Skip to content

Commit

Permalink
folder name changes...
Browse files Browse the repository at this point in the history 
github can't keep track of folder name changes apparently
  • Loading branch information
@xiuyechen
xiuyechen committed Jun 21, 2018
1 parent 31e8558 commit 07c99d8
Show file tree
Hide file tree
Showing 120 changed files with 279 additions and 88 deletions.
3 changes: 3 additions & 0 deletions .gitignore
View file
@@ -1,3 +1,6 @@
*.asv
*.mat

# Windows image file caches
Thumbs.db
ehthumbs.db
Expand Down
123 changes: 64 additions & 59 deletions GUI functions/DrawTimeSeries.m
View file
Expand Up @@ -28,7 +28,7 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
isPlotRegWithTS = getappdata(hfig,'isPlotRegWithTS');
clrmap = [];
numK = getappdata(hfig,'numK');
isAxTight = [];
isAxTight = 1;

% override with (optional) inputs
if exist('opts','var')
Expand Down Expand Up @@ -76,12 +76,17 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
i_fish = getappdata(hfig,'i_fish');

isPlotRegSameRow = 0;
if ~exist('isPlotRegWithTS','var'),
if ~exist('isPlotRegWithTS','var')
isPlotRegWithTS = 0;
end

M = getappdata(hfig,'M');

if 0 % manual adjustment!
M = circshift(M,30+45,2); % 15 for looming
stim = circshift(stim,30+45,2);
end

nFrames = size(M,2);
%
% if isPopout
Expand All @@ -100,21 +105,21 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
numK = max(max(gIX),numK);

%% Main plotting
if isPlotLines,
if 1, % (just to collapse isPlotLines = true)
if isPlotLines
if 1 % (just to collapse isPlotLines = true)
%% settings
len = pos(3);
% fpsec = getappdata(hfig,'fpsec');%1.97;

% set position grid
nClus = length(unique(gIX));

if isPlotBehavior,
if isPlotBehavior
nExtraRows = 3; % number of extra rows
else
nExtraRows = 2;
end
if isPlotRegWithTS && ~isPlotRegSameRow,
if isPlotRegWithTS && ~isPlotRegSameRow
nLines = nClus + 1;
if ~isAxTight
nRows = max(8,nLines)+nExtraRows+1;
Expand Down Expand Up @@ -154,8 +159,8 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
U = unique(gIX);

j_pos = 0;
if isPlotRegWithTS,
if ~isPlotRegSameRow,
if isPlotRegWithTS
if ~isPlotRegSameRow
j_pos = 1;
end

Expand All @@ -167,7 +172,7 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
axis tight;axis off
end

for j = 1:nClus,
for j = 1:nClus
k = U(j);
Ys = M(gIX==k,:);
ymean = mean(Ys,1);
Expand All @@ -185,17 +190,17 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
plot(xv,ymean,'-','Linewidth',1,'color',clrmap(k,:))
axis tight;axis off

if false %isPlotClusN
text (xv(end)+1,0,['n=',num2str(size(Ys,1))]);
end
% if false %isPlotClusN
% text(xv(end)+1,0,['n=',num2str(size(Ys,1))]);
% end
end

%% plot scale bar
axes('Position',[pos(1),pos(2)+pos(4)-lineH*(nLines+2),len,lineH]); hold on;
if nFrames<600, % <~10 min, plot 1min scale bar
if nFrames<600 % <~10 min, plot 1min scale bar
plot([1,10*fpsec],[0.75,0.75],'k-');
text(pos(1),0.5,'10 sec','HorizontalAlignment','left')
elseif nFrames<2400, % <~10 min, plot 1min scale bar
elseif nFrames<2400 % <~10 min, plot 1min scale bar
plot([1,60*fpsec],[0.75,0.75],'k-');
text(pos(1)+60*fpsec/2,0.5,'1 min','HorizontalAlignment','center')
else % >~10 min, plot 5 min scale bar
Expand All @@ -206,7 +211,7 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
axis off

%% draw behavior bar
if isPlotBehavior,
if isPlotBehavior
h = axes('Position',[pos(1),pos(2)+pos(4)-lineH*(nLines+3),len,0.7/nRows]);
DrawBehaviorBar(h,behavior,i_fish);

Expand All @@ -217,14 +222,14 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
end

else % ~isPlotLines, i.e. plot all traces as grayscale map
if isCentroid,
if isCentroid
M_ = FindClustermeans(gIX,M);
gIX_ = unique(gIX);
else
if ~isPopout, % down-sample
if ~isPopout % down-sample
displaymax_cell = 8000;
displaymax_frames = 5000;
if length(cIX) > displaymax_cell,
if length(cIX) > displaymax_cell
skip_cell = round(length(cIX)/displaymax_cell);

cIX = cIX(1:skip_cell:end,:);
Expand All @@ -234,8 +239,8 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
M_ = M;
end

if size(M_,2) > displaymax_frames,
skip_frames = round(length(cIX)/displaymax_frames);
if size(M_,2) > displaymax_frames
skip_frames = round(size(M_,2)/displaymax_frames);
M_ = M_(:,1:skip_frames:end);
stim = stim(:,1:skip_frames:end);
behavior = behavior(:,1:skip_frames:end);
Expand All @@ -249,7 +254,7 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)

%% set size of stimulus-bar relative to whole plot
% each stim bar (if applicable) takes up 1 unit, and behavior bar takes up 2.
if ~isPopout,
if ~isPopout
barratio = 0.025;
else
barratio = 0.05;
Expand Down Expand Up @@ -283,9 +288,9 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
ix_div = [find(diff(idx));length(idx)];

bars = ones(nLines,bwidth);
if numK>1,
if numK>1
bars(1:ix_div(1),:) = idx(ix_div(1));
for i = 2:length(ix_div),
for i = 2:length(ix_div)
% paint color
bars(ix_div(i-1)+1:ix_div(i),:) = idx(ix_div(i));
end
Expand All @@ -301,8 +306,8 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)

% plot 'im'
hold off;
if isPopout,
if ~isPlotBehavior,
if isPopout
if ~isPlotBehavior
set(h_ax,'Position',[pos(1),pos(2),pos(3),pos(4)*(1-barratio)]);
else
set(h_ax,'Position',[pos(1),pos(2)+pos(4)*barratio*2,pos(3),pos(4)*(1-barratio*3)]);
Expand All @@ -313,7 +318,7 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
end

% (if too few rows, pad to 30 rows with white background)
if s1<30,
if s1<30
temp = im;
im = ones(30,s2,s3);
im(1:s1,:,:) = temp;
Expand All @@ -325,15 +330,15 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)

% plot cluster division lines
plot([0.5,s2+0.5],[0.5,0.5],'k','Linewidth',0.5);
if numK>1,
for i = 1:length(ix_div),% = numK-1,
if numK>1
for i = 1:length(ix_div)% = numK-1,
y = ix_div(i)+0.5;
plot([0.5,s2+0.5],[y,y],'k','Linewidth',0.5);
end
end

% label axes
if ~exist('nCells','var'),
if ~exist('nCells','var')
nCells = nLines;
end
ylabel(['Number of cells: ' num2str(nCells)]);
Expand All @@ -343,19 +348,19 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
% write in text labels (numbers corresponding to vertical colorbar)
x = s2*1.003;
y_last = 0;
for i = 1:length(ix_div),
for i = 1:length(ix_div)
% avoid label crowding
margin = 0.015*s1;
y0 = ix_div(i)+0.5;
y = max(y_last+margin,y0);
if i<length(ix_div),
if i<length(ix_div)
ynext = ix_div(i+1);
else
ynext = y0+margin*2;
end
% draw if not squeezed too much away
if y < y0+margin*2 && y < 0.5*(y0+ynext), %nLines+stimheight-margin,
if exist('iswrite','var') && iswrite,
if y < y0+margin*2 && y < 0.5*(y0+ynext) %nLines+stimheight-margin,
if exist('iswrite','var') && iswrite
try
text(x,y,[num2str(idx(ix_div(i))) ': ' num2str(rankscore(i))],'HorizontalAlignment','Left','VerticalAlignment','Bottom',...
'FontUnits','normalized','FontSize',0.015,'Tag','label');
Expand Down Expand Up @@ -390,7 +395,7 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
plot([length(stim),length(stim)],[0,size(stimbar,1)],'k','Linewidth',0.5);

% bottom axis
if ~isPopout, % plot stimbar in the bottom too
if ~isPopout % plot stimbar in the bottom too
axes('Position',[pos(1),pos(2)+pos(4)*barratio*2,pos(3),pos(4)*barratio]);
image(stimbar);axis off;hold on;
plot([1,length(stim)],[size(stimbar,1),size(stimbar,1)],'k','Linewidth',0.5); % plot bottom border
Expand All @@ -399,13 +404,13 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
end

%% Draw behavior
if isPlotBehavior,
if isPlotBehavior
h = axes('Position',[pos(1),pos(2),pos(3),pos(4)*barratio*2]);
DrawBehaviorBar(h,behavior,i_fish,barlength);
axes('Position',[0.015,pos(2),0.03,pos(4)*barratio*2]);
DrawArrowsIcon(isPopout);
else
h = h_ax;
axes(h_ax);
end

% % label horizontal axis: approximate time length
Expand All @@ -417,7 +422,7 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
% end

%% Draw fish icon:
if ~isPopout,
if ~isPopout
axes('Position',[0.015, pos(2)+pos(4)*barratio*2, 0.03, pos(4)*barratio]);
else
axes('Position',[0.015,pos(2)+pos(4)*(1-barratio),0.03,pos(4)*barratio]);
Expand Down Expand Up @@ -446,7 +451,7 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
end

function DrawFishIcon
if exist('fishpic.jpg','file')==2,
if exist('fishpic.jpg','file')==2
pic = imread('fishpic.jpg');
fishpic = imresize(pic,0.5);

Expand All @@ -455,14 +460,14 @@ function DrawTimeSeries(hfig,cIX_plot,gIX_plot,opts)
end

function DrawArrowsIcon(isPopout)
if ~isPopout,
if exist('arrows.jpg','file')==2,
if ~isPopout
if exist('arrows.jpg','file')==2
pic = imread('arrows.jpg');
arrowpic = imresize(pic,0.2);
image(arrowpic); axis off; axis image; axis tight
end
else
if exist('arrows_wide.jpg','file')==2,
if exist('arrows_wide.jpg','file')==2
pic = imread('arrows_wide.jpg');
arrowpic = imresize(pic,0.2);
image(arrowpic); axis off; axis image; axis tight
Expand All @@ -477,18 +482,18 @@ function DrawBehaviorBar(h,behavior,i_fish,barlength)
m = AutoScaleImage0to1(m);

% additional line-by-line normalization! (optional)
for i = 1:numReg,
for i = 1:numReg
temp = m(i,:);
m(i,:) = (temp-min(temp))/(max(temp)-min(temp));
end

if exist('barlength','var'),
if exist('barlength','var')
temp = ones(size(m,1),barlength);
temp(:,1:length(m)) = m;
else
temp = m;
end
if numReg == 2,
if numReg == 2
imagesc(temp);colormap gray
set(h,'YTick',[],'XTick',[]);
set(h, 'box', 'off')
Expand All @@ -499,15 +504,15 @@ function DrawBehaviorBar(h,behavior,i_fish,barlength)
y = 1.5;
plot([0.5,length(behavior)+0.5],[y,y],'w','Linewidth',0.5);

elseif 1, % plot all 5 lines
else % plot all 5 lines
imagesc(temp(1:5,:));colormap gray
set(h,'YTick',[],'XTick',[]);
set(h, 'box', 'off')
axis off
hold on;axis ij;

% plot division lines
for i = 0:3,
for i = 0:3
y = i+0.5;
plot([0.5,length(behavior)+0.5],[y,y],'w','Linewidth',0.5);
end
Expand All @@ -519,18 +524,18 @@ function DrawBehaviorBar(h,behavior,i_fish,barlength)
% text(x,y,names{i},'Fontsize',7);
% end

else % only plot top 3 lines
m = vertcat(temp(1,:),temp(2,:),temp(3,:));
imagesc(m);colormap gray
set(h,'YTick',[],'XTick',[]);
set(h, 'box', 'off')
axis off
hold on;axis ij;

% plot division lines
for i = 0:2,
y = i+0.5;
plot([0.5,length(behavior)+0.5],[y,y],'w','Linewidth',0.5);
end
% else % only plot top 3 lines
% m = vertcat(temp(1,:),temp(2,:),temp(3,:));
% imagesc(m);colormap gray
% set(h,'YTick',[],'XTick',[]);
% set(h, 'box', 'off')
% axis off
% hold on;axis ij;
%
% % plot division lines
% for i = 0:2
% y = i+0.5;
% plot([0.5,length(behavior)+0.5],[y,y],'w','Linewidth',0.5);
% end
end
end

0 comments on commit 07c99d8

Please sign in to comment.