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R8218/measureSCase.m
8566b2f9bc32aterrier-plotUpdate

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measureSCase.m
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function output = measureScase(varargin)
measureSCaseStart = tic;
Logger.start("measureSCase");
config = getConfig();
% Initialise cases
if nargin > 0
casesToMeasure = [string(varargin)];
else
casesToMeasure = config.casesToMeasure;
end
if config.overwriteMeasurements
SCases = createEmptySCase(casesToMeasure);
else
SCases = loadSCase(casesToMeasure);
end
% Run measurements
for i = 1:length(SCases)
SCaseStart = tic;
Logger.newDelimitedSection(SCases(i).id);
if config.runMeasurements.loadData
Logger.logn("");
SCases(i).patient.loadData();
end
if config.shouldersToMeasure.rightAuto
Logger.newDelimitedSection("Shoulder Right Auto");
runShoulderMeasurements(SCases(i).shoulders.right.auto);
Logger.closeSection();
end
if config.shouldersToMeasure.rightManual
Logger.newDelimitedSection("Shoulder Right Manual");
runShoulderMeasurements(SCases(i).shoulders.right.manual);
Logger.closeSection();
end
if config.shouldersToMeasure.leftAuto
Logger.newDelimitedSection("Shoulder Left Auto");
runShoulderMeasurements(SCases(i).shoulders.left.auto);
Logger.closeSection();
end
if config.shouldersToMeasure.leftManual
Logger.newDelimitedSection("Shoulder Left Manual");
runShoulderMeasurements(SCases(i).shoulders.left.manual);
Logger.closeSection();
end
Logger.newDelimitedSection(...
sprintf("SCase measured in %.2fs", toc(SCaseStart)));
Logger.closeBlock();
end
% Save results
if config.saveMeasurements
saveMeasurements(SCases);
end
if config.saveAllMeasurementsInOneFile
saveAllMeasurementsInOneFile(SCases, casesToMeasure);
end
Logger.newDelimitedSection(...
sprintf("Whole measureSCase() ran in %.2fs", toc(measureSCaseStart)));
Logger.stop();
output = SCases;
end
function runShoulderMeasurements(shoulder)
shoulderStart = tic;
config = getConfig();
% Measurements
if config.runMeasurements.loadData
shoulder.loadData();
end
if shoulder.isempty()
Logger.logn("Not enough data loaded to perform further measurements.")
return
end
if config.runMeasurements.sliceAndSegmentRotatorCuffMuscles
Logger.newDelimitedSection("Segment"); Logger.logn("");
Logger.timeLogExecution("Slice and segment rotator cuff muscles: ",...
@(shoulder) shoulder.rotatorCuff.sliceAndSegment(), shoulder);
Logger.closeSection();
end
if config.runMeasurements.morphology
shoulder.morphology();
end
if config.runMeasurements.measureFirst
shoulder.measureFirst();
end
if config.runMeasurements.measureSecond
shoulder.measureSecond();
end
if config.runMeasurements.measureGlenoidDensity
Logger.newDelimitedSection("Glenoid density"); Logger.logn("");
Logger.timeLogExecution("Glenoid density: ",...
@(shoulder) shoulder.scapula.glenoid.measureDensity(), shoulder);
Logger.closeSection();
end
Logger.newDelimitedSection(...
sprintf("Shoulder measured in %.2fs", toc(shoulderStart)));
Logger.closeSection();
end
function saveMeasurements(SCases)
savingStart = tic;
Logger.log("Saving new measurements: ")
try
arrayfun(@(SCase) SCase.saveMatlab, SCases);
Logger.logn("Done in %.2fs", toc(savingStart));
catch ME
Logger.logn(ME.message);
end
end
function saveAllMeasurementsInOneFile(SCases, casesToMeasure)
savingStart = tic;
Logger.log("Saving whole database in one file: ")
try
if not(isequal(casesToMeasure, "*"))
SCaseDB = loadSCase("*");
else
SCaseDB = SCases;
end
save(fullfile(getConfig().dataDir, "matlab", "SCaseDB.mat"), "SCaseDB");
Logger.logn("Done in %.2fs", toc(savingStart));
catch ME
Logger.logn(ME.message);
end
end
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