diff --git a/leversc/src/MATLAB/@leversc/leversc.m b/leversc/src/MATLAB/@leversc/leversc.m
index 35ed034c9eb5ccf9bf815a7c9882ac72089aefe9..73a002abf3a6bcba691c3a09746de4fc5178f51a 100644
--- a/leversc/src/MATLAB/@leversc/leversc.m
+++ b/leversc/src/MATLAB/@leversc/leversc.m
@@ -30,6 +30,7 @@ classdef leversc <handle
optional_figNumber=1;
end
[im,imD,figNumber]=parseArgs(optional_im,optional_imD,optional_figNumber);
+ im = imPad4(im);
obj.figNumber=figNumber;
if isfield(imD,'imageData')
CONSTANTS=imD;
@@ -122,3 +123,19 @@ end
end
+function im = imPad4(im)
+
+pad = [0,0,0];
+for d = 1:3
+ if 0~=mod(size(im,d),4)
+ pad(d) = size(im,d) + 4-mod(size(im,d),4);
+ end
+end
+if any(pad)
+ sz = size(im);
+ sz = sz(1:3);
+ pad = max(pad,sz);
+ im(pad(1),pad(2),pad(3),:) = 0;
+end
+
+end
\ No newline at end of file
diff --git a/matlab/+Batch/batchProc.m b/matlab/+Batch/batchProc.m
index 9bdb4cf09f4a35430284d67d58cbbd5f2432b523..a2ddcb3fbf776dcac79f64bdbe8184999aca1497 100644
--- a/matlab/+Batch/batchProc.m
+++ b/matlab/+Batch/batchProc.m
@@ -1,7 +1,7 @@
function batchProc(ROOT,nproc,nthread)
-parpool(nproc)
+ljsStartParallel(nproc);
flist = dir(fullfile(ROOT,'*.LEVER'));
parfor ff=1:length(flist)
diff --git a/matlab/+Batch/processMovie.m b/matlab/+Batch/processMovie.m
index 745d9486ad33326ee494fc607326f98798bd8711..8bbce04fe7dfb4215df267d69c2cc6739b83af35 100644
--- a/matlab/+Batch/processMovie.m
+++ b/matlab/+Batch/processMovie.m
@@ -49,7 +49,8 @@ processInfo.tPatch=getElapsed(tx);
tx=tic();
% nMerged = Smooth.Merge.goMerge(conn,CONSTANTS,segParams,nProcessors);
-nMerged = Smooth.Merge.goMerge2(conn, CONSTANTS, segParams);
+% nMerged = Smooth.Merge.goMerge2(conn, CONSTANTS, segParams);
+nMerged = -1;
processInfo.tMerge=getElapsed(tx);
tx=tic();
diff --git a/matlab/+DenoiseCache/denoiseFolder.m b/matlab/+DenoiseCache/denoiseFolder.m
index 72f1770409af637c8e40a6a986c344bf8126f0f0..0d12c85aa0b395a4fd28c82d2aeb6201361ec179 100644
--- a/matlab/+DenoiseCache/denoiseFolder.m
+++ b/matlab/+DenoiseCache/denoiseFolder.m
@@ -8,7 +8,7 @@ if 2==length(nProcessors)
nProcessors=nProcessors(2);
end
-nProcessors = min(nProcessors,16);
+nProcessors = min(nProcessors,8);
flist=dir(fullfile(folderName,'*.h5'));
if 0==length(flist)
diff --git a/matlab/+Helpers/cellEccentricity.m b/matlab/+Helpers/cellEccentricity.m
new file mode 100644
index 0000000000000000000000000000000000000000..0f76c5e048e30167a23d4dcded626b238925212d
--- /dev/null
+++ b/matlab/+Helpers/cellEccentricity.m
@@ -0,0 +1,4 @@
+function ecc = cellEccentricity(cx)
+
+evals = eig(cov(cx.pts));
+ecc = min(evals)/max(evals);
\ No newline at end of file
diff --git a/matlab/+Lineage/eraseLineage.m b/matlab/+Lineage/eraseLineage.m
new file mode 100644
index 0000000000000000000000000000000000000000..79116adb6bbfe7c6db1479c2034302740ac3621f
--- /dev/null
+++ b/matlab/+Lineage/eraseLineage.m
@@ -0,0 +1,9 @@
+function eraseLineage(conn)
+
+exec(conn,'delete from tblFamilies;delete from uiExtFamilies');
+strDB = conn.DataSource;
+Batch.batchTrack(strDB);
+Smooth.Patch.patch11(conn);
+Smooth.Patch.patch12(conn);
+Smooth.Patch.patch21(conn);
+Smooth.Patch.patchOcclusion(conn);
\ No newline at end of file
diff --git a/matlab/+MovieMaker/ssfMovie_erk.m b/matlab/+MovieMaker/ssfMovie_erk.m
index 4d68eb566b48208882be651f8709f9f70f809b07..7b850a4a63f18275100ecfa88c7c70371e62c495 100644
--- a/matlab/+MovieMaker/ssfMovie_erk.m
+++ b/matlab/+MovieMaker/ssfMovie_erk.m
@@ -5,8 +5,6 @@ function ssfMovie1(strDB)
bPreview = true
-
-
bwx = bwLoG_pos;
bwx(:,:,:,2) = bwLoG_neg;
imd = MicroscopeData.MakeMetadataFromImage(bwx);
diff --git a/matlab/+Read/findImageFolder.m b/matlab/+Read/findImageFolder.m
index 02e7b12f4efa03f96eb6a04b0e0799cf7e717b85..0e381a5925076bc2d1cd104fae5600b84ab92646 100644
--- a/matlab/+Read/findImageFolder.m
+++ b/matlab/+Read/findImageFolder.m
@@ -42,7 +42,7 @@ if ~exist(ljs,'file')
end
[fid,message]=fopen(fullfile(leverFolder,'lever.json'));
if (fid<=0)
- fprintf(1,'ERROR -- getConstants.m -- image path invalid and no lever.json ROOT override (message=%s)\n',message);
+ fprintf(1,'ERROR %s -- getConstants.m -- image path invalid and no lever.json ROOT override (message=%s)\n',CONSTANTS.imageData.DatasetName,message);
return;
end
diff --git a/matlab/+Read/getCell.m b/matlab/+Read/getCell.m
index ce9a54819e278d227a15574b77d7f295c2ca632f..72e20413e3ab5dbb8e7d1d5f55b96588ec07e52c 100644
--- a/matlab/+Read/getCell.m
+++ b/matlab/+Read/getCell.m
@@ -1,18 +1,22 @@
function Cell=getCell(conn,cellID,CONSTANTS)
Cell=[];
-
+qTable=fetch(conn,'pragma table_info(tblCells)');
+bLoG = any(cellfun(@length,(strfind(qTable.name,'LoG'))));
try
- cmd=['SELECT cellID,time,trackID,centroid,u16pixels,maxRadius,channel,area,surface,segCC '...
- ' FROM tblCells WHERE cellID=' num2str(cellID)];
+ cmd=['SELECT cellID,time,trackID,centroid,u16pixels,maxRadius,channel,area,surface,segCC '];
+ if bLoG
+ cmd = [cmd ' ,LoG '];
+ end
+ cmd =[cmd ' FROM tblCells WHERE cellID=' num2str(cellID)];
Q=ljsFetch(conn,cmd);
catch
try
Cell=Read.getCell3D(conn,cellID);
catch
fprintf(2,'unable to read cell from %s\n',CONSTANTS.imageData.DatasetName);
- return
end
+ return
end
if isempty(Q)
return
@@ -32,6 +36,9 @@ Cell.area=Q{8};
Cell.surface=jsondecode(Q{9});
Cell.segCC=Q{10};
+if bLoG
+ Cell.LoG = Q{11};
+end
if exist('CONSTANTS','var')
Cell = Read.setCellsIdxPts(Cell,CONSTANTS);
end
diff --git a/matlab/+Read/getCell3D.m b/matlab/+Read/getCell3D.m
index 59bff1b43d28bf6f6fe88c902c08ea9a4c587770..7ade71dea7999ec240c7d9df7a07f64cb5fd3126 100644
--- a/matlab/+Read/getCell3D.m
+++ b/matlab/+Read/getCell3D.m
@@ -2,7 +2,14 @@ function Cell=getCell3D(conn,cellID,CONSTANTS)
Cell=[];
-cmd=['SELECT time,trackID,centroid,channel,area,maxRadius,verts,faces,edges,normals,u16pixels FROM tblCells WHERE cellID=' num2str(cellID)];
+qTable=fetch(conn,'pragma table_info(tblCells)');
+bLoG = any(cellfun(@length,(strfind(qTable.name,'LoG'))));
+
+cmd=['SELECT time,trackID,centroid,channel,area,maxRadius,verts,faces,edges,normals,u16pixels '];
+if bLoG
+ cmd = [cmd ',LoG '];
+end
+cmd = [cmd ' FROM tblCells WHERE cellID=' num2str(cellID)];
Q=ljsFetch(conn,cmd);
% cellid time trackID centroid channel area, maxRadius,
% verts,edges,normals,faces,u16pixels
diff --git a/matlab/+SSF/catKymographs.m b/matlab/+SSF/catKymographs.m
new file mode 100644
index 0000000000000000000000000000000000000000..dbc4f2d70f775cd11f7a9f6532e2595af19f3ca5
--- /dev/null
+++ b/matlab/+SSF/catKymographs.m
@@ -0,0 +1,26 @@
+% pads time between images
+function i12 = catKymographs(i1,i2,dim)
+[i1,i2] = padIm(i1,i2);
+i12 = cat(dim,i1,i2);
+4;
+
+function [i1,i2] = padIm(i1,i2)
+
+if size(i1,3)>size(i2,3)
+ i2(:,:,end:size(i1,3),:)=0;
+else
+ i1(:,:,end:size(i2,3),:)=0;
+end
+
+if size(i1,2)>size(i2,2)
+ i2(:,end:size(i1,2),:,:)=0;
+else
+ i1(:,end:size(i2,2),:,:)=0;
+end
+
+if size(i1,1)>size(i2,1)
+ i2(end:size(i1,1),:,:,:)=0;
+else
+ i1(end:size(i2,1),:,:,:)=0;
+end
+
diff --git a/matlab/+SSF/cropKymo.m b/matlab/+SSF/cropKymo.m
new file mode 100644
index 0000000000000000000000000000000000000000..c86c14812892d6bd762924e73d6f8b84ce784d1e
--- /dev/null
+++ b/matlab/+SSF/cropKymo.m
@@ -0,0 +1,22 @@
+function im_crop = cropKymo(imSrc,idxPixels)
+
+% first copy over target pixels
+im = 0 * imSrc;
+im(idxPixels) = imSrc(idxPixels);
+
+[r,c,z]=ind2sub(size(im),idxPixels);
+
+r = cropDim(r,size(im,1));
+c = cropDim(c,size(im,2));
+z = cropDim(z,size(im,3));
+
+im_crop = im(min(r):max(r),min(c):max(c),min(z):max(z),:);
+
+
+function y = cropDim(x,sz)
+
+y = [min(x)-1:max(x)+1];
+y = min(y,sz);
+y = max(y,1);
+
+
diff --git a/matlab/+SSF/drawMitoticSSFtracks.m b/matlab/+SSF/drawMitoticSSFtracks.m
new file mode 100644
index 0000000000000000000000000000000000000000..d852790910a56a878784506820612d26d6e40fd7
--- /dev/null
+++ b/matlab/+SSF/drawMitoticSSFtracks.m
@@ -0,0 +1,57 @@
+% erk1D = Y(:,1);
+% [~,idxSort] = sort(erk1D);
+% qMitoSorted = qMitotic(idxSort,:);
+%
+function imx = drawMitoticSSFtracks(qMitotic,erkClipLimits,bDraw)
+
+if ~exist('bDraw','var')
+ bDraw = false;
+end
+
+for i = 1:height(qMitotic)
+ if ~isa(qMitotic.erk{i},'uint8')
+ qMitotic.erk{i} = SSF.quantize8(qMitotic.erk{i},erkClipLimits);
+ end
+end
+
+tmax = max(cellfun(@length,qMitotic.erk));
+imx = zeros(2*height(qMitotic),tmax);
+for i = 1:height(qMitotic)
+ erk_i = qMitotic.erk{i};
+ imx(2*i,end-length(erk_i)+1:end) = erk_i;
+end
+
+if ~bDraw
+ return
+end
+
+
+cmPos = colormap('parula');
+cmNeg = colormap('cool');
+cm = [cmNeg(1:2:end,:);cmPos(1:2:end,:)];
+cm(1,:) = [1,1,1];
+
+
+figure;imagesc(imx);colormap(cm);
+c = colorbar();
+clim = [min(c.Ticks),max(c.Ticks)];
+cticks = [clim(1), mean([clim(1),mean(clim)]), mean(clim), mean([clim(2),mean(clim)]),clim(2)];
+c.Ticks = cticks;
+c.TickLabels = {'BG','-0.5','0','0.5','1'}
+c.Label.String = 'Erk SSF';
+
+% close all
+
+% cm = colormap('parula');
+% cm(1:13,:)=repmat([1,1,1],13,1);
+% % c = colorbar('ticks',round(linspace(double(erkLimits(1)),double(erkLimits(2)),10)));
+% c = colorbar
+% c.Label.String = 'Erk SSF (8 bit, clipped to 95%)'
+%
+% xx = round(linspace(50,size(imx,2),5));
+% set(gca,'XTickLabel',arrayfun(@(y) num2str((y-308),xx,'UniformOutput',false))
+% xlabel('frames before mitosis');
+% ylabel('mitotic parent track sorted by NCD principal component')
+% yy = yticks();
+% set(gca,'YTickLabel',arrayfun(@(y) num2str(y/2),yticks()))
+% 4;
diff --git a/matlab/+SSF/drawSSFclusters.m b/matlab/+SSF/drawSSFclusters.m
new file mode 100644
index 0000000000000000000000000000000000000000..2e71a714a664dab1a0852ce74a93214d0ab0a191
--- /dev/null
+++ b/matlab/+SSF/drawSSFclusters.m
@@ -0,0 +1,68 @@
+% erk1D = Y(:,1);
+% [~,idxSort] = sort(erk1D);
+% qMitoSorted = qMitotic(idxSort,:);
+%
+% function imx = drawSSFtracks(qMitotic,idx,bDraw)
+
+% if ~exist('bDraw','var')
+% bDraw = false;
+% end
+tmax = max(cellfun(@length,qMitotic.erk));
+imx = [];
+imxH = 1;
+clusterPts = [];
+for k = 1:max(idx)
+ idxk = find(idx==k);
+ qk = qMitotic(idxk,:);
+ qk.yk = Y(idxk,1);
+ qk = sortrows(qk,'yk');
+ for i = 1:height(qk)
+ erk_i = qk.erk{i};
+ imx(imxH,tmax-length(erk_i)+1:tmax) = erk_i;
+ imxH = imxH+2;
+ end
+ imxH = imxH + 2;
+ clusterPts=[clusterPts,imxH];
+ imxH = imxH + 4;
+
+end
+
+
+
+% if ~bDraw
+% return
+% end
+
+
+close all
+
+cm = colormap('parula');
+cm(1,:) = [1,1,1];
+
+figure;imagesc(imx);colormap(cm);hold on
+c = colorbar('ticks',[2,64,128,192,255], 'ticklabels',{'-1.0','-0.5','0','0.5','1'});
+c.Label.String = 'Erk SSF';
+for p = 1:length(clusterPts)
+ plot([1,size(imx,2)],[clusterPts(p),clusterPts(p)],'-..k')
+end
+
+%
+
+% cm = colormap('parula');
+% cm(1:13,:)=repmat([1,1,1],13,1);
+% % c = colorbar('ticks',round(linspace(double(erkLimits(1)),double(erkLimits(2)),10)));
+% c = colorbar
+% c.Label.String = 'Erk SSF (8 bit, clipped to 95%)'
+%
+xx = round(linspace(50,size(imx,2),5));
+set(gca,'XTick',xx);
+set(gca,'XTickLabel',arrayfun(@(y) num2str(y-308),xx,'UniformOutput',false))
+xlabel('frames before mitosis');
+ylabel('mitotic parent track sorted by cluster and NCD principal component')
+yy = yticks();
+set(gca,'YTickLabel',arrayfun(@(y) num2str(y/2),yticks(),'uniformOutput',false))
+% h=gca; h.YAxis.TickLength = [0 0];
+yticks([])
+% 4;
+set(gcf,'color','w')
+% exportgraphics(gcf,'erk ssf heat map tracks NCD sorted cluster FLIF1d.pdf','Resolution',600,'contenttype','image')
diff --git a/matlab/+SSF/drawSSFtracks.m b/matlab/+SSF/drawSSFtracks.m
new file mode 100644
index 0000000000000000000000000000000000000000..1578eb1ffe731c9d7b4c7fdc167cf34188d461c4
--- /dev/null
+++ b/matlab/+SSF/drawSSFtracks.m
@@ -0,0 +1,85 @@
+% strDB = '/g/leverjs/Olivier/Agne/march_2023_20x/2022-04-05_steady_state_48h_deprived_13_ori.LEVER';
+
+function drawSSFtracks(ROOT,cache, kymo_channel, channel_description,fnames)
+
+[~,dsName,ext] = fileparts(ROOT);
+if ~exist('fnames','var')
+ fnames = [];
+end
+
+outfile = [dsName ' ' channel_description ' SSF projection_y_t.pdf'];
+if isempty(ext)
+ flist = dir(fullfile(ROOT,'*.LEVER'));
+else
+ flist = dir(ROOT);
+end
+f=figure(1);
+f.WindowState = 'maximized';
+pause(1)
+
+kymoPixels = {};
+for ff=1:length(flist)
+ strDB = fullfile(flist(ff).folder,flist(ff).name);
+ [ROOT,lf] = fileparts(strDB);
+ strKymoDB = fullfile(ROOT,cache,[lf '.LEVER_ssf_cache.LEVER']);
+ if ~exist(strKymoDB,'file')
+ continue
+ end
+ imKymo = SSF.loadImage(strKymoDB,kymo_channel);
+ kymoPixels{ff} = imKymo(find(imKymo));
+end
+kymoPixels = vertcat(kymoPixels{:});
+erkClipLimits = [prctile(kymoPixels,2.5),prctile(kymoPixels,97.5)];
+
+for ff = 1:length(flist)
+ strDB = fullfile(flist(ff).folder,flist(ff).name);
+ [ROOT,lf] = fileparts(strDB);
+ strKymoDB = fullfile(ROOT,cache,[lf '.LEVER_ssf_cache.LEVER']);
+ if ~exist(strKymoDB,'file')
+ continue
+ end
+ imKymo = SSF.loadImage(strKymoDB,kymo_channel);
+ %
+ imp = squeeze(max(imKymo,[],2));
+ imn = squeeze(min(imKymo,[],2));
+ imn = abs(imn);
+ idx = find(imn>imp);
+ imp(idx) = -1 .* imn(idx);
+% imp(imp<-0.5) = 0;
+ impq = SSF.quantize8(imp,erkClipLimits);
+% impq(imp==0 & imn==0) = 0;
+
+% % keep just [0,1] SSF
+% imp = squeeze(max(imKymo,[],2));
+% erkClipLimits = [0,prctile(kymoPixels,99.9)];
+% impq = SSF.quantize8(imp,erkClipLimits);
+% impq(imp==0) = 0; % set the background
+%
+
+ clf;imagesc(impq)
+ cm = colormap('parula');
+ cm(1,:) = [1,1,1]; % make the background white!
+ colormap(cm)
+ c = colorbar();
+ clim = [min(impq(:)),max(impq(:))];
+ cticks = [clim(1)+1, mean([clim(1),mean(clim)]), mean(clim), mean([clim(2),mean(clim)]),clim(2)];
+ c.Ticks = cticks;
+ % c.TickLabels = {'-1','-0.5','0','0.5','1'}
+
+ ticksSSF = linspace(erkClipLimits(1),erkClipLimits(2),5);
+ ticksSSF = arrayfun(@(x) num2str(x,2),ticksSSF,'UniformOutput',false);
+ c.TickLabels = ticksSSF;
+ c.Label.String = [channel_description ' SSF (dataset reference)'];
+ if ~isempty(fnames)
+ lf = fnames{ff};
+ end
+ hold on
+ yl = ylim();
+ plot([62,62],[yl(1),yl(2)],'--r','linewidth',2)
+ title([lf ' ' channel_description ' SSF projection to (Y/2,time)'],'interpreter','none')
+ xlabel('time (frames)')
+ ylabel('Y (max intensity projection along X)')
+ bAppend = ff>1;
+ exportgraphics(gcf,outfile,'Resolution',600,'contenttype','image','append',bAppend);
+
+end
\ No newline at end of file
diff --git a/matlab/+SSF/draw_ssf_ncd.m b/matlab/+SSF/draw_ssf_ncd.m
index a52d16003b60ab31a9fa81d0a0984bb60ff5072d..4c4acb5b8ef8caf077c51efbc45355a800b9dbcc 100644
--- a/matlab/+SSF/draw_ssf_ncd.m
+++ b/matlab/+SSF/draw_ssf_ncd.m
@@ -1,12 +1,12 @@
% load('agne_72_8bpp.mat')
flist = dir(fullfile(ROOT,'*.LEVER'));
-className = {};
-for ff=1:length(flist)
- cn = regexp(flist(ff).name,'(\d+-\d+-\d+)_.*(\d\d)_ori*','tokens');
- cn = [cn{1}{1} '_' cn{1}{2}];
- className{ff} = classMap(cn);
-end
+% className = {};
+% for ff=1:length(flist)
+% cn = regexp(flist(ff).name,'(\d+-\d+-\d+)_.*(\d\d)_ori*','tokens');
+% cn = [cn{1}{1} '_' cn{1}{2}];
+% className{ff} = classMap(cn);
+% end
% targetClass = {'AKT1_E17K','WT','PIK3CA_E545K'}
% idx = find(cellfun(@(x) ~isempty(find(strcmp(targetClass,x))),className));
% A=d(idx,idx);
@@ -28,7 +28,7 @@ clf;hold off;
sym = {'ko','cv','m^','r*','gx','<k','b>','gs','bd'};
-classList = unique(classMap.values);
+classList = unique(className);
hx = zeros(size(classList));
hold on
diff --git a/matlab/+SSF/draw_ssf_tracks.m b/matlab/+SSF/draw_ssf_tracks.m
deleted file mode 100644
index d677a8a056c95fcb91a10802c52e2cb2636b5499..0000000000000000000000000000000000000000
--- a/matlab/+SSF/draw_ssf_tracks.m
+++ /dev/null
@@ -1,41 +0,0 @@
-close all
-classList = unique(classMap.values);
-for ff = 1:length(flist)
- strDB = fullfile(flist(ff).folder,flist(ff).name);
- [conn,CONSTANTS,segParams]=openDB(strDB);
-
- cmd = 'select trackID from tblCells inner join tblFamilies on cellID = cellID_parent';
- q = fetch(conn,cmd);
- close(conn);
-
- erk_tracks = movie_tracks{ff};
- class = classMap(flist(ff).name(1:13));
- id = find(cellfun(@length,strfind(classList,class)));
- figure(id) ; hold on
-
- tids = erk_tracks.keys;
- tids = [tids{:}];
- tids = intersect(tids,q.trackID);
- for i = 1:length(tids)
- ssf = erk_tracks(tids(i));
- if size(ssf,2) <= 10 || all(0==ssf(1,:))
- continue
- end
- plot(5*ssf(2,:),ssf(1,:),'-');
- end
-end
-
-for i = 1:length(classList)
- figure(i)
- set(gcf,'color','w')
- title(classList{i},'Interpreter','none')
- xlabel('time (minutes)')
- ylabel('SSF')
- fname = ['erk_tracks_' classList{i} '.tif'];
- print(fname,'-dtiffn');
-end
-
-cx={}
-for ff = 1:length(flist)
- cx{ff} = classMap(flist(ff).name(1:13))
-end
\ No newline at end of file
diff --git a/matlab/+SSF/gen_SSF_kymo.m b/matlab/+SSF/gen_SSF_kymo.m
index 24b4e020818f2c901a74e5b8927865f0f9428d08..130871e45a57944087497af420d4619e9c97716e 100644
--- a/matlab/+SSF/gen_SSF_kymo.m
+++ b/matlab/+SSF/gen_SSF_kymo.m
@@ -1,36 +1,56 @@
+% BE CAREFUL HERE! BE DRAGONS! GET THESE target names & numbers RIGHT OR PERISH
+% 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,outfolder,bDownscale, startFrame)
-function gen_SSF_kymo(ROOT)
-targetChannelNames = {'Erk SSF'; 'Akt SSF' ; 'DHB SSF'; 'H2B SSF'; 'velocity SSF'}; % channel names in the kymo
-targetChannelNumbers = [-2, -3, 1, -4]; % maps image channel names to kymo channel names
+if ~exist('bDownscale','var')
+ bDownscale = false;
+end
+if ~exist('startFrame','var')
+ startFrame = 1;
+end
-cacheFolder = fullfile(ROOT,'kymoV2');
-if ~exist(cacheFolder,'dir')
- mkdir(cacheFolder);
+[fx,nx,ext]=fileparts(strDB);
+if strcmp(ext,'.LEVER')
+ flist = dir(strDB);
+ ROOT = fx;
+else
+ ROOT = strDB;
+ flist = dir(fullfile(strDB,'*.LEVER'));
end
-flist = dir(fullfile(ROOT,'*.LEVER'));
L = length(flist);
+
+if ~exist(outfolder,'dir')
+ mkdir(outfolder);
+end
+
imd={};
+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
t0 = tic();
- imVolume = SSF.ssf_volume(str_ff,targetChannelNumbers);
+ imVolume = SSF.ssf_volume(str_ff,targetChannelNumbers, bDownscale);
if isempty(imVolume)
continue
end
- imVolume(:,:,:,5) = SSF.velocity_kymo(str_ff);
- imVolume = imVolume(:,:,31:end,:); % trim off first 30 frames
+% imVolume(:,:,:,length(targetChannelNumbers)+1) = SSF.velocity_kymo(str_ff);
+ 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
diff --git a/matlab/+SSF/goErkCN.m b/matlab/+SSF/goErkCN.m
new file mode 100644
index 0000000000000000000000000000000000000000..1c7ae124eb937c61971f4571c2c873fe3c298117
--- /dev/null
+++ b/matlab/+SSF/goErkCN.m
@@ -0,0 +1,42 @@
+% strDB = '/f/leverjs/Olivier/Yannick/20210924/20210924_pos3.LEVER';
+% tblCN = goErkCN(strDB,174279)
+% tblCN = goErkCN(strDB,224589)
+function tblCN = goErkCN(strDB,targetTrack)
+
+[conn,CONSTANTS,segParams]=openDB(strDB);
+[ROOT,lf] = fileparts(strDB);
+strKymo = fullfile(ROOT,'kymoV',[lf '.LEVER_ssf_cache.LEVER']);
+imKymo = leversc.loadImage(strKymo,1,1);
+
+cmd = ['select cellID,trackID,centroid,time,LoG from tblCells where trackID = '...
+ num2str(targetTrack)];
+q=fetch(conn,cmd);
+
+erkSSF = [];
+for i = 1:height(q)
+ centroid = jsondecode(q.centroid{i});
+ centroid = [round(centroid(1:2))', q.time(i)];
+ sample_value = SSF.ssf_sample(imKymo,centroid);
+ erkSSF(i) = sample_value;
+end
+
+featureParams.channel = 2;
+featureParams.name='CytoToNuclearRatio';
+featureParams.color="#00ffff";
+tblCN = table();
+for i = 1:height(q)
+ t = q.time(i);
+ cellList = Read.getCellsTime(conn,t,segParams.channels(1),CONSTANTS);
+ nt = SSF.cytoToNuclearRatio(cellList,q.cellID(i),t,CONSTANTS,featureParams,segParams);
+ nt.erkSSF = erkSSF(i);
+ tblCN = [tblCN;nt]
+end
+ee = imKymo(find(imKymo));
+erkClipLimits = [prctile(ee,2.5), prctile(ee,97.5)];
+
+erk = tblCN.erkSSF;
+erk = SSF.quantize8(erk,erkClipLimits);
+erk = 2 * (double(erk) / 255) -1;
+figure;plot(erk)
+hold on
+plot(tblCN.cnRatio)
\ No newline at end of file
diff --git a/matlab/+SSF/goTrackSSFkymo.m b/matlab/+SSF/goTrackSSFkymo.m
new file mode 100644
index 0000000000000000000000000000000000000000..6461c99111f6b7e7ace956edf4da2fbd94be7224
--- /dev/null
+++ b/matlab/+SSF/goTrackSSFkymo.m
@@ -0,0 +1,117 @@
+
+ROOT = '/f/leverjs/Olivier/Yannick/20210924/';
+flist = dir(fullfile(ROOT,'*.LEVER'));
+
+cxKymo = {};
+qMitotic = {};
+
+for ff = 1:length(flist)
+ strDB = fullfile(flist(ff).folder,flist(ff).name);
+ [ROOT,lf] = fileparts(strDB);
+ strKymoDB = fullfile(ROOT,'kymoV',[lf '.LEVER_ssf_cache.LEVER']);
+ cxKymo{ff} = SSF.loadImage(strKymoDB,1);
+ [conn,CONSTANTS,segParams]=openDB(strDB);
+ imErk = cxKymo{ff}(:,:,:,1);
+ qm = fetch(conn,'select * from (select cellID,trackID,count(time) as nt from tblCells where trackID in (select trackID from tblCells inner join tblFamilies on cellID_parent=cellID) group by trackID) where nt>23');
+ for i = 1:length(qm.trackID)
+ qcx = fetch(conn,['select centroid,time from tblCells where trackID = ' num2str(qm.trackID(i))]);
+ centroids = cellfun(@jsondecode,qcx.centroid,'UniformOutput',false);
+ centroids = reshape(vertcat(centroids{:}),3,[])';
+ centroids = round(centroids);
+ qm.centroids{i} = [centroids(:,1:2),qcx.time];
+ qm.idxCentroids{i} = sub2ind(size(cxKymo{ff}),centroids(:,2),centroids(:,1),qcx.time);
+ qm.movieID(i) = ff;
+ qm.erk{i} = SSF.ssf_sample_idx(imErk,qm.idxCentroids{i});
+ qm.isEmpty(i) = all(0==qm.erk{i});
+ end
+ qm(qm.isEmpty,:)=[];
+ qMitotic = [qMitotic;qm];
+end
+% qMitotic.erk is the signal. quantize it to 8 bit now
+erkCombined =[qMitotic.erk{:}]' ;
+erkClipLimits = [prctile(erkCombined,2.5), prctile(erkCombined,97.5)];
+for c = 1:length(cxKymo)
+ cxKymo{c} = SSF.quantize8(cxKymo{c},erkClipLimits);
+end
+% % a bit slow, but steady. find distancefrom each mitotis
+for i = 1:height(qMitotic)
+
+ strDB = fullfile(flist(qMitotic.movieID(i)).folder,flist(qMitotic.movieID(i)).name);
+ [conn,CONSTANTS,segParams]=openDB(strDB);
+ q1 = fetch(conn,['select centroid,time from tblCells where cellID = ' num2str(qMitotic.cellID(i))]);
+ colony = Read.getCellsTime(conn,q1.time,4,CONSTANTS);
+ for c = 1:length(colony)
+ bw = zeros(CONSTANTS.imageData.Dimensions(2),CONSTANTS.imageData.Dimensions(1));
+ bw(colony(c).idxPts) = 1;
+ centroid1 = round(jsondecode(q1.centroid{1}));
+ if ~bw(centroid1(2),centroid1(1))
+ continue
+ end
+ bwd = bwdist(~bw);
+ bwd = bwd./max(bwd(:));
+ qMitotic.dNormalized(i) = bwd(centroid1(2),centroid1(1));
+ qMitotic.time(i) = q1.time;
+ end
+end
+
+
+
+for i = 1:height(qMitotic)
+ erk_i = medfilt1(qMitotic.erk{i}, 5);
+ erk_i = SSF.quantize8(erk_i, erkClipLimits);
+ qMitotic.erk{i} = erk_i;
+end
+
+d = [];
+L = height(qMitotic);
+parfor i = 1:L
+% im_i = SSF.cropKymo(cxKymo{qMitotic.movieID(i)},qMitotic.idxCentroids{i});
+ for j = 1:L
+% im_j = SSF.cropKymo(cxKymo{qMitotic.movieID(j)},qMitotic.idxCentroids{j});
+ erk_j = medfilt1(qMitotic.erk{j},5)
+ im_j = SSF.quantize8(erk_j,erkClipLimits);
+ d(i,j) = SSF.ncd_ssf_volume(im_i,im_j);
+ end
+end
+
+% for i = 1:length(d)
+% for j = 1 : length(d)
+% d(i,j)=max(d(i,j),d(j,i));
+% end
+% d(i,i) = max(d(i,i),0);
+% end
+
+close all
+A = d;
+K=3;
+[idx,Y] = Cluster.SpectralCluster(A,K);
+% Y(:,3) = [erkMitotic.d];
+figure;hold on
+hred = [];
+hgreen = [];
+for i = 1 : height(qMitotic)
+ if qMitotic.dNormalized(i)<.2929
+ hred = [hred,plot3(Y(i,1),Y(i,2),Y(i,3),'.r')];
+ else
+ hgreen = [hgreen,plot3(Y(i,1),Y(i,2),Y(i,3),'.g')];
+ end
+end
+xlabel('u1')
+ylabel('u2')
+zlabel('u3')
+legend([hred(1),hgreen(1)],'d_{normalized} < 0.29','d_{normalized} \geq .2929')
+
+set(gcf,'color','w')
+figure;hold on
+for i = 1 : height(qMitotic)
+ if qMitotic.dNormalized(i)<.2929
+ plot(Y(i,1),Y(i,2),'.r');
+ else
+ plot(Y(i,1),Y(i,2),'.g');
+ end
+end
+xlabel('u1')
+ylabel('u2')
+legend({'d_{normalized}>.2929','d_{normalized}<.2929'})
+set(gcf,'color','w')
+% exportgraphics(gcf,'erkMitoticParentTracksEmbedding_medfilt.pdf','Resolution',300,'contenttype','image')
\ No newline at end of file
diff --git a/matlab/+SSF/go_ssf_ncd.m b/matlab/+SSF/go_ssf_ncd.m
index b7d9c45067d13b448c75d69a808003aa2eec3ce6..f79c51b3104637c29891d5a0b65e7457aaa11ab3 100644
--- a/matlab/+SSF/go_ssf_ncd.m
+++ b/matlab/+SSF/go_ssf_ncd.m
@@ -4,40 +4,86 @@
% AKT_CHANNEL = 2;
% H2B_CHANNEL = 3;
% targetChannels = [ERK_CHANNEL,AKT_CHANNEL];
-function d=go_ssf_ncd(ROOT,targetChannels)
+function d=go_ssf_ncd(kROOT,targetChannels)
-flist = dir(fullfile(ROOT,'*.LEVER'));
+tStart = tic();
+
+flist = dir(fullfile(kROOT,'*.LEVER'));
d = zeros(length(flist));
-L = length(flist);
-imList = {};
+kymoPixels = {};
+
+p = ljsStartParallel(32);
-tStart = tic();
-%
-parfor ff=1:L
+parfor ff=1:length(flist)
strDB_ff = fullfile(flist(ff).folder,flist(ff).name);
- im_ff = SSF.loadImage(strDB_ff,targetChannels);
- for gg=1:L
- if gg<ff
+ im_ff = SSF.loadImage(strDB_ff,targetChannels);
+ kp = im_ff(find(im_ff));
+ kymoPixels{ff} = kp;
+end
+kymoPixels = vertcat(kymoPixels{:});
+erkClipLimits = [prctile(kymoPixels,2.5),prctile(kymoPixels,97.5)]
+% erkClipLimits = [0,prctile(kymoPixels,99)];
+
+%
+cmdList = NCD.dParallelCommandList(ones(length(flist)),p.NumWorkers);
+W = size(cmdList,2); % for slicing j in parfor
+H = size(cmdList,1);
+dxx = zeros(H,W);
+parfor i=1:H
+ str_ff_prev = '';
+ im_ff = [];
+
+ for j = 1:W
+ t0 = tic();
+ ff = cmdList(i,j,2); % ff is the row var -- repeats
+ gg = cmdList(i,j,1);
+ if 0 == ff || 0 == gg
continue
end
- t0 = tic();
+ strDB_ff = fullfile(flist(ff).folder,flist(ff).name);
+ if ~strcmp(strDB_ff,str_ff_prev)
+ im_ff = SSF.loadImage(strDB_ff,targetChannels);
+ im_ff = SSF.quantize8(im_ff,erkClipLimits);
+ str_ff_prev = strDB_ff;
+ end
+
if ff == gg
- d(ff,gg) = SSF.ncd_ssf_volume(im_ff,im_ff);
+ d1 = SSF.ncd_ssf_volume(im_ff,im_ff);
+ dxx(i,j) = d1;
else
strDB_gg = fullfile(flist(gg).folder,flist(gg).name);
- im_gg = SSF.loadImage(strDB_gg,targetChannels);
+ im_gg = SSF.loadImage(strDB_gg,targetChannels);
+ im_gg = SSF.quantize8(im_gg,erkClipLimits);
+
d1 = SSF.ncd_ssf_volume(im_ff,im_gg);
d2 = SSF.ncd_ssf_volume(im_gg,im_ff);
- d(ff,gg) = min(d1,d2);
+
+
+ dxx(i,j) = min(d1,d2);
end
tElapsed = toc(t0);
- fprintf('%s tElapsed = %0.2f\n',mat2str([ff,gg,d(ff,gg)]),tElapsed);
+ fprintf('%s tElapsed = %0.2f\n',mat2str([ff,gg,dxx(i,j)]),tElapsed);
end
end
-for i=1:L
- for j=1:i-1
- d(i,j) = d(j,i);
+% convert dxx to distance matrix d
+d = [];
+for i = 1 : size(dxx,1)
+ for j = 1 : size(dxx,2)
+ c = cmdList(i,j,1);
+ r = cmdList(i,j,2);
+ if 0 == r || 0 == c
+ continue
+ end
+ d(r,c) = dxx(i,j);
+ end
+end
+
+for i = 1 : size(d,1)
+ for j = 1 : size(d,2)
+ if 0 == d(i,j)
+ d(i,j) = d(j,i);
+ end
end
end
tElapsed = toc(tStart);
-fprintf('total time tElapsed = %0.2f\n',tElapsed);
\ No newline at end of file
+fprintf('total time tElapsed = %0.2f\n',tElapsed);
diff --git a/matlab/+SSF/loadImage.m b/matlab/+SSF/loadImage.m
index 289d75927ec2977fabfc149f0d4121d51e64d728..9e149c8d140985dc9473b36273bbf4483b2c4841 100644
--- a/matlab/+SSF/loadImage.m
+++ b/matlab/+SSF/loadImage.m
@@ -1,10 +1,11 @@
+
function im = loadImage(strDB,channelList)
+if ~exist('bDouble','var')
+ bDouble = false;
+end
im = [];
+time = 1; % kymo is single time point
for c=1:length(channelList)
- im(:,:,:,c) = leversc.loadImage(strDB,1,channelList(c));
-end
-if 2 == length(channelList)
- im(:,:,:,3) = 0 * im(:,:,:,1);
+ im(:,:,:,c) = leversc.loadImage(strDB,time,channelList(c));
end
-im = im2uint8(im);
diff --git a/matlab/+SSF/ncd_ssf_volume.m b/matlab/+SSF/ncd_ssf_volume.m
index 7126fcde848816060cdfea112f13cf02eeec1bb3..0c3427a496154cf7e7ca3f8e62c3e5f32c32eb74 100644
--- a/matlab/+SSF/ncd_ssf_volume.m
+++ b/matlab/+SSF/ncd_ssf_volume.m
@@ -3,11 +3,11 @@
% package to cell array by t and then pass to in memory FLI%F compressor
function ncd = ncd_ssf_volume(i1,i2)
-im12 = padcat1(i1,i2);
+im12 = SSF.catKymographs(i1,i2,1);
im12 = squeeze(num2cell(im12,[1,2,4]));
s12 = NCD.flifPress(im12);
-im21 = padcat2(i1,i2);
+im21 = SSF.catKymographs(i1,i2,2);
im21 = squeeze(num2cell(im21,[1,2,4]));
s21 = NCD.flifPress(im21);
@@ -22,22 +22,3 @@ s2 = NCD.flifPress(i2);
ncd = ( s12-min(s1,s2)) / (max(s1,s2));
4;
-
-% pads time between images
-function i12 = padcat1(i1,i2)
-if size(i1,3)>size(i2,3)
- i2(:,:,end:size(i1,3),:)=0;
-else
- i1(:,:,end:size(i2,3),:)=0;
-end
-i12 = cat(1,i1,i2);
-4;
-
-function i12 = padcat2(i1,i2)
-if size(i1,3)>size(i2,3)
- i2(:,:,end:size(i1,3),:)=0;
-else
- i1(:,:,end:size(i2,3),:)=0;
-end
-i12 = cat(2,i1,i2);
-4;
\ No newline at end of file
diff --git a/matlab/+SSF/quantize8.m b/matlab/+SSF/quantize8.m
new file mode 100644
index 0000000000000000000000000000000000000000..1a2a0f119da3e86867c2433fc4da199bb0480fd6
--- /dev/null
+++ b/matlab/+SSF/quantize8.m
@@ -0,0 +1,14 @@
+% clipLimits = [minVal,maxVal];
+function im = quantize8(im,clipLimits)
+
+if isa(im,'uint8')
+ return
+end
+im = max(im,clipLimits(1));
+im = min(im,clipLimits(2));
+
+im = (im - clipLimits(1)) ./ (clipLimits(2) - clipLimits(1));
+
+im = im2uint8(im);
+im = max(im,1); % exclude 0 -- only for background
+im(1,1) = 0; % make sure at least 1 pixel hits background
\ No newline at end of file
diff --git a/matlab/+SSF/ssf_channel.m b/matlab/+SSF/ssf_channel.m
index 49d18d232bdf8c7bf3a02f28df711376122622c1..ce62430a5ea41136d52ce539b19924d432999714 100644
--- a/matlab/+SSF/ssf_channel.m
+++ b/matlab/+SSF/ssf_channel.m
@@ -1,11 +1,12 @@
-function imSSF = ssf_channel(cellList,CONSTANTS,channel,t,refMax,segParams,centroidMap)
+function imSSF = ssf_channel(cellList,CONSTANTS,channel,t,refMax,segParams,centroidMap,bDownscale)
-if ~exist('bTube','var')
- bTube = false;
-end
im = MicroscopeData.Reader('imageData',CONSTANTS.imageData, 'chanList',abs(channel),'timeRange',[t t], 'outType','uint16','prompt',false);
im = Segment.denoise(im,segParams,false);
im = double(im)./2^16;
+% scale refMax by actual image statistics. median estimates background,
+% 99.99% represents max foreground intensity.
+refMax = refMax * ( prctile(im(:),99.99) - median(im(:)));
+
[imLoG, imp, imn] = LoG.getCompositeLoG(im,CONSTANTS,segParams);
bw = logical(0*imp);
@@ -16,7 +17,11 @@ d = bwdist(~bw);
imp(d<3)=0;
imn(d<3)=0;
-imSSF = zeros(size(imp,1),size(imp,2));
+szim = ceil(size(imp));
+if bDownscale
+ szim = szim ./ 2;
+end
+imSSF = zeros(szim(1),szim(2));
for i=1:length(cellList)
if is3D(CONSTANTS)
cx = centroidMap(cellList(i).cellID);
@@ -24,15 +29,18 @@ for i=1:length(cellList)
cx = round(cellList(i).centroid);
cx = [cx(2),cx(1)]; % [y,x]
end
+ if bDownscale
+ cx = round(cx/2);
+ end
val_Pos = max(imp(cellList(i).idxPts));
val_Neg = max(imn(cellList(i).idxPts));
if val_Pos > val_Neg
- % bright nucleus, dark cytoplasm
+ % dark nucleus, bright cytoplasm
% ssf sign is in direction of intensity gradient
- val = -1 * val_Pos;
+ val = val_Pos;
else
- % dark nucleus, bright cytoplasm
- val = val_Neg;
+ % bright nucleus, dark cytoplasm
+ val = -1 * val_Neg;
end
ratio = val./refMax;
ratio = min(ratio,1);
@@ -41,4 +49,16 @@ for i=1:length(cellList)
imSSF(cx(1),cx(2)) = ratio;
end
+
+% if channel < 0
+% % negative channel, keep negative LoG response
+% imSSF(imSSF>0) = 0;
+% imSSF = abs(imSSF);
+% else
+% % positive channel, keep positive LoG response
+% imSSF(imSSF<0) = 0;
+% end
+
+% imSSF = max(imSSF,0);
+% imSSF = min(imSSF,1);
4;
diff --git a/matlab/+SSF/ssf_sample.m b/matlab/+SSF/ssf_sample.m
new file mode 100644
index 0000000000000000000000000000000000000000..d39f114804581513bda4597295cc072da8592ca4
--- /dev/null
+++ b/matlab/+SSF/ssf_sample.m
@@ -0,0 +1,10 @@
+% check the neighborhood around centeroid in imkymo. used to eliminate
+% round off errors in kymo / cell centroid
+function sample_value = ssf_sample(imKymo,centroid,idxCentroid)
+
+sample_value = imKymo(centroid(1)-1:centroid(1)+1,centroid(2)-1:centroid(2)+1,centroid(3));
+if length(find(sample_value))>1
+ fprintf(2,'ack SSF kymo ack more than one ssf sample found at centroid. send help.\n');
+end
+sample_value = sample_value(find(sample_value));
+sample_value = sample_value(1);
\ No newline at end of file
diff --git a/matlab/+SSF/ssf_sample_idx.m b/matlab/+SSF/ssf_sample_idx.m
new file mode 100644
index 0000000000000000000000000000000000000000..0d3d500c518a55f21dd3e67f132852220bbd33af
--- /dev/null
+++ b/matlab/+SSF/ssf_sample_idx.m
@@ -0,0 +1,17 @@
+% check the neighborhood around centeroid in imkymo. used to eliminate
+% round off errors in kymo / cell centroid
+function sampleList = ssf_sample_idx(imKymo,idxCentroid)
+sampleList = [];
+for i = 1:length(idxCentroid)
+ [centroid(1),centroid(2),centroid(3)] = ind2sub(size(imKymo),idxCentroid(i));
+ sv = imKymo(centroid(1)-1:centroid(1)+1,centroid(2)-1:centroid(2)+1,centroid(3));
+ if length(find(sv))>1
+ fprintf(2,'ack SSF kymo ack more than one ssf sample found at centroid. send help.\n');
+ end
+ sv = sv(find(sv));
+ if isempty(sv)
+ sv = 0;
+ end
+ sv = sv(1);
+ sampleList(i) = sv;
+end
\ No newline at end of file
diff --git a/matlab/+SSF/ssf_volume.m b/matlab/+SSF/ssf_volume.m
index 7e778db02da9b4e38465ce731aea390daf31f557..7e2927ea01a46987baed927ab1d189cf7dd9c757 100644
--- a/matlab/+SSF/ssf_volume.m
+++ b/matlab/+SSF/ssf_volume.m
@@ -1,4 +1,4 @@
-function im_ssf = ssf_volume(strDB,targetChannelNumbers)
+function im_ssf = ssf_volume(strDB,targetChannelNumbers, bDownscale)
refMax = 0.7; % from cacheReferenceLoG
@@ -20,6 +20,9 @@ xyzct_size = Helpers.volumeSize(CONSTANTS);
% FUN NOTE :: if you compute kymo_size wrong here, then when we iterate
% below you will propagate that mistake exponentially and run out of memory
kymo_size = [xyzct_size(1:2) xyzct_size(5) xyzct_size(4) 1];
+if bDownscale
+ kymo_size(1:2) = ceil(kymo_size(1:2) ./ 2);
+end
if is3D(CONSTANTS)
centroidMap = SSF.mapCentroids(connx,CONSTANTS);
else
@@ -33,7 +36,7 @@ for t=1:CONSTANTS.imageData.NumberOfFrames
cellList = Read.getCellsTime(connx,t,segParams.channels(1),CONSTANTS);
for c=1:length(targetChannelNumbers)
% 5-D x,y,1,c,t -> 3-D x,y,t(z),c
- im_ssf(:,:,t,c) = SSF.ssf_channel(cellList,CONSTANTS,targetChannelNumbers(c),t,refMax,segParams,centroidMap);
+ im_ssf(:,:,t,c) = SSF.ssf_channel(cellList,CONSTANTS,targetChannelNumbers(c),t,refMax,segParams,centroidMap,bDownscale);
end
end
close(connx);
\ No newline at end of file
diff --git a/matlab/+SSF/trackDistance.m b/matlab/+SSF/trackDistance.m
new file mode 100644
index 0000000000000000000000000000000000000000..4f018e942bae2444aafe3a2dc62234220edd76fd
--- /dev/null
+++ b/matlab/+SSF/trackDistance.m
@@ -0,0 +1,18 @@
+function d = trackDistance(ci,cj)
+tOverlap = intersect(ci(:,3),cj(:,3));
+if isempty(tOverlap)
+ d = Inf;
+ return
+end
+idxDel = find(arrayfun(@(x) isempty(intersect(x,tOverlap)),ci(:,3)));
+ci(idxDel,:) = [];
+idxDel = find(arrayfun(@(x) isempty(intersect(x,tOverlap)),cj(:,3)));
+cj(idxDel,:) = [];
+
+
+if isempty(ci) || isempty(cj)
+ d = Inf;
+ return
+end
+dx = sqrt( (ci(:,1) - cj(:,1)).^2 + (ci(:,2)-cj(:,2)).^2);
+d = median(dx);
\ No newline at end of file
diff --git a/matlab/+Segment/frameSegment.m b/matlab/+Segment/frameSegment.m
index 4b314b8fca358923f76c27286d84f096b39cddd2..58756230a73dbb0f87c25dd2734cd0cc6728d7bf 100644
--- a/matlab/+Segment/frameSegment.m
+++ b/matlab/+Segment/frameSegment.m
@@ -130,7 +130,7 @@ for n=1:max(L(:))
end
end
newCell.idxPts = idx;
-
+ newCell.n = n;
segL=unique(L2(idx));
segL(0==segL)=[];
if length(segL)>1
@@ -141,27 +141,35 @@ for n=1:max(L(:))
newCell=Ensemble.setCellFeatures(newCell,rp,n,segParams);
end
newCell.LoG = LoG.sampleCell(newCell,CONSTANTS,imLoG);
- if is3D(imLoG)
- threshLoG = -1e-2;
- else
- threshLoG = -1e-3;
- end
- if (newCell.LoG >threshLoG)
- % disallow segmentation based on centroid LoG thresholding
+
+ % check ecc
+ v = eig(cov(newCell.pts));
+ ecc = max(v)/min(v);
+ if ecc>50
continue
end
+% if is3D(imLoG)
+% threshLoG = -1e-2;
+% else
+% threshLoG = -1e-3;
+% end
+% if (newCell.LoG >threshLoG)
+% % disallow segmentation based on centroid LoG thresholding
+% continue
+% end
Cells=[Cells newCell];
end
-
-threshLoG = mean([Cells.LoG])/10;
-idx = find([Cells.LoG]>threshLoG); % use > since LoG is negative on nuclear channel
-Cells(idx) = [];
-% % on ensembleSeg
-if 1 || bEnsemble
- Cells=Ensemble.setCellEfficiency(Cells,CONSTANTS,im,imLoG,segParams,medianMask);
-% Cells = Ensemble.set_LoG_score(Cells,CONSTANTS,im,imLoG,segParams);
-end
+if ~isempty(Cells)
+ threshLoG = mean([Cells.LoG])/10;
+ idx = find([Cells.LoG]>threshLoG); % use > since LoG is negative on nuclear channel
+% Cells(idx) = [];
+ % % on ensembleSeg
+ if 1 || bEnsemble
+ Cells=Ensemble.setCellEfficiency(Cells,CONSTANTS,im,imLoG,segParams,medianMask);
+ % Cells = Ensemble.set_LoG_score(Cells,CONSTANTS,im,imLoG,segParams);
+ end
+end
if DRAW && ~is3D(im)
for i=1:length(Cells)
diff --git a/matlab/+Segment/segReduce.m b/matlab/+Segment/segReduce.m
index 08e5a1789f212d7de83aa79da308eedcf730d721..654da8f96e0c52d15a57230ffb19fe0c7e64a27a 100644
--- a/matlab/+Segment/segReduce.m
+++ b/matlab/+Segment/segReduce.m
@@ -2,7 +2,8 @@
function L = segReduce(bw,imn,min_area_pixels)
% use the LoG image instead of distance for watershed xform
% empirical maxima surpression with first watershed
-L = watershed(-1 * imhmax(imn,0.01));
+hmax = 0.01;
+L = watershed(-1 * imhmax(imn,hmax));
% % L=watershed(-1 * imn);
L(~bw)=0;
diff --git a/matlab/+Segment/thresholdLoG_negative.m b/matlab/+Segment/thresholdLoG_negative.m
index e0b043bd7ef6746b40a2495612231d74833e906c..29aa79124ee71827f938a801a954a8c2f6038a11 100644
--- a/matlab/+Segment/thresholdLoG_negative.m
+++ b/matlab/+Segment/thresholdLoG_negative.m
@@ -10,6 +10,9 @@ else
sensitivity = segParams.sensitivity;
end
+% ACK! hardcode! ACK!
+sensitivity = 0;
+
imn = imLoG;
imn(imn>0)=0;
imn=abs(imn);
diff --git a/matlab/+Smooth/+Classify/getMitosisFeatures.m b/matlab/+Smooth/+Classify/getMitosisFeatures.m
index e47ce7446ca54d136c91d425ae6eaa42a7548f73..204e9fcbc8cbe172bb28c634aa14dbced2fd37b5 100644
--- a/matlab/+Smooth/+Classify/getMitosisFeatures.m
+++ b/matlab/+Smooth/+Classify/getMitosisFeatures.m
@@ -44,15 +44,12 @@ centroids=cellfun(@jsondecode,q(:,3),'uniformoutput',false);
centroids=reshape(cell2mat(centroids),3,[])';
parentCandidates=[cell2mat(q(:,1:2)) centroids];
-d1=Read.getCell(conn,d1CellID);
+d1=Read.getCell(conn,d1CellID,CONSTANTS);
costs=findD2Candidates(conn,parentCandidates,time,d1);
if isempty(costs)
return
end
-[~,idx]=min([costs.ratioD1D2]);
-if costs(idx).ratioD1D2>25
- return
-end
+[~,idx]=min(abs(1-[costs.ratioD1D2]));
mitosisNode.ratioD1D2=costs(idx).ratioD1D2;
% make sure daughter is not already in family tree. if density is high
@@ -70,20 +67,20 @@ end
cmd=['select max(time) from tblCells where trackID IN(' num2str(costs(idx).parentDaughterTID(2)), ',' num2str(costs(idx).parentDaughterCID(2)) ') '];
q=ljsFetch(conn,cmd);
t1=q{1};
-if (t1-time)<5 && ~bDebug
- return
-end
+% if (t1-time)<5 && ~bDebug
+% return
+% end
mitosisNode.parentCellID=costs(idx).parentDaughterCID(1);
mitosisNode.siblingCellID=costs(idx).parentDaughterCID(2);
mitosisNode.parentDaughterTID=costs(idx).parentDaughterTID;
-d2=Read.getCell(conn,mitosisNode.siblingCellID);
-p=Read.getCell(conn,mitosisNode.parentCellID);
+d2=Read.getCell(conn,mitosisNode.siblingCellID,CONSTANTS);
+p=Read.getCell(conn,mitosisNode.parentCellID,CONSTANTS);
-% for parent area, select max over last 3 frames
+% for parent area, select max over last 2 frames
cmd=['select area from tblCells where trackID=' num2str(mitosisNode.parentDaughterTID(1))...
- ' and time<' num2str(d1.time) ' and time>=' num2str(p.time-3)];
+ ' and time<' num2str(d1.time) ' and time>=' num2str(d1.time-2)];
q=ljsFetch(conn,cmd);
aparent=cell2mat(q);
@@ -95,40 +92,43 @@ else
areaRatio=ar2;
end
mitosisNode.areaRatio=areaRatio;
-if areaRatio<minAreaRatio || areaRatio>2.5
- return
-end
+
bOcclusionEdge1=Mitosis.checkOcclusionEdge(conn,d1);
bOcclusionEdge2=Mitosis.checkOcclusionEdge(conn,d2);
if bOcclusionEdge1 || bOcclusionEdge2
+ % ???
+ mitosisNode.areaRatio = Inf;
return
end
mitosisNode.sibAreaRatio=max([d1.area,d2.area])/min([d1.area,d2.area]);
+% parent LoG
+cmd=['select LoG from tblCells where trackID=' num2str(p.trackID)...
+ ' and time<' num2str(d1.time) ' and time>=' num2str(p.time-3)];
+q=ljsFetch(conn,cmd);
+parentLoG = min(cell2mat(q));
+% d1 LoG
+cmd=['select LoG from tblCells where trackID=' num2str(d1.trackID)...
+ ' and time>=' num2str(d1.time) ' and time<' num2str(d1.time+3)];
+q=ljsFetch(conn,cmd);
+d1LoG = min(cell2mat(q));
-segParams=Read.getSegmentationParams(conn);
-imCache=Mitosis.getImageCache(conn,CONSTANTS,time,segParams);
-if isempty(imCache)
- return;
-end
+% d1 LoG
+cmd=['select LoG from tblCells where trackID=' num2str(d2.trackID)...
+ ' and time>=' num2str(d1.time) ' and time<' num2str(d2.time+3)];
+q=ljsFetch(conn,cmd);
+d2LoG = min(cell2mat(q));
-d1br=brightShape(d1,imCache.im);
-d2br=brightShape(d2,imCache.im);
-d1t1=getNextDaughter(conn,d1);
-if ~isempty(d1t1)
- d1br=max([d1br,brightShape(d1t1,imCache.imP1)]);
-end
-d2t1=getNextDaughter(conn,d2);
-if ~isempty(d2t1)
- d2br=max([d2br,brightShape(d2t1,imCache.imP1)]);
-end
+mitosisNode.pd1d2LoG = [parentLoG,d1LoG,d2LoG];
-pbr=getParentBR(conn,CONSTANTS,p,imCache);
-mitosisNode.brightRatio=[d1br,d2br,pbr];
-eccParent=getParentECC(conn,imCache,p);
-mitosisNode.eccParent=eccParent;
+mitosisNode.pd1d2Ecc = [Helpers.cellEccentricity(p),Helpers.cellEccentricity(d1),...
+ Helpers.cellEccentricity(d2)];
+
+o1 = length(intersect(p.idxPts,d1.idxPts))/min(length(p.idxPts),length(d1.idxPts));
+o2 = length(intersect(p.idxPts,d2.idxPts))/min(length(p.idxPts),length(d2.idxPts));
+mitosisNode.pd1d2overlap = [o1,o2];
4;
% end of find family
@@ -140,113 +140,41 @@ for i=1:size(parentCandidates,1)
% % target sibling 2 is the cell parent candidate tracked 2
% parentCandidates are [cellID,trackID,centroid]
- [d2TrackID,d2CellID,d2Centroid]=getDaughter2(conn,parentCandidates(i,:),time,d1);
- if isempty(d2TrackID)
+ d2 = getDaughter2(conn,parentCandidates(i,:),time,d1);
+ if isempty(d2)
continue
end
- if d2CellID==d1.cellID
+ if d2.cellID==d1.cellID
% need to come in via the other sibling!
return
end
-
+ d1d2LoG = abs([d1.LoG,d2.LoG]);
+ d1d2LoG = min(d1d2LoG)/max(d1d2LoG);
+% if d1d2LoG < 0.5
+% continue
+% end
pCentroid=parentCandidates(i,3:5);
% midpoint of line between daughters -- this is where we'd like to see
% the parent
- pmid=(d2Centroid+d1.centroid)/2;
+ pmid=(d2.centroid+d1.centroid)/2;
nc=[];
- nc.parentDaughterCID=[parentCandidates(i,1),d2CellID,];
+ nc.parentDaughterCID=[parentCandidates(i,1),d2.cellID,];
nc.parentToDaughterMidpoint=norm(pCentroid-pmid);
nc.dParentD1=Mitosis.cellDistance(conn,d1.cellID,parentCandidates(i,1));
- nc.dParentD2=Mitosis.cellDistance(conn,d2CellID,parentCandidates(i,1));
- nc.parentDaughterTID=[parentCandidates(i,2),d2TrackID];
+ nc.dParentD2=Mitosis.cellDistance(conn,d2.cellID,parentCandidates(i,1));
+ nc.parentDaughterTID=[parentCandidates(i,2),d2.trackID];
+
+ ratioD1D2 = min(nc.dParentD1,nc.dParentD2) / max(nc.dParentD1,nc.dParentD2);
nc.ratioD1D2=nc.dParentD1/nc.dParentD2;
+ nc.d1d2LoG = d1d2LoG;
costs=[costs nc];
end
-function eccParent=getParentECC(conn,imCache,p)
-eccParent=getEcc(size(imCache.im),p);
-cmd=['select cellID from tblCells where time=' num2str(p.time-1) ' and '...
- ' trackID= ' num2str(p.trackID)];
-q=ljsFetch(conn,cmd);
-if isempty(q)
- return
-end
-p1=Read.getCell(conn,q{1});
-eccParent1=getEcc(size(imCache.im),p1);
-eccParent=min([eccParent,eccParent1]);
-
-
-function pbr=getParentBR(conn,CONSTANTS,p,imCache)
-
-% parent needs to be in frame t-1
-pbr=brightShape(p,imCache.imM1);
-cmd=['select cellID from tblCells where time=' num2str(p.time-1) ' and '...
- ' trackID= ' num2str(p.trackID)];
-q=ljsFetch(conn,cmd);
-if isempty(q)
- return
-end
-p1=Read.getCell(conn,q{1});
-pbr1=brightShape(p1,imCache.imM2);
-pbr=max([pbr,pbr1]);
-
-function d=getNextDaughter(conn,cell)
-
-cmd=['select cellID from tblCells where trackID=' num2str(cell.trackID) ' and time=' num2str(cell.time)];
-q=ljsFetch(conn,cmd);
-if isempty(q)
- d=[];
- return;
-end
-nextID=q{1};
-d=Read.getCell(conn,nextID);
-
-% mse between distance transform and intensity profile
-function br=brightShape(cell,im)
-
-if isempty(im)
- br=0;
- return;
-end
-imx=0*im;
-if (size(im,3))>1
- idx=sub2ind(size(im),cell.pts(:,2),cell.pts(:,1),cell.pts(:,3));
-else
- idx=sub2ind(size(im),cell.pts(:,2),cell.pts(:,1));
-end
-imx(idx)=im(idx);
-if (0==max(imx(:)))
- br=0;
- return
-end
-
-bwd=bwdist(~imx);
-imx=imx.*max(bwd(:))/max(imx(:));
-br=sum(bwd(:)-imx(:))/length(find(bwd));
-
-function ecc=getEcc(szImage,cell)
-
-if length(szImage)>2 && szImage(3)>1
- ecc=0;
- return;
-end
-imx=zeros(szImage);
-idx=sub2ind(szImage,cell.pts(:,2),cell.pts(:,1));
-imx(idx)=1;
-if (0==max(imx(:)))
- ecc=1;
- return
-end
-rp=regionprops(imx,'Eccentricity');
-ecc=rp.Eccentricity;
-
-function [d2TrackID,d2CellID,d2Centroid]=getDaughter2(conn,parentCandidate,time,d1)
+function d2 = getDaughter2(conn,parentCandidate,time,d1)
-d2TrackID=[];
-d2CellID=[];
-d2Centroid=[];
+d2 = [];
itid=parentCandidate(2); % trackID for parent/daughter 2
% try to use parent trackID in time t-1 to find daughter in time t
@@ -257,9 +185,7 @@ if size(q,1)>1
fprintf(2,'rut roh! duplicate track entries conn=%s time=%d\n',conn.DataSource,time);
end
if ~isempty(q)
- d2TrackID=itid;
- d2CellID=q{1};
- d2Centroid=jsondecode(q{1,2})';
+ d2 = Read.getCell(conn,q{1});
else
% parent did not track to a d2
% so, there first choice is still out there and is not d1 (since d1 is
@@ -272,26 +198,24 @@ else
% to find a daughter that the parent wanted, but later the parent may
% get the track they actually wanted. pfad.
% for now, no go
- return;
-
- cmd=['select * from tblDistCC where cellID_src=' num2str(parentCandidate(1)) ...
- ' and cellID_dst in (select cellID from (select cellID,trackID,min(time) ' ...
- ' as tStart from tblCells group by trackID)) and cellID_dst<>' num2str(d1.cellID)];
- q=fetch(conn,cmd);
- if ~isempty(q)
- % make sure d2 is not already in table
- cmd=['select * from tblFamilies where cellID_child1=' num2str(q.cellID_dst(1))];
- qfamily=fetch(conn,cmd);
- if isempty(qfamily)
- d2=Read.getCell(conn,q.cellID_dst(1));
- if d2.time~=d1.time
- return
- end
- d2TrackID=d2.trackID;
- d2CellID=d2.cellID;
- d2Centroid=d2.centroid;
+ cmd = ['select * from tblDistCC where cellID_src = ' num2str(parentCandidate(1)) ' order by cost asc'];
+ qp = fetch(conn,cmd);
+ cmd = ['select cellID,LoG from tblCells where cellID in ' Helpers.sqlEncodeVector(qp.cellID_dst)];
+ qd = fetch(conn,cmd);
+ qd(qd.LoG>-0.1,:) = [];
+ qd(qd.cellID == d1.cellID,:) = [];
+ i = 1;
+ while i <= length(qp.cellID_dst)
+ if isempty(intersect(qp.cellID_dst(i),qd.cellID))
+ qp(i,:) = [];
+ else
+ i = i+1;
end
end
+ if ~isempty(qp)
+ d2 = Read.getCell(conn,qp.cellID_dst(1));
+ end
+
end
diff --git a/matlab/+Smooth/+Classify/goClassifyMitosis.m b/matlab/+Smooth/+Classify/goClassifyMitosis.m
index b1dd86c29e34ff999064fa38a9d0c29304627025..b2542ead4a500033e82d7f29cd2991f149e144cb 100644
--- a/matlab/+Smooth/+Classify/goClassifyMitosis.m
+++ b/matlab/+Smooth/+Classify/goClassifyMitosis.m
@@ -13,43 +13,23 @@ end
if ~exist('nProcessors','var') || isempty(nProcessors)
nProcessors=ljsNProcs();
end
-p=ljsStartParallel(nProcessors);
+% p=ljsStartParallel(nProcessors);
mParams=Read.getMitosisParams(conn);
+segParams = Read.getSegmentationParams(conn);
targetTracks=Smooth.getTargetTracks(conn,5);
-strDB=conn.DataSource;
-mnode=Smooth.Classify.newMitosisNode(-1);
-cxComp=Composite();
-spmd
- cxComp=openDB(strDB);
-end
-mnode=[];
-for i=1:ceil(size(targetTracks,1)/p.NumWorkers)
- mx=[];
- spmd
- idx = ((i - 1) * numlabs) + labindex;
- if idx<=size(targetTracks,1)
- if targetTracks.t0(idx)==1
- mx=Smooth.Classify.newMitosisNode(targetTracks.trackID(idx));
- else
- mx=Smooth.Classify.getMitosisFeatures(cxComp,CONSTANTS,mParams,targetTracks.trackID(idx));
- end
- end
- end
- mres=[mx{:}]';
- mnode=[mnode;mres];
-end
-spmd
- close(cxComp);
-end
+mnode = [];
+
+for i = 1:length(targetTracks.trackID)
+ mn = Smooth.Classify.getMitosisFeatures(conn,CONSTANTS,mParams,targetTracks.trackID(i)) ;
-for i=1:length(mnode)
- if Smooth.Classify.isValidMitosis(mnode(i),mParams)
- c1=Read.getCell(conn,mnode(i).d1CellID);
- c2=Read.getCell(conn,mnode(i).siblingCellID);
- p=Read.getCell(conn,mnode(i).parentCellID);
- ljsLog('resegMitosis: adding new mitosis at child = %d\n',mnode(i).d1CellID);
- Mitosis.addMitosis(conn,p,c1,c2);
+ if Smooth.Classify.isValidMitosis(mn,mParams)
+ c1=Read.getCell(conn,mn.d1CellID);
+ c2=Read.getCell(conn,mn.siblingCellID);
+ p=Read.getCell(conn,mn.parentCellID);
+% drawMitosis(conn.DataSource,p,c1,c2,segParams,mn);
+ ljsLog('resegMitosis: adding new mitosis at child = %d\n',mn.d1CellID);
+ Mitosis.addMitosis(conn,p,c1,c2);
end
end
\ No newline at end of file
diff --git a/matlab/+Smooth/+Classify/isValidMitosis.m b/matlab/+Smooth/+Classify/isValidMitosis.m
index 154d6d3b13ab94d8a7fbe3c12077310e11b74470..f2eb47765e065a8865d969c1263e9832354a48c9 100644
--- a/matlab/+Smooth/+Classify/isValidMitosis.m
+++ b/matlab/+Smooth/+Classify/isValidMitosis.m
@@ -3,19 +3,27 @@ bValid=false;
if mnode.parentCellID<0
return;
end
-if any(isinf(mnode.brightRatio))
+threshLoG = [-0.05,-0.1,-0.35];
+if any(mnode.pd1d2LoG > threshLoG(1))
return;
end
-if ~isinf(mParams.brightThreshold)
- if any(mnode.brightRatio<mParams.brightThreshold)
- return;
- end
+if any(mnode.pd1d2LoG < threshLoG(3))
+ return;
end
-if ~isinf(mParams.eccentricityThreshold)
- if mnode.eccParent>mParams.eccentricityThreshold
- return;
+if ~any(mnode.pd1d2LoG < threshLoG(2))
+ return
+end
+if any(mnode.pd1d2overlap>0.25)
+ if ~all(mnode.pd1d2LoG<threshLoG(2))
+ return
end
end
+
+daughterLoG = abs(mnode.pd1d2LoG(2:3));
+dRatio = min(daughterLoG)/max(daughterLoG);
+if dRatio < 0.5
+ return
+end
if ~isinf(mParams.parentDaughterAreaRatio)
if mnode.areaRatio<mParams.parentDaughterAreaRatio
return;
diff --git a/matlab/+Smooth/+Classify/newMitosisNode.m b/matlab/+Smooth/+Classify/newMitosisNode.m
index 599f7716a7fdeecf93f26e268363d45682122f7e..7ee0e1dc4030806221d5d86245ac6781cfd5e702 100644
--- a/matlab/+Smooth/+Classify/newMitosisNode.m
+++ b/matlab/+Smooth/+Classify/newMitosisNode.m
@@ -6,7 +6,8 @@ mitosisNode.parentCellID=-1;
mitosisNode.siblingCellID=-1;
mitosisNode.parentDaughterTID=[-1,d1CellID];
mitosisNode.areaRatio=0;
-mitosisNode.brightRatio=[-Inf,-Inf,-Inf];
+mitosisNode.pd1d2LoG=[-Inf,-Inf,-Inf];
mitosisNode.sibAreaRatio=0;
-mitosisNode.eccParent=2;
+mitosisNode.pd1d2Ecc=[-Inf,-Inf,-Inf];
mitosisNode.d1CellID=d1CellID;
+mitosisNode.pd1d2overlap = [-Inf,-Inf];
diff --git a/matlab/+Smooth/getTargetTracks.m b/matlab/+Smooth/getTargetTracks.m
index de010390f3c6b8a40e1f160880e1af4167d26e5c..bbdf4640e4bd55b9017c81420f127b1910fea5e7 100644
--- a/matlab/+Smooth/getTargetTracks.m
+++ b/matlab/+Smooth/getTargetTracks.m
@@ -1,9 +1,16 @@
function targetTracks=getTargetTracks(conn,nFrames)
-cmd=['select * from (select trackID,min(time) as t0,max(time) as t1,count(time) as lifespan '...
- ' from tblCells group by trackID) where lifespan>' num2str(nFrames)];
-targetTracks=fetch(conn,cmd);
+% cmd=['select * from (select trackID,min(time) as t0,max(time) as t1,count(time) as lifespan '...
+% ' from tblCells group by trackID) where lifespan>' num2str(nFrames)];
+% targetTracks=fetch(conn,cmd);
+cmd = ['select tblCells.trackID,tblCells.time,tblCells.LoG from tblCells '...
+ ' inner join (select trackID,count(time) as nt '...
+ ' from tblCells group by trackID) as qx on tblCells.trackID = qx.trackID '...
+ ' where nt>5 and tblCells.cellID=tblCells.trackID and tblCells.time>1 and '...
+ ' tblCells.LoG<-0.05 order by tblCells.LoG asc'];
+
+targetTracks = fetch(conn,cmd);
diff --git a/matlab/+Write/CreateCells.m b/matlab/+Write/CreateCells.m
index 94eb5644662538dbb3ae71a2599b22514b4b37c0..221f409341693f376d3d21df6a5baba3d2049a5a 100644
--- a/matlab/+Write/CreateCells.m
+++ b/matlab/+Write/CreateCells.m
@@ -9,16 +9,27 @@ if isempty(Cells)
end
[~,tblFields]=Write.prepareCell([],Cells(1));
+qTable=fetch(conn,'pragma table_info(tblCells)');
if isfield(Cells,'nest')
- tblFields.iNest=max(tblFields{1,:})+1;
- q=fetch(conn,'pragma table_info(tblCells)');
- if ~any(cellfun(@length,(strfind(q.name,'iNest'))))
+ tblFields.iNest=max(tblFields{1,:})+1;
+ if ~any(cellfun(@length,(strfind(qTable.name,'iNest'))))
cmd = ['ALTER TABLE tblCells ADD COLUMN iNest INTEGER default -1'];
exec(conn,cmd);
cmd = ['ALTER TABLE tblZombies ADD COLUMN iNest INTEGER'];
exec(conn,cmd);
end
end
+
+if isfield(Cells,'LoG')
+ tblFields.LoG=max(tblFields{1,:})+1;
+ if ~any(cellfun(@length,(strfind(qTable.name,'LoG'))))
+ cmd = ['ALTER TABLE tblCells ADD COLUMN LoG REAL'];
+ exec(conn,cmd);
+ cmd = ['ALTER TABLE tblZombies ADD COLUMN LoG REAL'];
+ exec(conn,cmd);
+ end
+end
+
cmd=Write.buildPreparedStatement(tblFields,'tblCells');
insertCells = conn.handle.prepareStatement(cmd);
@@ -33,6 +44,11 @@ for i=1:length(Cells)
insertCells.setInt(tblFields.iNest,-1);
end
end
+ if isfield(Cells,'LoG')
+ if ~isempty(Cells(i).nest)
+ insertCells.setDouble(tblFields.LoG,Cells(i).LoG);
+ end
+ end
Write.tryUpdateDB(insertCells);
end
diff --git a/package-lock.json b/package-lock.json
index e74e8f153bf0b91378a862079eea664272ebce5c..37d82ac109c3a80e999b30b9dfa7eb3ac1d4ca33 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -21,7 +21,7 @@
"minimist": "^1.2.5",
"multer": "^1.4.3",
"semver": "^6.3.0",
- "sqlite3": "^4.1.1",
+ "sqlite3": "^5.1.6",
"xlsx": "^0.15.6"
},
"devDependencies": {
@@ -130,6 +130,12 @@
"node": ">= 10.0.0"
}
},
+ "node_modules/@gar/promisify": {
+ "version": "1.1.3",
+ "resolved": "https://registry.npmjs.org/@gar/promisify/-/promisify-1.1.3.tgz",
+ "integrity": "sha512-k2Ty1JcVojjJFwrg/ThKi2ujJ7XNLYaFGNB/bWT9wGR+oSMJHMa5w+CUq6p/pVrKeNNgA7pCqEcjSnHVoqJQFw==",
+ "optional": true
+ },
"node_modules/@malept/cross-spawn-promise": {
"version": "1.1.1",
"resolved": "https://registry.npmjs.org/@malept/cross-spawn-promise/-/cross-spawn-promise-1.1.1.tgz",
@@ -226,6 +232,109 @@
"node": ">= 10.0.0"
}
},
+ "node_modules/@mapbox/node-pre-gyp": {
+ "version": "1.0.10",
+ "resolved": "https://registry.npmjs.org/@mapbox/node-pre-gyp/-/node-pre-gyp-1.0.10.tgz",
+ "integrity": "sha512-4ySo4CjzStuprMwk35H5pPbkymjv1SF3jGLj6rAHp/xT/RF7TL7bd9CTm1xDY49K2qF7jmR/g7k+SkLETP6opA==",
+ "dependencies": {
+ "detect-libc": "^2.0.0",
+ "https-proxy-agent": "^5.0.0",
+ "make-dir": "^3.1.0",
+ "node-fetch": "^2.6.7",
+ "nopt": "^5.0.0",
+ "npmlog": "^5.0.1",
+ "rimraf": "^3.0.2",
+ "semver": "^7.3.5",
+ "tar": "^6.1.11"
+ },
+ "bin": {
+ "node-pre-gyp": "bin/node-pre-gyp"
+ }
+ },
+ "node_modules/@mapbox/node-pre-gyp/node_modules/node-fetch": {
+ "version": "2.6.11",
+ "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.11.tgz",
+ "integrity": "sha512-4I6pdBY1EthSqDmJkiNk3JIT8cswwR9nfeW/cPdUagJYEQG7R95WRH74wpz7ma8Gh/9dI9FP+OU+0E4FvtA55w==",
+ "dependencies": {
+ "whatwg-url": "^5.0.0"
+ },
+ "engines": {
+ "node": "4.x || >=6.0.0"
+ },
+ "peerDependencies": {
+ "encoding": "^0.1.0"
+ },
+ "peerDependenciesMeta": {
+ "encoding": {
+ "optional": true
+ }
+ }
+ },
+ "node_modules/@mapbox/node-pre-gyp/node_modules/semver": {
+ "version": "7.5.1",
+ "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.1.tgz",
+ "integrity": "sha512-Wvss5ivl8TMRZXXESstBA4uR5iXgEN/VC5/sOcuXdVLzcdkz4HWetIoRfG5gb5X+ij/G9rw9YoGn3QoQ8OCSpw==",
+ "dependencies": {
+ "lru-cache": "^6.0.0"
+ },
+ "bin": {
+ "semver": "bin/semver.js"
+ },
+ "engines": {
+ "node": ">=10"
+ }
+ },
+ "node_modules/@npmcli/fs": {
+ "version": "1.1.1",
+ "resolved": "https://registry.npmjs.org/@npmcli/fs/-/fs-1.1.1.tgz",
+ "integrity": "sha512-8KG5RD0GVP4ydEzRn/I4BNDuxDtqVbOdm8675T49OIG/NGhaK0pjPX7ZcDlvKYbA+ulvVK3ztfcF4uBdOxuJbQ==",
+ "optional": true,
+ "dependencies": {
+ "@gar/promisify": "^1.0.1",
+ "semver": "^7.3.5"
+ }
+ },
+ "node_modules/@npmcli/fs/node_modules/semver": {
+ "version": "7.5.1",
+ "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.1.tgz",
+ "integrity": "sha512-Wvss5ivl8TMRZXXESstBA4uR5iXgEN/VC5/sOcuXdVLzcdkz4HWetIoRfG5gb5X+ij/G9rw9YoGn3QoQ8OCSpw==",
+ "optional": true,
+ "dependencies": {
+ "lru-cache": "^6.0.0"
+ },
+ "bin": {
+ "semver": "bin/semver.js"
+ },
+ "engines": {
+ "node": ">=10"
+ }
+ },
+ "node_modules/@npmcli/move-file": {
+ "version": "1.1.2",
+ "resolved": "https://registry.npmjs.org/@npmcli/move-file/-/move-file-1.1.2.tgz",
+ "integrity": "sha512-1SUf/Cg2GzGDyaf15aR9St9TWlb+XvbZXWpDx8YKs7MLzMH/BCeopv+y9vzrzgkfykCGuWOlSu3mZhj2+FQcrg==",
+ "deprecated": "This functionality has been moved to @npmcli/fs",
+ "optional": true,
+ "dependencies": {
+ "mkdirp": "^1.0.4",
+ "rimraf": "^3.0.2"
+ },
+ "engines": {
+ "node": ">=10"
+ }
+ },
+ "node_modules/@npmcli/move-file/node_modules/mkdirp": {
+ "version": "1.0.4",
+ "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-1.0.4.tgz",
+ "integrity": "sha512-vVqVZQyf3WLx2Shd0qJ9xuvqgAyKPLAiqITEtqW0oIUjzo3PePDd6fW9iFz30ef7Ysp/oiWqbhszeGWW2T6Gzw==",
+ "optional": true,
+ "bin": {
+ "mkdirp": "bin/cmd.js"
+ },
+ "engines": {
+ "node": ">=10"
+ }
+ },
"node_modules/@sindresorhus/is": {
"version": "0.14.0",
"resolved": "https://registry.npmjs.org/@sindresorhus/is/-/is-0.14.0.tgz",
@@ -489,6 +598,74 @@
"resolved": "https://registry.npmjs.org/ms/-/ms-2.1.2.tgz",
"integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w=="
},
+ "node_modules/agentkeepalive": {
+ "version": "4.3.0",
+ "resolved": "https://registry.npmjs.org/agentkeepalive/-/agentkeepalive-4.3.0.tgz",
+ "integrity": "sha512-7Epl1Blf4Sy37j4v9f9FjICCh4+KAQOyXgHEwlyBiAQLbhKdq/i2QQU3amQalS/wPhdPzDXPL5DMR5bkn+YeWg==",
+ "optional": true,
+ "dependencies": {
+ "debug": "^4.1.0",
+ "depd": "^2.0.0",
+ "humanize-ms": "^1.2.1"
+ },
+ "engines": {
+ "node": ">= 8.0.0"
+ }
+ },
+ "node_modules/agentkeepalive/node_modules/debug": {
+ "version": "4.3.4",
+ "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.4.tgz",
+ "integrity": "sha512-PRWFHuSU3eDtQJPvnNY7Jcket1j0t5OuOsFzPPzsekD52Zl8qUfFIPEiswXqIvHWGVHOgX+7G/vCNNhehwxfkQ==",
+ "optional": true,
+ "dependencies": {
+ "ms": "2.1.2"
+ },
+ "engines": {
+ "node": ">=6.0"
+ },
+ "peerDependenciesMeta": {
+ "supports-color": {
+ "optional": true
+ }
+ }
+ },
+ "node_modules/agentkeepalive/node_modules/depd": {
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/depd/-/depd-2.0.0.tgz",
+ "integrity": "sha512-g7nH6P6dyDioJogAAGprGpCtVImJhpPk/roCzdb3fIh61/s/nPsfR6onyMwkCAR/OlC3yBC0lESvUoQEAssIrw==",
+ "optional": true,
+ "engines": {
+ "node": ">= 0.8"
+ }
+ },
+ "node_modules/agentkeepalive/node_modules/ms": {
+ "version": "2.1.2",
+ "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.2.tgz",
+ "integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w==",
+ "optional": true
+ },
+ "node_modules/aggregate-error": {
+ "version": "3.1.0",
+ "resolved": "https://registry.npmjs.org/aggregate-error/-/aggregate-error-3.1.0.tgz",
+ "integrity": "sha512-4I7Td01quW/RpocfNayFdFVk1qSuoh0E7JrbRJ16nH01HhKFQ88INq9Sd+nd72zqRySlr9BmDA8xlEJ6vJMrYA==",
+ "optional": true,
+ "dependencies": {
+ "clean-stack": "^2.0.0",
+ "indent-string": "^4.0.0"
+ },
+ "engines": {
+ "node": ">=8"
+ }
+ },
+ "node_modules/aggregate-error/node_modules/indent-string": {
+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/indent-string/-/indent-string-4.0.0.tgz",
+ "integrity": "sha512-EdDDZu4A2OyIK7Lr/2zG+w5jmbuk1DVBnEwREQvBzspBJkCEbRa8GxU1lghYcaGJCnRWibjDXlq779X1/y5xwg==",
+ "optional": true,
+ "engines": {
+ "node": ">=8"
+ }
+ },
"node_modules/ajv": {
"version": "6.12.6",
"resolved": "https://registry.npmjs.org/ajv/-/ajv-6.12.6.tgz",
@@ -736,17 +913,33 @@
"integrity": "sha1-HjRA6RXwsSA9I3SOeO3XubW0PlY="
},
"node_modules/aproba": {
- "version": "1.2.0",
- "resolved": "https://registry.npmjs.org/aproba/-/aproba-1.2.0.tgz",
- "integrity": "sha512-Y9J6ZjXtoYh8RnXVCMOU/ttDmk1aBjunq9vO0ta5x85WDQiQfUF9sIPBITdbiiIVcBo03Hi3jMxigBtsddlXRw=="
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/aproba/-/aproba-2.0.0.tgz",
+ "integrity": "sha512-lYe4Gx7QT+MKGbDsA+Z+he/Wtef0BiwDOlK/XkBrdfsh9J/jPPXbX0tE9x9cl27Tmu5gg3QUbUrQYa/y+KOHPQ=="
},
"node_modules/are-we-there-yet": {
- "version": "1.1.5",
- "resolved": "https://registry.npmjs.org/are-we-there-yet/-/are-we-there-yet-1.1.5.tgz",
- "integrity": "sha512-5hYdAkZlcG8tOLujVDTgCT+uPX0VnpAH28gWsLfzpXYm7wP6mp5Q/gYyR7YQ0cKVJcXJnl3j2kpBan13PtQf6w==",
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/are-we-there-yet/-/are-we-there-yet-2.0.0.tgz",
+ "integrity": "sha512-Ci/qENmwHnsYo9xKIcUJN5LeDKdJ6R1Z1j9V/J5wyq8nh/mYPEpIKJbBZXtZjG04HiK7zV/p6Vs9952MrMeUIw==",
"dependencies": {
"delegates": "^1.0.0",
- "readable-stream": "^2.0.6"
+ "readable-stream": "^3.6.0"
+ },
+ "engines": {
+ "node": ">=10"
+ }
+ },
+ "node_modules/are-we-there-yet/node_modules/readable-stream": {
+ "version": "3.6.2",
+ "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-3.6.2.tgz",
+ "integrity": "sha512-9u/sniCrY3D5WdsERHzHE4G2YCXqoG5FTHUiCC4SIbr6XcLZBY05ya9EKjYek9O5xOAwjGq+1JdGBAS7Q9ScoA==",
+ "dependencies": {
+ "inherits": "^2.0.3",
+ "string_decoder": "^1.1.1",
+ "util-deprecate": "^1.0.1"
+ },
+ "engines": {
+ "node": ">= 6"
}
},
"node_modules/argparse": {
@@ -1407,6 +1600,47 @@
"node": ">= 0.8"
}
},
+ "node_modules/cacache": {
+ "version": "15.3.0",
+ "resolved": "https://registry.npmjs.org/cacache/-/cacache-15.3.0.tgz",
+ "integrity": "sha512-VVdYzXEn+cnbXpFgWs5hTT7OScegHVmLhJIR8Ufqk3iFD6A6j5iSX1KuBTfNEv4tdJWE2PzA6IVFtcLC7fN9wQ==",
+ "optional": true,
+ "dependencies": {
+ "@npmcli/fs": "^1.0.0",
+ "@npmcli/move-file": "^1.0.1",
+ "chownr": "^2.0.0",
+ "fs-minipass": "^2.0.0",
+ "glob": "^7.1.4",
+ "infer-owner": "^1.0.4",
+ "lru-cache": "^6.0.0",
+ "minipass": "^3.1.1",
+ "minipass-collect": "^1.0.2",
+ "minipass-flush": "^1.0.5",
+ "minipass-pipeline": "^1.2.2",
+ "mkdirp": "^1.0.3",
+ "p-map": "^4.0.0",
+ "promise-inflight": "^1.0.1",
+ "rimraf": "^3.0.2",
+ "ssri": "^8.0.1",
+ "tar": "^6.0.2",
+ "unique-filename": "^1.1.1"
+ },
+ "engines": {
+ "node": ">= 10"
+ }
+ },
+ "node_modules/cacache/node_modules/mkdirp": {
+ "version": "1.0.4",
+ "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-1.0.4.tgz",
+ "integrity": "sha512-vVqVZQyf3WLx2Shd0qJ9xuvqgAyKPLAiqITEtqW0oIUjzo3PePDd6fW9iFz30ef7Ysp/oiWqbhszeGWW2T6Gzw==",
+ "optional": true,
+ "bin": {
+ "mkdirp": "bin/cmd.js"
+ },
+ "engines": {
+ "node": ">=10"
+ }
+ },
"node_modules/cacheable-request": {
"version": "6.1.0",
"resolved": "https://registry.npmjs.org/cacheable-request/-/cacheable-request-6.1.0.tgz",
@@ -1519,9 +1753,12 @@
}
},
"node_modules/chownr": {
- "version": "1.1.4",
- "resolved": "https://registry.npmjs.org/chownr/-/chownr-1.1.4.tgz",
- "integrity": "sha512-jJ0bqzaylmJtVnNgzTeSOs8DPavpbYgEr/b0YL8/2GO3xJEhInFmhKMUnEJQjZumK7KXGFhUy89PrsJWlakBVg=="
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/chownr/-/chownr-2.0.0.tgz",
+ "integrity": "sha512-bIomtDF5KGpdogkLd9VspvFzk9KfpyyGlS8YFVZl7TGPBHL5snIOnxeshwVgPteQ9b4Eydl+pVbIyE1DcvCWgQ==",
+ "engines": {
+ "node": ">=10"
+ }
},
"node_modules/chromium-pickle-js": {
"version": "0.2.0",
@@ -1540,6 +1777,15 @@
"resolved": "https://registry.npmjs.org/classnames/-/classnames-2.3.1.tgz",
"integrity": "sha512-OlQdbZ7gLfGarSqxesMesDa5uz7KFbID8Kpq/SxIoNGDqY8lSYs0D+hhtBXhcdB3rcbXArFr7vlHheLk1voeNA=="
},
+ "node_modules/clean-stack": {
+ "version": "2.2.0",
+ "resolved": "https://registry.npmjs.org/clean-stack/-/clean-stack-2.2.0.tgz",
+ "integrity": "sha512-4diC9HaTE+KRAMWhDhrGOECgWZxoevMc5TlkObMqNSsVU62PYzXZ/SMTjzyGAFF1YusgxGcSWTEXBhp0CPwQ1A==",
+ "optional": true,
+ "engines": {
+ "node": ">=6"
+ }
+ },
"node_modules/cli-boxes": {
"version": "2.2.1",
"resolved": "https://registry.npmjs.org/cli-boxes/-/cli-boxes-2.2.1.tgz",
@@ -1740,6 +1986,14 @@
"integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
"dev": true
},
+ "node_modules/color-support": {
+ "version": "1.1.3",
+ "resolved": "https://registry.npmjs.org/color-support/-/color-support-1.1.3.tgz",
+ "integrity": "sha512-qiBjkpbMLO/HL68y+lh4q0/O1MZFj2RX6X/KmMa3+gJD3z+WwI1ZzDHysvqHGS3mP6mznPckpXmw1nI9cJjyRg==",
+ "bin": {
+ "color-support": "bin.js"
+ }
+ },
"node_modules/colors": {
"version": "1.0.3",
"resolved": "https://registry.npmjs.org/colors/-/colors-1.0.3.tgz",
@@ -1818,7 +2072,7 @@
"node_modules/console-control-strings": {
"version": "1.1.0",
"resolved": "https://registry.npmjs.org/console-control-strings/-/console-control-strings-1.1.0.tgz",
- "integrity": "sha1-PXz0Rk22RG6mRL9LOVB/mFEAjo4="
+ "integrity": "sha512-ty/fTekppD2fIwRvnZAVdeOiGd1c7YXEixbgJTNzqcxJWKQnjJ/V1bNEEE6hygpM3WjwHFUVK6HTjWSzV4a8sQ=="
},
"node_modules/content-disposition": {
"version": "0.5.3",
@@ -1964,6 +2218,7 @@
"resolved": "https://registry.npmjs.org/debug/-/debug-3.2.6.tgz",
"integrity": "sha512-mel+jf7nrtEl5Pn1Qx46zARXKDpBbvzezse7p7LqINmdoIk8PYP5SySaxEmYv6TZ0JyEKA1hsCId6DIhgITtWQ==",
"deprecated": "Debug versions >=3.2.0 <3.2.7 || >=4 <4.3.1 have a low-severity ReDos regression when used in a Node.js environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (https://github.com/visionmedia/debug/issues/797)",
+ "dev": true,
"dependencies": {
"ms": "^2.1.1"
}
@@ -1971,7 +2226,8 @@
"node_modules/debug/node_modules/ms": {
"version": "2.1.2",
"resolved": "https://registry.npmjs.org/ms/-/ms-2.1.2.tgz",
- "integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w=="
+ "integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w==",
+ "dev": true
},
"node_modules/decamelize": {
"version": "1.2.0",
@@ -1998,6 +2254,7 @@
"version": "0.6.0",
"resolved": "https://registry.npmjs.org/deep-extend/-/deep-extend-0.6.0.tgz",
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}
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"resolved": "https://registry.npmjs.org/delegates/-/delegates-1.0.0.tgz",
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+ "integrity": "sha512-bd2L678uiWATM6m5Z1VzNCErI3jiGzt6HGY8OVICs40JQq/HALfbyNJmp0UDakEY4pMMaN0Ly5om/B1VI/+xfQ=="
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- "integrity": "sha1-+hN8S9aY7fVc1c0CrFWfkaTEups=",
- "bin": {
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- "node": ">=0.10"
+ "node": ">=8"
}
},
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@@ -2727,6 +2981,12 @@
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}
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+ "resolved": "https://registry.npmjs.org/err-code/-/err-code-2.0.3.tgz",
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"resolved": "https://registry.npmjs.org/error-ex/-/error-ex-1.3.2.tgz",
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+ "minipass": "^3.0.0"
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}
},
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- "resolved": "https://registry.npmjs.org/gauge/-/gauge-2.7.4.tgz",
- "integrity": "sha1-LANAXHU4w51+s3sxcCLjJfsBi/c=",
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+ "engines": {
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+ "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz",
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+ "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-3.0.0.tgz",
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+ "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz",
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+ "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
+ "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==",
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}
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"node_modules/get-caller-file": {
@@ -3264,9 +3576,9 @@
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+ "version": "4.2.11",
+ "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.11.tgz",
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"resolved": "https://registry.npmjs.org/has-unicode/-/has-unicode-2.0.1.tgz",
- "integrity": "sha1-4Ob+aijPUROIVeCG0Wkedx3iqLk="
+ "integrity": "sha512-8Rf9Y83NBReMnx0gFzA8JImQACstCYWUplepDa9xprwwtmgEZUF0h/i5xSA625zB/I37EtrswSST6OXxwaaIJQ=="
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},
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+ "resolved": "https://registry.npmjs.org/humanize-ms/-/humanize-ms-1.2.1.tgz",
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- "dev": true,
+ "devOptional": true,
"engines": {
"node": ">=0.8.19"
}
@@ -3572,6 +3885,12 @@
"node": ">=0.10.0"
}
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+ "resolved": "https://registry.npmjs.org/infer-owner/-/infer-owner-1.0.4.tgz",
+ "integrity": "sha512-IClj+Xz94+d7irH5qRyfJonOdfTzuDaifE6ZPWfx0N0+/ATZCbuTPq2prFl526urkQd90WyUKIh1DfBQ2hMz9A==",
+ "optional": true
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"resolved": "https://registry.npmjs.org/inflight/-/inflight-1.0.6.tgz",
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"deprecated": "Please update to ini >=1.3.6 to avoid a prototype pollution issue",
+ "dev": true,
"engines": {
"node": "*"
}
},
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+ "resolved": "https://registry.npmjs.org/ip/-/ip-2.0.0.tgz",
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"resolved": "https://registry.npmjs.org/ipaddr.js/-/ipaddr.js-1.9.0.tgz",
@@ -3660,6 +3986,12 @@
"url": "https://github.com/sponsors/sindresorhus"
}
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+ "resolved": "https://registry.npmjs.org/is-lambda/-/is-lambda-1.0.1.tgz",
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+ "optional": true
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"resolved": "https://registry.npmjs.org/is-npm/-/is-npm-5.0.0.tgz",
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- "dev": true
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},
@@ -4171,6 +4502,33 @@
"url": "https://github.com/sponsors/sindresorhus"
}
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+ "resolved": "https://registry.npmjs.org/make-fetch-happen/-/make-fetch-happen-9.1.0.tgz",
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+ "resolved": "https://registry.npmjs.org/minipass/-/minipass-3.3.6.tgz",
+ "integrity": "sha512-DxiNidxSEK+tHG6zOIklvNOwm3hvCrbUrdtzY74U6HKTJxvIDfOUL5W5P2Ghd3DTkhhKPYGqeNUIh5qcM4YBfw==",
"dependencies": {
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- "yallist": "^3.0.0"
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}
},
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- "url": "https://github.com/sponsors/feross"
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- "url": "https://www.patreon.com/feross"
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- "url": "https://feross.org/support"
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+ "node_modules/minipass-collect": {
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+ "node_modules/minipass-flush": {
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+ "node_modules/minipass-pipeline": {
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@@ -4361,27 +4766,6 @@
"node": ">=0.4"
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"resolved": "https://registry.npmjs.org/negotiator/-/negotiator-0.6.2.tgz",
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- "integrity": "sha1-Ca5p+9YJnfuGAoHaZv8nkPoAmVQ=",
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+ "nopt": "^5.0.0",
+ "npmlog": "^6.0.0",
+ "rimraf": "^3.0.2",
+ "semver": "^7.3.5",
+ "tar": "^6.1.2",
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- "node": ">=0.1.9"
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}
},
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- "deprecated": "Please upgrade to @mapbox/node-pre-gyp: the non-scoped node-pre-gyp package is deprecated and only the @mapbox scoped package will recieve updates in the future",
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+ }
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- "rimraf": "^2.6.1",
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+ "delegates": "^1.0.0",
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},
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}
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+ "optional": true,
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+ "optional": true,
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+ "console-control-strings": "^1.1.0",
+ "gauge": "^4.0.3",
+ "set-blocking": "^2.0.0"
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+ }
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+ "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-3.6.2.tgz",
+ "integrity": "sha512-9u/sniCrY3D5WdsERHzHE4G2YCXqoG5FTHUiCC4SIbr6XcLZBY05ya9EKjYek9O5xOAwjGq+1JdGBAS7Q9ScoA==",
+ "optional": true,
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+ "integrity": "sha512-Wvss5ivl8TMRZXXESstBA4uR5iXgEN/VC5/sOcuXdVLzcdkz4HWetIoRfG5gb5X+ij/G9rw9YoGn3QoQ8OCSpw==",
+ "optional": true,
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+ "semver": "bin/semver.js"
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+ "engines": {
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+ }
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+ "node_modules/node-gyp/node_modules/string-width": {
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+ "optional": true,
+ "dependencies": {
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+ "is-fullwidth-code-point": "^3.0.0",
+ "strip-ansi": "^6.0.1"
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+ "engines": {
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+ "node_modules/node-gyp/node_modules/strip-ansi": {
+ "version": "6.0.1",
+ "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
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+ "optional": true,
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+ "node_modules/node-jsxml": {
+ "version": "0.9.0",
+ "resolved": "https://registry.npmjs.org/node-jsxml/-/node-jsxml-0.9.0.tgz",
+ "integrity": "sha1-Ca5p+9YJnfuGAoHaZv8nkPoAmVQ=",
+ "dev": true,
+ "engines": {
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}
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- "resolved": "https://registry.npmjs.org/nopt/-/nopt-4.0.3.tgz",
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+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/nopt/-/nopt-5.0.0.tgz",
+ "integrity": "sha512-Tbj67rffqceeLpcRXrT7vKAN8CwfPeIBgM7E6iBkmKLV7bEMwpGgYLGv0jACUsECaa/vuxP0IjEont6umdMgtQ==",
"dependencies": {
- "abbrev": "1",
- "osenv": "^0.1.4"
+ "abbrev": "1"
},
"bin": {
"nopt": "bin/nopt.js"
+ },
+ "engines": {
+ "node": ">=6"
}
},
"node_modules/normalize-package-data": {
@@ -4486,38 +5002,15 @@
"node": ">=8"
}
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- "resolved": "https://registry.npmjs.org/npm-bundled/-/npm-bundled-1.1.1.tgz",
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- "resolved": "https://registry.npmjs.org/npmlog/-/npmlog-4.1.2.tgz",
- "integrity": "sha512-2uUqazuKlTaSI/dC8AzicUck7+IrEaOnN/e0jd3Xtt1KcGpwx30v50mL7oPyr/h9bL3E4aZccVwpwP+5W9Vjkg==",
+ "version": "5.0.1",
+ "resolved": "https://registry.npmjs.org/npmlog/-/npmlog-5.0.1.tgz",
+ "integrity": "sha512-AqZtDUWOMKs1G/8lwylVjrdYgqA4d9nu8hc+0gzRxlDb1I10+FHBGMXs6aiQHFdCUUlqH99MUMuLfzWDNDtfxw==",
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- "console-control-strings": "~1.1.0",
- "gauge": "~2.7.3",
- "set-blocking": "~2.0.0"
+ "are-we-there-yet": "^2.0.0",
+ "console-control-strings": "^1.1.0",
+ "gauge": "^3.0.0",
+ "set-blocking": "^2.0.0"
}
},
"node_modules/nugget": {
@@ -4605,31 +5098,6 @@
"wrappy": "1"
}
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- "integrity": "sha1-u+Z0BseaqFxc/sdm/lc0VV36EnQ=",
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"version": "1.1.0",
"resolved": "https://registry.npmjs.org/p-cancelable/-/p-cancelable-1.1.0.tgz",
@@ -4639,6 +5107,21 @@
"node": ">=6"
}
},
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+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/p-map/-/p-map-4.0.0.tgz",
+ "integrity": "sha512-/bjOqmgETBYB5BoEeGVea8dmvHb2m9GLy1E9W43yeyfP6QQCZGFNa+XRceJEuDB6zqr+gKpIAmlLebMpykw/MQ==",
+ "optional": true,
+ "dependencies": {
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+ },
+ "engines": {
+ "node": ">=10"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/sindresorhus"
+ }
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"resolved": "https://registry.npmjs.org/package-json/-/package-json-6.5.0.tgz",
@@ -4853,6 +5336,25 @@
"asap": "~2.0.3"
}
},
+ "node_modules/promise-inflight": {
+ "version": "1.0.1",
+ "resolved": "https://registry.npmjs.org/promise-inflight/-/promise-inflight-1.0.1.tgz",
+ "integrity": "sha512-6zWPyEOFaQBJYcGMHBKTKJ3u6TBsnMFOIZSa6ce1e/ZrrsOlnHRHbabMjLiBYKp+n44X9eUI6VUPaukCXHuG4g==",
+ "optional": true
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+ "node_modules/promise-retry": {
+ "version": "2.0.1",
+ "resolved": "https://registry.npmjs.org/promise-retry/-/promise-retry-2.0.1.tgz",
+ "integrity": "sha512-y+WKFlBR8BGXnsNlIHFGPZmyDf3DFMoLhaflAnyZgV6rG6xu+JwesTo2Q9R6XwYmtmwAFCkAk3e35jEdoeh/3g==",
+ "optional": true,
+ "dependencies": {
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+ "retry": "^0.12.0"
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+ "engines": {
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"version": "15.8.1",
"resolved": "https://registry.npmjs.org/prop-types/-/prop-types-15.8.1.tgz",
@@ -4962,6 +5464,7 @@
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+ "dev": true,
"dependencies": {
"deep-extend": "^0.6.0",
"ini": "~1.3.0",
@@ -5239,15 +5742,27 @@
"lowercase-keys": "^1.0.0"
}
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+ "node_modules/retry": {
+ "version": "0.12.0",
+ "resolved": "https://registry.npmjs.org/retry/-/retry-0.12.0.tgz",
+ "integrity": "sha512-9LkiTwjUh6rT555DtE9rTX+BKByPfrMzEAtnlEtdEwr3Nkffwiihqe2bWADg+OQRjt9gl6ICdmB/ZFDCGAtSow==",
+ "optional": true,
+ "engines": {
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+ }
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"node_modules/rimraf": {
- "version": "2.7.1",
- "resolved": "https://registry.npmjs.org/rimraf/-/rimraf-2.7.1.tgz",
- "integrity": "sha512-uWjbaKIK3T1OSVptzX7Nl6PvQ3qAGtKEtVRjRuazjfL3Bx5eI409VZSqgND+4UNnmzLVdPj9FqFJNPqBZFve4w==",
+ "version": "3.0.2",
+ "resolved": "https://registry.npmjs.org/rimraf/-/rimraf-3.0.2.tgz",
+ "integrity": "sha512-JZkJMZkAGFFPP2YqXZXPbMlMBgsxzE8ILs4lMIX/2o0L9UBw9O/Y3o6wFw/i9YLapcUJWwqbi3kdxIPdC62TIA==",
"dependencies": {
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},
"bin": {
"rimraf": "bin.js"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/isaacs"
}
},
"node_modules/safe-buffer": {
@@ -5352,7 +5867,7 @@
"node_modules/set-blocking": {
"version": "2.0.0",
"resolved": "https://registry.npmjs.org/set-blocking/-/set-blocking-2.0.0.tgz",
- "integrity": "sha1-BF+XgtARrppoA93TgrJDkrPYkPc="
+ "integrity": "sha512-KiKBS8AnWGEyLzofFfmvKwpdPzqiy16LvQfK3yv/fVH7Bj13/wl3JSR1J+rfgRE9q7xUJK4qvgS8raSOeLUehw=="
},
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@@ -5399,9 +5914,9 @@
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- "integrity": "sha1-tf3AjxKH6hF4Yo5BXiUTK3NkbG0="
+ "version": "3.0.7",
+ "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-3.0.7.tgz",
+ "integrity": "sha512-wnD2ZE+l+SPC/uoS0vXeE9L1+0wuaMqKlfz9AMUo38JsyLSBWSFcHR1Rri62LZc12vLr1gb3jl7iwQhgwpAbGQ=="
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@@ -5441,13 +5956,63 @@
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- "dev": true,
"optional": true,
"engines": {
"node": ">= 6.0.0",
"npm": ">= 3.0.0"
}
},
+ "node_modules/socks": {
+ "version": "2.7.1",
+ "resolved": "https://registry.npmjs.org/socks/-/socks-2.7.1.tgz",
+ "integrity": "sha512-7maUZy1N7uo6+WVEX6psASxtNlKaNVMlGQKkG/63nEDdLOWNbiUMoLK7X4uYoLhQstau72mLgfEWcXcwsaHbYQ==",
+ "optional": true,
+ "dependencies": {
+ "ip": "^2.0.0",
+ "smart-buffer": "^4.2.0"
+ },
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+ "dev": true,
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- "url": "https://www.patreon.com/feross"
- },
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@@ -6719,6 +7311,12 @@
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@@ -6785,6 +7383,79 @@
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@@ -7021,6 +7692,58 @@
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@@ -7214,17 +7937,29 @@
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+ "version": "2.0.0",
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},
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@@ -9484,6 +10310,12 @@
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@@ -9547,6 +10386,12 @@
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@@ -10526,6 +11479,22 @@
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@@ -10832,10 +11802,16 @@
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"resolved": "https://registry.npmjs.org/set-blocking/-/set-blocking-2.0.0.tgz",
- "integrity": "sha1-BF+XgtARrppoA93TgrJDkrPYkPc="
+ "integrity": "sha512-KiKBS8AnWGEyLzofFfmvKwpdPzqiy16LvQfK3yv/fVH7Bj13/wl3JSR1J+rfgRE9q7xUJK4qvgS8raSOeLUehw=="
},
"setimmediate": {
"version": "1.0.5",
@@ -10972,9 +11948,9 @@
}
},
"signal-exit": {
- "version": "3.0.2",
- "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-3.0.2.tgz",
- "integrity": "sha1-tf3AjxKH6hF4Yo5BXiUTK3NkbG0="
+ "version": "3.0.7",
+ "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-3.0.7.tgz",
+ "integrity": "sha512-wnD2ZE+l+SPC/uoS0vXeE9L1+0wuaMqKlfz9AMUo38JsyLSBWSFcHR1Rri62LZc12vLr1gb3jl7iwQhgwpAbGQ=="
},
"single-line-log": {
"version": "1.1.2",
@@ -11010,9 +11986,46 @@
"version": "4.2.0",
"resolved": "https://registry.npmjs.org/smart-buffer/-/smart-buffer-4.2.0.tgz",
"integrity": "sha512-94hK0Hh8rPqQl2xXc3HsaBoOXKV20MToPkcXvwbISWLEs+64sBq5kFgn2kJDHb1Pry9yrP0dxrCI9RRci7RXKg==",
- "dev": true,
"optional": true
},
+ "socks": {
+ "version": "2.7.1",
+ "resolved": "https://registry.npmjs.org/socks/-/socks-2.7.1.tgz",
+ "integrity": "sha512-7maUZy1N7uo6+WVEX6psASxtNlKaNVMlGQKkG/63nEDdLOWNbiUMoLK7X4uYoLhQstau72mLgfEWcXcwsaHbYQ==",
+ "optional": true,
+ "requires": {
+ "ip": "^2.0.0",
+ "smart-buffer": "^4.2.0"
+ }
+ },
+ "socks-proxy-agent": {
+ "version": "6.2.1",
+ "resolved": "https://registry.npmjs.org/socks-proxy-agent/-/socks-proxy-agent-6.2.1.tgz",
+ "integrity": "sha512-a6KW9G+6B3nWZ1yB8G7pJwL3ggLy1uTzKAgCb7ttblwqdz9fMGJUuTy3uFzEP48FAs9FLILlmzDlE2JJhVQaXQ==",
+ "optional": true,
+ "requires": {
+ "agent-base": "^6.0.2",
+ "debug": "^4.3.3",
+ "socks": "^2.6.2"
+ },
+ "dependencies": {
+ "debug": {
+ "version": "4.3.4",
+ "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.4.tgz",
+ "integrity": "sha512-PRWFHuSU3eDtQJPvnNY7Jcket1j0t5OuOsFzPPzsekD52Zl8qUfFIPEiswXqIvHWGVHOgX+7G/vCNNhehwxfkQ==",
+ "optional": true,
+ "requires": {
+ "ms": "2.1.2"
+ }
+ },
+ "ms": {
+ "version": "2.1.2",
+ "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.2.tgz",
+ "integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w==",
+ "optional": true
+ }
+ }
+ },
"source-map": {
"version": "0.6.1",
"resolved": "https://registry.npmjs.org/source-map/-/source-map-0.6.1.tgz",
@@ -11068,12 +12081,21 @@
"dev": true
},
"sqlite3": {
- "version": "4.2.0",
- "resolved": "https://registry.npmjs.org/sqlite3/-/sqlite3-4.2.0.tgz",
- "integrity": "sha512-roEOz41hxui2Q7uYnWsjMOTry6TcNUNmp8audCx18gF10P2NknwdpF+E+HKvz/F2NvPKGGBF4NGc+ZPQ+AABwg==",
+ "version": "5.1.6",
+ "resolved": "https://registry.npmjs.org/sqlite3/-/sqlite3-5.1.6.tgz",
+ "integrity": "sha512-olYkWoKFVNSSSQNvxVUfjiVbz3YtBwTJj+mfV5zpHmqW3sELx2Cf4QCdirMelhM5Zh+KDVaKgQHqCxrqiWHybw==",
"requires": {
- "nan": "^2.12.1",
- "node-pre-gyp": "^0.11.0"
+ "@mapbox/node-pre-gyp": "^1.0.0",
+ "node-addon-api": "^4.2.0",
+ "node-gyp": "8.x",
+ "tar": "^6.1.11"
+ },
+ "dependencies": {
+ "node-addon-api": {
+ "version": "4.3.0",
+ "resolved": "https://registry.npmjs.org/node-addon-api/-/node-addon-api-4.3.0.tgz",
+ "integrity": "sha512-73sE9+3UaLYYFmDsFZnqCInzPyh3MqIwZO9cw58yIqAZhONrrabrYyYe3TuIqtIiOuTXVhsGau8hcrhhwSsDIQ=="
+ }
}
},
"ssf": {
@@ -11109,6 +12131,15 @@
}
}
},
+ "ssri": {
+ "version": "8.0.1",
+ "resolved": "https://registry.npmjs.org/ssri/-/ssri-8.0.1.tgz",
+ "integrity": "sha512-97qShzy1AiyxvPNIkLWoGua7xoQzzPjQ0HAH4B0rWKo7SZ6USuPcrUiAFrws0UH8RrbWmgq3LMTObhPIHbbBeQ==",
+ "optional": true,
+ "requires": {
+ "minipass": "^3.1.1"
+ }
+ },
"stat-mode": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/stat-mode/-/stat-mode-1.0.0.tgz",
@@ -11172,7 +12203,8 @@
"strip-json-comments": {
"version": "2.0.1",
"resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-2.0.1.tgz",
- "integrity": "sha1-PFMZQukIwml8DsNEhYwobHygpgo="
+ "integrity": "sha1-PFMZQukIwml8DsNEhYwobHygpgo=",
+ "dev": true
},
"sumchecker": {
"version": "2.0.2",
@@ -11279,28 +12311,27 @@
}
},
"tar": {
- "version": "4.4.13",
- "resolved": "https://registry.npmjs.org/tar/-/tar-4.4.13.tgz",
- "integrity": "sha512-w2VwSrBoHa5BsSyH+KxEqeQBAllHhccyMFVHtGtdMpF4W7IRWfZjFiQceJPChOeTsSDVUpER2T8FA93pr0L+QA==",
- "requires": {
- "chownr": "^1.1.1",
- "fs-minipass": "^1.2.5",
- "minipass": "^2.8.6",
- "minizlib": "^1.2.1",
- "mkdirp": "^0.5.0",
- "safe-buffer": "^5.1.2",
- "yallist": "^3.0.3"
+ "version": "6.1.15",
+ "resolved": "https://registry.npmjs.org/tar/-/tar-6.1.15.tgz",
+ "integrity": "sha512-/zKt9UyngnxIT/EAGYuxaMYgOIJiP81ab9ZfkILq4oNLPFX50qyYmu7jRj9qeXoxmJHjGlbH0+cm2uy1WCs10A==",
+ "requires": {
+ "chownr": "^2.0.0",
+ "fs-minipass": "^2.0.0",
+ "minipass": "^5.0.0",
+ "minizlib": "^2.1.1",
+ "mkdirp": "^1.0.3",
+ "yallist": "^4.0.0"
},
"dependencies": {
- "safe-buffer": {
- "version": "5.2.1",
- "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.2.1.tgz",
- "integrity": "sha512-rp3So07KcdmmKbGvgaNxQSJr7bGVSVk5S9Eq1F+ppbRo70+YeaDxkw5Dd8NPN+GD6bjnYm2VuPuCXmpuYvmCXQ=="
+ "minipass": {
+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/minipass/-/minipass-5.0.0.tgz",
+ "integrity": "sha512-3FnjYuehv9k6ovOEbyOswadCDPX1piCfhV8ncmYtHOjuPwylVWsghTLo7rabjC3Rx5xD4HDx8Wm1xnMF7S5qFQ=="
},
- "yallist": {
- "version": "3.1.1",
- "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz",
- "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g=="
+ "mkdirp": {
+ "version": "1.0.4",
+ "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-1.0.4.tgz",
+ "integrity": "sha512-vVqVZQyf3WLx2Shd0qJ9xuvqgAyKPLAiqITEtqW0oIUjzo3PePDd6fW9iFz30ef7Ysp/oiWqbhszeGWW2T6Gzw=="
}
}
},
@@ -11392,17 +12423,6 @@
"dev": true,
"requires": {
"rimraf": "^3.0.0"
- },
- "dependencies": {
- "rimraf": {
- "version": "3.0.2",
- "resolved": "https://registry.npmjs.org/rimraf/-/rimraf-3.0.2.tgz",
- "integrity": "sha512-JZkJMZkAGFFPP2YqXZXPbMlMBgsxzE8ILs4lMIX/2o0L9UBw9O/Y3o6wFw/i9YLapcUJWwqbi3kdxIPdC62TIA==",
- "dev": true,
- "requires": {
- "glob": "^7.1.3"
- }
- }
}
},
"tmp-promise": {
@@ -11514,6 +12534,24 @@
"resolved": "https://registry.npmjs.org/unfetch/-/unfetch-4.2.0.tgz",
"integrity": "sha512-F9p7yYCn6cIW9El1zi0HI6vqpeIvBsr3dSuRO6Xuppb1u5rXpCPmMvLSyECLhybr9isec8Ohl0hPekMVrEinDA=="
},
+ "unique-filename": {
+ "version": "1.1.1",
+ "resolved": "https://registry.npmjs.org/unique-filename/-/unique-filename-1.1.1.tgz",
+ "integrity": "sha512-Vmp0jIp2ln35UTXuryvjzkjGdRyf9b2lTXuSYUiPmzRcl3FDtYqAwOnTJkAngD9SWhnoJzDbTKwaOrZ+STtxNQ==",
+ "optional": true,
+ "requires": {
+ "unique-slug": "^2.0.0"
+ }
+ },
+ "unique-slug": {
+ "version": "2.0.2",
+ "resolved": "https://registry.npmjs.org/unique-slug/-/unique-slug-2.0.2.tgz",
+ "integrity": "sha512-zoWr9ObaxALD3DOPfjPSqxt4fnZiWblxHIgeWqW8x7UqDzEtHEQLzji2cuJYQFCU6KmoJikOYAZlrTHHebjx2w==",
+ "optional": true,
+ "requires": {
+ "imurmurhash": "^0.1.4"
+ }
+ },
"unique-string": {
"version": "2.0.0",
"resolved": "https://registry.npmjs.org/unique-string/-/unique-string-2.0.0.tgz",
@@ -11689,17 +12727,17 @@
"version": "2.0.2",
"resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
"integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==",
- "dev": true,
+ "devOptional": true,
"requires": {
"isexe": "^2.0.0"
}
},
"wide-align": {
- "version": "1.1.3",
- "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.3.tgz",
- "integrity": "sha512-QGkOQc8XL6Bt5PwnsExKBPuMKBxnGxWWW3fU55Xt4feHozMUhdUMaBCk290qpm/wG5u/RSKzwdAC4i51YigihA==",
+ "version": "1.1.5",
+ "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.5.tgz",
+ "integrity": "sha512-eDMORYaPNZ4sQIuuYPDHdQvf4gyCF9rEEV/yPxGfwPkRodwEgiMUUXTx/dex+Me0wxx53S+NgUHaP7y3MGlDmg==",
"requires": {
- "string-width": "^1.0.2 || 2"
+ "string-width": "^1.0.2 || 2 || 3 || 4"
}
},
"widest-line": {
diff --git a/package.json b/package.json
index 59d64bdd0d9d59fec0eb08c05532f40c2fa587e2..f5e43ff94b0bda9740506e31e107f45816e47de0 100644
--- a/package.json
+++ b/package.json
@@ -29,7 +29,7 @@
"minimist": "^1.2.5",
"multer": "^1.4.3",
"semver": "^6.3.0",
- "sqlite3": "^4.1.1",
+ "sqlite3": "^5.1.6",
"xlsx": "^0.15.6"
},
"devDependencies": {