diff --git a/matlab/+SSF/gen_SSF_kymo.m b/matlab/+SSF/gen_SSF_kymo.m index d73fac9cd151518af5f3821136150c5de7b49d42..130871e45a57944087497af420d4619e9c97716e 100644 --- a/matlab/+SSF/gen_SSF_kymo.m +++ b/matlab/+SSF/gen_SSF_kymo.m @@ -3,7 +3,7 @@ % targetChannelNames = {'Erk SSF'; 'Akt SSF' ; 'DHB SSF'; 'H2B SSF'; 'velocity SSF'}; % channel names in the kymo % targetChannelNames = {'Erk SSF'; 'Oct4 SSF' ; 'H2B SSF'; 'velocity SSF'}; % channel names in the kymo % targetChannelNumbers = [2, 3, -1]; % maps image channel names to kymo channel names -function gen_SSF_kymo(strDB,targetChannelNames,targetChannelNumbers,bDownscale, startFrame) +function gen_SSF_kymo(strDB,targetChannelNames,targetChannelNumbers,outfolder,bDownscale, startFrame) if ~exist('bDownscale','var') bDownscale = false; @@ -22,9 +22,9 @@ else end L = length(flist); -cacheFolder = fullfile(ROOT,'kymoV2'); -if ~exist(cacheFolder,'dir') - mkdir(cacheFolder); + +if ~exist(outfolder,'dir') + mkdir(outfolder); end imd={}; @@ -33,7 +33,7 @@ p = ljsStartParallel(16); parfor ff=1:L % for ff=1:L str_ff = fullfile(flist(ff).folder,flist(ff).name); - if exist(fullfile(cacheFolder,[flist(ff).name '_ssf_cache.json']),'file') + if exist(fullfile(outfolder,[flist(ff).name '_ssf_cache.json']),'file') fprintf(1,'genKymo skipping %s kymo exists\n',str_ff); continue end @@ -46,11 +46,11 @@ parfor ff=1:L imVolume = imVolume(:,:,startFrame:end,:); % trim off first 30 frames imd{ff}=MicroscopeData.MakeMetadataFromImage(imVolume); imd{ff}.DatasetName=[flist(ff).name '_ssf_cache']; - imd{ff}.imageDir = cacheFolder; + imd{ff}.imageDir = outfolder; imd{ff}.ChannelNames = targetChannelNames; - MicroscopeData.WriterH5(imVolume,'imageData',imd{ff},'path',cacheFolder); + MicroscopeData.WriterH5(imVolume,'imageData',imd{ff},'path',outfolder); tElapsed = toc(t0); fprintf(1,'ssf_volume %d tElapsed=%0.2f\n',ff,tElapsed); end -Import.leverImport('',cacheFolder); \ No newline at end of file +Import.leverImport('',outfolder); \ No newline at end of file