MAJOR: drop TissueCyte support and re-factor.

README.md

@@ -2,8 +2,7 @@
 
 # StitchIt
 
-*StitchIt* is a MATLAB package that was originally built for stitching data from the TissueVision 2-photon tomography system.
-However, *StitchIt* is sufficiently modular that it can handle other tiled data sets too (e.g. from a slide scanner or tiled images obtained from *in vivo* experiments using [ScanImage](http://scanimage.vidriotechnologies.com/)).
+*StitchIt* is a MATLAB package for stitching data acquired via our [ScanImage](http://scanimage.vidriotechnologies.com/))-based acquisition system (BakingTray).
 To get started, please read the [Wiki](https://github.com/BaselLaserMouse/StitchIt/wiki). 
 There is a [changelog](https://raw.githubusercontent.com/BaselLaserMouse/StitchIt/master/changelog.txt).
 

changelog.txt

@@ -1,5 +1,8 @@
 StitchIt Change Log
 
+12/03/2020
+- DEVELOPER MAJOR: Dev branch. Drop TissueCyte support. StitchIt handles only BakingTray data now. There is a release associated with this commit. Refactor BakingTray stitching files and remove possibility of adding other stitching system systems. The flexibility isn't being used and it's worth the confusion. 
+
 20/03/2020
 - USER: Downsampled stacks now contain the channel name (as a string -- "red" or "green") in the file name.
 - USER: stitchedPlanesToVolume produces stacks that contain the channel name the file name.

code/SystemClasses/determineStitchItSystemType.m → code/INI/determineStitchItSystemType.m

@@ -10,20 +10,17 @@
 % 
 % Outputs
 % systemType - a string defining the name of the acquisition system used.
-%              Currently returns one of 'TissueCyte' or 'BakingTray'
+%              Currently only 'BakingTray' or nothing, to indicate that no file was found. 
 %
 %
 %
 %
 
 
 %Assign particular file names found in the experiment path to sub-directories in the SystemSpecifc directory
-if ~isempty(dir('Mosaic_*.txt'))
-    systemType='TissueCyte';
-elseif ~isempty(dir('Recipe*.yml')) || ~isempty(dir('recipe*.yml'))
+if ~isempty(dir('Recipe*.yml')) || ~isempty(dir('recipe*.yml'))
     systemType='BakingTray';
 else
     fprintf('Can not find acquisition system log file in %s\n',pwd)
     systemType=-1;
 end
-

code/INI/readStitchItINI.m

@@ -59,14 +59,6 @@
 
     if isnumeric(systemType) && systemType==-1 ;
         INIfname=defaultINIfname; %Try reading the default INI file
-    elseif strcmpi(systemType,'TissueCyte')
-        disp('TissueCyte')
-        % This is really crap, but I need to read TissueCyte stuff in separately 
-        % because we will get a recursive function call otherwise. TODO: fix this shit
-        % In the unlikely event we have data generated by Orchestrator
-        T=tissuecyte;
-        M=T.readMosaicMetaData(T.getTiledAcquisitionParamFile);
-        systemID = M.System.ID;
     elseif strcmpi(systemType,'BakingTray');
         % This is to populate the System.ID field from which we can get the system ID.
         % The following line will only work if we are in a sample directory