Rollup interactions.R

workflow/apps/matlab/easy/DgenResults.m

@@ -1,7 +1,5 @@
-%% CALLED BY EASYconsole.m %%
-% Updated 240724 Bryan C Roessler to improve file operations and portability
-%
 global projectScansDir
+global projectName
 global matFile
 global defImParMat
 global printResultsDir
@@ -27,7 +25,7 @@ end
 % MPnum=ImParMat(1);
 % opt=questdlg('Print Results Only (RES), DB Only (DB), or Both','Results Printout Options','Res','DB','Both','Both');
 opt='Res';
-if ~exist('defImParMat','var') || isempty(defImParMat) % TODO needs better explanation
+if ~exist('defImParMat','var') || isempty(defImParMat) % TODO needs explanation
   load(pointMapsFile);
 end
 destPerMP=ImParMat(2); % TODO this is weird, needs explanation
@@ -37,7 +35,7 @@ numOfDrgs=length(DM.drug);
 numOfMeds=length(DM.media);
 destPerMP=numOfDrgs;
 
-% TODO this should be rewritten or is uncessary, what is this for
+% TODO this should be rewritten or is unnecessary, what is this for
 % Determine the longest set of intensity(tPts) for the Experiment Data Set
 maxNumIntens=0;
 for n=1:size(scan,2)
@@ -53,22 +51,12 @@ end
 % end
 
 % TODO this seems weird
-expNm=projectScansDir(max(strfind(projectScansDir,'/'))+1:end);
 drivePos=min(strfind(projectScansDir,'/'));
 drive=projectScansDir(1:(drivePos-1));
-DBupload=fullfile(drive,'EZdbFiles','DBupLOADfiles');
+% DBupload=fullfile(drive,'EZdbFiles','DBupLOADfiles');
 
-% Added to allow backward compatability
+resultsFilename=fullfile(printResultsDir, 'results_elr.txt');
-% Test for CFoutStd as indication of 2018version with r_refined fit code;If
+DBfilename=fullfile(printResultsDir, 'DbaseELr.txt');
-% earlier version with only a standard composite fite, Print results to !!ResultsStd_...txt only
-try
-  scan(1).plate(1).CFoutStd(1,1);
-  resultsFilename=fullfile(printResultsDir, strcat('!!ResultsELr_',expNm,'.txt'));
-  DBfilename=fullfile(printResultsDir, strcat('!!DbaseELr_',expNm,'.txt'));
-catch
-  resultsFilename=fullfile(printResultsDir, strcat('!!ResultsStd_',expNm,'.txt'));
-  DBfilename=fullfile(printResultsDir, strcat('!!DbaseStd_',expNm,'.txt'));
-end
 
 if isequal(opt,'Res')||isequal(opt,'Both'),fid=fopen(resultsFilename,'w');end
 if isequal(opt,'DB')||isequal(opt,'Both'),fid2=fopen(DBfilename,'w');end
@@ -271,7 +259,7 @@ for s=1:size(scan,2)
           end 
 
           if isequal(opt,'DB')||isequal(opt,'Both')
-            fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',expNm,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
+            fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',projectName,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
             fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
                 outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
                 outCmat(n,5),dbRsq,dbKup,dbKlo,dbrup,dbrlo,dbLlo,dbLup);   %\t%.5f\t%.5f\t%.5f\t%.5f
@@ -361,24 +349,24 @@ if isequal(opt,'Res')||isequal(opt,'Both')
   fclose(fid); 
 end
 
-if isequal(opt,'DB')||isequal(opt,'Both')
+% if isequal(opt,'DB')||isequal(opt,'Both')
-  fclose(fid2);
+%   fclose(fid2);
-  try
+%   try
-    copyfile(DBfilename,DBupload)
+%     copyfile(DBfilename,DBupload)
-  catch ME
+%   catch ME
-    fprintf('DB upload failed with error: %s\n', getReport(ME, 'basic'));
+%     fprintf('DB upload failed with error: %s\n', getReport(ME, 'basic'));
-    rep=sprintf('Failed copyfile to %s - %s', DBupload, rep);
+%     rep=sprintf('Failed copyfile to %s - %s', DBupload, rep);
-    errordlg(rep);
+%     errordlg(rep);
-  end
+%   end
-end
+% end
 
 % Print results using the standard method
 try
   scan(1).plate(1).CFoutStd(1,1) %Test for 2018 r_refined version 
 
   ln=1;
-  resultsFilename=fullfile(printResultsDir, strcat('!!ResultsStd_',expNm,'.txt'));
+  resultsFilename=fullfile(printResultsDir, 'results_std.txt');
-  DBfilename=fullfile(printResultsDir, strcat('!!DbaseStd_',expNm,'.txt'));
+  DBfilename=fullfile(printResultsDir, 'DbaseStd.txt');
   if isequal(opt,'Res')||isequal(opt,'Both'),fid=fopen(resultsFilename,'w');end
   if isequal(opt,'DB')||isequal(opt,'Both'),fid2=fopen(DBfilename,'w');end  %121012 Combo
   if isequal(opt,'Res')||isequal(opt,'Both') %print Results
@@ -553,7 +541,7 @@ try
             end
 
             if isequal(opt,'DB')||isequal(opt,'Both')
-              fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',expNm,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
+              fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',projectName,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
               fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
                 outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
                 outCmat(n,5),dbRsq,dbKup,dbKlo,...
@@ -649,20 +637,20 @@ try
     fclose(fid); 
   end
 
-  if isequal(opt,'DB')||isequal(opt,'Both')
+  % if isequal(opt,'DB')||isequal(opt,'Both')
-    fclose(fid2);
+  %   fclose(fid2);
-    try
+  %   try
-      copyfile(DBfilename,DBupload)
+  %     copyfile(DBfilename,DBupload)
-    catch ME
+  %   catch ME
-      fsprintf('DB upload failed with error: %s\n', getReport(ME, 'basic'));
+  %     fsprintf('DB upload failed with error: %s\n', getReport(ME, 'basic'));
-      rep=sprintf('Failed copyfile to %s - %s\n', DBupload, rep);
+  %     rep=sprintf('Failed copyfile to %s - %s\n', DBupload, rep);
-      errordlg(rep)
+  %     errordlg(rep)
-    end
+  %   end
-  end
+  % end
 
-  msgbox([sprintf('Printing Script complete. Check !!Results sheets in %s for results.', printResultsDir)])
+  msgbox([sprintf('Printing script complete. Check results sheets in %s for results.', printResultsDir)])
 
 catch ME
-  fprintf('Printing Script failed with error: %s\n', getReport(ME, 'basic'));
+  fprintf('Printing script failed with error: %s\n', getReport(ME, 'basic'));
 end
 

workflow/apps/matlab/easy/EASYconsole.m

@@ -141,8 +141,7 @@ function varargout = EASYconsole(varargin)
   if ~isempty(getenv('MASTER_PLATE_FILE'))
     masterPlateFile=fullfile(getenv('MASTER_PLATE_FILE'));
     fprintf('Using drug media file: %s from environment variable MASTER_PLATE_FILE\n', masterPlateFile);
-  else
+  else % try to find MasterPlate_ file on our own
-    % Try to find MasterPlate_ file on our own
     mp=fullfile(easyResultsDir, strcat('MasterPlate_', projectName,'.xlsx'));
     if exist(mp, 'file')
       masterPlateFile=mp;
@@ -281,7 +280,7 @@ function NewExpDat_Callback(~, ~, ~)
 
   % Create a new experiment
   try
-    questdlg('\fontsize{20} NAME the file and NAVIGATE to the directory with the image folders.','File Creation','OK', struct('Default','OK','Interpreter','tex'));
+    questdlg('Name the file and navigate to the directory with the image folders.','File Creation','OK', struct('Default','OK','Interpreter','tex'));
     [matfile,easyResultsDir]=uiputfile('.mat');
     inputFileName=strrep(inputFile,'.mat','');
     

workflow/apps/matlab/easy/NIscanIntensBGpar4GblFnc.m

@@ -791,7 +791,7 @@ function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2,
           else
             refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));             
           end
-          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx))); % return from lunch fix start here!!!!!
+          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));
           if rem(r,numRows)==0
             refBG(3)=refP(1)+widthEx+ floor(0.5*(plateBotSpace));          
           else

workflow/apps/matlab/easy/par4Gbl_Main8c.m

@@ -1,5 +1,3 @@
-%% CALLED BY EASYconsole.m %%
-
 global SWgrowthArea
 global scLst
 global ImParMat
@@ -62,9 +60,9 @@ end
 % after each run to allow previous version of EASY to access data made
 % by EASY versions after 20_0819.
 try
-  load(fullfile(fotosResultsDir,'Nbdg')); %Modified to load from 'Fotos' 20_0819
+  load(fullfile(fotosResultsDir,'Nbdg')); % modified to load from 'Fotos' 20_0819
 catch
-  load(fullfile(pointMapsResultsDir,'Nbdg')); %Left in to accomodate loads of work before 20_0819
+  load(fullfile(pointMapsResultsDir,'Nbdg')); % left in to accomodate loads of work before 20_0819
 end
 % Load Fotos stored data
 fotosToLoad={'Coordinates', 'BGatTpts', 'anlZones', 'NCFparms'};
@@ -211,11 +209,11 @@ end
 
 % Save data in .mat files
 save(matFile,'scan');
-% save((fullfile(easyResultsDir,'PTmats','Nbdg')), 'sbdg'); %legacy location can probably get rid of in time
+% save((fullfile(easyResultsDir,'PTmats','Nbdg')), 'sbdg'); % legacy location can probably get rid of in time
 save((fullfile(fotosResultsDir,'Nbdg')), 'sbdg');
-save((fullfile(fotosResultsDir,'Coordinates')),'FexpScanSpots') %Saves frames at each tPt
+save((fullfile(fotosResultsDir,'Coordinates')),'FexpScanSpots') % saves frames at each tPt
 save((fullfile(fotosResultsDir,'BGatTpts')),'FexpScanBMtp')
-save((fullfile(fotosResultsDir,'anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt
+save((fullfile(fotosResultsDir,'anlZones')),'anlZoneRefs') % saves anl Positions at each tPt
 
 % Print FitResults
 fileExt='.txt';

workflow/templates/scans-demo/20240719_RyanMan2_PDR1CYC8_P6_TC/1/InitialPoints.txt

@@ -1 +0,0 @@
-384,76,75,70,145

workflow/templates/scans-demo/20240719_RyanMan2_PDR1CYC8_P6_TC/1/Points.txt

@@ -1,384 +0,0 @@
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-2,70,220,0,0,0,0,0,0,0,0,0,0,0,0
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workflow/templates/scans-demo/20240719_RyanMan2_PDR1CYC8_P6_TC/2/StartTime.txt

@@ -1 +0,0 @@
-7/19/2024 2:47:54 PM