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Remove old TissueCyte setting from INI file
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@raacampbell
raacampbell committed Jun 9, 2020
1 parent dea6bfe commit f43ef1e
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Showing 6 changed files with 112 additions and 133 deletions.
31 changes: 10 additions & 21 deletions code/INI/readStitchItINI.m
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Expand Up @@ -22,7 +22,7 @@
% Inputs
% All inputs as *optional* parameter/value pairs
% 'INIfname' - Path to INI file to read. If empty or missing the above rules apply.
% 'systemType' = either 'TissueCyte' or the ID of a system (the microscope name).
% 'systemType' = The ID of a system (the microscope name).
%
% Outputs
% out - the contents of the INI file (plus some minor processing) as a structure
Expand Down Expand Up @@ -130,29 +130,18 @@

end

%Pull out the current objective from the structure
% TODO: the following is system specific and very much tied to the TV.
% Need to get rid of it -- too complicated
if ~isfield(out, out.experiment.objectiveName)
error('No objective name field %s found\nPlease check your INI file!', out.experiment.objectiveName')
end
thisObjective = out.(out.experiment.objectiveName);
%Note that for TV data sets, the number of microns per pixel is with respect to the 1664 image size
out.micsPerPixel.micsPerPixelMeasured=thisObjective.micsPerPixelMeasured;
out.micsPerPixel.micsPerPixelRows=thisObjective.micsPerPixelRows;
out.micsPerPixel.micsPerPixelCols=thisObjective.micsPerPixelCols;


function out=readThisINI(fname)
ini = IniConfig();
ini.ReadFile(fname);
ini = IniConfig();
ini.ReadFile(fname);

sections = ini.GetSections;
sections = ini.GetSections;

for ii=1:length(sections)
keys = ini.GetKeys(sections{ii});
values = ini.GetValues(sections{ii}, keys);
for jj=1:length(values)
out.(sections{ii}(2:end-1)).(keys{jj})=values{jj};
for ii=1:length(sections)
keys = ini.GetKeys(sections{ii});
values = ini.GetValues(sections{ii}, keys);
for jj=1:length(values)
out.(sections{ii}(2:end-1)).(keys{jj})=values{jj};
end
end
end
72 changes: 0 additions & 72 deletions code/INI/stitchitConf_DEFAULT.ini
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Expand Up @@ -30,78 +30,6 @@ stitchedDirBaseName=stitchedImages
WEBdir=forWWW


;;----------------------------------------------------------------------------
;; Our TissueVision system does not correctly report the number of microns per
;; pixel in the Mosaic file. We therefore measured this and the following few
;; sections are responsible for correctly telling StitchIt what this value is.
;; We define the number of microns per pixel with respect to a particular image
;; size. It might have been better to define it using scan angle, but right now
;; we do it with respect to an image size of 1664 x 1664.
;; Note that [experiment], [micsPerPixel], and the objective sections are only
;; for the TissueVision. We assume that other systems will correctly report the
;; number of microns per pixel in the image meta-data.

;;----------------------------------------------------------------------------
[experiment]
;; Set this to be the objective used in your experiment. This value is
;; used to determine where to place the tiles. Its name must correspond to one of the
;; the objective name sections below. The _x_x that suffixes some names refers to the
;; scan angle. e.g. _2_2 is a scan angle of 2.2
objectiveName=Nikon16x_2_2
;;objectiveName=Nikon16x_3_0
;;objectiveName=Zeiss20x



;;----------------------------------------------------------------------------
;;This section determines how StitchIt will calculate the number of microns
;;per pixel. This is important because StitchIt uses this number to position
;;the tiles. It needs to know the number of microns per pixel both for
;;naive positioning and stage coordinate positioning.
;;


[micsPerPixel]
;;We calculate the number of microns per pixel by imaging an EM grid. The number of
;;microns per pixel must be in reference to a particular image size. This is defined
;;here. e.g. 1664 by 1664 pixels
numPix=1664

;;The following setting allows us to choose whether we want to use a single number
;;for both X and Y or different numbers. Using a single number (usemeasured=1)
;;causes us to use "micsPerPixel" and setting usemeasured to 0 casuses us to use
;;the two separate row and col values. The need to tweak the number may arise from
;;the sampling accuracy of the measurements which creates rounding errors in the FFT.
;;1 means use the measured, single, value for both x and y. 0 means use the other
;;two values (micsPerPixelRows and micsPerPixelCols.
usemeasured=0


;; Objectives follow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[Zeiss20x]
;;In case the user tweaks this value, we log here in the comments that the
;;default value for the 20x at 1664^2 is 0.485 microns/pixel
micsPerPixelMeasured=0.485

;;The following two numbers are based on the above but tweaked. The
;;tweaking was done by trying out a bunch of different conversion factors
;;and seeing what worked best. They allow for setting different numbers
;;of microns per pixel in x and y. This may not be necessary and may be
;;removed in future.
micsPerPixelRows=0.468
micsPerPixelCols=0.450


[Nikon16x_2_2]
micsPerPixelMeasured=0.480
micsPerPixelRows=0.474
micsPerPixelCols=0.459

[Nikon16x_3_0]
micsPerPixelMeasured=0.650
micsPerPixelRows=0.650
micsPerPixelCols=0.650



;;----------------------------------------------------------------------------
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5 changes: 2 additions & 3 deletions code/preProcessTiles/preProcessTiles.m
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Expand Up @@ -119,9 +119,8 @@
verbose=params.Results.verbose;


if ~strcmp(determineStitchItSystemType,'TissueCyte') && ...
(length(combCorChans)>1 || combCorChans~=0)
fprintf('\nYou have requested to run a comb-correction on non-TissueVision data. Please see:\n ')
if length(combCorChans)>1 || combCorChans~=0
fprintf('\nYou have requested to run a comb-correction. This is not working right now. Please see:\n ')
fprintf('https://github.com/BaselLaserMouse/StitchIt/wiki/Tile-pre-processing\n\n')
end

Expand Down
106 changes: 99 additions & 7 deletions code/stitching/determineStitchedImageExtent.m
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Expand Up @@ -7,7 +7,7 @@
% With auto-ROI the sections will be very different sizes. In order to produces a series of
% stitched images having the same size from section to section we need to determine the
% locations of all the tiles in the whole sample and find the extrema in the x/y plane.
% This functio does this.
% This function does this.
%
% Inputs - none. just run from sample directory
%
Expand All @@ -18,6 +18,13 @@
% Rob Campbell - SWC 2020


verbose=true; %report to screen lots on info on
plotboxes=true; %make a plot with the imaged areas overlain

if verbose
fprintf('%s is determining the extent of the imaged area\n', mfilename)
end

out=[];
[data,successfulRead]=readMetaData2Stitchit;

Expand All @@ -42,30 +49,115 @@
out.maxXPos = nan(1,length(rDataDirs));
out.maxYPos = nan(1,length(rDataDirs));

tp = {}; %cache all loaded position arrays in case we want to do stuff with them later
for ii=1:length(rDataDirs)
posFname = fullfile(userConfig.subdir.rawDataDir,rDataDirs(ii).name,'tilePositions.mat');
if ~exist(posFname,'file')
continue
end

load(posFname,'positionArray')
tp{ii} = positionArray;

% Log the minimum X and Y positions
% Log the actual minimum X and Y positions
% TODO - we should maybe allow for predicted stage positions instead of actual
out.minXPos(ii)=min(positionArray(:,5));
out.minYPos(ii)=min(positionArray(:,6));

out.maxXPos(ii)=max(positionArray(:,5));
out.maxYPos(ii)=max(positionArray(:,6));

if verbose
fprintf('%d/%d Front/Left -- x=%0.2f y=%0.2f (%d by %d tiles)\n', ...
ii, ...
length(rDataDirs), ...
out.maxXPos(ii), ...
out.maxYPos(ii), ...
length(unique(positionArray(:,1))), ...
length(unique(positionArray(:,2))) )
end

end


tileStepSizeMM = abs(mode(diff(positionArray(:,3))))

% The tile step size is the distance moved by the microscope in mm as it travels from one x/y stage
% location to the next. It is equal to the tile size (image FOV) minus the overlap between tiles.
tileStepSizeMM = abs(mode(diff(positionArray(:,3))));

% The tile extent in mm is the image FOV
tileExtentInMM = tileStepSizeMM / (1-data.mosaic.overlapProportion);

%out.minXY = [min(out.minXPos), min(out.minYPos)] - tileExtentInMM; % % TODO -- I would have thought this is correct, but it seems not to be

% The number of mm of overlap between adjacent tiles
tileOverlapInMM = tileExtentInMM - tileStepSizeMM;

out.minXY = [min(out.minXPos), min(out.minYPos)] - tileStepSizeMM;
out.maxXY = [max(out.maxXPos), max(out.maxYPos)];

out.maxXY = [max(out.maxXPos), max(out.maxYPos)]; % This is the "origin" front/left


% This is a call to a test function to ensure that all is running as expected
checkMinMax


if plotboxes
% Use the minimum x/y position and the tile position array to produce pixel positions for
% where the tiles ought to go.
voxSize = [data.voxelSize.X, data.voxelSize.Y];
tileStep = [(tileStepSizeMM*1E3) / voxSize(1), (tileStepSizeMM*1E3) / voxSize(2)];
tileSizeInPixels = [(tileExtentInMM*1E3) / voxSize(1), (tileExtentInMM*1E3) / voxSize(2)];
figure(4592)
clf
hold on
jj = jet(length(rDataDirs));
for ii=1:length(rDataDirs)

tmp=stagePos2PixelPos(tp{ii}(:,5:6), voxSize, out.maxXY);
minPix = min(tmp);
maxPix = max(tmp) + tileSizeInPixels;
d = maxPix-minPix; % This is the size of the box

% Plot the box
x = [minPix(2), minPix(2), minPix(2)+d(2), minPix(2)+d(2), minPix(2)];
y = [minPix(1), minPix(1)+d(1), minPix(1)+d(1), minPix(1), minPix(1)];
plot(x, y, '-', 'Color', jj(ii,:), 'LineWidth', 2)

% Print to screen the size and location of the box
fprintf('%d/%d %dx%d pixels. With far corner at pixel pos %d/%d (%0.2f by %0.2f tile step sizes).\n', ...
ii, length(rDataDirs), ...
ceil(d), ...
ceil(max(x)), ceil(max(y)), ...
d(1)/tileStep(1), d(2)/tileStep(2))
fprintf(' min pixel: %d / %d\n\n', ceil(min(x)), ceil(min(y)))
end
hold off
axis ij
end




function checkMinMax
% This is somewhat of a test function. If the min and max positions we have extracted are all
% correct, we should fit an integer number of tiles into the space they demarcate for each section.
fprintf('Do the min/max stage coords results in an integer number of tiles?\n')

for ii = 1:length(out.minYPos)

% If we just do the following we will be num tiles minus 1 because it does not
% take into account the area imaged by the final tile row and tile column.
dX = out.maxXPos(ii) - out.minXPos(ii);
dY = out.maxYPos(ii) - out.minYPos(ii);

% Therefore we add one tile step size (tile FOV minus the overlap)
dX = out.maxXPos(ii) - out.minXPos(ii) + tileStepSizeMM;
dY = out.maxYPos(ii) - out.minYPos(ii) + tileStepSizeMM;
fprintf('%d/%d. Tiles plus on step size: %0.1f x %0.1f\n', ...
ii, length(out.minYPos), ...
dX/tileStepSizeMM, dY/tileStepSizeMM)

end
end %checkMinMax


end % Main enclosing function

25 changes: 1 addition & 24 deletions code/stitching/gridPos2Pixels.m
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Expand Up @@ -26,7 +26,7 @@
% stepSize - step in microns between one tile and the next. If a scalar the step size is the same in both
% rows and columns. If a vector of length 2, it defines the step size along the rows (1) and
% cols (2). By default stepSize is obtained from the parameter file.
%
%
%
% OUTPUTS
% pixelPositions - n by 2 array. n tiles. [pixel row, pixel column]
Expand All @@ -40,29 +40,6 @@
tileCol = tileCoords(:,2);


if nargin<2 | isempty(pixelRes) %read in number of microns per pixel if needed

userConfig=readStitchItINI;
if userConfig.micsPerPixel.usemeasured
pixResR = userConfig.micsPerPixel.micsPerPixelMeasured;
pixResC = userConfig.micsPerPixel.micsPerPixelMeasured;
else
pixResR = userConfig.micsPerPixel.micsPerPixelRows;
pixResC = userConfig.micsPerPixel.micsPerPixelCols;
end

else

if length(pixelRes)==1
pixResR = pixelRes;
pixResC = pixelRes;
elseif length(pixelRes)>1
pixResR = pixelRes(1);
pixResC = pixelRes(2);
end

end


if nargin<3 | isempty(stepSize)
M=readMetaData2Stitchit;
Expand Down
6 changes: 0 additions & 6 deletions code/stitching/stitchAllChannels.m
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Expand Up @@ -48,12 +48,6 @@ function stitchAllChannels(chansToStitch,stitchedSize,illumChans,combCorChans)
return
end

%Bail out if we can't determin the acquisition system name
if determineStitchItSystemType<1
%error message generated by determineStitchItSystemType
return
end


% Check input arguments
if nargin<1
Expand Down

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