Squashed initial commit

2024-09-10 13:47:29 -04:00
commit 8ebb6ad265
6221 changed files with 2512206 additions and 0 deletions
--- a/qhtcp-workflow/apps/matlab/easy/NCsingleDisplay.m
+++ b/qhtcp-workflow/apps/matlab/easy/NCsingleDisplay.m
@@ -0,0 +1,89 @@
+%% CALLED WHEN ACCESSING 'CurveFit Display' %%
+global scLst
+global scan
+
+hf=figure;
+% Parameter Entry
+[scLst, row, col]=NCdisplayGui(projectScansDir);
+close(hf)
+selSpot=(row-1)*24 + col;
+for iPlate=1:length(scLst)
+  scanPltNum=str2double(scLst(iPlate));
+  K=scan(scanPltNum).plate(1).CFout((selSpot),3);
+  r=scan(scanPltNum).plate(1).CFout((selSpot),4);
+  l=scan(scanPltNum).plate(1).CFout((selSpot),5);
+  suffix=strcat('Scan-Plate', scLst(iPlate)); % char(QspLst(n));
+  % fileSpotSuffix=strcat('-Spot#',num2str(selSpot),'-Row=',selSpotRC(1),'-Col=',selSpotRC(2),'-FitData','-L=',num2str(l),'-r=',num2str(r),'-K=',num2str(K));    
+  fileSpotSuffix=strcat('-Spot#',num2str(selSpot),'-Row=',num2str(row),'-Col=',num2str(col),'-FitData','-L=',num2str(l),'-r=',num2str(r),'-K=',num2str(K));    
+  filenameNoExt=[suffix fileSpotSuffix];
+  timeArr=scan(scanPltNum).plate(1).tSeries;
+  rawIntens=scan(scanPltNum).plate(1).intens((selSpot),:)/scan(scanPltNum).plate(1).Ag((selSpot));
+  try
+    filterTms=scan(scanPltNum).plate(1).filterTimes{(selSpot)};
+    normInts=scan(scanPltNum).plate(1).normIntens{(selSpot)};
+  catch
+  end
+  if (exist('K','var')&& exist('r','var') && exist('l','var'))
+    t=(0:1:200);   
+    Growth=K ./ (1 +  exp(-r.* (t - l )));
+  end 
+  if length(scLst)>1 
+    figure
+  else
+    cla
+  end
+  hold on
+  plot(timeArr,rawIntens,'g*');
+  try
+    plot(filterTms,normInts,'o');
+  catch
+  end
+  hold on;
+  title(filenameNoExt); % this didn't make sense so changed
+  xlabel('Hours');
+  ylabel('Intensities Normalized by Area');
+  grid on;
+  if (exist('K','var')&& exist('r','var') && exist('l','var'))
+    plot(t, Growth,'b-');
+    % Plot L on curvefit figure
+    grL=Growth(round(l)); % growthCurve timePT for l in hours 
+    plot(l,0:grL,'-b') % to display position of l 
+    plot(l,grL,'^b') % to display l position on curve as an arrowhead
+
+    % Plot Arbitrary User Entry AUC "finalTimePt"  
+    % plot(finalTimePt,0,'+m')
+    % plot(0:finalTimePt,bl,'-m')
+  end  
+end
+
+%Spot entry form------------------------------------------------------
+%{
+prompt={'Enter spot to analyse:'};
+dlg_title='Input spot to curve fit';
+num_lines=1;
+def={'1'};
+selSpot=inputdlg(prompt,dlg_title,num_lines,def);
+K=scan(scanPltNum).plate(1).CFout(str2double(selSpot),3);
+r=scan(scanPltNum).plate(1).CFout(str2double(selSpot),4);
+l=scan(scanPltNum).plate(1).CFout(str2double(selSpot),5);
+
+suffix=strcat('Scan-Plate', scLst);    %char(QspLst(n));
+fileSpotSuffix=strcat('-Spot#',selSpot,'-FitData','-L=',num2str(l),'-r=',num2str(r),'-K=',num2str(K));    
+filenameNoExt=[suffix fileSpotSuffix];
+
+timeArr=scan(scanPltNum).plate(1).tSeries;
+rawIntens=scan(scanPltNum).plate(1).intens(str2double(selSpot),:)/scan(scanPltNum).plate(1).Ag(str2double(selSpot));
+filterTms=scan(scanPltNum).plate(1).filterTimes{str2double(selSpot)};
+normInts=scan(scanPltNum).plate(1).normIntens{str2double(selSpot)};
+
+%}
+%-----------------------------------------------------------------------
+%{
+prompt={'Enter Spot row:','Enter Spot column:'};
+dlg_title='Input spot to curve fit';
+num_lines=2;
+def={'1','1'};
+selSpotRC=inputdlg(prompt,dlg_title,num_lines,def);
+row=str2double(selSpotRC(1));  col=str2double(selSpotRC(2));
+%}
+%row=cell2mat(row);