IMAGE_PREVIEW
%resize image for preview
resizeX = min(xImagePixels,5000);
resizeY = min(yImagePixels,5000);
gradeImage = imresize(gradeImage,[resizeX,resizeY],'nearest');
fprintf("%s - %s %.0f%s%.0f %s\n", string(datetime),"Resized tumor grade image to", resizeX,"x",resizeY, "for output preview")
else
clear gradeImage;
end % End IF: app.OUTPUT_IMAGE_PREVIEW
catch ME
% alert user that an error occured if not already done
if ~app.ErrorAlertAlreadyCreated
app.ErrorAlertAlreadyCreated = true;
message_text = "GLASS-AI encountered an error during tumor grade image creation." + ...
newline + "[ERROR MESSAGE]" + newline + ME.message;
uialert(app.GLASSAIUIFigure,message_text,"Analysis error")
end
fprintf("%s - %s %s %s\n",string(datetime),"[ERROR]: An error occured during tumor grade image creation for",app.currentFileNameExt)
%rethrow error to stop execution
rethrow(ME);
end % End TRY: make tumor grade image
%% create an overall tumor grade image if requested
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
if app.ASSIGN_OVERALL_GRADES
statusupdate(app,"Assigning overall grades to tumors")
try
%Make a mask of the tumors where the pixel
%intensity is equal to the overall grade based on
%the method defined by the user
classifications = makeoveralltumorgrademask(app,classifications,segmentedTumorMask,individualTumorStats);
%Save overall tumor grade mask to file
statusupdate(app,"Saving overall tumor grade mask")
overallTumorGradeOutputFilePath = fullfile(app.OUTPUT_PATH, strcat(app.currentFileName,'_overall_tumor_grades.mat'));
[overallTumorGradeOutputFilePath, overwriteAll] = promptreplacexistingfile(app,overallTumorGradeOutputFilePath,overwriteAll,".mat","_new.mat");
fprintf("%s - %s %s %s %s\n", string(datetime),"Saving overall tumor grade mask for",app.currentFileNameExt,"to",overallTumorGradeOutputFilePath)
save(overallTumorGradeOutputFilePath,'classifications', '-v7.3');
fprintf("%s - %s %s %s %s\n", string(datetime),"Saved overall tumor grade mask for",app.currentFileNameExt,"to",overallTumorGradeOutputFilePath)
catch ME
% alert user that an error occured if not already done
if ~app.ErrorAlertAlreadyCreated
app.ErrorAlertAlreadyCreated = true;
message_text = "GLASS-AI encountered an error while saving overall tumor grade mask." + ...
newline + "[ERROR MESSAGE]" + newline + ME.message;
uialert(app.GLASSAIUIFigure,message_text,"Analysis error")
end
fprintf("%s - %s %s\n",string(datetime),"[ERROR]: An error occured during saving of overall tumor grade mask for",app.currentFileNameExt)
%rethrow error to stop execution
rethrow(ME);
end % End TRY: save overall tumor grade mask to file
%Make an RGB image of overall tumor grades using the
%colormap defined in the 'Grade Map Colors' tab
statusupdate(app,"Making overall tumor grade map");
try
%Use the same function to make overall grade
%image that was used to make the pixel grade image
%since the classifications matrix has been adjusted
overallTumorGradeImage = createtumorgradeimage(app,classifications);
fprintf("%s - %s %s\n", string(datetime),"Finished making overall tumor grade image for", app.currentFileNameExt)
%Clear classifications to reduce memory load
clear classifications;
%Resize overallTumorGradeImage to set scaling factors
overallTumorGradeImage = imresize(overallTumorGradeImage, app.OUTPUT_GRADE_IMAGE_SCALE, 'nearest');
fprintf("%s - %s %.2f%s\n", string(datetime),"Resized tumor grade image to", app.OUTPUT_GRADE_IMAGE_SCALE,"x")
% save overallTumorGradeImage to file
statusupdate(app,"Saving overall tumor grade map")
overallTumorGradeImageFilePath = fullfile(app.OUTPUT_PATH,strcat(app.currentFileName+"_overall_grades.tif"));
[overallTumorGradeImageFilePath, overwriteAll] = promptreplacexistingfile(app,overallTumorGradeImageFilePath,overwriteAll);
if (xImagePixels * yImagePixels) > 40000000 % use writetiff() for large images
writetiff(app,overallTumorGradeImage,overallTumorGradeImageFilePath);
fprintf("%s - %s %s %s %s %s\n", string(datetime),"Saved tumor grade image for", app.currentFileNameExt, "to",overallTumorGradeImageFilePath,"using writetiff")
else %use imwrite for smaller images
imwrite(overallTumorGradeImage,overallTumorGradeImageFilePath,'tif','Compression','lzw');
fprintf("%s - %s %s %s %s %s\n", string(datetime),"Saved tumor grade image for", app.currentFileNameExt, "to",overallTumorGradeImageFilePath,"using imwrite with LZW compression")
end % End IF: use writetiff() for large images
%Resize or clear overallTumorGradeImage to
%reduce memory load
if app.OUTPUT_IMAGE_PREVIEW
resizeX = min(xImagePixels,5000);
resizeY = min(yImagePixels,5000);
overallTumorGradeImage = imresize(overallTumorGradeImage,[resizeX,resizeY],'nearest');
fprintf("%s - %s %.0f%s%.0f %s\n", string(datetime),"Resized overall tumor grade image to", resizeX,"x",resizeY, "for output preview")
else
clear overallTumorGradeImage;
end % End IF: app.OUTPUT_IMAGE_PREVIEW
catch ME
% alert user that an error occured if not already done
if ~app.ErrorAlertAlreadyCreated
app.ErrorAlertAlreadyCreated = true;
message_text = "GLASS-AI encountered an error during overall tumor grade image creation." + ...
newline + "[ERROR MESSAGE]" + newline + ME.message;
uialert(app.GLASSAIUIFigure,message_text,"Analysis error")
end
fprintf("%s - %s %s %s\n",string(datetime),"[ERROR]: An error occured during overall tumor grade image creation for",app.currentFileNameExt)
%rethrow error to stop execution
rethrow(ME);
end % End TRY: make overall tumor grade image if requested
end %if: app.ASSIGN_OVERALL_GRADES
%Reduce segmentedTumorMask size to requested output scale
%of semgentation image or clear from memory to reduce load
if app.MAKE_SEGMENTATION_IMAGE
segmentedTumorMask = imresize(segmentedTumorMask,app.OUTPUT_SEGMENTATION_IMAGE_SCALE);
else
clear segmentedTumorMask
end
%% make tumor segmentation image if requested
%check stop button status before proceeding
drawnow
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
if app.MAKE_SEGMENTATION_IMAGE
statusupdate(app,"Making tumor segmentation image");
try
% use stain normalized image if available
if app.NORMALIZE_STAINS
fprintf("%s - %s %s\n", string(datetime),"Gathering stain normalized image for making segmentation image of", app.currentFileNameExt)
segmentationImage = gather(normalizedImage);
fprintf("%s - %s %s\n", string(datetime),"Finished gathering stain normalized image for making segmentation image of", app.currentFileNameExt)
%Adjust inputs to output scale to prevent
%distortion of added text.
segmentationImage = imresize(segmentationImage,app.OUTPUT_SEGMENTATION_IMAGE_SCALE);
segmentationImage = createsegmentationimage(app,segmentationImage, segmentedTumorMask, individualTumorStats);
fprintf("%s - %s %s\n", string(datetime),"Finished making tumor segmentation image for", app.currentFileNameExt)
else
fprintf("%s - %s %s\n", string(datetime),"Gathering input image for making segmentation image of", app.currentFileNameExt)
segmentationImage = gather(wholeImage);
fprintf("%s - %s %s\n", string(datetime),"Finished gathering input image for making segmentation image of", app.currentFileNameExt)
%Adjust inputs to output scale to prevent
%distortion of added text.
segmentationImage = imresize(segmentationImage,app.OUTPUT_SEGMENTATION_IMAGE_SCALE);
segmentationImage = createsegmentationimage(app,segmentationImage, segmentedTumorMask, individualTumorStats);
fprintf("%s - %s %s\n", string(datetime),"Finished making tumor segmentation image for", app.currentFileNameExt)
end
%No longer need segmentedTumorMask. Free up memory.
clear segmentedTumorMask
%Save tumor segmentation image to file
statusupdate(app,"Saving tumor segmentation image");
segmentationImageFilePath = fullfile(app.OUTPUT_PATH,strcat(app.currentFileName+"_segmentation.tif"));
[segmentationImageFilePath, overwriteAll] = promptreplacexistingfile(app,segmentationImageFilePath,overwriteAll);
if (xImagePixels * yImagePixels) > 40000000 %write as tiled tiff for large images
writetiff(app,segmentationImage,segmentationImageFilePath);
fprintf("%s - %s %s %s %s %s\n", string(datetime),"Saved tumor segmentation image for", app.currentFileNameExt, "to",segmentationImageFilePath,"using writetiff")
else
imwrite(segmentationImage,segmentationImageFilePath,'tif','Compression','lzw');
fprintf("%s - %s %s %s %s %s\n", string(datetime),"Saved tumor segmentation image for", app.currentFileNameExt, "to",segmentationImageFilePath,"using imwrite with LZW compression")
end
%Resize or clear segmentationImage to
%reduce memory load
if app.OUTPUT_IMAGE_PREVIEW
segmentationImage = imresize(segmentationImage, [resizeX resizeY],'nearest');
fprintf("%s - %s %.0f%s%.0f %s\n", string(datetime),"Resized tumor segmentation image to", resizeX,"x",resizeY, "for output preview")
else
clear segmentationImage;
end % End IF: app.OUTPUT_IMAGE_PREVIEW
catch ME
% alert user that an error occured if not already done
if ~app.ErrorAlertAlreadyCreated
app.ErrorAlertAlreadyCreated = true;
message_text = "GLASS-AI encountered an error during tumor segmentation image creation." + ...
newline + "[ERROR MESSAGE]" + newline + ME.message;
uialert(app.GLASSAIUIFigure,message_text,"Analysis error")
end
fprintf("%s - %s %s %s\n",string(datetime),"[ERROR]: An error occured during tumor segmentation image creation for",app.currentFileNameExt)
%rethrow error to stop execution
rethrow(ME);
end % End TRY: make tumor segmentation image if requested
end % End IF: app.MAKE_SEGMENTATION_IMAGE
%% save stain normalized image if requested
%check stop button status before proceeding
drawnow
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
if app.NORMALIZE_STAINS
if app.NormalizedImageOutputCheckBox.Value
statusupdate(app,"Saving stain normalized image");
try
%normalizedImage is still a blockedImage. When
%used for making the segmentationImage it is
%gathered to a different variable name.
normalizedImageFilePath = fullfile(app.OUTPUT_PATH,strcat(app.currentFileName+"_normalized.tif"));
adapter = images.blocked.TIFF;
adapter.Compression = Tiff.Compression.JPEG;
%Write function can't overwrite by default.
%prompt user to replace existing file or rename
%current output
[normalizedImageFilePath, overwriteAll] = promptreplacexistingfile(app,normalizedImageFilePath,overwriteAll);
fprintf("%s - %s %s %s %s\n", string(datetime),"Saving stain normalized image for", app.currentFileNameExt, "to",normalizedImageFilePath)
write(normalizedImage,normalizedImageFilePath,'Adapter',adapter);
fprintf("%s - %s %s %s %s\n", string(datetime),"Finished saving stain normalized image for", app.currentFileNameExt, "to",normalizedImageFilePath)
catch ME
% alert user that an error occured if not already done
if ~app.ErrorAlertAlreadyCreated
app.ErrorAlertAlreadyCreated = true;
message_text = "GLASS-AI encountered an error while saving stain normalized image." + ...
newline + "[ERROR MESSAGE]" + newline + ME.message;
uialert(app.GLASSAIUIFigure,message_text,"Analysis error")
end
fprintf("%s - %s %s %s\n",string(datetime),"[ERROR]: An error occured during normalized H&E image output for",app.currentFileNameExt)
%rethrow error to stop execution
rethrow(ME);
end % End TRY: make stain normalization image
end % End IF: app.NormalizedImageOutputCheckbox.Value
end % End IF: app.NORMALIZE_STAINS
%% create max class score map if requested
%- convert matrix to RGB image and reload for preview
%check stop button status before proceeding
drawnow
if app.StopAnalysisButton.Value == 1
app.StopAnalysisButton.Text = "Stopped";
app.StopAnalysisButton.Enable = "off";
fprintf("%s - %s\n",string(datetime),"ANALYSIS STOP REQUESTED BY USER. Returning control from runglassai().")
return
end
try
if app.MAKE_CONFIDENCE_MAP
statusupdate(app,"Making class confidence map")
%generate 256 element colormap based on selected
%color palette
maxClassProbablityColorMap = getcolormap(app);
%gather blockedImage for saving
fprintf("%s - %s %s\n", string(datetime),"Gathering max class probility map of", app.currentFileNameExt)
maxClassProbability = gather(maxClassProbability);
fprintf("%s - %s %s\n", string(datetime),"Finished gathering max class probility map of", app.currentFileNameExt)
%Change from 0-1 scaled double to 0-255 scaled
%uint8
maxClassProbability = uint8(maxClassProbability*255);
% resize to user defined scale and apply colormap