Skip to content

Commit

Permalink
Merge pull request #100 from bahanonu/bahanonu/functionUpdates
Browse files Browse the repository at this point in the history 
Misc. improvements, GUI speed-ups, and new options
  • Loading branch information
@bahanonu
bahanonu authored Mar 1, 2022
2 parents c1a12aa + 5ba519b commit 0dc144f
Show file tree
Hide file tree
Showing 43 changed files with 1,068 additions and 577 deletions.
4 changes: 3 additions & 1 deletion +ciapkg/+api/convertInscopixIsxdToHdf5.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@
% inputMoviePath - char: path to ISXD file.
% outputs
%
% changelog
% 2022.01.26 [07:46:01] - Update +image package to +inscopix.

[success] = ciapkg.image.convertInscopixIsxdToHdf5(inputFilePath,'passArgs', varargin);
[success] = ciapkg.inscopix.convertInscopixIsxdToHdf5(inputFilePath,'passArgs', varargin);
end
21 changes: 21 additions & 0 deletions +ciapkg/+api/getMovieFileType.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
function [movieType, supported, movieType2] = getMovieFileType(thisMoviePath)
% Determine how to load movie, don't assume every movie in list is of the same type
% Biafra Ahanonu
% started: 2020.09.01 [‏‎14:16:57]
% inputs
% thisMoviePath - String: path to movie file.
% outputs
% movieType - Movie type
% supported - logical, whether movie is supported by CIAtah.
% movieType2 - Second movie type name (e.g. for NWB, where primary is HDF5).

% changelog
% 2021.08.08 [19:30:20] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
% 2021.08.13 [02:31:48] - Added HDF5 capitalized file extension.
% 2022.01.04 [12:23:47] - Update all strcmp to endsWith to ensure finding file extension as there are cases where software will export metadata into files with naming schema like NAME.tif.xml for NAME.tif and this can cause issues when using strcmp without endsWith-like checks.
% 2022.01.04 [13:28:05] - Update docs.
% TODO
%

[movieType, supported, movieType2] = ciapkg.io.getMovieFileType(thisMoviePath,'passArgs', varargin);
end
17 changes: 17 additions & 0 deletions +ciapkg/+api/getMovieInfo.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
function [movieInfo] = getMovieInfo(inputMovie,varargin)
% Wrapper to quickly get movie information. Options are the same as loadMovieList.
% Biafra Ahanonu
% started: 2020.09.29 [13:23:57]
% inputs
% inputMovie - [x y frames] or char string (path to movie).
% outputs
%

% changelog
% 2021.08.08 [19:30:20] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
% 2022.01.20 [22:50:25] - Directly call loadMovieList and bypass ciapkg.api.
% TODO
%

[movieInfo] = ciapkg.io.getMovieInfo(inputMovie,'passArgs', varargin);
end
25 changes: 25 additions & 0 deletions +ciapkg/+api/readFrame.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
function [thisFrame,movieFileID,inputMovieDims] = readFrame(inputMoviePath,frameNo,varargin)
% Fast reading of frame from files on disk. This is an alternative to loadMovieList that is much faster when only a single frame needs to be read.
% Biafra Ahanonu
% started: 2020.10.19 [11:45:24]
% inputs
% inputMoviePath | Str: path to a movie. Supports TIFF, AVI, HDF5, NWB, or Inscopix ISXD.
% frameNo | Int: frame number.
% outputs
%
% Usage
% For non-HDF5 file types, need to open a link to the
% [thisFrame,movieFileID,inputMovieDims] = ciapkg.io.readFrame(inputMoviePath,frameNo);
% Then for the second call, feed in movieFileID and inputMovieDims to improve read speed.
% [thisFrame] = ciapkg.io.readFrame(inputMoviePath,frameNo,'movieFileID',movieFileID,'inputMovieDims',inputMovieDims);

% changelog
% 2021.06.30 [01:26:29] - Updated handling of no file path character input.
% 2021.07.03 [09:02:14] - Updated to have backup read method for different tiff styles.
% 2021.08.08 [19:30:20] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
% TODO
%


[thisFrame,movieFileID,inputMovieDims] = ciapkg.io.readFrame(inputMoviePath,frameNo,'passArgs', varargin);
end
4 changes: 2 additions & 2 deletions +ciapkg/+api/viewAddTextToMovie.m
View file
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
function [movieTmp] = viewAddTextToMovie(movieTmp,inputText,fontSize)
function [movieTmp] = viewAddTextToMovie(movieTmp,inputText,fontSize,varargin)
% Adds text to movie matrix.
% Biafra Ahanonu
% inputs
% inputSignal - input signal (or matrix)
% outputs
%

[movieTmp] = ciapkg.video.viewAddTextToMovie(movieTmp,inputText,'passArgs', varargin);
[movieTmp] = ciapkg.video.viewAddTextToMovie(movieTmp,inputText,fontSize,'passArgs', varargin);
end
137 changes: 82 additions & 55 deletions +ciapkg/+classification/signalSorter.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,9 @@
% 2021.07.12 [10:14:21] - Changed call to overloaded functions to `ciapkg.overloaded` to avoid altering users Matlab workspace native functions.
% 2021.07.12 [11:15:06] - Change selection of cell on the maps to be instantaneous for where the mouse location is, much faster, don't have to wait for ginputCustom cross-hairs to show. Users can still show crosshairs with 'V'.
% 2021.08.08 [19:30:20] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
% 2021.12.22 [08:19:19] - Updated suptitle to ciapkg.overloaded.suptitle. Also limit number of GUI re-runs to prevent infinite looping.
% 2022.01.19 [12:35:42] - Fixed issue with `gca.XRuler.Axle.LineStyle` being an empty object when axes created, leading to failure to assign and error loops.
% 2022.02.06 [20:06:19] - Make all openFigure to ciapkg.api.openFigure.
% TODO
% DONE: New GUI interface to allow users to scroll through video and see cell activity at that point
% DONE: allow option to mark rest as bad signals
Expand Down Expand Up @@ -237,6 +240,8 @@
options.minEventsAddPeaks = 4;
% Int: font size of GUI elements
options.fontSize = 8;
% Int: number of times to re-run GUI in case of errors
options.guiReRunNo = 5;
% get options
options = getOptions(options,varargin);
% unpack options into current workspace
Expand Down Expand Up @@ -323,7 +328,7 @@
% pre-open all needed figures
for figNoFake = [1996 1997 1776 1777 1778 1779 42 1]
try;close(figNoFake);end
[~, ~] = openFigure(figNoFake, '');
[~, ~] = ciapkg.api.openFigure(figNoFake, '');
clf
drawnow
end
Expand Down Expand Up @@ -600,19 +605,23 @@

% Re-run in case of any errors or problems with the GUI
safeExit = 0;
while safeExit==0
% Re-run only a limited number of times to prevent infinite looping
nReRuns = options.guiReRunNo;
runNo = 1;
while safeExit==0&runNo<nReRuns
try
% Run the main decision-making function
[choices, safeExit] = chooseSignals(options,1:nSignals, inputImages,inputSignals,objMap, valid, inputStr,tmpDir,sessionID,signalPeakIdx,signalSnr,inputImagesThres,inputImageSizes,peakOutputStat,ROItraces,imgStats,inputSignalSignal,inputSignalNoise,inputImagesBoundaryIndices,signalPeakIdxOriginal,signalPeaksOriginal,instructionStr);
catch err
runNo = runNo+1;
disp(repmat('@',1,7))
disp(getReport(err,'extended','hyperlinks','on'));
disp(repmat('@',1,7))
end
end

% Assume all skips were good ICs that user forgot to enter
validChoices = choices;;
validChoices = choices;
validChoices(validChoices==-1)=1;
validChoices = logical(validChoices);

Expand Down Expand Up @@ -673,30 +682,30 @@ function plotSignalStatistics(inputSignals,inputImageSizes,inputStr,pointColor,
if ~isempty(slopeRatio)&&~isempty(signalSnr)
% start plotting!
figNo = 1776;%AMERICA
[~, figNo] = openFigure(figNo, '');
[~, figNo] = ciapkg.api.openFigure(figNo, '');
hold off;
plot(normalizeVector(slopeRatio),'Color',[4 4 4]/5);hold on;
plot(normalizeVector(signalSnr),'r');
title(['SNR in trace signal for ' inputStr])
hleg1 = legend('S-ratio','SNR');
xlabel('ic rank');ylabel('SNR');box off;hold off;

[~, figNo] = openFigure(figNo, '');
[~, figNo] = ciapkg.api.openFigure(figNo, '');
hold off;
plot(slopeRatio,'Color',[4 4 4]/5);hold on;
plot(signalSnr,'r');
title(['SNR in trace signal for ' inputStr])
hleg1 = legend('S-ratio','SNR');
xlabel('ic rank');ylabel('SNR');box off;hold off;

[~, figNo] = openFigure(figNo, '');
[~, figNo] = ciapkg.api.openFigure(figNo, '');
scatter(signalSnr,slopeRatio,[pointColor '.']);hold on;
plot(signalSnr, r, 'k-');
title(['SNR v S-ratio for ' inputStr])
xlabel('SNR');ylabel('S-ratio');box off;
eval(holdState);

[~, figNo] = openFigure(figNo, '');
[~, figNo] = ciapkg.api.openFigure(figNo, '');
scatter3(signalSnr,slopeRatio,inputImageSizes,[pointColor '.'])
title(['SNR, S-ratio, filter size for ' inputStr])
xlabel('SNR');ylabel('S-ratio');zlabel('ic size');
Expand Down Expand Up @@ -1266,8 +1275,9 @@ function plotSignalStatistics(inputSignals,inputImageSizes,inputStr,pointColor,

plotPeakSignal(thisTrace,testpeaks,cellIDStr,instructionStr,minValTraces,maxValTraces,peakROI,peakOutputStat.avgSpikeTrace(i,:),peakOutputStat.slopeRatio(i),peakOutputStat.spikeCenterTrace{i},valid);
axisH = gca;
axisH.XRuler.Axle.LineStyle = 'none';
axisH.YRuler.Axle.LineStyle = 'none';
set(axisH,'XTick',[],'YTick',[]);
% axisH.XRuler.Axle.LineStyle = 'none';
% axisH.YRuler.Axle.LineStyle = 'none';
% add in the ratio of the rise/decay slopes. Should be >>1 for calcium

if i==1
Expand Down Expand Up @@ -1679,7 +1689,7 @@ function subfxnUserInputGui(replyTmp)
% 'M' make a montage of peak frames
if isequal(reply, 109)&&~isempty(options.inputMovie)
try
% [~, ~] = openFigure(options.secondFigNo, '');
% [~, ~] = ciapkg.api.openFigure(options.secondFigNo, '');
figure(options.secondFigNo)
clf
croppedPeakImages2 = viewMontage(options.inputMovie,thisImage,options,thisTrace,[signalPeakIdx{i}],minValMovie,maxValMovie,options.cropSizeLength,i,1);
Expand All @@ -1696,7 +1706,7 @@ function subfxnUserInputGui(replyTmp)

colorbar('Location','eastoutside');

suptitle('Press any key to exit')
ciapkg.overloaded.suptitle('Press any key to exit')
set(gcf,'currentch','3');
keyIn = get(gcf,'CurrentCharacter');
drawnow
Expand Down Expand Up @@ -1768,7 +1778,7 @@ function subfxnUserInputGui(replyTmp)
subfxnCreateLegend();
% 'I' display trace with median removed
elseif isequal(reply, 105)
% [~, ~] = openFigure(options.secondFigNo, '');
% [~, ~] = ciapkg.api.openFigure(options.secondFigNo, '');
figure(options.secondFigNo)
clf
set(gcf,'currentch','3');
Expand All @@ -1783,7 +1793,7 @@ function subfxnUserInputGui(replyTmp)
axis equal tight
colormap([options.colormap]);
colorbar
suptitle('Current signal source image | Press any key to exit')
ciapkg.overloaded.suptitle('Current signal source image | Press any key to exit')
drawnow
while strcmp(keyIn,'3')
keyIn = get(gcf,'CurrentCharacter');
Expand All @@ -1792,7 +1802,7 @@ function subfxnUserInputGui(replyTmp)
close(options.secondFigNo)
% 'R' display trace with median removed
elseif isequal(reply, 114)
% [~, ~] = openFigure(options.secondFigNo, '');
% [~, ~] = ciapkg.api.openFigure(options.secondFigNo, '');
figure(options.secondFigNo)
clf
set(gcf,'currentch','3');
Expand Down Expand Up @@ -1905,7 +1915,7 @@ function subfxnUserInputGui(replyTmp)
title('All traces')
% legend()

suptitle('Press any key to exit | Zoom is enabled on traces, x axes are linked')
ciapkg.overloaded.suptitle('Press any key to exit | Zoom is enabled on traces, x axes are linked')
linkaxes(linkAx,'x');
drawnow
while strcmp(keyIn,'3')
Expand Down Expand Up @@ -2029,7 +2039,7 @@ function mouseWheelChange(hObject, callbackdata, handles)
end
end
function [conMenu] = subfxn_createShortcutInfo()

sepMenuLins = {'','',''};
% {'Drag edges to resize legend window.','',''},...
menuListInfo = {...
Expand Down Expand Up @@ -2084,7 +2094,7 @@ function mouseWheelChange(hObject, callbackdata, handles)
if isempty([menuListInfo{mNo}{1}])
labelStr = [''];
else
labelStr = ['<HTML><PRE>' menuListInfo{mNo}{1} ' ' menuListInfo{mNo}{3} '</PRE>'];
labelStr = ['<HTML><PRE>' menuListInfo{mNo}{1} ' ' menuListInfo{mNo}{3} '</PRE>'];
end
mitemAll{mNo} = uimenu(conMenu,'label',labelStr,'MenuSelectedFcn',@(src,evnt) subfxnUserInputGui(double(menuListInfo{mNo}{2})));
end
Expand Down Expand Up @@ -2248,26 +2258,34 @@ function movieCallback(source,eventdata)
validData(:,i,3) = 1;

if i==1
if ~isempty(axValid)
delete(findobj(mainFig,'Tag','colorProgressBar1'));
end
colorbar(inputMoviePlotLoc2Handle,'off')
s2Pos = plotboxpos(inputMoviePlotLoc2Handle);
cbh = colorbar(inputMoviePlotLoc2Handle,'Location','eastoutside','Position',[s2Pos(1)+s2Pos(3)+0.005 s2Pos(2) 0.01 s2Pos(4)],'FontSize',options.fontSize-2);
ylabel(cbh,'Fluorescence (e.g. \DeltaF/F or \DeltaF/\sigma)','FontSize',options.fontSize-1);

set(mainFig,'CurrentAxes',inputMoviePlotLocHandle);
s3Pos = plotboxpos(gca);

axValid = axes('Position',[s3Pos(1) 0.98 s3Pos(3) 0.02],'XTick',[],'YTick',[]);
validImgHandle = imagesc(axValid,validData);
set(axValid,'XTick',[],'YTick',[],'Tag','colorProgressBar1')
xlabel(['Cell (green), non-cell (red), unknown (gray) | ' 'signal ' cellIDStr ' (' num2str(sum(valid==1)) ' good)'],'FontSize',options.fontSize-2)

box off
axValid.XRuler.Axle.LineStyle = 'none';
axValid.YColor = [1,1,1,0];
% axValid.YRuler.Axle.LineStyle = 'none';
try
if ~isempty(axValid)
delete(findobj(mainFig,'Tag','colorProgressBar1'));
end
colorbar(inputMoviePlotLoc2Handle,'off')
s2Pos = plotboxpos(inputMoviePlotLoc2Handle);
cbh = colorbar(inputMoviePlotLoc2Handle,'Location','eastoutside','Position',[s2Pos(1)+s2Pos(3)+0.005 s2Pos(2) 0.01 s2Pos(4)],'FontSize',options.fontSize-2);
ylabel(cbh,'Fluorescence (e.g. \DeltaF/F or \DeltaF/\sigma)','FontSize',options.fontSize-1);

set(mainFig,'CurrentAxes',inputMoviePlotLocHandle);
s3Pos = plotboxpos(gca);

axValid = axes('Position',[s3Pos(1) 0.98 s3Pos(3) 0.02],'XTick',[],'YTick',[]);
validImgHandle = imagesc(axValid,validData);
set(axValid,'XTick',[],'YTick',[],'Tag','colorProgressBar1')
xlabel(['Cell (green), non-cell (red), unknown (gray) | ' 'signal ' cellIDStr ' (' num2str(sum(valid==1)) ' good)'],'FontSize',options.fontSize-2)

box off
% axValid
set(axValid,'XTick',[],'YTick',[]);
% axValid.XRuler.Axle.LineStyle = 'none';
axValid.YColor = [1,1,1,0];
% axValid.YRuler.Axle.LineStyle = 'none';
catch err
disp(repmat('@',1,7))
disp(getReport(err,'extended','hyperlinks','on'));
disp(repmat('@',1,7))
end
else
thisHandle = findobj(axValid,'Type','image');
set(thisHandle,'CData',validData);
Expand All @@ -2280,21 +2298,29 @@ function movieCallback(source,eventdata)
validData(:,validSorted==0,1) = 1;
validData(:,validSorted==1,2) = 1;
if i==1
if ~isempty(axValidAll)
delete(findobj(mainFig,'Tag','colorProgressBar2'));
end
set(mainFig,'CurrentAxes',inputMoviePlotLoc2Handle);
s3Pos = plotboxpos(gca);
axValidAll = axes('Position',[s3Pos(1) 0.98 s3Pos(3) 0.02],'XTick',[],'YTick',[]);
validImgHandle = imagesc(axValidAll,validData);
set(axValidAll,'XTick',[],'YTick',[],'Tag','colorProgressBar2')
% xlabel(['Percent: cell (green), non-cell (red), unknown (gray).'],'FontSize',options.fontSize-2)
xlabel(['<---see.'],'FontSize',options.fontSize-2)

box off
axValidAll.XRuler.Axle.LineStyle = 'none';
axValidAll.YColor = [1,1,1,0];
% axValidAll.YRuler.Axle.LineStyle = 'none';
try
if ~isempty(axValidAll)
delete(findobj(mainFig,'Tag','colorProgressBar2'));
end
set(mainFig,'CurrentAxes',inputMoviePlotLoc2Handle);
s3Pos = plotboxpos(gca);
axValidAll = axes('Position',[s3Pos(1) 0.98 s3Pos(3) 0.02],'XTick',[],'YTick',[]);
validImgHandle = imagesc(axValidAll,validData);
set(axValidAll,'XTick',[],'YTick',[],'Tag','colorProgressBar2')
% xlabel(['Percent: cell (green), non-cell (red), unknown (gray).'],'FontSize',options.fontSize-2)
xlabel(['<---see.'],'FontSize',options.fontSize-2)

box off
% axValidAll
set(axValidAll,'XTick',[],'YTick',[]);
% axValidAll.XRuler.Axle.LineStyle = 'none';
axValidAll.YColor = [1,1,1,0];
% axValidAll.YRuler.Axle.LineStyle = 'none';
catch err
disp(repmat('@',1,7))
disp(getReport(err,'extended','hyperlinks','on'));
disp(repmat('@',1,7))
end
else
thisHandle = findobj(axValidAll,'Type','image');
set(thisHandle,'CData',validData);
Expand Down Expand Up @@ -2359,7 +2385,7 @@ function subfxnLostFocusMainFig(jAxis, jEventData, hFig)
clf
set(tmpHandle,'Name','Key legend','NumberTitle','off')
uicontrol('style','text','string',instructionStr,'Units', 'normalized','position',[1 1 80 90]/100,'horizontalAlignment', 'left','FontSize',9)
suptitle('signalSorter shortcuts/legend')
ciapkg.overloaded.suptitle('signalSorter shortcuts/legend')
axis off

% s.Interpreter = 'tex';
Expand Down Expand Up @@ -2631,8 +2657,9 @@ function subfxnLostFocusMainFig(jAxis, jEventData, hFig)
uistack(h,'bottom');

axisH = gca;
axisH.XRuler.Axle.LineStyle = 'none';
axisH.YRuler.Axle.LineStyle = 'none';
set(axisH,'XTick',[],'YTick',[]);
% axisH.XRuler.Axle.LineStyle = 'none';
% axisH.YRuler.Axle.LineStyle = 'none';

hold off;
catch err
Expand Down
Loading

0 comments on commit 0dc144f

Please sign in to comment.