Move unused python/math scripts to DEPRECATE folders

PreProcess/PullOutProcessRecruitData.m

@@ -3,7 +3,7 @@
 % grp 4 as a single row.
 %
 % Processing continues on this array.
-% - Dredge Data, if chosend,  requires further processing to adjust for scallops detected vs actual
+% - Dredge Data, if chosen,  requires further processing to adjust for scallops detected vs actual
 %   and depth adjustments. HabCam needs no further adjustment.
 %
 % Dredge and HabCam data are combined into a single array and then sorted by year

PythonScripts/GUI/GeoSAM/InverseDistanceWeigthing.py → PythonScripts/DEPRECATE/InverseDistanceWeigthing.py

@@ -68,16 +68,19 @@ def Interpolate(self):
         #---------------------------------------------------
         # Read in grid data
         #---------------------------------------------------
-        numGrid = self.GetNumberOfRecords(self.gridFname, hasHeader=False)
+        numGrid = self.GetNumberOfRecords(self.gridFname, hasHeader=True)
+        print('GRID LEN: ', numGrid)
 
         gridX = np.zeros(numGrid)
         gridY = np.zeros(numGrid)
         gridLat = np.zeros(numGrid)
         gridLon = np.zeros(numGrid)
 
         with open(self.gridFname, 'r') as f:
+            inputStr = f.readline() # read and ignore header
             for n in range(numGrid):
                 inputStr = f.readline()
+                #print(n, inputStr)
                 inputArr = [s.strip() for s in inputStr.split(',')]
                 gridX[n] = float(inputArr[0])
                 gridY[n] = float(inputArr[1])

PythonScripts/GUI/GeoSAM/GeoSams.py

@@ -319,12 +319,12 @@ def Run_Sim(self):
 
             if result.returncode == 0:
                 if not self.skipStatusMsgs.get(): messagebox.showinfo("GeoSAM Sim", 
-                    f'Completed Successfully\n{result.args}\nStarting UK Interp\nIf all output selected this will run over an hour.\nPlease be patient.')
+                    f'Completed Successfully\n{result.args}\nStarting Interp&Plot\nIf all output selected this will run over an hour.\nPlease be patient.')
 
                 # Then Continue with Interpolation and Plotting Results -----------------------------------------------------------
                 (retDict, procID) = self.InterpAndPlotResults()
                 if sum(retDict.values()) == 0:
-                    messagebox.showinfo("GeoSAMS/UK/Plotting", f'ALL DONE\nRan {procID} processes')
+                    messagebox.showinfo("GeoSAMS/Interp/Plotting", f'ALL DONE\nRan {procID} processes')
                 else:
                     messagebox.showerror("InterpAndPlotResults", 'Failed')
             else:
@@ -472,6 +472,8 @@ def InterpAndPlotResults(self):
         # Intepolate using OK
         # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
         # all survey data residuals computed now to interpolate. 
+        # At this point all parallel processing is complete, restart procID counter
+        procID = 0
         for pStr in self.paramStr:
             for r in region:
                 for year in years:
@@ -486,6 +488,17 @@ def InterpAndPlotResults(self):
                         cmd = ['python3', ex, inputFile ]
                     with open(stdOutFile, 'w') as fid:
                         result = subprocess.run(cmd, stdout=fid)
+
+                    retDict[procID] = result.returncode
+
+                    # could wait until all scripts have run. If failure most likely with python itself
+                    # so fail at first occurance.
+                    if sum(retDict.values()) != 0:
+                        messagebox.showerror("GeoSAM OK", f'Failed\n{result.args}\nReturn Code = {result.returncode}')
+                        return (retDict, procID)
+            procID += 1
+
+
         # 
         # Process CSV files to combine the years
         pfix = 'Results/Lat_Lon_Grid_'
@@ -506,7 +519,7 @@ def InterpAndPlotResults(self):
 
                 if r == region[0]: 
                     dfFinal.to_csv(flout, index=False)
-                else:
+                else: # append MA to GB
                     dfFinal.to_csv(flout, mode='a', index=False,header=False)
 
         # Lat_Lon_Grid_BIOM_AL2022_2026.csv

mfiles/CheckInRegionPolygon.m

@@ -1,4 +1,6 @@
 function [zone, region]= CheckInRegionPolygon(isOctave, X_t, Y_t, shape)
+% Called from HabCamData5mmbin and TrawlData5mmbin
+%
 % Takes X,Y UTM coordinates and determins which, if any
 % Zone region geopoint is located.
 % Returns Zone name and alphabetical index

mfiles/ZvsRCurve.m → mfiles/DEPRECATE/ZvsRCurve.m

@@ -5,15 +5,15 @@
 [z,j]=sort(z);r=r(j);
 plot(z,r,'k.');
 n=0;
-for z0=0:250,
+for z0=0:250
   n=n+1;
   k=find(and(z<z0+5,z>z0-5));
   if ~isempty(k)
     r0(n)=max(r(k));
   else
     r0(n)=NaN;
-  endif
-endfor
+  end
+end
  z0=0:250;
  close all
 clf; plot(z,r,'k.',z0,r0,'r');
@@ -24,7 +24,7 @@
 b=15;
 fr=a+b*exp(-((z-zc)/w).^2);
 j=find(r>fr);
-length(j)/length(z)
+length(j)/length(z);
 clf; plot(z,r,'k.',z,fr,'r',z0,r0,'b',z(j),r(j),'rx');title(num2str(length(j)/length(z)))
 
 figure
@@ -35,15 +35,15 @@
 [z,j]=sort(z);r=r(j);
 plot(z,r,'k.');
 n=0;
-for z0=0:250,
+for z0=0:250
   n=n+1;
   k=find(and(z<z0+5,z>z0-5));
   if ~isempty(k)
     r0(n)=max(r(k));
   else
     r0(n)=NaN;
-  endif
-endfor
+  end
+end
  z0=0:250;
 
 clf; plot(z,r,'k.',z0,r0,'r');
@@ -58,7 +58,7 @@
 fr(j)=a+b*exp(-((z(j)-zc)/w2).^2);
 
 j=find(r>fr);
-length(j)/length(z)
+length(j)/length(z);
 clf; plot(z,r,'k.',z,fr,'r',z0,r0,'b',z(j),r(j),'rx');title(num2str(length(j)/length(z)))
 
 
@@ -72,15 +72,15 @@
 [z,j]=sort(z);r=r(j);
 plot(z,r,'k.');
 n=0;
-for z0=0:250,
+for z0=0:250
   n=n+1;
   k=find(and(z<z0+5,z>z0-5));
   if ~isempty(k)
     r0(n)=max(r(k));
   else
     r0(n)=NaN;
-  endif
-endfor
+  end
+end
  z0=0:250;
 figure;
 clf; plot(z,r,'k.',z0,r0,'r');
@@ -95,7 +95,7 @@
 fr(j)=a+b*exp(-((z(j)-zc)/w2).^2);
 
 j=find(r>fr);
-length(j)/length(z)
+length(j)/length(z);
 clf; plot(z,r,'k.',z,fr,'r',z0,r0,'b',z(j),r(j),'rx');title(num2str(length(j)/length(z)))
 
 

mfiles/GetRegion.m

@@ -1,5 +1,7 @@
 function x = GetRegion(isOctave, lat_t, lon_t, stratum_t)
-
+% Called from HabCamData5mmbin and TrawlData5mmbin
+%
+% Determines which region, as defined by stratum, the point lat_t, lon_t is in
 
 region_none=0;
 regionGB_N=1;

mfiles/GetShapeData.m

@@ -1,4 +1,6 @@
 function x = GetShapeData()
+% Called from HabCamData5mmbin and TrawlData5mmbin
+%
 % reads in shape files named by environment variables
 % Concatenates MAB and GB structures into a single structure
 % getZone is true if the region data is desired

mfiles/GetUnits.m

@@ -3,6 +3,8 @@
 %              or   'Lat_Lon_Survey_ABUN...'
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 function units = GetUnits(fileName)
+% Called from PlotLatLonGridSurvey
+%
     units ='';
     k=strfind(fileName,'ABUN');
     if k>0, units = 'scallops/m^2';end

mfiles/PlotXYDepth.m

@@ -1,25 +1,21 @@
-% Reads in data From DNxyzLatLon and converts it to a table
+% Reads in data From DNRegionGrid and converts it to a table
 % Then plots depth using color grid
 
 function PlotXYDepth(fname)
 D=readtable(fname,"FileType","spreadsheet");
 
-X=table2array(D(:,2));
-Y=table2array(D(:,3));
-[lat, lon] = utm2ll(X,Y,19);
-depth=array2table(table2array(D(:,5)),'VariableNames',{'Depth'});
-lon = array2table(lon,'VariableNames',{'Longitude'});
-lat = array2table(lat,'VariableNames',{'Latitude'});
-tbl = [lat, lon, depth];
+depth_t=array2table(table2array(D(:,3)),'VariableNames',{'Depth'});
+lat_t = array2table(table2array(D(:,4)),'VariableNames',{'Longitude'});
+lon_t = array2table(table2array(D(:,5)),'VariableNames',{'Latitude'});
+tbl = [lat_t, lon_t, depth_t];
 
-%figure('Name',fname)
-s=geoscatter(tbl,"Latitude", "Longitude", "filled");
+figure('Name',fname)
+s=geoscatter(tbl,"Longitude", "Latitude", "filled");
 hold on
 geobasemap darkwater;
-
 s.SizeData = 5; % size of dots
 s.ColorVariable = "Depth";
 c=hot(100);
 colormap(c);
 c = colorbar;
-c.Label.String = "Depth";
+c.Label.String = "Depth";