Removing Use HabCam

.octaverc

@@ -1,3 +1,4 @@
+warning('off', 'Octave:shadowed-function');
 addpath mfiles/
 addpath mfiles/latlonutm/
 addpath PreProcess/

Configuration/Simulation/Scallop.cfg

@@ -1,6 +1,5 @@
 # input file for Scallops 
 Time steps per Year = 13
-Use HabCam Data = T
 # Configuration files are expected to be in the Configuration directory
 Mortality Config File = Growth.cfg
 Recruit Config File = Recruitment.cfg

PreProcess/AddXY.m

@@ -0,0 +1,23 @@
+function AddXY()
+
+M=dlmread('OriginalData/dredgetowbysize7917.csv');
+lat=M(:,18);
+lon=-M(:,19);
+% preallocate
+xx=lon;
+yy=lat;
+n = size(lon,1);
+for i = 1:n
+    if lon(i)>-70.5
+        zone=19;
+    else
+        zone=18;
+    end
+    if mod(i,10000) == 0; fprintf('i : %d of %d\n', i, n); end
+    [xx(i),yy(i)]=ll2utm(lat(i),lon(i),zone);
+end
+
+M = [M, xx, yy];
+dlmwrite('OriginalData/dredgetowbysizeXY.csv', M);
+end
+

PreProcess/HabCamData5mmbin.m

@@ -1,4 +1,4 @@
-function HabCamData5mmbin(yrStart, yrEnd, domain)
+function HabCamData5mmbin(yrStart, yrEnd, domain, appendResults)
 
 dataFile = 'OriginalData/Habcam_BySegment_2000_2014-2020.csv';
 
@@ -29,6 +29,7 @@ function HabCamData5mmbin(yrStart, yrEnd, domain)
         yrStart = str2num(cell2mat(arg_list(1)));
         yrEnd = str2num(cell2mat(arg_list(2)));
         domain = cell2mat(arg_list(3));
+        appendResults = cell2mat(arg_list(4));
     else
         yrStart = str2num(yrStart);
         yrEnd = str2num(yrEnd);
@@ -147,12 +148,20 @@ function HabCamData5mmbin(yrStart, yrEnd, domain)
                 end
             end
         end
-        flnm=strcat('Data/HCbin5mm',int2str(yr),domain,'.csv');
+        flnm=strcat('Data/bin5mm',int2str(yr),domain,'.csv');
         fprintf('Size of grid %d\n', size(X,1))
         if isOctave
-            csvwrite(flnm,X);
+            if strcmp(appendResults(1), 'T')
+                dlmwrite(flnm, X, "-append")
+            else
+                dlmwrite(flnm,X);
+            endif
         else
-            writetable(X,flnm,'WriteVariableNames',0);
+            if strcmp(appendResults(1), 'T')
+                writematrix(X,flnm,'WriteMode','append')
+            else
+                writematrix(X,flnm);
+            endif
         end
     end % if sum(j) == 0
 end  % for yr=yrStart:yrEnd

PreProcess/PullOutRecruitData.m

@@ -8,7 +8,7 @@
 % VIMSRSA ==> 4444
 % NMFSSHRP ==> 5555
 % ALL ==> 0
-function PullOutRecruitData(src, useHabCam)
+function PullOutRecruitData(src, useHabCam, appendResults)
 
 isOctave = (exist('OCTAVE_VERSION', 'builtin') ~= 0);
 
@@ -17,7 +17,8 @@ function PullOutRecruitData(src, useHabCam)
     arg_list=argv();
     if ~strcmp(arg_list(1), '--gui');
         src = str2num(cell2mat(arg_list(1)));
-        useHabCam = cell2mat(arg_list(2))
+        useHabCam = cell2mat(arg_list(2));
+        appendResults = cell2mat(arg_list(3));
     else
         src = str2num(src);
     end
@@ -49,12 +50,14 @@ function PullOutRecruitData(src, useHabCam)
                "statype","SVGEAR","haul","gearcon","sdefid","newstra","clop","lat","lon","tnms",...
                "setdpth","bottemp","dopdisb","distused","towadj","towdur","sizegrp","catchnu",...
                "catchwt","surv_n","partrecn","fullrecn","surv_b","partrecb","fullrecb","postow",...
-               "datasource","lwarea","SETLW","SVSPP","PropChains","AREAKIND","STRATMAP","SQNM"};
+               "datasource","lwarea","SETLW","SVSPP","PropChains","AREAKIND","STRATMAP","SQNM", "UTM X", "UTM Y"};
     yearCol    = find(strcmpi("year", header), 1);
     monCol     = find(strcmpi("month", header), 1);
     dayCol     = find(strcmpi("day",   header), 1);
     latCol     = find(strcmpi("lat"    , header), 1);
     lonCol     = find(strcmpi("lon"    , header), 1);
+    utmxCol    = find(strcmpi("UTM X"   , header), 1);
+    utmyCol    = find(strcmpi("UTM Y"   , header), 1);
     zCol       = find(strcmpi("setdpth", header), 1);
     sgCol      = find(strcmpi("sizegrp", header), 1);
     svCol      = find(strcmpi("surv_n" , header), 1);
@@ -125,34 +128,21 @@ function PullOutRecruitData(src, useHabCam)
 else
     j=size_grp==4 & dataSrc==srcText;
 end
-if useHC
-    utmX = F(j, utmxCol);
-    utmY = F(j, utmyCol);
-else
-    % Correct sign of longitude
-    F(j,lonCol) = -F(j,lonCol);
-    lon = F(j,lonCol);
-    lat = F(j,latCol);
-
-    utmX = zeros(size(lon,1),1);
-    utmY = zeros(size(lon,1),1);
-
-    for i = 1:size(lon,1)
-        if lon(i)>-70.5
-            zone=19;
-        else
-            zone=18;
-        end
-        [utmX(i),utmY(i)]=ll2utm(lat(i),lon(i),zone);
-    end
-end
 
-M = [F(j,yearCol) F(j,monCol) F(j,dayCol) F(j,latCol) F(j,lonCol) utmX utmY F(j,zCol) recr_t];
+M = [F(j,yearCol) F(j,monCol) F(j,dayCol) F(j,latCol) F(j,lonCol) F(j, utmxCol) F(j, utmyCol) F(j,zCol) recr_t];
 
 flnm = 'OriginalData/NewRecruits.csv';
 
 if isOctave
-  csvwrite(flnm, M);
+    if strcmp(appendResults(1), 'T') && useHC
+        dlmwrite(flnm, M, "-append")
+    else
+        dlmwrite(flnm,M);
+    endif
 else
-  writetable(M,flnm);
+    if strcmp(appendResults(1), 'T') && useHC
+        writematrix(M,flnm,'WriteMode','append')
+    else
+        writematrix(M,flnm);
+    endif
 end

PreProcess/TrawlData5mmbin.m

@@ -34,15 +34,14 @@ function TrawlData5mmbin(yrStart, yrEnd, src, domain)
 end
 
 if isOctave
-
     M=csvreadK('OriginalData/dredgetowbysize7917.csv');
     mon=M(:,5);
     j=find(mon>0);
     M=M(j,:);
-    %------- new M table ----------------------
 
+    %------- new M table ----------------------
     if ~strcmp(domain, 'AL')
-        lon=-M(:,19);
+        lon=M(:,19);
         if strcmp(domain, 'GB')
             j = lon>-70.5;%GB
             zone=19;
@@ -53,41 +52,20 @@ function TrawlData5mmbin(yrStart, yrEnd, src, domain)
 
         %------- new M with just MA or GB ----------------------
         M = M(j,:);
-        lat=table2array(M(:,18));
-        lon=-table2array(M(:,19));
-        [xx,yy]=ll2utm(lat,lon,zone);
-
-    else % working with AL
-        lat=M(:,18);
-        lon=-M(:,19);
-        % preallocate
-        xx=lon;
-        yy=lat;
-        n = size(lon,1);
-        for i = 1:n
-            if lon(i)>-70.5
-                zone=19;
-            else
-                zone=18;
-            end
-            if mod(i,10000) == 0; fprintf('i : %d of %d\n', i, n); end
-            [xx(i),yy(i)]=ll2utm(lat(i),lon(i),zone);
-        end
     end
 
     year = M(:,4);
     sg = M(:,27);
     dataSrc = M(:,37);
 else % NOT Octave
     M = readtable('OriginalData/dredgetowbysize7917.csv',"FileType","text");
-
     mon=table2array(M(:,5));
     j=mon>0;
     M=M(j,:);
-    %------- new M table ----------------------
 
+    %------- new M table ----------------------
     if ~strcmp(domain, 'AL')
-        lon = -table2array(M(:,19));
+        lon = table2array(M(:,19));
         if strcmp(domain, 'GB')
             j = lon>-70.5;
             zone=19;
@@ -98,24 +76,6 @@ function TrawlData5mmbin(yrStart, yrEnd, src, domain)
 
         %------- new M with just MA or GB ----------------------
         M = M(j,:);
-        lat=table2array(M(:,18));
-        lon=-table2array(M(:,19));
-        [xx,yy]=ll2utm(lat,lon,zone);
-
-    else % working with AL
-        lat=table2array(M(:,18));
-        lon=-table2array(M(:,19));
-        % preallocate
-        xx=lon;
-        yy=lat;
-        for i = 1:size(lon,1)
-            if lon(i)>-70.5
-                zone=19;
-            else
-                zone=18;
-            end
-            [xx(i),yy(i)]=ll2utm(lat(i),lon(i),zone);
-        end
     end
 
     year = table2array(M(:,4));
@@ -130,7 +90,6 @@ function TrawlData5mmbin(yrStart, yrEnd, src, domain)
 countPerSqm = detect / towArea_sqm;
 
 for yr=yrStart:yrEnd
-    yr
     X=[];
     %j=and(year==yr,sg==3.);
     if srcText == 0
@@ -153,7 +112,7 @@ function TrawlData5mmbin(yrStart, yrEnd, src, domain)
             stratum_t = M(j,8);
             is_closed_t = double(M(j,17)>0);
             lat_t = M(j,18);
-            lon_t = -(M(j,19));
+            lon_t = M(j,19);
             mon = M(j,5);
             day = M(j,6);
             yd = 0 * day;
@@ -162,23 +121,23 @@ function TrawlData5mmbin(yrStart, yrEnd, src, domain)
             end
             DecYr_t = year(j) + yd/365.25;
             z_t = cast(M(j,21),"double");
-            x_t = xx(j);
-            y_t = yy(j);
+            x_t = M(j,45);
+            y_t = M(j,46);
         else
             stratum_t = M(j,8);
             is_closed_t = array2table(int8(table2array(M(j,17)>0)),'VariableNames',{'isClosed'});
-            lat_t = M(j,18);
-            lon_t = array2table(-table2array(M(j,19)),'VariableNames',{'lon'});
+            lat_t = table2array(M(j,18));
+            lon_t = table2array(M(j,19));
             mon = table2array(M(j,5));
             day = table2array(M(j,6));
             yd = 0 * day;
             for k=1:length(day)
                 yd(k) = yearday(mon(k),day(k),0);
             end
             DecYr_t = array2table(year(j) + yd/365.25,'VariableNames',{'DecYr'});
-            z_t = M(j,21);
-            x_t = array2table(xx(j),'VariableNames',{'x'});
-            y_t = array2table(yy(j),'VariableNames',{'y'});
+            z_t = table2array(M(j,21));
+            x_t = table2array(M(j,45));
+            y_t = table2array(M(j,46));
         end
 
         n=find(and(year==yr,sg==3.));

PythonScripts/GUI/GeoSAM/GeoSams.py

@@ -186,14 +186,8 @@ def Run_Sim(self):
         # Ensure data is available, by first checking if data files have been created.
         # Typical data file name: Data/bin5mm2015AL.csv
         filesExist = True
-        if self.frame1.usingHabCam.get():
-            prefix = 'HCbin5mm'
-            dataSrcArg = 'H'
-        else:
-            prefix = 'bin5mm'
-            dataSrcArg = 'D'
         for yr in range(self.yearStart, self.yearStop+1):
-            dataFName = os.path.join(self.root, 'Data', prefix+str(yr)+self.domainName+'.csv')
+            dataFName = os.path.join(self.root, 'Data', 'bin5mm'+str(yr)+self.domainName+'.csv')
             if not os.path.isfile(dataFName): 
                 filesExist = False
                 break
@@ -206,9 +200,9 @@ def Run_Sim(self):
                 mathArg = 'O'
 
             if platform.system() == 'Windows':
-                cmd = [os.path.join(self.root, 'Unpack.bat'), startYear, stopYear, '0', self.domainName, mathArg, dataSrcArg]
+                cmd = [os.path.join(self.root, 'Unpack.bat'), startYear, stopYear, '0', self.domainName, mathArg]
             else:
-                cmd = [os.path.join(self.root, 'Unpack.sh'), startYear, stopYear, '0', self.domainName, mathArg, dataSrcArg]
+                cmd = [os.path.join(self.root, 'Unpack.sh'), startYear, stopYear, '0', self.domainName, mathArg]
                 subprocess.run(['chmod','744','Unpack.sh']) # make file executable
             messagebox.showinfo("Unpack", f'Starting Unpack.\nThis could take several minutes, longer if using Octave.\nPlease be patient.')
             result = subprocess.run(cmd)
@@ -458,7 +452,6 @@ def WriteScallopConfig(self):
         with open(simCfgFile, 'w') as f:
             f.write('# input file for Scallops \n')
             f.write('Time steps per Year = ' + str(self.frame1.tsPerYear.myEntry.get())+'\n')
-            f.write('Use HabCam Data = '     + str(self.frame1.usingHabCam.get())[0]+'\n')
             f.write('# Configuration files are expected to be in the Configuration directory\n')
             f.write('Mortality Config File = '   + self.frame1.mortCfgFile.myEntry.get() + '\n')
             f.write('Recruit Config File = '     + self.frame1.recrCfgFile.myEntry.get() + '\n')
@@ -712,8 +705,6 @@ def ReadSimConfigFile(self):
                 self.paramVal += 256
             elif (tag == 'Time steps per Year'):
                 self.tsPerYear = int(value)
-            elif (tag == 'Use HabCam Data'):
-                self.useHabCamData = value[0] == 'T'
 
     ## 
     # Read in the (tag, value) parameters from the UK configuration file.

PythonScripts/GUI/GeoSAM/MainInputFrame.py

@@ -137,15 +137,6 @@ def __init__(self, container, friend, tsPerYear, selectedOutputs, maxYears):
         self.domainNameCombo.current(2)
         self.domainNameCombo.grid(row=3, column=1, sticky='w', pady=5)
         #-------------------------------------------------------------------------------------------
-        self.usingHabCamLabel = ttk.Label(durationFrame, text='Domain Name')
-        self.usingHabCam = tk.BooleanVar(durationFrame, self.friend.useHabCamData)
-        self.usingHabCamLabel = ttk.Label(durationFrame, text='Data Source')
-        self.usingHabCamLabel.grid(row=4, column=0)
-        self.useHabCamRB = ttk.Radiobutton(durationFrame, text='Habcam', value=True, variable=self.usingHabCam, command=None)
-        self.useHabCamRB.grid(row=4, column=1,sticky='w')
-        self.useDredgeRB = ttk.Radiobutton(durationFrame, text='Dredge', value=False, variable=self.usingHabCam, command=None)
-        self.useDredgeRB.grid(row=5, column=1,sticky='w')
-        #-------------------------------------------------------------------------------------------
         durationFrame.grid(row=2, column=1, padx=5, sticky='w')
         # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
         outputSelFrame = ttk.LabelFrame(self, text='Output Selection', style='SAMS.TFrame')

SRC/GridManager.f90

@@ -97,7 +97,6 @@ module Grid_Manager_Mod
 integer, PRIVATE :: num_areas ! number of special access areas
 integer, PRIVATE :: num_grids
 logical, PRIVATE :: use_spec_access_data
-logical, PRIVATE :: use_habcam_data
 character(domain_len), PRIVATE :: domain_name
 character(fname_len), PRIVATE :: config_file_name
 character(fname_len), PRIVATE :: init_cond_fname
@@ -139,19 +138,17 @@ integer function Set_Num_Grids()
 !> Initializes growth for startup
 !>
 !==================================================================================================================
-subroutine Set_Grid_Manager(state_mat, grid, ngrids, dom_name, use_hc)
+subroutine Set_Grid_Manager(state_mat, grid, ngrids, dom_name)
 integer, intent(inout) :: ngrids
 real(dp), intent(out):: state_mat(1:ngrids, 1:num_size_classes)
 type(Grid_Data_Class), intent(out) :: grid(*)
 character(domain_len), intent(in) :: dom_name
-logical, intent(in) :: use_hc
 
 integer n, j, k
 character(fname_len) fname
 
 ! set private variables
 domain_name = dom_name
-use_habcam_data = use_hc
 
 ! Used to verify grid in special access area
 fname = 'Results/SurveyLoc.txt'