From 0ef1e10ed6f288da36f5c1e11c1fd5efb7138d46 Mon Sep 17 00:00:00 2001
From: Jurjen Broeke <jurjen.broeke@vu.nl>
Date: Thu, 7 Mar 2024 09:39:21 +0100
Subject: [PATCH] minor update
fixed implementation of importing ROIs.
added additional checks on user interaction (WIP).
---
sCaSpA.m | 56 +++++++++++++++++++++++++++++++++++++++++---------------
1 file changed, 41 insertions(+), 15 deletions(-)
diff --git a/sCaSpA.m b/sCaSpA.m
index 3893020..330b5cd 100644
--- a/sCaSpA.m
+++ b/sCaSpA.m
@@ -174,11 +174,12 @@ classdef sCaSpA < matlab.apps.AppBase
properties (Access = private)
majVer = 1;
% major versions - 230228 = 1 -> finish build the main interface, it will guide the user to the main steps of the analysis
- minVer = 3;
+ minVer = 4;
% minor versions - 230228 = 0 -> basic functionality implemented
% - 230320 = 1 -> add a new column for labeling the ROIs, one filter for the trace, and one filter for the FOV
% - 230405 = 2 -> Implemented loading *.nd2 files
% - 230425 = 3 -> Start implementation for cell clustering and out of network analysis
+ % - 240307 = 4 -> implemented ROI loading from ImageJ RoiSet files
dailyBuilt = 3;
% bug fixes - 230425 = 0 -> Several bug fixes and new implementations
% - 230504 = 1 -> Add batch import for movies
@@ -502,41 +503,62 @@ classdef sCaSpA < matlab.apps.AppBase
function ImportROIs(app)
roiPath = uigetdir(app.options.LastPath, 'Select ROI folder');
- fileExt = '*.csv';
+ if roiPath == 0
+ % user canceled
+ return;
+ end
+ % use the zip extension to select RoiSets derived from ImageJ
+ fileExt = '*.zip';
roiFiles = dir(fullfile(roiPath, fileExt));
+
+ % perform a check to see if any files are present
+ if numel(roiFiles) == 0
+ return;
+ end
+
togglePointer(app);
figure(app.UIFigure);
try
- % Get the name info
- nameList = regexprep({roiFiles.name}, fileExt, '');
+ % Get the name info (remove the asterisk for replacement)
+ nameList = regexprep({roiFiles.name}, fileExt(2:end), '');
nameParts = regexp(nameList, '_', 'split')';
nFiles = numel(nameList);
allRois = cell(size(app.imgT,1), 1);
for f = 1:nFiles
- % Match the ROI to the expetimentID
- expID = [nameParts{f}{2} '_' nameParts{f}{4}];
+ % Match the ROI to the experimentID, compensate for
+ % RoiSet_ prefix if required
+ if matches(nameParts{f}{1}, 'RoiSet')
+ expID = [nameParts{f}{3} '_' nameParts{f}{5}];
+ else
+ expID = [nameParts{f}{2} '_' nameParts{f}{4}];
+ end
cellFltr = matches(app.dicT.ExperimentID, expID);
+ if sum(cellFltr) == 0
+ % this experiment ID could not be found, skip
+ continue;
+ end
% Extract the ROIs
if contains(fileExt, '*.zip')
- tempRoi = ReadImageJROI(fullfile({roiFiles(f).folder}, {roiFiles(f).name}));
- tempRoi = cellfun(@(x) x.vnRectBounds, tempRoi{:}, 'UniformOutput', false);
+ tempRoi = ReadImageJROI(fullfile(roiFiles(f).folder, roiFiles(f).name));
+ tempRoi = cellfun(@(x) x.vnRectBounds, tempRoi, 'UniformOutput', false);
else
- tempRoi = ReadImageJROI(fullfile({roiFiles(f).folder}, {roiFiles(f).name}));
+ tempRoi = ReadImageJROI(fullfile(roiFiles(f).folder, roiFiles(f).name));
end
% Get the center coordinate
tempRoi = cellfun(@(x) round([mean(x([2 4])), mean(x([1 3]))]), tempRoi, 'UniformOutput', false);
% Add the ROI to the right cells
allRois{cellFltr} = cell2mat(tempRoi');
- % Load the data
- getIntensity(app)
end
+ %assign the updated ROIs
app.dicT.RoiSet = allRois;
+ % Load the data
+ getIntensity(app)
togglePointer(app)
catch ME
- delete(hWait);
togglePointer(app);
disp(ME)
errordlg('Failed to import the RoiSet. Please check command window for details', 'Import ROIs failed');
+ return;
end
modifyROIs(app, 'Modify')
end
@@ -1025,11 +1047,15 @@ classdef sCaSpA < matlab.apps.AppBase
tempDIC = contains(app.dicT.CellID, app.DropDownDIC.Value);
allRoi = app.dicT.RoiSet{tempDIC};
nRoi = size(allRoi,1);
+ if nRoi == 0
+ % there are no ROIs, so stop processing
+ return;
+ end
% Delete the existing mask and replace it
app.patchMask = [];
delete(findobj(app.UIAxesDIC, 'Type', 'Patch'));
delete(findobj(app.UIAxesMovie, 'Type', 'Patch'));
- for r=1:nRoi
+ for r=nRoi:-1:1
if strcmp(app.options.RoiShape, 'Square')
tempRoi = [allRoi(r,:) - app.options.RoiSize; allRoi(r,:) + app.options.RoiSize];
roiX = [tempRoi(1,1) tempRoi(2,1) tempRoi(2,1) tempRoi(1,1)];
@@ -2398,7 +2424,7 @@ classdef sCaSpA < matlab.apps.AppBase
%hWait = varargin{2};
end
for i = 1:nImages
- tic
+ %tic
nRoi = size(tempRoi,1);
hWait.Message = sprintf('Getting %d ROIs intensity in FOV: %s', nRoi, app.imgT.CellID{imgFltr(i)});
imgInfo = app.imgT.ImgProperties(imgFltr(i),:);
@@ -2433,7 +2459,7 @@ classdef sCaSpA < matlab.apps.AppBase
% Since we already loaded the data anyway, save the StdDev
tempImg = std(double(imgData),[],3);
app.stdT{tempDIC} = tempImg;
- loadTime = toc;
+ %loadTime = toc;
end
if nargin < 3
close(hWait);
--
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