Merge pull request #735 from aodn/release_2.6.11

Release 2.6.11, fixes #733

AutomaticQC/imosEchoIntensitySetQC.m

@@ -35,10 +35,8 @@
 
 if ~valid
     %TODO: we may need to include a global verbose flag to avoid pollution here.
-    for k = 1:numel(reason)
-        dispmsg('Skipping %s. Reason: \n', sample_data.toolbox_input_file, reason{k})
-    end
-
+    unwrapped_msg = ['Skipping %s. Reasons: ' cell2str(reason,'')];
+    dispmsg(unwrapped_msg,sample_data.toolbox_input_file)
     return
 end
 

AutomaticQC/imosEchoIntensityVelocitySetQC.m

@@ -71,10 +71,22 @@
         if strcmpi(paramName, ['ABSIC' cc]), idABSIC{j} = i; end
     end
 end
-idHeight = getVar(sample_data.dimensions, 'HEIGHT_ABOVE_SENSOR');
-Bins    = sample_data.dimensions{idHeight}.data';
-idDepth = getVar(sample_data.variables, 'DEPTH');
-depth = sample_data.variables{idDepth}.data;
+try
+    idHeight = getVar(sample_data.dimensions, 'HEIGHT_ABOVE_SENSOR');
+    Bins    = sample_data.dimensions{idHeight}.data';
+catch
+    dispmsg('No HEIGHT_ABOVE_SENSOR variable. Skipping...')
+    return
+end
+
+try
+    idDepth = getVar(sample_data.variables, 'DEPTH');
+    depth = sample_data.variables{idDepth}.data;
+catch
+    dispmsg('No DEPTH variable. Skipping...')
+    return
+end
+
 
 % check if the data is compatible with the QC algorithm
 idMandatory = (idUcur | idVcur | idWcur | idCspd | idCdir);

AutomaticQC/imosSurfaceDetectionByDepthSetQC.m

@@ -23,9 +23,8 @@
 [valid,reason] = IMOS.validate_dataset(sample_data,currentQCtest);
 if ~valid
     %TODO: we may need to include a global verbose flag to avoid pollution here.
-    for k=1:numel(reason)
-        dispmsg('Skipping %s. Reason: \n', sample_data.toolbox_input_file, reason{k})
-    end
+    unwrapped_msg = ['Skipping %s. Reasons: ' cell2str(reason,'')];
+    dispmsg(unwrapped_msg,sample_data.toolbox_input_file)
     return
 end
 

AutomaticQC/qcFilterMain.m

@@ -167,7 +167,7 @@
             % user cancelled
             if ~isempty(cancel) && getappdata(cancel, 'cancel'), return; end
 
-            if contains(filterName,'SpikeQC')
+            if contains(filterName,'TimeSeriesSpikeQC')
               varname = sam.(type{m}){k}.name;
               if ~exist('varflags','var')
                 [varflags, varlogs] = filter(sam, auto);

Preprocessing/depthPP.m

@@ -844,18 +844,17 @@
             continue;
         end
     end
-    
+
     if depthIdx(iCurSam)
         % update existing depth data in data set
-        sample_data{iCurSam}.(depthVarType).data = computedDepth;
-
-        depthComment = sample_data{iCurSam}.(depthVarType).comment;
+        depth_index = depthIdx(iCurSam);
+        sample_data{iCurSam}.(depthVarType){depth_index}.data = computedDepth;
+        depthComment = sample_data{iCurSam}.(depthVarType){depth_index}.comment;
         if isempty(depthComment)
-            sample_data{iCurSam}.(depthVarType).comment = computedDepthComment;
+            sample_data{iCurSam}.(depthVarType){depth_index}.comment = computedDepthComment;
         else
-            sample_data{iCurSam}.(depthVarType).comment = [comment ' ' computedDepthComment];
+            sample_data{iCurSam}.(depthVarType){depth_index}.comment = [comment ' ' computedDepthComment];
         end
-
     else
         % add depth data as new variable in data set
         sample_data{iCurSam} = addVar( ...

Util/genSampleDataDesc.m

@@ -54,12 +54,18 @@
 
 try
     time_coverage_start = sam.time_coverage_start;
+    if isempty(time_coverage_start)
+        time_coverage_start = 0;
+    end
 catch
     time_coverage_start = 0;
 end
 
 try 
     time_coverage_end = sam.time_coverage_end;
+    if isempty(time_coverage_end)
+        time_coverage_end = 0;
+    end
 catch
     time_coverage_end = 0;
 end
@@ -73,7 +79,7 @@
     filename = 'Unknown';
 end
 
-[~, fName, fSuffix] = fileparts(sam.toolbox_input_file);
+[~, fName, fSuffix] = fileparts(filename);
 
 fName = [fName fSuffix];
 
@@ -84,7 +90,19 @@
     alias_file = '';
 end
 
-instrument_entry = [sam.meta.instrument_make ' ' sam.meta.instrument_model];
+try
+    maker = sam.meta.instrument_make;
+catch
+    maker = 'None';
+end
+try
+    model = sam.meta.instrument_model;
+catch
+    model = 'None';
+end
+
+instrument_entry = [maker ' ' model ];
+
 if ~isempty(alias_file)
     try
         map = readMappings(alias_file);

build.py

@@ -180,7 +180,9 @@ def find_items(folder: str) -> dict:
     items["standard_matfiles"] = [
         x.as_posix()
         for x in all_files
-        if x.suffix == ".mat" and "/+" not in x.parent.as_posix()
+        if "data/testfiles/" not in x.as_posix()
+        if x.suffix == ".mat"
+        and "/+" not in x.parent.as_posix()
     ]
 
     items["standard_miscfiles"] = [

imosToolbox.m

@@ -37,7 +37,7 @@ function imosToolbox(auto, varargin)
 %
 
 % Set current toolbox version
-toolboxVersion = ['2.6.10 - ' computer];
+toolboxVersion = ['2.6.11 - ' computer];
 
 if nargin == 0, auto = 'manual'; end
 

test/Preprocessing/testDepthPP.m

@@ -0,0 +1,31 @@
+classdef testDepthPP < matlab.unittest.TestCase
+
+    % Test DepthPP
+    %
+    % by [email protected]
+    %
+    properties (TestParameter)
+        mode = {'profile','timeSeries'};
+    end
+
+    methods (Test)
+        function testDepthPPOverwriteDepth(~, mode)
+            d = IMOS.gen_dimensions(mode,1,{'TIME'},{@double},{randn(100,1)});
+            parr = 100*ones(100,1);
+            darr = randn(100,1);
+            v = IMOS.gen_variables(d,{'X','PRES','DEPTH'},{@double,@double,@double},{randn(1,1),parr,darr},'coordinates','');
+            dataset = struct();
+            dataset.dimensions = d;
+            dataset.variables = v;
+            dataset.instrument_nominal_depth = 200;
+            dataset.site_nominal_depth = 205;
+            dataset.toolbox_input_file = '';
+            dataset.meta = struct();
+            dataset = makeNetCDFCompliant(dataset);
+            disp('Select from PRES measurements to overwrite DEPTH and make this test pass')
+            x = depthPP({dataset},'qc',false); %select from PRES to overwrite DEPTH
+            assert(~isequal(x{1}.variables{end}.data,darr));
+        end
+    end
+
+end