tileLoad returns stage positions if required.

code/preProcessTiles/preProcessTiles.m

@@ -279,7 +279,7 @@
         combFile=fullfile(sectionStatsDirName,'phaseStats_01.mat');
         if length(sectionsToProcess)==1 && sectionsToProcess==0 && exist(combFile,'file')
             fprintf('%s exists. Skipping this comb correction\n',combFile)
-        else    
+        else
             % load channel if needed
             notLoaded = arrayfun(@(x) isempty(imStack{x,1}), combCorChans);
             [imStack, tileIndex, loadError] = load_imstack(imStack, tileIndex, param, ...

code/stitching/tileLoad.m

@@ -1,4 +1,4 @@
-function [im,index]=tileLoad(coords,varargin)
+function [im,index,stagePos]=tileLoad(coords,varargin)
 % Load raw tile data as a stack for processing by StitchIt
 %
 % function [im,index]=tileLoad(coords,'Param1', Val1, 'Param2', Val2, ...)
@@ -50,7 +50,8 @@
 % 3. optical section
 % 4. tile row
 % 5. tile column
-%
+% 
+% stagePos - structure containing stage positions in mm
 %
 %
 % EXAMPLES
@@ -334,7 +335,18 @@
 end
 
 
-
+% get stage positions if requested
+if nargout>2
+    stagePos=[];
+    posFname = fullfile(sectionDir,'tilePositions.mat');
+    if exist(posFname)
+        load(posFname,'positionArray')
+        stagePos.targetPos.X = positionArray(:,3);
+        stagePos.targetPos.Y = positionArray(:,4);
+        stagePos.actualPos.X = positionArray(:,5);
+        stagePos.actualPos.Y = positionArray(:,6);
+    end
+end
 
 %Calculate average filename from tile coordinates. We could simply load the
 %image for one layer and one channel, or we could try odd stuff like averaging
@@ -354,3 +366,4 @@
     end
 
 %/COMMON
+

code/utils/readMetaData2Stitchit.m

@@ -86,9 +86,6 @@
 out = recipe2StitchIt(rawOut,fname);
 
 
-% Add stage position data
-
-
 %------------------------------------------------------------------------
 % Internal functions follow. This is just for tidiness.
 
@@ -124,18 +121,3 @@
     if out.mosaic.sliceThickness<1
         out.mosaic.sliceThickness = out.mosaic.sliceThickness*1E3;
     end
-
-
-function out = addStagePositions(recipeStruct,positionMatrix)
-    % Add stage position data associated with each tile to the recipe file
-    if ~isempty(raw.XPos)
-        out.stageLocations.requestedStep.X = raw.XPos(:,1); %What was the motion step requested by the microscope?
-        out.stageLocations.expected.X = cumsum(raw.XPos(:,1)); %Infer what the position shoudld be
-        out.stageLocations.reported.X = raw.XPos(:,2);
-    end
-
-    if ~isempty(raw.YPos)
-        out.stageLocations.requestedStep.Y = raw.YPos(:,1); %What was the motion step requested by the microscope?
-        out.stageLocations.expected.Y = cumsum(raw.YPos(:,1)); %Infer what the position shoudld be
-        out.stageLocations.reported.Y = raw.YPos(:,2);
-    end

code/visualisations/peekSection.m

@@ -151,7 +151,7 @@
 % if the images haven't been illumination-corrected for vignetting. 
 %tileIndex=flipud(tileIndex);
 
-
+% Stitch using theoretical pixel positions
 pixelPositions=ceil(gridPos2Pixels(tileIndex,[param.voxelSize.X,param.voxelSize.Y]));
 stitchedImage = stitcher(im,pixelPositions);