fix(Parser): handle non binmapped oceancontour NetCDFs and add OceanC…

…ontour unittests

Parser/OceanContour/OceanContour.m

@@ -447,7 +447,7 @@ function warning_failed(failed_items, filename)
             %
             % %read from netcdf
             % file = [toolboxRootPath 'data/testfiles/netcdf/Nortek/OceanContour/Signature/s500_enu_avg.nc'];
-            % [sample_data] = readOceanContour(file);
+            % [sample_data] = OceanContour.readOceanContourFile(file);
             % assert(strcmpi(sample_data{1}.meta.instrument_model,'Signature500'))
             % assert(isequal(sample_data{1}.meta.instrument_avg_interval,60))
             % assert(isequal(sample_data{1}.meta.instrument_sample_interval,600))
@@ -458,7 +458,7 @@ function warning_failed(failed_items, filename)
             %
             % % read from matfile
             % file = [toolboxRootPath 'data/testfiles/mat/Nortek/OceanContour/Signature/s500_enu_avg.mat'];
-            % [sample_data] = readOceanContour(file);
+            % [sample_data] = OceanContour.readOceanContourFile(file);
             % assert(strcmpi(sample_data{1}.meta.instrument_model,'Signature500'))
             % assert(isequal(sample_data{1}.meta.instrument_avg_interval,60))
             % assert(isequal(sample_data{1}.meta.instrument_sample_interval,600))
@@ -548,12 +548,16 @@ function warning_failed(failed_items, filename)
 
                 meta.magDec = get_att('magDec');
                 custom_magnetic_declination = logical(meta.magDec);
-                meta.binMapping = get_att('binMapping');
-                binmapped = logical(meta.binMapping);                                               
+                try
+                    meta.binMapping = get_att('binMapping');
+                    binmapped = logical(meta.binMapping);
+                catch
+                    binmapped = false;
+                end
+
                 %Now that we know some preliminary info, we can load the variable
                 % name mappings and the list of variables to import.
-
-
+
                 var_mapping = OceanContour.get_varmap(ftype, group_name, nBeams, custom_magnetic_declination,binmapped);
                 import_mapping = OceanContour.get_importmap(nBeams, custom_magnetic_declination);
 
@@ -568,7 +572,7 @@ function warning_failed(failed_items, filename)
                     meta.dim_meta = data_metadata.(group_name).Dimensions;
                     meta.var_meta = data_metadata.(group_name).Variables;
                     gid = dataset_groups(k);
-                    get_var = @(x)(nc_get_var(gid, var_mapping.(x)));                   
+                    get_var = @(x)(nc_get_var(gid, var_mapping.(x))); 
                 else
                     fname = getindex(dataset_groups, k);
                     get_var = @(x)(transpose(matdata.(fname).(var_mapping.(x))));

test/Parser/GenericParser/testOceanContour.m

@@ -0,0 +1,47 @@
+classdef testOceanContour < matlab.unittest.TestCase
+
+    % Test Reading Nortek Signature files output by OceanContour software
+    % with the OceanContour
+    % function.
+    %
+    % author: laurent.besnard@utas.edu.au
+    %
+    % TODO: understand why fillValues for s500 and s1000 are different by a
+    % factor 10
+
+
+    properties (TestParameter)
+        mode = {'timeSeries'};
+        oceancontour_sig500_file = files2namestruct(rdir([toolboxRootPath 'data/testfiles/netcdf/Nortek/OceanContour/Signature/sig500']));
+        oceancontour_sig1000_file = files2namestruct(rdir([toolboxRootPath 'data/testfiles/netcdf/Nortek/OceanContour/Signature/sig1000']));
+    end
+
+    methods (Test)
+
+        function testOceanContourSig500(~, oceancontour_sig500_file)
+            data = OceanContour.readOceanContourFile(oceancontour_sig500_file);
+            assert(strcmp(data{1}.meta.instrument_model,'Signature500'));
+            assert(strcmp(data{1}.meta.instrument_make,'Nortek'));
+            assert(strcmp(data{1}.meta.coordinate_system,'ENU'));
+            assert(data{1}.meta.beam_angle==25);
+            assert(round(mean(data{1,1}.variables{1,5}.data)) == 19)  % TEMP var check
+
+            tolerance = 0.001;
+            assert(abs(min(data{1,1}.variables{1,16}.data(:,1)) - -32.7680) < tolerance);  % UCUR var check. fillvalue seems to be -32.7680
+        end
+
+        function testOceanContourSig1000(~, oceancontour_sig1000_file)
+            data = OceanContour.readOceanContourFile(oceancontour_sig1000_file);
+            assert(strcmp(data{1}.meta.instrument_model,'Signature1000'));
+            assert(strcmp(data{1}.meta.instrument_make,'Nortek'));
+            assert(strcmp(data{1}.meta.coordinate_system,'ENU'));
+            assert(data{1}.meta.beam_angle==25);
+            assert(round(mean(data{1,1}.variables{1,5}.data)) == 20)  % temperature var check
+
+            tolerance = 0.001;
+            assert(abs(min(data{1,1}.variables{1,16}.data(:,1)) - -3.27680) < tolerance);  % UCUR var check. fillvalue seems to be -3.27680
+        end
+    end
+
+end
+