diff --git a/.gitignore b/.gitignore
index bf29b9851..efcea30c5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,6 @@
 *.ppp
+*.mqc
+*.pqc
 .mypy_cache/*
 Java/bin
 *.pyc
@@ -8,3 +10,10 @@ data
 dist
 data/*
 dist/*
+Geomag/sample_coords.txt
+Geomag/sample_out_IGRF13.txt
+.python-version
+.standalone_canonical_version
+.build.py@*
+*.nc
+tmp/test_*
diff --git a/AutomaticQC/SpikeClassifiers/imosSpikeClassifierBurstHampel.m b/AutomaticQC/SpikeClassifiers/imosSpikeClassifierBurstHampel.m
index dddbba7a5..52cf1ce23 100644
--- a/AutomaticQC/SpikeClassifiers/imosSpikeClassifierBurstHampel.m
+++ b/AutomaticQC/SpikeClassifiers/imosSpikeClassifierBurstHampel.m
@@ -10,7 +10,7 @@
 % signal - A Burst 1-d signal.
 % use_burst_window  - a boolean to consider the half_window_width applied at burst scale. If false, will consider the burst series as continuous.
 % half_window_width - The half_window_width burst range (the full window size will be 1+2*half_window_width)
-% madfactor -  A multipling scale for the MAD.
+% madfactor - a scale for the mean absolute deviation which values above will be marked as a spike.
 % repeated_only - a boolean to mark spikes in burst only if they are detected more than one time (only for half_window_width>0).
 % lower_mad_limit - a lower threshold for the MAD values, which values below will be ignored.
 %
@@ -23,13 +23,11 @@
 %
 % % simple spikes
 % x = randn(1,100)*1e-2;
-% spikes = [3,7,33,92,99]
+% spikes = [3,7,33,92,99];
 % x(spikes) = 1000;
 % bduration = 6;
 % v = 1:bduration:length(x)+bduration;
-% for k=1:length(v)-1;
-% bind{k} = [v(k),min(v(k+1)-1,length(x))];
-% end
+% for k=1:length(v)-1; bind{k} = [v(k),min(v(k+1)-1,length(x))]; end
 % [dspikes] = imosSpikeClassifierBurstHampel(bind,x);
 % assert(isequal(dspikes,spikes));
 % % equal to Hampel
@@ -38,12 +36,18 @@
 % assert(isequal(dspikes,spikes));
 % assert(isequal(dspikes,dspikes2));
 %
-% % detecting entire burst as spike
+% % by ignoring the burst nature, we need to be aware
+% % that entire bursts as spike will be missing.
+%
 % x = randn(1,100)*1e-2;
-% fullburst_spiked = [3,7,13,14,15,16,17,18,33,92,99]
+% fullburst_spiked = [3,7,13,14,15,16,17,18,33,92,99];
 % x(fullburst_spiked) = 1000;
-% [dspikes] = imosSpikeClassifierBurstHampel(bind,x);
+% half_window_width = 1; % 3 point window
+% madfactor = mad([1000,0,0]); %pick only big spikes. 
+% [dspikes] = imosSpikeClassifierBurstHampel(bind,x,false,1,madfactor);
 % assert(isequal(dspikes,[3,7,33,92,99]));
+%
+% %considering the burst nature of sampling fix this
 % [dspikes2] = imosSpikeClassifierBurstHampel(bind,x,true,2);
 % assert(isequal(dspikes2,fullburst_spiked))
 %
diff --git a/AutomaticQC/SpikeClassifiers/imosSpikeClassifierBurstRunningStats.m b/AutomaticQC/SpikeClassifiers/imosSpikeClassifierBurstRunningStats.m
index 088c25b66..6751c05fc 100644
--- a/AutomaticQC/SpikeClassifiers/imosSpikeClassifierBurstRunningStats.m
+++ b/AutomaticQC/SpikeClassifiers/imosSpikeClassifierBurstRunningStats.m
@@ -25,8 +25,7 @@
 % z = randn(1,10);
 % z(10) = 10000;
 % [spikes] = imosSpikeClassifierRunningStats(z,@mean,@std,2);
-% assert(spikes(10)==1)
-% assert(spikes(1:9)==0)
+% assert(spikes==10)
 %
 % author: hugo.oliveira@utas.edu.au
 %
diff --git a/AutomaticQC/SpikeClassifiers/imosSpikeClassifierNonBurstSavGolOTSU.m b/AutomaticQC/SpikeClassifiers/imosSpikeClassifierNonBurstSavGolOTSU.m
index 23722b0e2..c290b4b53 100644
--- a/AutomaticQC/SpikeClassifiers/imosSpikeClassifierNonBurstSavGolOTSU.m
+++ b/AutomaticQC/SpikeClassifiers/imosSpikeClassifierNonBurstSavGolOTSU.m
@@ -26,7 +26,7 @@
 % signal = 10*sin(omega*t);
 % signal([20]) = max(signal).^3;
 % [spikes] = imosSpikeClassifierNonBurstSavGolOTSU(signal,5,2,100,5);
-% assert(spikes,20)
+% assert(spikes==20)
 %
 % author: Unknown
 % author: Ken Ridgway
diff --git a/AutomaticQC/SpikeClassifiers/imosSpikeClassifierOTSU.m b/AutomaticQC/SpikeClassifiers/imosSpikeClassifierOTSU.m
index 47afe8b0d..0447c47c4 100644
--- a/AutomaticQC/SpikeClassifiers/imosSpikeClassifierOTSU.m
+++ b/AutomaticQC/SpikeClassifiers/imosSpikeClassifierOTSU.m
@@ -21,24 +21,26 @@
 %
 % signal = [0,1,0];
 % [spikes] = imosSpikeClassifierOTSU(signal,3,1,false);
-% assert(spikes==2)
+% %limitation of otsu method - signal difference influence markups
+% assert(isequal(spikes,[1,2]))
 %
 % %non-centralized
-% signal = [0,0,0,1,0,1,0,0,0,0]
+% signal = [0,0,0,1,0,1,0,0,0,0];
 % [spikes] = imosSpikeClassifierOTSU(signal,3,1,false);
-% assert(spikes==[3,4,5,6])
-% centralized
+% assert(isequal(spikes,[3,4,5,6]))
+%
+% %centralized
 % [spikes] = imosSpikeClassifierOTSU(signal,3,1,true);
 % assert(~isequal(spikes,[4,6])) % fail
-% assert(spikes==[4]) % fail
+% assert(spikes==5) % fail
 %
 % %harmonic
 % omega = 2*pi/86400;
 % t = 0:3600:86400*5;
-% signal = 10*sin(omega*t)
+% signal = 10*sin(omega*t);
 % signal([10,20]) = max(signal)^3;
 % [spikes] = imosSpikeClassifierOTSU(signal,100,1,true);
-% assert(isequal(spikes,[10,20])
+% assert(isequal(spikes,[10,20]))
 %
 % %
 % omega = 2*pi/86400;
diff --git a/AutomaticQC/SpikeClassifiers/imosSpikeClassifierRunningStats.m b/AutomaticQC/SpikeClassifiers/imosSpikeClassifierRunningStats.m
index 5305f303a..00f6b9ec2 100644
--- a/AutomaticQC/SpikeClassifiers/imosSpikeClassifierRunningStats.m
+++ b/AutomaticQC/SpikeClassifiers/imosSpikeClassifierRunningStats.m
@@ -24,8 +24,7 @@
 % z = randn(1,10);
 % z(10) = 10000;
 % [spikes] = imosSpikeClassifierRunningStats(z,@mean,@std,2);
-% assert(spikes(10)==1)
-% assert(spikes(1:9)==0)
+% assert(spikes==10)
 %
 % author: hugo.oliveira@utas.edu.au
 %
diff --git a/AutomaticQC/SpikeClassifiers/imosSpikeClassifiersLimits.m b/AutomaticQC/SpikeClassifiers/imosSpikeClassifiersLimits.m
index 7d68a533e..496868af6 100644
--- a/AutomaticQC/SpikeClassifiers/imosSpikeClassifiersLimits.m
+++ b/AutomaticQC/SpikeClassifiers/imosSpikeClassifiersLimits.m
@@ -13,11 +13,11 @@
 %
 % Example:
 %
-% len = 100
-% [limits] = imosTimeSeriesSpikeQCLimits(len)
+% len = 100;
+% [limits] = imosSpikeClassifiersLimits(len);
 % assert(limits.hampel_half_window_width.min==1)
 % assert(limits.hampel_half_window_width.max==len/2)
-% assert(limits.hampel_madfactor.max = 20)
+% assert(limits.hampel_madfactor.max==20)
 %
 % author: hugo.oliveira@utas.edu.au
 %
diff --git a/AutomaticQC/SpikeClassifiers/otsu_threshold.m b/AutomaticQC/SpikeClassifiers/otsu_threshold.m
index b0085f27f..96aa783e0 100644
--- a/AutomaticQC/SpikeClassifiers/otsu_threshold.m
+++ b/AutomaticQC/SpikeClassifiers/otsu_threshold.m
@@ -18,9 +18,30 @@
 %
 % Example:
 %
+% % find different samplings
+% dsignal = diff([0:10:100, 101:110]);
+% [t] = otsu_threshold(dsignal,2);
+% assert(t>1);
+% assert(isequal(find(dsignal>t),1:10))
+% [t] = otsu_threshold(dsignal,100);
+% assert(t>1);
+%
+% % spike simple case
+% x = randn(1,100)*10;
+% spikes = [3,30:40,90];
+% x(spikes) = 100;
+% dsignal = diff(x);
+% t = otsu_threshold(dsignal,2);
+% assert(t<100);
+% assert(abs(x(3)-x(2))>t)
+% assert(abs(x(30)-x(29))>t)
+% assert(abs(x(90)-x(89))>t)
+% 
+% % simple threshold only detects the first
+% % occurence, and with a shifted index given
+% % the difference operation
+% assert(isequal(find(dsignal>t),[2,29,89]))
 %
-% [threshold] = compute_otsu_threshold(signal,nbins)
-% assert()
 %
 % author: hugo.oliveira@utas.edu.au
 %
diff --git a/AutomaticQC/imosEchoIntensitySetQC.m b/AutomaticQC/imosEchoIntensitySetQC.m
index 9791f505f..c6016cc7b 100644
--- a/AutomaticQC/imosEchoIntensitySetQC.m
+++ b/AutomaticQC/imosEchoIntensitySetQC.m
@@ -15,7 +15,7 @@
 % bad markings are bounded by the `bound_value` option.
 % This is useful to filter the echo amplitude QC markings to only
 % further specific depths or bin indexes.
-% 
+%
 % See imosEchoIntensitySetQC.txt options.
 %
 %
@@ -61,17 +61,15 @@
 
 nt = numel(IMOS.get_data(sample_data.dimensions, 'TIME'));
 
+
 if IMOS.adcp.is_along_beam(sample_data)
     bin_dist = IMOS.get_data(sample_data.dimensions, 'DIST_ALONG_BEAMS');
-    dims_tz = {'TIME', 'DIST_ALONG_BEAMS'};
-    nbeams = numel(absic_vars);
 else
     bin_dist = IMOS.get_data(sample_data.dimensions, 'HEIGHT_ABOVE_SENSOR');
-    dims_tz = {'TIME', 'HEIGHT_ABOVE_SENSOR'};
-    nbeams = numel(absic_vars);
 end
 
-flag_vars = IMOS.variables_with_dimensions(sample_data.dimensions, sample_data.variables, dims_tz);
+nbeams = numel(absic_vars);
+flag_vars = IMOS.adcp.echo_intensity_variables(sample_data);
 
 switch nbeams
     case 3
@@ -163,7 +161,6 @@
 
 flags = ones(size(beyond_threshold), 'int8') * goodFlag;
 flags(beyond_threshold) = badFlag;
-
 flag_vars_inds = IMOS.find(sample_data.variables, flag_vars);
 for k = 1:numel(flag_vars_inds)
     vind = flag_vars_inds(k);
@@ -176,7 +173,5 @@
 further_bad_bin = find(nbadbins, 1, 'last');
 
 paramsLog = ['echo_intensity_threshold=' threshold, 'propagate=', propagate, 'near_bad_bin=' near_bad_bin, 'further_bad_bin=' further_bad_bin];
-
 writeDatasetParameter(sample_data.toolbox_input_file, currentQCtest, 'echo_intensity_threshold', threshold);
-
 end
diff --git a/AutomaticQC/imosSurfaceDetectionByDepthSetQC.m b/AutomaticQC/imosSurfaceDetectionByDepthSetQC.m
index c8c39228a..c2bc59a93 100644
--- a/AutomaticQC/imosSurfaceDetectionByDepthSetQC.m
+++ b/AutomaticQC/imosSurfaceDetectionByDepthSetQC.m
@@ -7,7 +7,7 @@
 % observable water column height. Any bin beyond this height
 % is marked as bad.
 %
-% This test only works for datasets with available TIME dimension, 
+% This test only works for datasets with available TIME dimension,
 % HEIGHT_ABOVE_SENSOR or DIST_ALONG_BEAMS dimensions, DEPTH variable,
 % and adcp_site_nominal_depth or site_depth_at_deployment metadata.
 %
@@ -51,11 +51,11 @@
 flags = ones(size(wbins), 'int8') * badFlag;
 flags(wbins) = goodFlag;
 
-if along_beams
+if along_height
+    dims_tz = {'TIME','HEIGHT_ABOVE_SENSOR'};
+else
     dims_tz = {'TIME','DIST_ALONG_BEAMS'};
     dispmsg('No bin-mapping performed. Surface Detections will be contaminated by missing tilt corrections.')
-else
-    dims_tz = {'TIME','HEIGHT_ABOVE_SENSOR'};
 end
 
 vars_tz = IMOS.variables_with_dimensions(sample_data.dimensions,sample_data.variables,dims_tz);
diff --git a/Parser/+Workhorse/import_mappings.m b/Parser/+Workhorse/import_mappings.m
index ff0daff74..91536cddb 100644
--- a/Parser/+Workhorse/import_mappings.m
+++ b/Parser/+Workhorse/import_mappings.m
@@ -22,13 +22,16 @@
 % Examples:
 %
 % sensors = struct('Temperature',true,'Depth',true,'Conductivity',false,'SpeedOfSound',true,'Pitch',true,'Roll',true,'Heading',true);
-%
 % imap = Workhorse.import_mappings(sensors,4,'','beam');
 % fields = fieldnames(imap);
 % assert(inCell(fields,'VEL1'))
 % assert(~inCell(fields,'VCUR'))
 % assert(inCell(fields,'HEADING'))
 % assert(inCell(fields,'ABSIC4'))
+% assert(isequal(imap.('VEL1'),{'velocity','velocity1'}))
+% assert(isequal(imap.('VEL2'),{'velocity','velocity2'}))
+% assert(isequal(imap.('VEL3'),{'velocity','velocity3'}))
+% assert(isequal(imap.('VEL4'),{'velocity','velocity4'}))
 %
 % imap = Workhorse.import_mappings(sensors,4,'','earth');
 % fields = fieldnames(imap);
@@ -36,6 +39,10 @@
 % assert(~inCell(fields,'VEL1'))
 % assert(inCell(fields,'HEADING'))
 % assert(inCell(fields,'ABSIC4'))
+% assert(isequal(imap.('UCUR'),{'velocity','velocity1'}))
+% assert(isequal(imap.('VCUR'),{'velocity','velocity2'}))
+% assert(isequal(imap.('WCUR'),{'velocity','velocity3'}))
+% assert(isequal(imap.('ECUR'),{'velocity','velocity4'}))
 %
 % %MAG declination renaming.
 %
@@ -43,57 +50,88 @@
 % fields = fieldnames(imap);
 %
 % assert(~inCell(fields,'VEL1_MAG'))
-% assert(inCell(fields,'VCUR_MAG'))
-% assert(isequal(imap.('VCUR_MAG'),{'velocity','velocity1'}))
 % assert(inCell(fields,'UCUR_MAG'))
-% assert(isequal(imap.('UCUR_MAG'),{'velocity','velocity2'}))
-%
-% assert(inCell(fields,'ECUR'))
+% assert(isequal(imap.('UCUR_MAG'),{'velocity','velocity1'}))
+% assert(inCell(fields,'VCUR_MAG'))
+% assert(isequal(imap.('VCUR_MAG'),{'velocity','velocity2'}))
 % assert(inCell(fields,'WCUR'))
-%
-% assert(inCell(fields,'CMAG1'))
-% assert(isequal(imap.('CMAG1'),{'corrMag','field1'}))
-%
-% assert(inCell(fields,'PERG4'))
-% assert(isequal(imap.('PERG4'),{'percentGood','field4'}))
+% assert(isequal(imap.('WCUR'),{'velocity','velocity3'}))
+% assert(inCell(fields,'ECUR'))
+% assert(isequal(imap.('ECUR'),{'velocity','velocity4'}))
 %
 % assert(inCell(fields,'ABSIC4'))
 % assert(isequal(imap.('ABSIC4'),{'echoIntensity','field4'}))
+% assert(inCell(fields,'CMAG3'))
+% assert(isequal(imap.('CMAG3'),{'corrMag','field3'}))
+% assert(inCell(fields,'PERG2'))
+% assert(isequal(imap.('PERG2'),{'percentGood','field2'}))
 %
 % assert(inCell(fields,'HEADING_MAG'))
 % assert(isequal(imap.('HEADING_MAG'),{'variableLeader','heading'}))
 % assert(inCell(fields,'TX_VOLT'))
 % assert(isequal(imap.('TX_VOLT'),{'variableLeader','adcChannel1'}))
 %
+% %test beam_vars
+% [~,vel_vars,beam_vars,ts_vars] = Workhorse.import_mappings(sensors,3,'_MAG','earth');
+% assert(inCell(vel_vars,'UCUR_MAG'))
+% assert(inCell(vel_vars,'WCUR'))
+% assert(inCell(beam_vars,'ABSIC1'))
+% assert(inCell(beam_vars,'CMAG2'))
+% assert(inCell(beam_vars,'PERG3'))
+% assert(inCell(ts_vars,'HEADING_MAG'))
+% assert(~inCell(ts_vars,'PSAL'))
+%
+%
 % author: hugo.oliveira@utas.edu.au
 %
 
 narginchk(4, 4);
+
+imap = struct();
+
 switch frame_of_reference
     case 'earth'
-        vel_vars = {['VCUR' name_extension], ['UCUR' name_extension], 'WCUR'};
-        if num_beams>3
+        imap.(['UCUR' name_extension]) = {'velocity', 'velocity1'};
+        imap.(['VCUR' name_extension]) = {'velocity', 'velocity2'};
+        imap.('WCUR') = {'velocity', 'velocity3'};
+        vel_vars = {['UCUR' name_extension], ['VCUR' name_extension], 'WCUR'};
+        if num_beams == 4 
+            imap.('ECUR') = {'velocity', 'velocity4'};
             vel_vars{end+1} = 'ECUR';
         end
     case 'beam'
+        imap.('VEL1') = {'velocity', 'velocity1'};
+        imap.('VEL2') = {'velocity', 'velocity2'};
+        imap.('VEL3') = {'velocity', 'velocity3'};
         vel_vars = {'VEL1','VEL2','VEL3'};
-        if num_beams>3
+        if num_beams == 4 
+            imap.('VEL4') = {'velocity', 'velocity4'};
             vel_vars{end+1} = 'VEL4';
         end
+    otherwise
+        errormsg('Frame of reference %s not implemented.',frame_of_reference)
 end
 
-beam_vars = {'ABSIC1', 'ABSIC2', 'ABSIC3', 'ABSIC4', 'CMAG1', 'CMAG2', 'CMAG3', 'CMAG4', 'PERG1', 'PERG2', 'PERG3', 'PERG4'};
-ts_vars = {};
-
-imap = struct();
-
-for k = 1:num_beams
-    imap.(vel_vars{k}) = {'velocity', ['velocity' num2str(k)]};
+%follow the order of previous definitions for compatibility
+beam_vars = cell(1,num_beams*3); %ABSIC,CMAG,PERG
+c=0;
+for k=1:num_beams
+    c=c+1;
     imap.(['ABSIC' num2str(k)]) = {'echoIntensity', ['field' num2str(k)]}; %backscatter
+    beam_vars{c} = ['ABSIC' num2str(k)];
+end
+for k=1:num_beams
+    c=c+1;
     imap.(['CMAG' num2str(k)]) = {'corrMag', ['field' num2str(k)]}; %correlation
+    beam_vars{c} = ['CMAG' num2str(k)];
+end
+for k=1:num_beams
+    c=c+1;
     imap.(['PERG' num2str(k)]) = {'percentGood', ['field' num2str(k)]}; %percentGood
+    beam_vars{c} = ['PERG' num2str(k)];
 end
 
+ts_vars = {};
 if sensors.Temperature
     ts_vars = [ts_vars, 'TEMP'];
     imap.('TEMP') = {'variableLeader', 'temperature'};
diff --git a/Parser/GenericParser/InstrumentParsers/StaroddiParser.m b/Parser/GenericParser/InstrumentParsers/StaroddiParser.m
index 9205ee94a..66b226939 100644
--- a/Parser/GenericParser/InstrumentParsers/StaroddiParser.m
+++ b/Parser/GenericParser/InstrumentParsers/StaroddiParser.m
@@ -26,7 +26,7 @@
 %
 % Example:
 %
-% idata = StaroddiParser({'0-4T3769.DAT'},'timeSeries');
+% %see test/Parser/testStaroddi.m
 %
 % author: hugo.oliveira@utas.edu.au
 %
diff --git a/Parser/GenericParser/InstrumentRules/StaroddiRules.m b/Parser/GenericParser/InstrumentRules/StaroddiRules.m
index b6e1a3b79..c75b23e29 100644
--- a/Parser/GenericParser/InstrumentRules/StaroddiRules.m
+++ b/Parser/GenericParser/InstrumentRules/StaroddiRules.m
@@ -23,8 +23,9 @@
 % The outputs are used by the respective `Instrument`Parser function
 % to read the data into the Toolbox structure.
 %
-% For more information, see comments in the StaroddiRules.m file, which
-% explains all the functionality.
+% Example:
+% %For more information, see comments below which
+% %explains all the grammar functionality.
 %
 % author: hugo.oliveira@utas.edu.au
 
diff --git a/Parser/GenericParser/detectEncoding.m b/Parser/GenericParser/detectEncoding.m
index a71a6ad63..6523a16a1 100644
--- a/Parser/GenericParser/detectEncoding.m
+++ b/Parser/GenericParser/detectEncoding.m
@@ -16,7 +16,7 @@
 %
 % Example:
 % % automatic detection
-% filename = [toolboxRootPath() 'data/testfiles/RBR/duet3/v000/082533_20190525_0515_eng_rbrduet3.txt']
+% filename = [toolboxRootPath() 'data/testfiles/RBR/duet3/v000/082533_20190525_0515_eng_rbrduet3.txt'];
 % encoding = detectEncoding(filename);
 % assert(strcmp(encoding,'windows-1252'));
 %
diff --git a/Parser/oceanContourParse.m b/Parser/oceanContourParse.m
index 2182be68c..d5ce1e7b8 100644
--- a/Parser/oceanContourParse.m
+++ b/Parser/oceanContourParse.m
@@ -15,8 +15,9 @@
 %
 % Example:
 %
-% [data] = OceanContourParser(file,mode)
-% assert()
+% % this is a wrapper,
+% % check the `OceanContour.readOceanContourFile`
+% % docstring for tests.
 %
 % author: hugo.oliveira@utas.edu.au
 %
diff --git a/Parser/signatureParse.m b/Parser/signatureParse.m
index 4b8aae8bf..a7e1d5023 100644
--- a/Parser/signatureParse.m
+++ b/Parser/signatureParse.m
@@ -11,7 +11,11 @@
 % Outputs:
 %   sample_data - Struct containing sample data.
 %
-% Author: 		Guillaume Galibert <guillaume.galibert@utas.edu.au>
+% Example:
+%
+% % for tests, see tests/Parser/testSignature.m
+%
+% author: Guillaume Galibert <guillaume.galibert@utas.edu.au>
 %
 
 %
diff --git a/Parser/workhorseParse.m b/Parser/workhorseParse.m
index c752edcf1..ec0868616 100644
--- a/Parser/workhorseParse.m
+++ b/Parser/workhorseParse.m
@@ -102,7 +102,13 @@
     vaddr = imap.(vname);
     ogroup = vaddr{1};
     ovar = vaddr{2};
-    imported.(vname) = ensembles.(ogroup).(ovar);
+    try
+      imported.(vname) = ensembles.(ogroup).(ovar);
+    catch
+      %raise a nice error msg in case the ensembles functionality is changed 
+      % and we didn't update the import maps, or the import mapping is outdated.
+      errormsg('Trying to associate vname=%s with associated with ogroup=%s and ovar=%s failed!',vname,ogroup,ovar)
+    end
     ensembles.(ogroup) = rmfield(ensembles.(ogroup),ovar);
   end
 
@@ -196,7 +202,11 @@
       vars2d_vel = cell(1,numel(all_vel_vars));
       for k=1:numel(all_vel_vars)
         vname = all_vel_vars{k};
-        vars2d_vel{k} = struct('name',vname,'typeCastFunc',IMOS.resolve.imos_type(vname),'dimensions',earth_dims,'data',imported.(vname),'coordinates',coords2d_vel);
+        %force conversion for backward compatibility - this incur in at least 4 type-conversion from original data to netcdf - madness!
+        typecast_func = IMOS.resolve.imos_type(vname);
+        type_converted_var = typecast_func(imported.(vname));
+        imported = rmfield(imported,vname);
+        vars2d_vel{k} = struct('name',vname,'typeCastFunc',typecast_func,'dimensions',earth_dims,'data',type_converted_var,'coordinates',coords2d_vel);
       end          
     otherwise 
          errormsg('Frame of reference `%s` not supported',meta.adcp_info.coords.frame_of_reference)
diff --git a/Preprocessing/adcpBinMappingPP.m b/Preprocessing/adcpBinMappingPP.m
index 47ab6b7a4..feef80220 100644
--- a/Preprocessing/adcpBinMappingPP.m
+++ b/Preprocessing/adcpBinMappingPP.m
@@ -91,7 +91,7 @@
     roll = sample_data{k}.variables{rollIdx}.data * pi / 180;
     beamAngle = sample_data{k}.meta.beam_angle * pi / 180;
 
-    %TODO: the adjusted distances should be exported 
+    %TODO: the adjusted distances should be exported
     % as variables to enable further diagnostic plots and debugging.
     %TODO: the adjusted distances should be a Nx4 array or Nx3 array.
     if isRDI% RDI 4 beams
@@ -131,7 +131,7 @@
     % interpolation conditions. This would allow a progress bar here.
 
     for n = 1:number_of_beams
-        beam_vars = get_beam_vars(sample_data{k}, n);
+        beam_vars = IMOS.adcp.beam_vars(sample_data{k}, n);
         [all_beam_vars] = IMOS.concatenate_variables(sample_data{k}.variables, beam_vars);
 
         switch n
@@ -238,60 +238,3 @@
 end
 
 end
-
-function [ibvars] = get_beam_vars(sample_data, n)
-%function [ibvars] = get_beam_vars(sample_data,n)
-%
-% Get the available beam variable names
-% based on the beam number.
-%
-% Inputs:
-%
-% sample_data [struct] - the toolbox struct.
-% n [double] - the beam number [1-4]
-%
-% Outputs:
-%
-% ibvars [cell{str}] - the variable names associated
-%                      with the beam number.
-%
-%
-% author: hugo.oliveira@utas.edu.au
-%
-%
-
-narginchk(2, 2)
-
-if ~isstruct(sample_data)
-    error('Frist argument not a toolbox struct')
-end
-
-switch n
-    case 1
-        beam_vars = {'ABSI1', 'ABSIC1', 'CMAG1', 'SNR1', 'VEL1'};
-    case 2
-        beam_vars = {'ABSI2', 'ABSIC2', 'CMAG2', 'SNR2', 'VEL2'};
-    case 3
-        beam_vars = {'ABSI3', 'ABSIC3', 'CMAG3', 'SNR3', 'VEL3'};
-    case 4
-        beam_vars = {'ABSI4', 'ABSIC4', 'CMAG4', 'VEL4'};
-    otherwise
-        errormsg('Second argument not a valid beam number')
-end
-
-ibvars = cell(1, length(beam_vars));
-is_a_beam_var = @(sample_data, varname)(IMOS.var_contains_dim(sample_data, varname, 'DIST_ALONG_BEAMS'));
-
-c = 0;
-
-for k = 1:length(beam_vars)
-
-    if is_a_beam_var(sample_data, beam_vars{k})
-        c = c + 1;
-        ibvars{c} = beam_vars{k};
-    end
-
-end
-
-ibvars = ibvars(1:c);
-end
diff --git a/Preprocessing/adcpWorkhorseVelocityBeam2EnuPP.m b/Preprocessing/adcpWorkhorseVelocityBeam2EnuPP.m
index c642fc77d..1f50b7ff5 100644
--- a/Preprocessing/adcpWorkhorseVelocityBeam2EnuPP.m
+++ b/Preprocessing/adcpWorkhorseVelocityBeam2EnuPP.m
@@ -32,9 +32,14 @@
 
 sind = TeledyneADCP.find_teledyne_beam_datasets(sample_data,'HEIGHT_ABOVE_SENSOR');
 dind = TeledyneADCP.find_teledyne_beam_datasets(sample_data,'DIST_ALONG_BEAMS');
-if any(dind)
+if ~isempty(dind)
     for k=1:length(dind)
-        warnmsg('Performing beam2earth converison without bin-mapping/tilt correction for data in %s',sample_data{dind(k)}.toolbox_input_file)
+        dataset = sample_data{dind(k)};
+        warn_vars = IMOS.adcp.beam_vars(dataset);
+        for l=1:length(warn_vars)
+            vname = warn_vars{l};
+            dispmsg('Performing beam2earth converison without bin-mapping/tilt correction for variable %s in dataset %s',vname,dataset.toolbox_input_file);
+        end
     end
     sind = union(sind, dind);
 end
@@ -92,7 +97,6 @@
 
     Beam2EnuComment = ['adcpWorkhorseVelocityBeam2EnuPP.m: velocity data in Easting Northing Up (ENU) coordinates has been calculated from velocity data in Beams coordinates ' ...
         'using heading and tilt information and instrument coordinate transform matrix.'];
- 
 
     %change in place.
     sample_data{ind}.variables{vel1_ind}.name = vel_vars{1};
@@ -119,7 +123,8 @@
 
     no_toolbox_tilt_correction = isfield(sample_data{ind}, 'history') && ~contains(sample_data{ind}.history, 'adcpBinMappingPP');
     if no_toolbox_tilt_correction
-        warnmsg('WARNING: Bin-Mapping not applied for %s. Data is converted to ENU coordinates without tilt corrections.',sample_data{ind}.toolbox_input_file)
+        %TODO: using warnmsg here would be too verbose - we probably need another function with the scope report level as argument.
+        dispmsg('WARNING: Bin-Mapping not applied for %s. Data is converted to ENU coordinates without tilt corrections.',sample_data{ind}.toolbox_input_file)
         % compat: Change dimensions to HEIGHT_ABOVE_SENSOR, since this would be done at adcpBinMappingPP.
         %
         % height_above_sensor_ind = IMOS.find(sample_data{ind}.dimensions,'HEIGHT_ABOVE_SENSOR');
diff --git a/Util/+IMOS/+adcp/beam_vars.m b/Util/+IMOS/+adcp/beam_vars.m
new file mode 100644
index 000000000..9d79530d8
--- /dev/null
+++ b/Util/+IMOS/+adcp/beam_vars.m
@@ -0,0 +1,106 @@
+function [ibvars] = beam_vars(sample_data, n)
+%function [ibvars] = beam_vars(sample_data,n)
+%
+% Get the available beam variable names
+% based on the beam number.
+% If beam number is not provided, all variables
+% names that are along beams are returned.
+%
+% Inputs:
+%
+% sample_data [struct] - the toolbox struct.
+% n [double] - the beam number [1-4]
+%
+% Outputs:
+%
+% ibvars [cell{str}] - the variable names associated
+%                      with the beam number.
+%
+% Example:
+%
+% time = (1:100)';
+% dab = (1:10)';
+% dummy = zeros(100,10);
+% type = @double;
+% dims = IMOS.gen_dimensions('adcp',2,{'TIME','DIST_ALONG_BEAMS'},{type,type},{time,dab});
+% vars = IMOS.gen_variables(dims,{'VEL1','ABSIC1','VEL3','ABSIC3'},{type,type,type,type},{dummy,dummy,dummy,dummy});
+% sample_data.dimensions = dims;
+% sample_data.variables = vars;
+% beam_vars_1 = IMOS.adcp.beam_vars(sample_data,1);
+% assert(numel(whereincell(beam_vars_1,{'ABSIC1','VEL1'}))==2)
+% assert(numel(whereincell(beam_vars_1,{'VEL3','ABSIC3'}))==0)
+%
+% %beam 3
+% beam_vars_3 = IMOS.adcp.beam_vars(sample_data,3);
+% assert(numel(whereincell(beam_vars_3,{'ABSIC1','VEL1'}))==0)
+% assert(numel(whereincell(beam_vars_3,{'VEL3','ABSIC3'}))==2)
+%
+% %all beams available
+% all_beams = IMOS.adcp.beam_vars(sample_data);
+% assert(numel(whereincell(all_beams,{'VEL1','ABSIC1','ABSIC3','VEL3'}))==4)
+%
+% %got a beam_variable name but dimensions are not aligned with DIST_ALONG_BEAMS
+% dummy = zeros(100,100);
+% vars = IMOS.gen_variables(dims,{'VEL1'},{type},{dummy});
+% sample_data.dimensions = dims;
+% sample_data.variables = vars;
+% beam_vars_1 = IMOS.adcp.beam_vars(sample_data,1);
+% assert(isempty(beam_vars_1))
+%
+%
+% author: hugo.oliveira@utas.edu.au
+%
+%
+narginchk(1, 2)
+
+if nargin<2
+	get_all_beam_vars = true;
+	n=inf;
+else
+	get_all_beam_vars = false;
+end
+
+
+if ~isstruct(sample_data)
+    error('Frist argument not a toolbox struct')
+end
+
+beam_vars_1 = {'ABSI1', 'ABSIC1', 'CMAG1', 'SNR1', 'VEL1'};
+beam_vars_2 = {'ABSI2', 'ABSIC2', 'CMAG2', 'SNR2', 'VEL2'};
+beam_vars_3 = {'ABSI3', 'ABSIC3', 'CMAG3', 'SNR3', 'VEL3'};
+beam_vars_4 = {'ABSI4', 'ABSIC4', 'CMAG4', 'VEL4'};
+
+switch n
+    case 1
+        beam_vars = beam_vars_1;
+    case 2
+        beam_vars = beam_vars_2;
+    case 3
+        beam_vars = beam_vars_3;
+    case 4
+        beam_vars = beam_vars_4;
+    otherwise
+		if get_all_beam_vars
+			beam_vars = [beam_vars_1, beam_vars_2, beam_vars_3, beam_vars_4];
+		else
+   	        errormsg('Second argument not a valid beam number')
+		end
+end
+
+%double check if dimensions are
+ibvars = cell(1, length(beam_vars));
+is_a_beam_var = @(sample_data, varname)(IMOS.var_contains_dim(sample_data, varname, 'DIST_ALONG_BEAMS'));
+
+c = 0;
+
+for k = 1:length(beam_vars)
+
+    if is_a_beam_var(sample_data, beam_vars{k})
+        c = c + 1;
+        ibvars{c} = beam_vars{k};
+    end
+
+end
+
+ibvars = ibvars(1:c);
+end
diff --git a/Util/+IMOS/+adcp/echo_intensity_variables.m b/Util/+IMOS/+adcp/echo_intensity_variables.m
new file mode 100644
index 000000000..bf12645bf
--- /dev/null
+++ b/Util/+IMOS/+adcp/echo_intensity_variables.m
@@ -0,0 +1,63 @@
+function [evars] = echo_intensity_variables(sample_data)
+% function [bool] = echo_intensity_variables(sample_data)
+%
+% Return variables names associated with echo intensity.
+% These are the variable commonly bin-mapped
+% (velocity & counts).
+%
+% Inputs:
+%
+% sample_data [struct] - a toolbox dataset.
+%
+% Outputs:
+%
+% evars [cell] - A cell with variable names.
+%
+% Example:
+%
+% %basic usage
+% x.variables{1}.name = 'ABSIC1';
+% x.variables{2}.name = 'VEL1';
+% x.variables{3}.name = 'X';
+% assert(inCell(IMOS.adcp.echo_intensity_variables(x),'ABSIC1'))
+% assert(inCell(IMOS.adcp.echo_intensity_variables(x),'VEL1'))
+% assert(~inCell(IMOS.adcp.echo_intensity_variables(x),'X'))
+%
+% y.variables{1}.name = 'UCUR';
+% y.variables{2}.name = 'DEPTH';
+% assert(inCell(IMOS.adcp.echo_intensity_variables(y),'UCUR'))
+% assert(~inCell(IMOS.adcp.echo_intensity_variables(y),'DEPTH'))
+%
+% author: hugo.oliveira@utas.edu.au
+%
+narginchk(1, 1)
+
+var_pool = {
+        'ABSI1', ...
+            'ABSIC1', ...
+            'CMAG1', ...
+            'SNR1', ...
+            'VEL1', ...
+            'UCUR', ...
+            'UCUR_MAG', ...
+            'ABSI2', ...
+            'ABSIC2', ...
+            'CMAG2', ...
+            'SNR2', ...
+            'VEL2', ...
+            'VCUR', ...
+            'VCUR_MAG', ...
+            'ABSI3', ...
+            'ABSIC3', ...
+            'CMAG3', ...
+            'SNR3', ...
+            'VEL3', ...
+            'WCUR', ...
+            'ABSI4', ...
+            'ABSIC4', ...
+            'CMAG4', ...
+            'VEL4', ...
+            'ECUR'
+        };
+evars = intersect(var_pool, IMOS.get(sample_data.variables, 'name'));
+end
diff --git a/Util/+IMOS/+adcp/is_along_beam.m b/Util/+IMOS/+adcp/is_along_beam.m
index 2b1dd7bf9..45d952c7c 100644
--- a/Util/+IMOS/+adcp/is_along_beam.m
+++ b/Util/+IMOS/+adcp/is_along_beam.m
@@ -2,6 +2,8 @@
 % function [bool] = is_along_beam(sample_data)
 %
 % Check if a dataset is defined along beam coordinates.
+% An along_beam dataset is one without the
+% `HEIGHT_ABOVE_SENSOR` dimension.
 %
 % Inputs:
 %
@@ -17,13 +19,14 @@
 % x.dimensions = IMOS.gen_dimensions('adcp');
 % assert(IMOS.adcp.is_along_beam(x));
 % x.dimensions{3}.name = 'HEIGHT_ABOVE_SENSOR';
-% assert(IMOS.adcp.is_along_beam(x));
-% x.dimensions{2}.name = 'HEIGHT_ABOVE_SENSOR';
 % assert(~IMOS.adcp.is_along_beam(x));
 %
 %
 % author: hugo.oliveira@utas.edu.au
 %
+narginchk(1,1)
+
 avail_dims = IMOS.get(sample_data.dimensions,'name');
-bool = inCell(avail_dims,'DIST_ALONG_BEAMS');
+bool = ~inCell(avail_dims,'HEIGHT_ABOVE_SENSOR');
+
 end
diff --git a/Util/+IMOS/+meta/site_bathymetry.m b/Util/+IMOS/+meta/site_bathymetry.m
index 74a982fbf..ee82d6837 100644
--- a/Util/+IMOS/+meta/site_bathymetry.m
+++ b/Util/+IMOS/+meta/site_bathymetry.m
@@ -18,11 +18,11 @@
 % Example:
 % sample_data.site_nominal_depth = [];
 % sample_data.site_depth_at_deployment = [];
-% assert(isempty(IMOS.meta.get_site_bathymetry(sample_data)))
+% assert(isempty(IMOS.meta.site_bathymetry(sample_data)))
 % sample_data.site_nominal_depth = 20;
-% assert(IMOS.meta.get_site_bathymetry(sample_data)==20)
+% assert(IMOS.meta.site_bathymetry(sample_data)==20)
 % sample_data.site_depth_at_deployment = 10;
-% assert(IMOS.meta.get_site_bathymetry(sample_data)==10)
+% assert(IMOS.meta.site_bathymetry(sample_data)==10)
 %
 % author: hugo.oliveira@utas.edu.au
 %
diff --git a/Util/+IMOS/featuretype_variables.m b/Util/+IMOS/featuretype_variables.m
index 6392dfd65..001fa703a 100644
--- a/Util/+IMOS/featuretype_variables.m
+++ b/Util/+IMOS/featuretype_variables.m
@@ -40,17 +40,17 @@
         ts_names = {'TIMESERIES', 'LATITUDE', 'LONGITUDE', 'NOMINAL_DEPTH'};
         ts_types = cellfun(@getIMOSType, ts_names, 'UniformOutput', false);
         ts_data = {1, NaN, NaN, NaN};
-        variables = IMOS.gen_variables(IMOS.gen_dimensions(ft), ts_names, ts_types, ts_data, 'comments', '');
+        variables = IMOS.gen_variables(IMOS.gen_dimensions(ft), ts_names, ts_types, ts_data, 'comment', '');
     case 'ad_profile'
         p_names = {'TIME', 'DIRECTION', 'LATITUDE', 'LONGITUDE', 'BOT_DEPTH'};
         p_types = cellfun(@getIMOSType, p_names, 'UniformOutput', false);
         p_data = {NaN, {'A', 'D'}, [NaN NaN], [NaN NaN], [NaN NaN]};
-        variables = IMOS.gen_variables(IMOS.gen_dimensions(ft), p_names, p_types, p_data, 'comments', '');
+        variables = IMOS.gen_variables(IMOS.gen_dimensions(ft), p_names, p_types, p_data, 'comment', '');
     case 'profile'
         p_names = {'PROFILE', 'TIME', 'DIRECTION', 'LATITUDE', 'LONGITUDE', 'BOT_DEPTH'};
         p_types = cellfun(@getIMOSType, p_names, 'UniformOutput', false);
         p_data = {1, NaN, {'D'}, NaN, NaN, NaN};
-        variables = IMOS.gen_variables(IMOS.gen_dimensions(ft), p_names, p_types, p_data, 'comments', '');
+        variables = IMOS.gen_variables(IMOS.gen_dimensions(ft), p_names, p_types, p_data, 'comment', '');
     otherwise
         warnmsg('FeatureType `%s` is not available.',featureType);
         variables = {};
diff --git a/Util/Path/FolderAbove.m b/Util/Path/FolderAbove.m
index 6895fb883..80fd7e9b4 100644
--- a/Util/Path/FolderAbove.m
+++ b/Util/Path/FolderAbove.m
@@ -14,10 +14,10 @@
 % above - a string with the folder above `level`.
 %
 % Example:
-% path = '/dev/shm/';
+% path = [toolboxRootPath() filesep 'Util'];
 % level = 1;
 % [above] = FolderAbove(path,level);
-% assert(strcmp(above,'/dev/'));
+% assert(contains(toolboxRootPath(),above));
 %
 % path = '/';
 % levle = 10;
diff --git a/Util/Path/filter_extensions.m b/Util/Path/filter_extensions.m
new file mode 100644
index 000000000..ca3434d51
--- /dev/null
+++ b/Util/Path/filter_extensions.m
@@ -0,0 +1,64 @@
+function [clean,removed] = filter_extensions(filenames,extensions)
+% function [clean,removed] = filter_(filenames)
+%
+% Given a cell, filter out file names with certain
+% extensions.
+%
+% Inputs:
+%
+% filenames[cell] - cell of file names
+% extensions[cell] - cell of file extensions
+%
+% Outputs:
+%
+% filtered - the filtered cell
+% removed - the members left out
+%
+% Example:
+%
+% %basic usage
+% files = {'a.m','b.txt','c.mat','d.log','e.nc'};
+% x = filter_extensions(files,'.mat');
+% assert(~inCell(x,'c.mat'))
+% x = filter_extensions(files,'.m');
+% assert(~inCell(x,'a.m'))
+% x = filter_extensions(files,{'.m','.txt','.mat','.nc'});
+% assert(isequal(x,{'d.log'}))
+%
+%
+% author: hugo.oliveira@utas.edu.au
+%
+narginchk(2,2)
+if ~iscellstr(filenames)
+	errormsg('First argument is not a cell of strings')
+elseif ~ischar(extensions) && ~iscellstr(extensions)
+	errormsg('Second argument is not a cell of strings')
+end
+
+if ischar(extensions)
+	extensions={extensions};
+end
+
+
+nf = numel(filenames);
+clean = cell(1,nf);
+removed = cell(1,nf);
+
+cc=0;
+cr=0;
+for k=1:numel(filenames)
+	file = filenames{k};
+	[~,~,ext] = fileparts(file);
+	if inCell(extensions,ext)
+		cr=cr+1;
+		removed{cr} = file;
+	else
+		cc=cc+1;
+		clean{cc} = file;
+	end
+end
+
+removed=removed(1:cr);
+clean=clean(1:cc);
+
+end
diff --git a/Util/Path/rdir.m b/Util/Path/rdir.m
index f43604aa6..cefb026e9 100644
--- a/Util/Path/rdir.m
+++ b/Util/Path/rdir.m
@@ -17,7 +17,7 @@
 %
 % %simple test with nest folders
 % [allfiles,allfolders] = rdir([toolboxRootPath 'Java']);
-% assert(sum(contains(allfolders,'Java/bin'))==4)
+% assert(sum(contains(allfolders,['Java' filesep 'src' filesep 'org']))==3)
 % assert(sum(contains(allfiles,'ddb.jar'))==1)
 %
 % author: hugo.oliveira@utas.edu.au
diff --git a/Util/Schema/isequal_ctype.m b/Util/Schema/isequal_ctype.m
index a7a9f0923..a4aee7115 100644
--- a/Util/Schema/isequal_ctype.m
+++ b/Util/Schema/isequal_ctype.m
@@ -1,57 +1,60 @@
 function [bool] = isequal_ctype(a, b),
-    % function [bool] = isequal_ctype(a,b),
-    %
-    % An enhanced isequal that compare type and content.
-    % This will not compare types of individual [cell,struct]
-    % [indexes,fieldnames]. For this, use treeDiff.
-    %
-    % Inputs:
-    %
-    % a - any non-class matlab variable.
-    % b - any non-class matlab variable.
-    %
-    % Outputs:
-    %
-    % bool - a boolean number representing if the type and content of
-    %        a and b are the same.
-    %
-    % Example:
-    % >>> a = 0,b=false;
-    % >>> assert(~isequal_ctype(a,b))
-    % >>> a = {0,int8(1),single(2),3.}, b = {false,int8(1),single(2),3.}
-    % >>> assert(isequal_ctype(a,b))
-    % >>> b{4} = 4.
-    % >>> assert(~isequal_ctype(a,b))
-    % >>> %matlab caveat - use treeDiff.m instead
-    % >>> a = struct('x',false), b = struct('x',0)
-    % >>> assert(isequal_ctype(a,b))
-    %
-    % author: hugo.oliveira@utas.edu.au
-    %
+% function [bool] = isequal_ctype(a,b),
+%
+% An enhanced isequal that compare type and content.
+% This will not compare types of individual [cell,struct]
+% [indexes,fieldnames]. For this, use treeDiff.
+%
+% Inputs:
+%
+% a - any non-class matlab variable.
+% b - any non-class matlab variable.
+%
+% Outputs:
+%
+% bool - a boolean number representing if the type and content of
+%        a and b are the same.
+%
+% Example:
+% a = 0;
+% b=false;
+% assert(~isequal_ctype(a,b))
+% a = {0,int8(1),single(2),3.};
+% b = {false,int8(1),single(2),3.};
+% assert(isequal_ctype(a,b))
+% b{4} = 4.;
+% assert(~isequal_ctype(a,b))
+% %matlab caveat - use treeDiff.m instead
+% a = struct('x',false);
+% b = struct('x',0);
+% assert(isequal_ctype(a,b))
+%
+% author: hugo.oliveira@utas.edu.au
+%
 
-    % Copyright (C) 2019, Australian Ocean Data Network (AODN) and Integrated
-    % Marine Observing System (IMOS).
-    %
-    % This program is free software: you can redistribute it and/or modify
-    % it under the terms of the GNU General Public License as published by
-    % the Free Software Foundation version 3 of the License.
-    %
-    % This program is distributed in the hope that it will be useful,
-    % but WITHOUT ANY WARRANTY; without even the implied warranty of
-    % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-    % GNU General Public License for more details.
-    %
-    % You should have received a copy of the GNU General Public License
-    % along with this program.
-    % If not, see <https://www.gnu.org/licenses/gpl-3.0.en.html>.
-    %
+% Copyright (C) 2019, Australian Ocean Data Network (AODN) and Integrated
+% Marine Observing System (IMOS).
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation version 3 of the License.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.
+% If not, see <https://www.gnu.org/licenses/gpl-3.0.en.html>.
+%
 
-    atype = whichtype(a);
-    btype = whichtype(b);
-    bool = isequal(atype, btype);
+atype = whichtype(a);
+btype = whichtype(b);
+bool = isequal(atype, btype);
 
-    if bool,
-        bool = isequaln(a, b);
-    end
+if bool,
+    bool = isequaln(a, b);
+end
 
 end
diff --git a/Util/Schema/treeDiff.m b/Util/Schema/treeDiff.m
index f2505aad8..94008dc59 100644
--- a/Util/Schema/treeDiff.m
+++ b/Util/Schema/treeDiff.m
@@ -223,7 +223,7 @@
             msg{end + 1} = compose(this_root, [': Content mismatch - evaluation of `' func2str(func) '( arg1' strtrim(asinput) ', arg2' strtrim(asinput) ')`'' failed\n']);
         else
             disp(asinput)
-            msg{end + 1} = compose(this_root, [': Content mismatch - evaluation of `' func2str(func) '( a' strtrim(asinput) ', b' strtrim(asinput) ')`'' failed\n']);
+            msg{end + 1} = compose(this_root, [': Content mismatch - evaluation of `' func2str(func) '( a[' type_a ']' strtrim(asinput) ', b[' type_b ']' strtrim(asinput) ')`'' failed\n']);
         end
 
         finalmsg = compose(this_root, gather(msg, stopfirst));
@@ -425,8 +425,7 @@
         b_len_within_larger = len_within_b{k} > len_within_a{k};
 
         if a_len_within_larger || b_len_within_larger,
-            msg = [': Length of entries mismatch - expected ' num2str(len_within_a{k}) ' got ' num2str(len_within_b{k}) '\n'];
-            return;
+            msg = [': Length of entries mismatch at cellindex/fieldname n=' num2str(k) '. Expected ' num2str(len_within_a{k}) ' got ' num2str(len_within_b{k}) '\n'];            return;
         end
 
     end
diff --git a/Util/TestUtils/checkDocstrings.m b/Util/TestUtils/checkDocstrings.m
index c997726bb..18e9265e8 100644
--- a/Util/TestUtils/checkDocstrings.m
+++ b/Util/TestUtils/checkDocstrings.m
@@ -1,16 +1,21 @@
-function [ok, wrong_files] = checkDocstrings(folder)
-% function [ok, wrong_files] = checkDocstrings(folder)
+function [ok, wrong_files, nfiles, error_msgs, missing_comment, missing_example] = checkDocstrings(folder)
+% function [ok, wrong_files, nfiles, error_msgs, missing_comment, missing_example] = checkDocstrings(folder)
 %
 % Check all matlab source file IMOS docstrings in a folder.
 %
 % Inputs:
-% 
+%
 % folder [str] - a string with the folder location.
 %
 % Outputs:
-% 
+%
 % ok [bool] - All docstrings are fine.
 % wrong_files - A cell where the evaluation of the docstring failed.
+% nfiles - The total number of files tested.
+% error_msgs - the msg triggered by the test evaluation.
+% missing_comment - A cell with files that are missing comments.
+% missing_example - A cell with files that are missing the Example
+%                  block from the toolbox docstring standard.
 %
 % Example:
 %
@@ -18,10 +23,11 @@
 % [ok,wrong_files] = checkDocstrings(folder);
 % assert(ok)
 % assert(isempty(wrong_files));
+% assert(false)
 %
 % author: hugo.oliveira@utas.edu.au
 %
-ok = false;
+narginchk(1,1)
 wrong_files = {};
 
 files = rdir(folder);
@@ -29,6 +35,11 @@
 	errormsg('No files present at %s folder',folder)
 end
 
+xunit_folder = fullfile(toolboxRootPath(),'test');
+not_a_xunit_test = @(x)(~contains(x,xunit_folder));
+non_xunit_tests = cellfun(not_a_xunit_test,files);
+files = files(non_xunit_tests);
+
 srcfiles = cell2mat(cellfun(@is_matlab,files,'UniformOutput',false));
 matlab_files = files(srcfiles);
 self_calling = contains(matlab_files,'checkDocstrings');
@@ -36,23 +47,40 @@
 	matlab_files(self_calling) = [];
 end
 nfiles = numel(matlab_files);
-
 oks = zeros(1,nfiles);
-for k=1:nfiles
+msgs = cell(1,nfiles);
+for k=1:numel(matlab_files)
 	file = matlab_files{k};
 	fprintf('%s: checking %s\n',mfilename,file)
-	[oks(k),~] = testDocstring(file);
+	[oks(k),msgs{k}] = testDocstring(file);
 end
 
 if all(oks)
 	ok = true;
+else
+	ok = false;
 end
 
-report = ~ok && nargout>1;
-if report
+if nargout > 1
 	wrong_files = matlab_files(~oks);
 end
 
+if nargout > 2
+	error_msgs = msgs(~oks);
+end
+
+if nargout > 3
+    check_comment = @(x)(contains(x,'No docstring block found in '));
+    lack_comment = cellfun(check_comment,msgs);
+    missing_comment = matlab_files(lack_comment);
+end
+
+if nargout > 4
+    check_example = @(x)(contains(x,'No docstring Example block found in '));
+    lack_example = cellfun(check_example,msgs);
+    missing_example = matlab_files(lack_example);
+end
+
 end
 
 function is_matlab = is_matlab(filestr)
diff --git a/Util/TestUtils/testDocstring.m b/Util/TestUtils/testDocstring.m
index e78ef124e..5c32d38ac 100644
--- a/Util/TestUtils/testDocstring.m
+++ b/Util/TestUtils/testDocstring.m
@@ -54,13 +54,20 @@
 
 [docstring_text, block_start_line] = readUntilMatch(fid, docstring_start_re, use_regex);
 if isempty(docstring_text)
-    ok = false;
-    msg = sprintf('No docstring Example block found in %s',filename);
+    ok = true;
+    msg = sprintf('No docstring block found in %s',filename);
+    fclose(fid);
     return
 end
 
 text_to_evaluate = readUntilMatch(fid, docstring_end_re, use_regex);
 text_to_evaluate = text_to_evaluate(1:end-1); % remove docstring_end_re match
+if isempty(text_to_evaluate)
+    ok = true;
+    msg = sprintf('No docstring Example block found in %s',filename);
+    fclose(fid);
+    return
+end
 
 [ok, msg] = commentEvalWrapper(text_to_evaluate, block_start_line, dbreak);
 
diff --git a/Util/detectMappingDelimiter.m b/Util/detectMappingDelimiter.m
index 29b8da894..a77fdc97c 100644
--- a/Util/detectMappingDelimiter.m
+++ b/Util/detectMappingDelimiter.m
@@ -16,7 +16,7 @@
 % %basic usage
 % comma_file = [toolboxRootPath 'GUI/instrumentAliases.txt'];
 % assert(isequal(detectMappingDelimiter(comma_file),','))
-% equal_file = [toolboxRootPath 'AutomaticQC/imosEchoIntensityQC.txt'];
+% equal_file = [toolboxRootPath 'AutomaticQC/imosEchoIntensitySetQC.txt'];
 % assert(isequal(detectMappingDelimiter(equal_file),'='))
 %
 %
@@ -38,7 +38,7 @@
 catch
 end
 
-try 
+try
 	equal_opts = readMappings(fname,'=');
 	equal_ok = true;
 catch
@@ -53,7 +53,7 @@
 	return
 elseif comma_ok
 	delimiter = ',';
-elseif equal_ok 
+elseif equal_ok
 	delimiter = '=';
 end
 
diff --git a/Util/memuse.m b/Util/memuse.m
index 5eeeea0af..27dcc3668 100644
--- a/Util/memuse.m
+++ b/Util/memuse.m
@@ -15,17 +15,17 @@
 %
 % Example:
 %
-% x = memuse(1048576,'logical')
+% x = memuse(1048576,'logical');
 % assert(x==1)
-% x = memuse(1048576,'double')
+% x = memuse(1048576,'double');
 % assert(x==8)
-% x = memuse(1048576,'single')
+% x = memuse(1048576,'single');
 % assert(x==4)
 %
 % %we dont introspect content for cells/struct
-% x = memuse(1,'struct')
+% x = memuse(1,'struct');
 % assert(isinf(x))
-% x = memuse(1,'cell')
+% x = memuse(1,'cell');
 % assert(isinf(x))
 %
 %
diff --git a/Util/updateMappings.m b/Util/updateMappings.m
index bd3b4b6b1..30e46e7c5 100644
--- a/Util/updateMappings.m
+++ b/Util/updateMappings.m
@@ -5,10 +5,10 @@ function updateMappings(fname, name, value)
 % preserving the previous state of the file,
 % including comments.
 %
-% A mapping/property file is a text file with the 
+% A mapping/property file is a text file with the
 % the first column of the file is a key,
 % the second column is a value.
-% 
+%
 % The function will fail if the property can't be found.
 %
 %
@@ -23,7 +23,7 @@ function updateMappings(fname, name, value)
 %
 % Example:
 %
-% file = [toolboxRootPath 'test_updateMappings'];
+% file = [toolboxRootPath 'tmp/test_updateMappings'];
 % nf = fopen(file,'w');
 % fprintf(nf,'%s\n','%1st line is a comment');
 % fprintf(nf,'%s\n','zero = a');
diff --git a/batchTesting.m b/batchTesting.m
index ea7c37938..f7b943957 100644
--- a/batchTesting.m
+++ b/batchTesting.m
@@ -1,16 +1,19 @@
-function batchTesting(parallel)
+function batchTesting(parallel,print_stats)
 % function batchTesting(parallel)
 %
-% Execute all the xunit Test functions of the toolbox
-% in batch mode.
+% Execute all the xunit Test functions
+% and docstring tests
 %
 % Inputs:
 %
-% parallel - true for parallel execution
+% parallel[bool] - true for parallel execution.
+% print_stats[bool] = true for printing statistics.
 %
 % Example:
 %
-% batchTesting(1)
+% % trigger all tests hiding the output
+% % and running all serially
+% %batchTesting(0,1);
 %
 % author: hugo.oliveira@utas.edu.au
 %
@@ -31,97 +34,167 @@ function batchTesting(parallel)
 % along with this program.
 % If not, see <https://www.gnu.org/licenses/gpl-3.0.en.html>.
 %
+narginchk(0, 2)
 
-csplit = strsplit(mfilename('fullpath'),[ filesep 'batchTesting']);
+if nargin == 0
+    parallel = false;
+    print_stats = true;
+elseif nargin == 1
+    print_stats = true;
+end
+
+csplit = strsplit(mfilename('fullpath'), 'batchTesting');
 root_folder = csplit{1};
 addpath([root_folder filesep 'Util' filesep 'Path'])
 setToolboxPaths(root_folder)
 
 try
-    results = runAllTests(parallel)%do not supress report output
-catch
-    error('Tests failed')
+    sdisp('Executing `xunit` tests...')
+    results = runAllTests(parallel);
+    total_xunit_tests = length(results);
+catch me
+    sdisp('`xunit` tests aborted. Please investigate the error:')
+    rethrow(me)
+end
+
+xunit_failed = [results(:).Failed];
+xunit_n_failed = sum(xunit_failed);
+xunit_skipped = ~xunit_failed & [results(:).Incomplete];
+xunit_n_skipped = sum(xunit_skipped);
+[xunit_failed_files, xunit_failed_tests, xunit_failed_lines] = get_xunit_stats(results(xunit_failed));
+[xunit_skipped_files, xunit_skipped_tests, xunit_skipped_lines] = get_xunit_stats(results(xunit_skipped));
+
+try
+    sdisp('Executing `docstring` tests...')
+    [ok, wrong_files, total_docstring_tests, error_msgs, missing_comment, missing_example] = checkDocstrings(toolboxRootPath());
+catch me
+    sdisp('Could not run `docstring` tests!')
+    rethrow(me)
 end
 
-failed = {'    Tests failed:\n'};
-c = 2;
+docstring_n_failed = length(wrong_files);
+docstring_n_skipped = length(missing_comment) + length(missing_example);
+
+failed_files = [xunit_failed_files, wrong_files];
+failed_tests = [xunit_failed_tests, wrong_files];
+failed_lines = [xunit_failed_lines, get_docstring_failed_lines(error_msgs)];
 
-%pretty print the results of failed tests.
-for k = 1:length(results)% loop through all results
-    ktest = results(k); %get k-results
+total_tests = total_xunit_tests + total_docstring_tests;
+total_failed = xunit_n_failed + docstring_n_failed;
+total_skipped = xunit_n_skipped + docstring_n_skipped;
 
-    if ~ktest.Passed
-        fparam = extract_param(ktest.Name); % extract all test parameters
-        fnames = fieldnames(fparam); %get parameter names
-        fnames = fnames(2:end); % remove the testname from the list
+total_missing_comment = length(missing_comment);
+total_missing_docstrings = length(missing_example);
 
-        %now create a pretty string
-        fstr = [repmat(' ', 1, length(failed{1})) fparam.testname ':\n'];
-        lfstr = length(fstr)
+if ~print_stats
+    return
+end
 
-        for kk = 1:length(fnames)
-            fstr = [fstr repmat(' ', 1, lfstr) fnames{kk} '->' fparam.(fnames{kk}) '\n'];
+sdisp('    ')
+sdisp('    ')
+sdisp('----IMOS toolbox Test Coverage Summary----')
+sdisp('----XUnit` test statistics and `docstrings` inspection in all matlab files in the repository----')
+sdisp('    Total number of tests evaluations: %d (%d `xunit` tests and %d docstrings',total_tests,total_xunit_tests,total_docstring_tests);
+sdisp('    Total number of failed tests: %d (%d xunit, %d source files)',total_failed,xunit_n_failed,docstring_n_failed);
+sdisp('    Total number of skipped tests: %d (%d xunit, %d source files)',total_skipped,xunit_n_skipped,docstring_n_skipped);
+sdisp('    ');
+if total_failed > 0
+    sdisp('Failed tests are:')
+    for k=1:length(failed_files)
+        if strcmp(failed_files{k},failed_tests{k})
+            sdisp('    file/test=%s,line=%s',failed_files{k},failed_lines{k})
+        else
+            sdisp('    file=%s,test=%s,line=%s',failed_files{k},failed_tests{k},failed_lines{k})
         end
+    end
+end
+
 
-        fstr = [fstr '\n'];
-        failed{c} = fstr; % store the string for subsequent failed tests if any
-        c = c + 1;
+if total_skipped > 0
+    if ~isempty(xunit_skipped_files)
+        sdisp('Skipped xunit tests are:')
+        for k=1:length(xunit_skipped_files)
+            sdisp('    test=%s',xunit_skipped_files{k})
+        end
+    end
+    if ~isempty(missing_comment)
+        sdisp('Skipped docstring tests are:')
+        for k=1:length(missing_comment)
+            sdisp('    file=%s, reason: missing docstring block',missing_comment{k});
+        end
     end
 
+    if ~isempty(missing_example)
+        for k=1:length(missing_example)
+            sdisp('    test=%s, reason: missing example block',missing_example{k});
+        end
+    end
 end
 
-if length(failed) > 1
-    error(sprintf(strjoin(failed)))
+
 end
 
+function [failed_files, failed_tests, failed_lines] = get_xunit_stats(results)
+n = length(results);
+failed_files = cell(1, n);
+failed_tests = cell(1, n);
+failed_lines = cell(1, n);
+
+for k = 1:n
+    test = results(k);
+    failed_files{k} = get_testfile(test);
+    failed_tests{k} = get_testname(test);
+    failed_lines{k} = get_blameline(test);
 end
 
-function params = extract_param(namestr)
-% function extract_param(namestr)
-%
-% Extract the name parameters used in the test
-% based on the name of the test.
-%
-% Inputs:
-%
-% namestr - the name of the test in the TestResult array.
-%
-% Example:
-%
-% testname_str='mytest(myparam='abc',myparam2='cba',folder='p__home_user_S');
-% params=extract_param(testname_str);
-% assert(strcmpi(params.testname,'mytest'))
-% assert(strcmpi(params.myparam,'abc'))
-% assert(strcmpi(params.myparam2,'cba'))
-% assert(strcmpi(params.folder='/home/user'))
-%
-% author: hugo.oliveira@utas.edu.au
+end
+
+function [clines] = get_docstring_failed_lines(error_msgs)
+clines = cell(1, length(error_msgs));
+
+for k = 1:length(clines)
+    s = find(error_msgs{k} == '(', 1);
+    e = find(error_msgs{k} == ')', 1);
+    clines{k} = error_msgs{k}(s:e);
+end
+
+end
+
+function file = get_testfile(r)
+
+try
+    file = r.Details.DiagnosticRecord.Stack(1).file;
+catch
+    sname = split(r.Name,'/');
+    file = sname{1};
+end
+
+end
 
-params = struct();
+function testname = get_testname(r)
 
-tmp = strsplit(namestr, '(');
-tmp2 = strsplit(tmp{1}, fileSep);
-params.testname = tmp2{end};
+try
+    testname = r.Details.DiagnosticRecord.Stack(1).name;
+catch
+    try
+        testname = replace(r.Details.DiagnosticRecord.EventLocation, '/', '.');
+    catch
+        testname = 'Unknown test';
+    end
+end
 
-pcell = strsplit(namestr, ',');
+end
 
-tmp = strsplit(pcell{1}, '(');
-tmp2 = strsplit(tmp{end}, '=');
-pname = tmp2{1};
-pval = tmp2{2};
-params.(pname) = pval;
+function blameline = get_blameline(r)
 
-for k = 2:length(pcell) - 1
-    tmp = strsplit(pcell{k}, '=');
-    pname = tmp{1};
-    pval = tmp{2};
-    params.(pname) = pval;
+try
+    blameline = r.Details.DiagnosticRecord.Stack(1).line;
+catch
+    blameline = 'Unknown line';
 end
 
-tmp = strsplit(pcell{end}, ')');
-tmp2 = strsplit(tmp{1}, '=');
-pname = tmp2{1};
-pval = tmp2{2};
-params.(pname) = pval;
+end
 
+function sdisp(varargin)
+    disp(sprintf(varargin{:}));
 end
diff --git a/build.py b/build.py
index 2cda57abd..377aeb1ae 100755
--- a/build.py
+++ b/build.py
@@ -1,25 +1,29 @@
 #!/usr/bin/env python3
-"""Build the imos stand-alone toolbox GUI using only the Matlab compiler.
+"""This script will build the imos stand-alone toolbox GUI using the Matlab compiler.
 
-This script ignores untracked and testfiles within the repository and weakly
-attach a string version to the binary filename.
-The string is related to the repo state.
+Support both Linux and Windows. See the `--arch` flag.
 
 Usage:
-  build.py  --arch=<architecture> [--root_path=<imostoolboxpath> --mcc_path=<mccpath> --dist_path=<distpath>]
+    build.py [--arch=<architecture> --check-repo-only --dry-run --build-java-deps  --root_path=<imostoolboxpath> --matlab_path=<mccpath> --dist_path=<distpath>]
 
 Options:
-  -h --help     Show this screen.
-  --version     Show version.
-  --mcc_path=<mccpath>           The Matlab runtime Path
-  --root_path=<imostoolboxpath>  The repository root path
-  --dist_path=<distpath>  Where Compiled items should be stored
-  --arch=<architecture>   One of win64,glnxa64,maci64
+    -h --help    Show this screen.
+    --version    Show version.
+    --arch=<architecture>    One of win64,glnxa64,maci64.
+    --check-repo-only   Just do a Repository check, no build steps.
+    --dry-run   Just do all the checks, but don't build anything
+    --build-java-deps    Build of java libraries.
+    --matlab_path=<matlabpath>    The Matlab install path.
+    --root_path=<imostoolboxpath>    The repository root path
+    --dist_path=<distpath>    Where Compiled items should be stored
 
 """
 
 import os
+import sys
+import platform
 import subprocess as sp
+from socket import gethostname
 from getpass import getuser
 from pathlib import Path
 from shutil import copy
@@ -35,41 +39,54 @@
 }
 VERSION_FILE = ".standalone_canonical_version"
 MATLAB_VERSION = "R2018b"
+
+#below are the toolboxes root folder within R2018b/
 MATLAB_TOOLBOXES_TO_INCLUDE: List[str] = [
-    "signal/signal",
-    "stats/stats",
-    "images/imuitools",
+    ['signal','signal'],
+    ['stats','stats'],
+    ['images','imuitools'],
 ]
 
+DEFAULT_MATLAB_ROOT_PATH = {
+    "glnxa64": os.path.join("/opt/MATLAB/", MATLAB_VERSION),
+    "maci64": os.path.join("/Applications/MATLAB/", MATLAB_VERSION),
+    "win64": os.path.join("C:\\Program Files\\", "\\MATLAB\\", MATLAB_VERSION),
+}
+
+MATLAB_ROOT_PATH_OPTS = {
+    "glnxa64": [
+        "/opt/",
+        "/usr/local/",
+        os.path.join("/home", getuser()),
+        os.path.join("/home", getuser(), "." + gethostname(), "apps"),
+    ],
+    "maci64": ["/Applications/", "/Users", "/"],
+    "win64": ["C:\\Program Files\\"],
+}
+
+MATLAB_COMPILER_FILENAME = {"glnxa64": "mcc", "maci64": "mcc", "win64": "mcc.bat"}
+
 
 def find_matlab_rootpath(arch_str):
     """Locate the matlab installation root path."""
 
-    if arch_str != "win64":
-        fname = f"*/MATLAB/{MATLAB_VERSION}"
-        if arch_str == "glnxa64":
-            lookup_folders = [
-                "/usr/local/",
-                "/opt",
-                f"/home/{os.environ['USER']}",
-                "/usr",
-            ]
-        elif arch_str == "maci64":
-            lookup_folders = ["/Applications/", "/Users"]
-    else:
-        fname = f"**\\MATLAB\\{MATLAB_VERSION}"
-        lookup_folders = ["C:\\Program Files\\"]
+    default_root_path = Path(DEFAULT_MATLAB_ROOT_PATH[arch_str])
+    if default_root_path.exists():
+        return str(default_root_path)
+
+    print(f"Matlab is not installed in the default directory. Searching some common options for arch={arch_str}...")
 
+    lookup_folders = MATLAB_ROOT_PATH_OPTS[arch_str]
     for folder in lookup_folders:
-        m_rootpath = list(Path(folder).glob(fname))
-        if m_rootpath:
-            return m_rootpath[0]
+        rootpath = Path(folder, "MATLAB", MATLAB_VERSION)
+        if rootpath.exists():
+            return rootpath
     raise ValueError("Unable to find matlab root path")
 
 
 def run(command: str):
     """Run a command at shell/cmdline."""
-    return sp.run(command, shell=True, check=True)
+    return sp.run(command, shell=True, stdout=sp.PIPE, stderr=sp.PIPE)
 
 
 def create_java_call_sig_compile(root_path: str) -> str:
@@ -116,16 +133,16 @@ def git_info(root_path: str) -> dict:
         version += info["tag"]
     else:
         version += info["branch"]
-        version += "-" + info["username"]
-        version += "-" + info["tag"]
+        version += "|" + info["username"]
+        version += "|" + info["tag"]
         if info["is_dirty"]:
-            version += "-dirty"
+            version += "|dirty"
 
     info["version"] = version
     return info
 
 
-def find_files_and_folders(path: str) -> [list, list]:
+def find_files_and_folders(path: str) -> (list, list):
     """Find both files and folders recursively in a current path."""
     pfolder: Path.PosixPath = Path(path)
     all_folders: list = [
@@ -181,8 +198,7 @@ def find_items(folder: str) -> dict:
         x.as_posix()
         for x in all_files
         if "data/testfiles/" not in x.as_posix()
-        if x.suffix == ".mat"
-        and "/+" not in x.parent.as_posix()
+        if x.suffix == ".mat" and "/+" not in x.parent.as_posix()
     ]
 
     items["standard_miscfiles"] = [
@@ -211,12 +227,6 @@ def get_required_files(root_path: str, info: dict) -> (list, list):
     allpackages = items["standard_packages"]
     allmiscfiles = items["standard_miscfiles"]
 
-    if info["is_dirty"]:
-        print(f"Warning: {root_path} repository is dirty")
-    if info["modified_files"]:
-        print(f"Warning: {root_path} got modified files not staged")
-    if info["staged_files"]:
-        print(f"Warning: {root_path} got staged files not commited")
     if info["untracked_files"]:
         print(f"Warning: {root_path} got untracked files - Ignoring them all...")
         for ufile in info["untracked_files"]:
@@ -237,6 +247,7 @@ def get_required_files(root_path: str, info: dict) -> (list, list):
 
 
 def create_mcc_call_sig(
+    matlab_root_path: str,
     mcc_path: str,
     root_path: str,
     dist_path: str,
@@ -260,9 +271,8 @@ def create_mcc_call_sig(
     matpackages_str = " ".join([f"-a {folder}" for folder in matpackages])
 
     if MATLAB_TOOLBOXES_TO_INCLUDE:
-        matlab_root_path = find_matlab_rootpath(arch)
         extra_toolbox_paths = [
-            os.path.join(matlab_root_path, "toolbox", x)
+            os.path.join(matlab_root_path, "toolbox", *x) #beware of path joins in windows
             for x in MATLAB_TOOLBOXES_TO_INCLUDE
         ]
 
@@ -282,8 +292,11 @@ def create_mcc_call_sig(
     )
 
     if arch == "win64":
+        # overcome the incapacity to execute a file with a valid full path in windows
+        mcc_path = 'mcc'
+        # overcome cmd.exe char limitation creating a tmp mfile and asking
+        # matlab to evaluate a string. (yes...)
         tmpscript = os.path.join(root_path, "tmpbuild.m")
-        # overcome cmd.exe limitation of characters by creating a tmp mfile
         with open(tmpscript, "w") as tmpfile:
             # overcome limitation of spaces within eval.
             if MATLAB_TOOLBOXES_TO_INCLUDE:
@@ -311,9 +324,9 @@ def create_mcc_call_sig(
     return rlist
 
 
-def get_args(args: dict) -> Tuple[str, str, str, str]:
-    """process the cmdline arguments to return the root_path, dist_path, mcc binary, and
-    architecture."""
+def get_args(args: dict) -> Tuple[str, str, str, str, str, str]:
+    """process the cmdline arguments."""
+
     if not args["--root_path"]:
         root_path = os.getcwd()
     else:
@@ -327,19 +340,52 @@ def get_args(args: dict) -> Tuple[str, str, str, str]:
     else:
         dist_path = args["--dist_path"]
 
-    if not args["--mcc_path"]:
-        mcc_path = "mcc"
+
+    if not args["--arch"]:
+        bits,linkage = platform.architecture()
+        if bits != '64bit':
+            raise Exception("32bit platforms are not supported.")
+
+        if linkage == 'ELF':
+            arch = 'glnxa64'
+        elif linkage == 'WindowsPE':
+            arch = 'win64'
+        else:
+            raise Exception(f"Architecture {linkage} is not supported")
     else:
-        mcc_path = args["--mcc_path"]
+        if args["--arch"] in VALID_ARCHS:
+            ind = VALID_ARCHS.index(args["--arch"])
+            arch = VALID_ARCHS[ind]
+        else:
+            raise Exception(
+                f"{args['--arch']} is not one of the valid architectures {VALID_ARCHS}",
+            )
+
+    compiler_filename = MATLAB_COMPILER_FILENAME[arch]
 
-    if args["--arch"] in VALID_ARCHS:
-        ind = VALID_ARCHS.index(args["--arch"])
-        arch = VALID_ARCHS[ind]
+    if args["--matlab_path"] and isinstance(args["--matlab_path"], str):
+        matlab_root_path = Path(args["--matlab_path"])
+        if matlab_root_path.exists():
+            mcc_path = Path(matlab_root_path, "bin", compiler_filename)
     else:
+        matlab_root_path = find_matlab_rootpath(arch)
+        mcc_path = Path(matlab_root_path, "bin", compiler_filename)
+
+    if not mcc_path.exists():
         raise Exception(
-            f"{args['--arch']} is not one of the valid architectures {VALID_ARCHS}",
+            f"Missing the mcc compiler at {matlab_root_path}. Please install the Matlab compiler toolbox."
         )
-    return root_path, dist_path, mcc_path, arch
+    else:
+        mcc_path = str(mcc_path)
+
+    return (
+        root_path,
+        dist_path,
+        matlab_root_path,
+        mcc_path,
+        arch,
+        args["--build-java-deps"],
+    )
 
 
 def write_version(afile: str, version: str) -> None:
@@ -351,21 +397,45 @@ def write_version(afile: str, version: str) -> None:
 if __name__ == "__main__":
     args = docopt(__doc__, version="0.1")
 
-    root_path, dist_path, mcc_path, arch = get_args(args)
+    root_path, dist_path, matlab_root_path, mcc_path, arch, build_java = get_args(args)
     repo_info = git_info(root_path)
 
-    print("Starting build process.")
-    print(f"Marking {repo_info['version']} as the standalone version")
-    write_version(VERSION_FILE, repo_info["version"])
+    print(f"Starting build process for {ARCH_NAMES[arch]}")
+    print(
+        f"The repository version mashup [branch|user|tag|rstatus] is : {repo_info['version']}"
+    )
+    print("Current repo information:")
+    for k, v in repo_info.items():
+        print(f"    {k}:{v}")
+
+    if not repo_info["untracked_files"]:
+        print("Warning: Untracked files in the repository. These will NOT be included.")
+
+    if not repo_info["staged_files"]:
+        print(
+            "Warning: Found non-commited changes! These modifications will be included in the stand-alone app!"
+        )
+
+    if not repo_info["modified_files"]:
+        print(
+            "Warning: Found non-staged files in the repository! These modifications will be included in the stand-alone app!"
+        )
+
+    if args['--check-repo-only']:
+        sys.exit()
+
+    if not args['--dry-run']:
+        write_version(VERSION_FILE, repo_info["version"])
 
     # output name of binary is restricted in mcc
     tmp_name = f"imosToolbox_{ARCH_NAMES[arch]}"
 
-    print("Gathering files to be included")
+    print("Gathering files to be included...")
     mfiles, datafiles, matpackages = get_required_files(root_path, repo_info)
     java_call = create_java_call_sig_compile(root_path)
 
     mcc_call = create_mcc_call_sig(
+        matlab_root_path,
         mcc_path,
         root_path,
         dist_path,
@@ -376,37 +446,40 @@ def write_version(afile: str, version: str) -> None:
         matpackages=matpackages,
     )
 
-    print("Current repo information:")
-    print(repo_info)
-
-    print(f"Building Java dependencies")
-    print(f"Calling {java_call}..")
-    ok = run(java_call)
-    if not ok:
-        raise Exception(f"{jcall} failed")
+    if build_java:
+        print(f"Building Java dependencies")
+        print(f"Calling `{java_call}`")
+        if not args['--dry-run']:
+            rstatus = run(java_call)
+            if rstatus.returncode is not 0:
+                raise Exception(f"`{java_call}` command failed. Stderr is: {rstatus.stderr}")
+            else:
+                if not rstatus.stdout:
+                    print(f"{rstatus.stdout}")
+    else:
+        print(f"Building Java dependencies skipped.")
 
     print(f"Building Matlab dependencies")
-    print(f"Calling {mcc_call}...")
+    print(f"Calling `{mcc_call}`")
     for mcall in mcc_call:
-        print(f"Executing {mcall}")
-        ok = run(mcall)
-        if not ok:
-            raise Exception(f"{mcall} failed")
-
-    print(f"The toolbox architecture is {ARCH_NAMES[arch]}.")
-    print(f"Git version information string is {repo_info['version']}")
-    print(f"Updating binary at {root_path}....")
+        print(f"Executing the mcc call: {mcall}")
+        if not args['--dry-run']:
+            ok = run(mcall)
+            if not ok:
+                raise Exception(f"{mcall} failed")
 
+    print(f"Updating binary at {root_path}")
     # mcc append .exe to end of file
-    if arch == "win64":
-        copy(
-            os.path.join(dist_path, tmp_name + ".exe"),
-            os.path.join(root_path, tmp_name + ".exe"),
-        )
-    else:
-        copy(
-            os.path.join(dist_path, tmp_name),
-            os.path.join(root_path, tmp_name + ".bin"),
-        )
+    if not args['--dry-run']:
+        if arch == "win64":
+            copy(
+                os.path.join(dist_path, tmp_name + ".exe"),
+                os.path.join(root_path, tmp_name + ".exe"),
+            )
+        else:
+            copy(
+                os.path.join(dist_path, tmp_name),
+                os.path.join(root_path, tmp_name + ".bin"),
+            )
 
     print("Build Finished.")
diff --git a/imosToolbox.m b/imosToolbox.m
index 519733b0a..f97c8e1bf 100644
--- a/imosToolbox.m
+++ b/imosToolbox.m
@@ -37,7 +37,7 @@ function imosToolbox(auto, varargin)
 %
 
 % Set current toolbox version
-toolboxVersion = ['2.6.12 - ' computer];
+toolboxVersion = ['2.6.13 - ' computer];
 
 if nargin == 0, auto = 'manual'; end
 
diff --git a/imosToolbox_Linux64.bin b/imosToolbox_Linux64.bin
index 3018708ec..d8d961fa7 100755
Binary files a/imosToolbox_Linux64.bin and b/imosToolbox_Linux64.bin differ
diff --git a/imosToolbox_Win64.exe b/imosToolbox_Win64.exe
index e28c2e865..341190e00 100644
Binary files a/imosToolbox_Win64.exe and b/imosToolbox_Win64.exe differ
diff --git a/runalltests.bat b/runalltests.bat
index 4244ab31e..accec1664 100755
--- a/runalltests.bat
+++ b/runalltests.bat
@@ -1,7 +1,7 @@
 @echo off
 if exist data (
 echo "Loading the IMOS-Toolbox Tests..."
-matlab -nosplash -nodesktop -r "batchTesting(0)"
+matlab -nosplash -r "batchTesting(0,1);"
 echo "Please check the tests reports in the command line window...") else (
 echo "Cannot run tests - please obtain all test files first with the get_testfiles.py script."
 )
diff --git a/runalltests.sh b/runalltests.sh
index b886d2585..fe19d8372 100755
--- a/runalltests.sh
+++ b/runalltests.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 if [ -d "data" ]; then
-  matlab -nosplash -nodesktop -r "batchTesting(0);exit"
+  matlab -nosplash -nodesktop -r "batchTesting(1,1);exit"
 else
   echo "Cannot run tests - please obtain all test files first with the get_testfiles.py script."
   exit 1
diff --git a/test/AutomaticQC/test_SpikeClassifiers.m b/test/AutomaticQC/test_SpikeClassifiers.m
index a745071b3..4b08ba528 100644
--- a/test/AutomaticQC/test_SpikeClassifiers.m
+++ b/test/AutomaticQC/test_SpikeClassifiers.m
@@ -1,7 +1,7 @@
 classdef test_SpikeClassifiers < matlab.unittest.TestCase
 
     properties (TestParameter)
-        plot_figure = {true}; %,false};
+        plot_figure = {ismember('plot_test_figures',who('global'))};
     end
 
     methods (Test)
@@ -208,7 +208,7 @@ function test_bursthampel(~,plot_figure)
             burst_interval = 3600/86400;
             bind = {[1,60], [61,120], [121,180],[181,240]};
             time = [0:1:59, 3600:1:3659, 7200:1:7259, 10800:1:10859];
-            osig = [12+randc(1,60),12+randc(1,60),18+randc(1,60),18+randc(1,60)];
+            osig = [12+randomBetween(-.5,.5,60),12+randomBetween(-.5,.5,60),18+randomBetween(-.5,.5,60),18+randomBetween(-.5,.5,60)];
             ssig = osig;
             spikes = 121;
             ssig(spikes) = 25;
@@ -239,7 +239,7 @@ function test_burststats(~,plot_figure)
             burst_interval = 3600/86400;
             bind = {[1,60], [61,120], [121,180],[181,240]};
             time = [0:1:59, 3600:1:3659, 7200:1:7259, 10800:1:10859];
-            osig = [12+randc(1,60),12+randc(1,60),18+randc(1,60),18+randc(1,60)];
+            osig = [12+randomBetween(-.5,.5,60),12+randomBetween(-.5,.5,60),18+randomBetween(-.5,-.5,60),18+randomBetween(-.5,.5,60)];
             ssig = osig;
             spikes = 121;
             ssig(spikes) = 25;
diff --git a/test/AutomaticQC/test_imosEchoIntensitySetQC.m b/test/AutomaticQC/test_imosEchoIntensitySetQC.m
index 34920acfa..b5f9412be 100644
--- a/test/AutomaticQC/test_imosEchoIntensitySetQC.m
+++ b/test/AutomaticQC/test_imosEchoIntensitySetQC.m
@@ -1,223 +1,247 @@
 classdef test_imosEchoIntensitySetQC < matlab.unittest.TestCase
 
     properties (TestParameter)
-        zdim = {'HEIGHT_ABOVE_SENSOR','DIST_ALONG_BEAMS'}
+        zdim = {'HEIGHT_ABOVE_SENSOR', 'DIST_ALONG_BEAMS'}
     end
 
     methods (TestMethodTeardown)
+
         function reset_default_options(~)
             file = which('imosEchoIntensitySetQC');
-            file(end:end+2) = 'txt';
-            updateMappings(file,'echo_intensity_threshold',50);
-            updateMappings(file,'bound_by_depth',0);
-            updateMappings(file,'bound_by_index',0);
-            updateMappings(file,'bound_value',99999);
-            updateMappings(file,'propagate',0);
+            file(end:end + 2) = 'txt';
+            updateMappings(file, 'echo_intensity_threshold', 50);
+            updateMappings(file, 'bound_by_depth', 0);
+            updateMappings(file, 'bound_by_index', 0);
+            updateMappings(file, 'bound_value', 99999);
+            updateMappings(file, 'propagate', 0);
         end
+
     end
 
     methods (Test)
 
-        function test_simple_detection(~,zdim)
+        function test_simple_detection(~, zdim)
             % only data 500:600,11 is bad.
             sample_data = create_simple_data(zdim);
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag(500:600,1:13)==1,'all'))
-            assert(all(flag(500:600,14)==4,'all'))
-            assert(all(flag(500:600,15:end)==1,'all'))
+            assert(all(flag(500:600, 1:13) == 1, 'all'))
+            assert(all(flag(500:600, 14) == 4, 'all'))
+            assert(all(flag(500:600, 15:end) == 1, 'all'))
         end
 
-        function test_simple_detection_upward_propagate(~,zdim)
+        function test_simple_detection_upward_propagate(~, zdim)
             % only data 500:600,11 is bad.
             sample_data = create_simple_data(zdim);
-            switch_option('propagate',1);
+            switch_option('propagate', 1);
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag(500:600,1:13)==1,'all'))
-            assert(all(flag(500:600,14:end)==4,'all'))
+            assert(all(flag(500:600, 1:13) == 1, 'all'))
+            assert(all(flag(500:600, 14:end) == 4, 'all'))
         end
 
-        function test_simple_detection_downward_propagate(~,zdim)
+        function test_simple_detection_downward_propagate(~, zdim)
             % only data 500:600,11 is bad.
-            sample_data = create_simple_data(zdim,-1*(10:10:200)');
-            switch_option('propagate',1);
+            sample_data = create_simple_data(zdim, -1 * (10:10:200)');
+            switch_option('propagate', 1);
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag(500:600,1:13)==1,'all'))
-            assert(all(flag(500:600,14:end)==4,'all'))
+            assert(all(flag(500:600, 1:13) == 1, 'all'))
+            assert(all(flag(500:600, 14:end) == 4, 'all'))
         end
 
-        function test_bound_by_depth_upward_clean_marked(~,zdim)
+        function test_simple_detection_both_dimensions_mark_only_echo_vars(~)
+            sample_data = create_simple_data('HEIGHT_ABOVE_SENSOR');
+            hdim = sample_data.dimensions{2};
+            new_dim = IMOS.gen_dimensions('', 1, {'DIST_ALONG_BEAMS'}, {@double}, {hdim.data});
+            sample_data.dimensions{end + 1} = new_dim{1};
+            new_var = sample_data.variables{end};
+            new_var.name = 'PERG1';
+            new_var.dimensions = [1, 3]; %cant use gen_variables since dimensions are the dubious.
+            sample_data.variables{end + 1} = new_var;
+
+            new = imosEchoIntensitySetQC(sample_data);
+            v = IMOS.as_named_struct(new.variables);
+            flag = v.('ABSIC1').flags;
+            assert(all(flag(500:600, 1:13) == 1, 'all'))
+            assert(all(flag(500:600, 14) == 4, 'all'))
+            assert(all(flag(500:600, 15:end) == 1, 'all'))
+
+            f = fieldnames(v.('PERG1'));
+            assert(~inCell(f,'flags'))
+
+        end
+
+        function test_bound_by_depth_upward_clean_marked(~, zdim)
             depth_constraint = 30; %only shallower than 30m is allowed markings.
             site_nominal_depth = 170; % 14th bad bin will be at 30m, so will be clear out
-            sample_data = create_simple_data(zdim,(10:10:200)',site_nominal_depth);
-            switch_option('bound_by_depth',1);
-            switch_option('bound_value',depth_constraint);
-            switch_option('propagate',0);
+            sample_data = create_simple_data(zdim, (10:10:200)', site_nominal_depth);
+            switch_option('bound_by_depth', 1);
+            switch_option('bound_value', depth_constraint);
+            switch_option('propagate', 0);
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag==1,'all'))
+            assert(all(flag == 1, 'all'))
         end
 
-        function test_bound_by_depth_downward_clean_marked(~,zdim)
+        function test_bound_by_depth_downward_clean_marked(~, zdim)
             depth_constraint = 140; %only deeper than 140m is allowed markings.
             site_nominal_depth = 0; % 14th bin will be clear.
-            sample_data = create_simple_data(zdim,-1*(10:10:200)',site_nominal_depth);
-            switch_option('bound_by_depth',1);
-            switch_option('bound_value',depth_constraint);
-            switch_option('propagate',0);
+            sample_data = create_simple_data(zdim, -1 * (10:10:200)', site_nominal_depth);
+            switch_option('bound_by_depth', 1);
+            switch_option('bound_value', depth_constraint);
+            switch_option('propagate', 0);
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag==1,'all'))
+            assert(all(flag == 1, 'all'))
         end
 
-        function test_bound_by_depth_upward_simple(~,zdim)
+        function test_bound_by_depth_upward_simple(~, zdim)
             depth_constraint = 40; %above 40m to be marked.
             site_nominal_depth = 140 + depth_constraint; % bindepth of 14th bin  + constraint
             zrange = 0;
-            sample_data = create_simple_data(zdim,(10:10:200)',site_nominal_depth,zrange);
-            echo_ind = IMOS.find(sample_data.variables,'ABSIC1');
-            sample_data.variables{echo_ind}.data(500:600,14) = 205; % increase gradient so 15th bin is also marked.
+            sample_data = create_simple_data(zdim, (10:10:200)', site_nominal_depth, zrange);
+            echo_ind = IMOS.find(sample_data.variables, 'ABSIC1');
+            sample_data.variables{echo_ind}.data(500:600, 14) = 205; % increase gradient so 15th bin is also marked.
             % we now unmark all bins deeper than 40m. and keep everything as detected above 40m.
-            switch_option('bound_by_depth',1);
-            switch_option('bound_value',depth_constraint);
-            switch_option('propagate',0);
+            switch_option('bound_by_depth', 1);
+            switch_option('bound_value', depth_constraint);
+            switch_option('propagate', 0);
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag(500:600,1:14)==1,'all'))
-            assert(all(flag(500:600,15)==4,'all'))
-            assert(all(flag(500:600,16:end)==1,'all'))
+            assert(all(flag(500:600, 1:14) == 1, 'all'))
+            assert(all(flag(500:600, 15) == 4, 'all'))
+            assert(all(flag(500:600, 16:end) == 1, 'all'))
         end
 
-        function test_bound_by_depth_upward_zeta(~,zdim)
+        function test_bound_by_depth_upward_zeta(~, zdim)
             depth_constraint = 40; %above 40m to be marked.
             site_nominal_depth = 140 + depth_constraint; % bindepth of 14th bin  + constraint
             zrange = 2;
-            sample_data = create_simple_data(zdim,(10:10:200)',site_nominal_depth,zrange);
-            echo_ind = IMOS.find(sample_data.variables,'ABSIC1');
-            sample_data.variables{echo_ind}.data(500:600,14) = 205; % increase gradient so 15th bin is also marked.
+            sample_data = create_simple_data(zdim, (10:10:200)', site_nominal_depth, zrange);
+            echo_ind = IMOS.find(sample_data.variables, 'ABSIC1');
+            sample_data.variables{echo_ind}.data(500:600, 14) = 205; % increase gradient so 15th bin is also marked.
             % we now unmark some bins deeper than 40m. and keep everything as detected shallower than 40m.
-            switch_option('bound_by_depth',1);
-            switch_option('bound_value',depth_constraint);
-            switch_option('propagate',0);
+            switch_option('bound_by_depth', 1);
+            switch_option('bound_value', depth_constraint);
+            switch_option('propagate', 0);
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag(500:600,1:13)==1,'all'))
-            assert(any(flag(500:600,1:14)==4,'all'))
-            assert(all(flag(500:600,15)==4,'all'))
-            assert(all(flag(500:600,16:end)==1,'all'))
-            switch_option('propagate',1)
+            assert(all(flag(500:600, 1:13) == 1, 'all'))
+            assert(any(flag(500:600, 1:14) == 4, 'all'))
+            assert(all(flag(500:600, 15) == 4, 'all'))
+            assert(all(flag(500:600, 16:end) == 1, 'all'))
+            switch_option('propagate', 1)
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag(500:600,1:13)==1,'all'))
-            assert(any(flag(500:600,1:14)==4,'all'))
-            assert(all(flag(500:600,15:end)==4,'all'))
+            assert(all(flag(500:600, 1:13) == 1, 'all'))
+            assert(any(flag(500:600, 1:14) == 4, 'all'))
+            assert(all(flag(500:600, 15:end) == 4, 'all'))
 
         end
 
-        function test_bound_by_depth_downward_simple(~,zdim)
+        function test_bound_by_depth_downward_simple(~, zdim)
             depth_constraint = 140; %only deeper than 600m is allowed markings.
             site_nominal_depth = 300; % bindepth of 14th bin will be 440m
-            sample_data = create_simple_data(zdim,-1*(10:10:200)',site_nominal_depth);
-            echo_ind = IMOS.find(sample_data.variables,'ABSIC1');
-            sample_data.variables{echo_ind}.data(500:600,14) = 205; % increase gradient so 15th bin is also marked.
+            sample_data = create_simple_data(zdim, -1 * (10:10:200)', site_nominal_depth);
+            echo_ind = IMOS.find(sample_data.variables, 'ABSIC1');
+            sample_data.variables{echo_ind}.data(500:600, 14) = 205; % increase gradient so 15th bin is also marked.
             % now unmark bins at 440m but keep all detected towards the bottom.
-            switch_option('bound_by_depth',1);
-            switch_option('bound_value',depth_constraint);
-            switch_option('propagate',0);
+            switch_option('bound_by_depth', 1);
+            switch_option('bound_value', depth_constraint);
+            switch_option('propagate', 0);
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag(500:600,1:14)==1,'all'))
-            assert(all(flag(500:600,15)==4,'all'))
-            assert(all(flag(500:600,16:end)==1,'all'))
+            assert(all(flag(500:600, 1:14) == 1, 'all'))
+            assert(all(flag(500:600, 15) == 4, 'all'))
+            assert(all(flag(500:600, 16:end) == 1, 'all'))
         end
 
-        function test_bound_by_depth_downward_zeta(~,zdim)
+        function test_bound_by_depth_downward_zeta(~, zdim)
             depth_constraint = 140; %only deeper than 600m is allowed markings.
             site_nominal_depth = 300; % bindepth of 14th bin will be 440m
             zrange = 2;
-            sample_data = create_simple_data(zdim,-1*(10:10:200)',site_nominal_depth,zrange);
-            echo_ind = IMOS.find(sample_data.variables,'ABSIC1');
-            sample_data.variables{echo_ind}.data(500:600,14) = 205; % increase gradient so 15th bin is also marked.
+            sample_data = create_simple_data(zdim, -1 * (10:10:200)', site_nominal_depth, zrange);
+            echo_ind = IMOS.find(sample_data.variables, 'ABSIC1');
+            sample_data.variables{echo_ind}.data(500:600, 14) = 205; % increase gradient so 15th bin is also marked.
             % now unmark some bins around 40m but keep all beyond 40m to the surface.
-            switch_option('bound_by_depth',1);
-            switch_option('bound_value',depth_constraint);
-            switch_option('propagate',0);
+            switch_option('bound_by_depth', 1);
+            switch_option('bound_value', depth_constraint);
+            switch_option('propagate', 0);
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag(500:600,1:13)==1,'all'))
-            assert(any(flag(500:600,1:14)==4,'all'))
-            assert(all(flag(500:600,15)==4,'all'))
-            assert(all(flag(500:600,16:end)==1,'all'))
-            switch_option('propagate',1);
+            assert(all(flag(500:600, 1:13) == 1, 'all'))
+            assert(any(flag(500:600, 1:14) == 4, 'all'))
+            assert(all(flag(500:600, 15) == 4, 'all'))
+            assert(all(flag(500:600, 16:end) == 1, 'all'))
+            switch_option('propagate', 1);
             new = imosEchoIntensitySetQC(sample_data);
             flag = new.variables{end}.flags;
-            assert(all(flag(500:600,1:13)==1,'all'))
-            assert(any(flag(500:600,1:14)==4,'all'))
-            assert(all(flag(500:600,15:end)==4,'all'))
+            assert(all(flag(500:600, 1:13) == 1, 'all'))
+            assert(any(flag(500:600, 1:14) == 4, 'all'))
+            assert(all(flag(500:600, 15:end) == 4, 'all'))
         end
 
         function test_realdata_bound_index(~)
-            % this file is clipped to out of water points. 
+            % this file is clipped to out of water points.
             % There are several above the threshold at the first bin interface and two points at bin26.
             % We will ignore the first bin interface gradients with a bound index, and match the two bad data.
             adcp_file = fullfile(toolboxRootPath, 'data/testfiles/Teledyne/workhorse/v000/beam/16072000.000.reduced');
             sample_data = load_binmapped_sample_data(adcp_file);
-            time = IMOS.get_data(sample_data.dimensions,'TIME');
+            time = IMOS.get_data(sample_data.dimensions, 'TIME');
             height_above_sensor = IMOS.get_data(sample_data.dimensions, 'HEIGHT_ABOVE_SENSOR');
-            nbins = numel(height_above_sensor);
             beam_height = IMOS.adcp.beam_height(height_above_sensor);
-            idepth = transpose(randomBetween(100,200,numel(time)));
+            idepth = transpose(randomBetween(100, 200, numel(time)));
             sdepth = IMOS.gen_variables(sample_data.dimensions, {'DEPTH'}, {@double}, {idepth}, 'positive', 'down');
             sample_data.variables{end + 1} = sdepth{1};
             sample_data.site_nominal_depth = beam_height - mode(idepth);
-         
+
             new = imosEchoIntensitySetQC(sample_data);
-            u_flag = new.variables{IMOS.find(new.variables,'VEL1')}.flags;
-            assert(all(u_flag(:,1)==1,'all'))
-            assert(any(u_flag(:,2)==4,'all'))
-            assert(all(u_flag(:,3:25)==1,'all'))
-            assert(sum(u_flag(:,26)==4)==2)
-            assert(all(u_flag(:,27:end)==1,'all'))
+            u_flag = new.variables{IMOS.find(new.variables, 'VEL1')}.flags;
+            assert(all(u_flag(:, 1) == 1, 'all'))
+            assert(any(u_flag(:, 2) == 4, 'all'))
+            assert(all(u_flag(:, 3:25) == 1, 'all'))
+            assert(sum(u_flag(:, 26) == 4) == 2)
+            assert(all(u_flag(:, 27:end) == 1, 'all'))
 
-            switch_option('bound_by_index',1)
-            switch_option('bound_value',25);% 1:25 always good.
+            switch_option('bound_by_index', 1)
+            switch_option('bound_value', 25); % 1:25 always good.
 
             new = imosEchoIntensitySetQC(sample_data);
-            u_flag = new.variables{IMOS.find(new.variables,'VEL1')}.flags;
-            v_flag = new.variables{IMOS.find(new.variables,'VEL2')}.flags;
-            w_flag = new.variables{IMOS.find(new.variables,'VEL3')}.flags;
-            e_flag = new.variables{IMOS.find(new.variables,'VEL4')}.flags;
-            a1_flag = new.variables{IMOS.find(new.variables,'ABSIC1')}.flags;
-            a2_flag = new.variables{IMOS.find(new.variables,'ABSIC2')}.flags;
-            a3_flag = new.variables{IMOS.find(new.variables,'ABSIC3')}.flags;
-            a4_flag = new.variables{IMOS.find(new.variables,'ABSIC4')}.flags;
-            assert(isequal(u_flag,v_flag,w_flag,e_flag,a1_flag,a2_flag,a3_flag,a4_flag));
-            assert(all(u_flag(:,1:25)==1,'all'))
-            assert(sum(u_flag(:,26)==4)==2)
-            assert(all(u_flag(:,27:end)==1,'all'))
-
-            converted = adcpWorkhorseVelocityBeam2EnuPP({sample_data},'');
-            switch_option('bound_by_index',1)
-            switch_option('bound_value',26)
+            u_flag = new.variables{IMOS.find(new.variables, 'VEL1')}.flags;
+            v_flag = new.variables{IMOS.find(new.variables, 'VEL2')}.flags;
+            w_flag = new.variables{IMOS.find(new.variables, 'VEL3')}.flags;
+            e_flag = new.variables{IMOS.find(new.variables, 'VEL4')}.flags;
+            a1_flag = new.variables{IMOS.find(new.variables, 'ABSIC1')}.flags;
+            a2_flag = new.variables{IMOS.find(new.variables, 'ABSIC2')}.flags;
+            a3_flag = new.variables{IMOS.find(new.variables, 'ABSIC3')}.flags;
+            a4_flag = new.variables{IMOS.find(new.variables, 'ABSIC4')}.flags;
+            assert(isequal(u_flag, v_flag, w_flag, e_flag, a1_flag, a2_flag, a3_flag, a4_flag));
+            assert(all(u_flag(:, 1:25) == 1, 'all'))
+            assert(sum(u_flag(:, 26) == 4) == 2)
+            assert(all(u_flag(:, 27:end) == 1, 'all'))
+
+            converted = adcpWorkhorseVelocityBeam2EnuPP({sample_data}, '');
+            switch_option('bound_by_index', 1)
+            switch_option('bound_value', 26)
             new = imosEchoIntensitySetQC(converted{1});
-            u_flag = new.variables{IMOS.find(new.variables,'UCUR_MAG')}.flags;
-            v_flag = new.variables{IMOS.find(new.variables,'VCUR_MAG')}.flags;
-            w_flag = new.variables{IMOS.find(new.variables,'WCUR')}.flags;
-            e_flag = new.variables{IMOS.find(new.variables,'ECUR')}.flags;
-            assert(isequal(u_flag,v_flag,w_flag,e_flag));
-            assert(all(u_flag==1,'all'))
+            u_flag = new.variables{IMOS.find(new.variables, 'UCUR_MAG')}.flags;
+            v_flag = new.variables{IMOS.find(new.variables, 'VCUR_MAG')}.flags;
+            w_flag = new.variables{IMOS.find(new.variables, 'WCUR')}.flags;
+            e_flag = new.variables{IMOS.find(new.variables, 'ECUR')}.flags;
+            assert(isequal(u_flag, v_flag, w_flag, e_flag));
+            assert(all(u_flag == 1, 'all'))
 
         end
+
     end
 
 end
 
-function switch_option(optname,optvalue)
+function switch_option(optname, optvalue)
     file = which('imosEchoIntensitySetQC');
-    file(end:end+2) = 'txt';
-    updateMappings(file,optname,optvalue);
+    file(end:end + 2) = 'txt';
+    updateMappings(file, optname, optvalue);
 end
 
 function [binmapped] = load_binmapped_sample_data(file)
@@ -226,40 +250,46 @@ function switch_option(optname,optvalue)
     binmapped = binmapped{1};
 end
 
-function [sample_data] = create_simple_data(zdim_name,bin_dist, site_nominal_depth,zrange)
-    % Create a simple test adcp dataset
-    % The instrument depth is at the bottom for upward looking, and at the surface
-    % for downward looking.
-    % The depth is contaminated with oscillations of ~[-zrange,+zrange] dbar,
-    % and echo intensity is randomized between 100-150 counts. 
-    % A detectable echo intensity count is found between 500-600 timestamps
-    % at the 14th bin with magnitude == 51 counts, which is above
-    % the default threshold of the test.
-    time = (1:1000)';
-    if nargin<2
-        bin_dist = (10:10:200)';
-    end
-    if nargin<3
-        site_nominal_depth = NaN;
-    end
-    if nargin<4
-        zrange = 0;
-    end
-    dims = IMOS.gen_dimensions('adcp', 2, {'TIME', zdim_name}, {@double, @double}, {time, bin_dist}); %upward looking == positive depth
-    zeta = randomBetween(-zrange,zrange,numel(time));
-    if all(bin_dist>0)
-        instrument_depth = transpose(site_nominal_depth + zeta);
-    else
-        instrument_depth = transpose(zeta);
-    end
-    vars_0 = randomBetween(100,150,1000*20);
-    vars_0 = reshape(vars_0,1000,20);
-    vars_0(500:600,14) = 201; % default threshold is 50, so fail at index 14.
-    vars_0(500:600,15) = 151; %drop off to only actually mark at index 14.
-    vars_0(500:600,16) = 141; %as above
-    vars = IMOS.gen_variables(dims, {'DEPTH','UCUR', 'ABSIC1'}, {@double, @double,@double}, {instrument_depth, vars_0, vars_0});
-    sample_data.dimensions = dims;
-    sample_data.variables = vars;
-    sample_data.site_nominal_depth = site_nominal_depth;
-    sample_data.toolbox_input_file = 'testdriven';
+function [sample_data] = create_simple_data(zdim_name, bin_dist, site_nominal_depth, zrange)
+% Create a simple test adcp dataset
+% The instrument depth is at the bottom for upward looking, and at the surface
+% for downward looking.
+% The depth is contaminated with oscillations of ~[-zrange,+zrange] dbar,
+% and echo intensity is randomized between 100-150 counts.
+% A detectable echo intensity count is found between 500-600 timestamps
+% at the 14th bin with magnitude == 51 counts, which is above
+% the default threshold of the test.
+time = (1:1000)';
+
+if nargin < 2
+    bin_dist = (10:10:200)';
+end
+
+if nargin < 3
+    site_nominal_depth = NaN;
+end
+
+if nargin < 4
+    zrange = 0;
+end
+
+dims = IMOS.gen_dimensions('adcp', 2, {'TIME', zdim_name}, {@double, @double}, {time, bin_dist}); %upward looking == positive depth
+zeta = randomBetween(-zrange, zrange, numel(time));
+
+if all(bin_dist > 0)
+    instrument_depth = transpose(site_nominal_depth + zeta);
+else
+    instrument_depth = transpose(zeta);
+end
+
+vars_0 = randomBetween(100, 150, 1000 * 20);
+vars_0 = reshape(vars_0, 1000, 20);
+vars_0(500:600, 14) = 201; % default threshold is 50, so fail at index 14.
+vars_0(500:600, 15) = 151; %drop off to only actually mark at index 14.
+vars_0(500:600, 16) = 141; %as above
+vars = IMOS.gen_variables(dims, {'DEPTH', 'UCUR', 'ABSIC1'}, {@double, @double, @double}, {instrument_depth, vars_0, vars_0});
+sample_data.dimensions = dims;
+sample_data.variables = vars;
+sample_data.site_nominal_depth = site_nominal_depth;
+sample_data.toolbox_input_file = fullfile(toolboxRootPath, 'tmp', 'testdriven');
 end
diff --git a/test/AutomaticQC/test_imosSurfaceDetectionByDepthSetQC.m b/test/AutomaticQC/test_imosSurfaceDetectionByDepthSetQC.m
index 0f623f717..8e4ec74b5 100644
--- a/test/AutomaticQC/test_imosSurfaceDetectionByDepthSetQC.m
+++ b/test/AutomaticQC/test_imosSurfaceDetectionByDepthSetQC.m
@@ -18,6 +18,24 @@ function test_simple_raw_detection_minimal_input(~)
             assert(first_bin_at_surface == 10);
         end
 
+        function test_simple_detection_both_dimensions_present(~)
+            sample_data = create_simple_data('HEIGHT_ABOVE_SENSOR');
+            hdim = sample_data.dimensions{2};
+            new_dim = IMOS.gen_dimensions('', 1, {'DIST_ALONG_BEAMS'}, {@double}, {hdim.data});
+            sample_data.dimensions{end + 1} = new_dim{1};
+            new_var = sample_data.variables{end};
+            new_var.name = 'PERG1';
+            new_var.dimensions = [1, 3]; %cant use gen_variables since dimensions are the dubious.
+            sample_data.variables{end + 1} = new_var;
+
+            new = imosSurfaceDetectionByDepthSetQC(sample_data);
+            flag = new.variables{1}.flags;
+            first_bin_at_surface = find(sum(flag == 1, 1) == 0, 1, 'first');
+            assert(first_bin_at_surface == 10);
+            assert(~isfield(new.variables{end},'flags'))
+        end
+
+
         function test_raw_file_downward_adcp_bottom_detection(~)
             adcp_file = fullfile(toolboxRootPath, 'data/testfiles/Teledyne/workhorse/v000/beam/16072000.000.reduced');
             sample_data = workhorseParse({adcp_file},'');
diff --git a/test/AutomaticQC/test_imosTiltVelocitySetQC.m b/test/AutomaticQC/test_imosTiltVelocitySetQC.m
index 9decbaf14..0171ddb69 100644
--- a/test/AutomaticQC/test_imosTiltVelocitySetQC.m
+++ b/test/AutomaticQC/test_imosTiltVelocitySetQC.m
@@ -1,7 +1,7 @@
 classdef test_imosTiltVelocitySetQC < matlab.unittest.TestCase
 
-    properties
-        testUI = true;
+    properties (TestParameter)
+        interactive = {ismember('interactive_tests',who('global'))};
     end
 
     methods (Test)
@@ -97,41 +97,34 @@ function test_load_sentinel(~)
             assert(isequal(e_logentry, logentry))
         end
 
-        function test_below_secondThreshold_ui(testCase)
-            if testCase.testUI
-                ssize = [100, 33];
-                sample_data = create_sample_data(ssize);
-                sample_data.variables{end}.data = zeros(100,1); %roll
-                sample_data.variables{end - 1}.data = zeros(100,1) +90; %pitch
-                sample_data.instrument = 'ADCP sentinel abcdefg';
-                e_logentry = 'firstTiltThreshold=15, secondTiltThreshold=91';
-                disp('Set firstFlagThreshold to be 4 and SecondTiltThreshold to be 91 for this test to pass');
-                v = zeros(ssize)+4;
-                [pdata, ~, logentry] = imosTiltVelocitySetQC(sample_data, false);
-                assert(isequal(pdata.variables{1}.flags, v))
-                assert(isequal(e_logentry, logentry))
-            else
-                disp("testUI is False...skipping UI testing")
-            end
-
+        function test_below_secondThreshold_ui(testCase,interactive)
+            testCase.assumeTrue(interactive,'Interactive test skipped')
+            ssize = [100, 33];
+            sample_data = create_sample_data(ssize);
+            sample_data.variables{end}.data = zeros(100,1); %roll
+            sample_data.variables{end - 1}.data = zeros(100,1) +90; %pitch
+            sample_data.instrument = 'ADCP sentinel abcdefg';
+            e_logentry = 'firstTiltThreshold=15, secondTiltThreshold=91';
+            disp('Set firstFlagThreshold to be 4 and SecondTiltThreshold to be 91 for this test to pass');
+            v = zeros(ssize)+4;
+            [pdata, ~, logentry] = imosTiltVelocitySetQC(sample_data, false);
+            assert(isequal(pdata.variables{1}.flags, v))
+            assert(isequal(e_logentry, logentry))
         end
 
-        function test_above_secondThreshold_ui(testCase)
-            if testCase.testUI
-                ssize = [100, 33];
-                sample_data = create_sample_data(ssize);
-                sample_data.variables{end}.data = zeros(100,1); %roll
-                sample_data.variables{end - 1}.data = zeros(100,1)+81.; %pitch
-                sample_data.instrument = 'ADCP sentinel abcdefg';
-                e_logentry = 'firstTiltThreshold=15, secondTiltThreshold=80';
-                disp('Set SecondTiltThreshold to be 80 for this test to pass');
-                v = zeros(ssize)+3;
-                [pdata, ~, logentry] = imosTiltVelocitySetQC(sample_data, false);
-                assert(isequal(pdata.variables{1}.flags, v))
-                assert(isequal(e_logentry, logentry))
-            else
-                disp("testUI is False...skipping UI testing")
-            end
+        function test_above_secondThreshold_ui(testCase,interactive)
+            testCase.assumeTrue(interactive,'Interactive test skipped')
+            ssize = [100, 33];
+            sample_data = create_sample_data(ssize);
+            sample_data.variables{end}.data = zeros(100,1); %roll
+            sample_data.variables{end - 1}.data = zeros(100,1)+81.; %pitch
+            sample_data.instrument = 'ADCP sentinel abcdefg';
+            e_logentry = 'firstTiltThreshold=15, secondTiltThreshold=80';
+            disp('Set SecondTiltThreshold to be 80 for this test to pass');
+            v = zeros(ssize)+3;
+            [pdata, ~, logentry] = imosTiltVelocitySetQC(sample_data, false);
+            assert(isequal(pdata.variables{1}.flags, v))
+            assert(isequal(e_logentry, logentry))
         end
 
     end
diff --git a/test/Parser/testOnlyCPHL.m b/test/Parser/testOnlyCPHL.m
index d23c9098e..c0203eb02 100644
--- a/test/Parser/testOnlyCPHL.m
+++ b/test/Parser/testOnlyCPHL.m
@@ -151,11 +151,13 @@ function test_aquatrackapp(~,sbe19p_reader,sbe19p_v000_param,mode)
 %
 fullpath = @fullfile;
 
-e.root_folder = toolboxRootPath();    
-e.ecot_folder = fullpath(e.root_folder, 'data/testfiles/ECOTriplet/v000/');
+exclude_extensions = {'.pqc','.mqc','.ppp'};
+find_valid_test_files = @(x)(FilesInFolder(x,exclude_extensions));
 
-ecot_v000 = FilesInFolder(e.ecot_folder);
+e.root_folder = toolboxRootPath();
+e.ecot_folder = fullpath(e.root_folder, 'data/testfiles/ECOTriplet/v000/');
 
+ecot_v000 = find_valid_test_files(e.ecot_folder);
 c = 0;
 for k = 1:length(ecot_v000)
 
@@ -168,50 +170,50 @@ function test_aquatrackapp(~,sbe19p_reader,sbe19p_v000_param,mode)
 e.ecot_v000_param = files2namestruct(e.ecot_v000_files);
 
 e.jfe_folder = fullpath(e.root_folder, 'data/testfiles/JFE/v000/');
-e.jfe_v000_files = FilesInFolder(e.jfe_folder);
+e.jfe_v000_files = find_valid_test_files(e.jfe_folder);
 e.jfe_v000_param = files2namestruct(e.jfe_v000_files);
 
 e.solo_folder = fullpath(e.root_folder, 'data/testfiles/RBR/solo/v000/');
-e.solo_v000_files = FilesInFolder(e.solo_folder);
+e.solo_v000_files = find_valid_test_files(e.solo_folder);
 e.solo_v000_param = files2namestruct(e.solo_v000_files);
 % e.tr1060_folder = fullpath(e.root_folder, 'data/testfiles/RBR/TR-1060/v000/');
-% e.tr1060_v000_files = FilesInFolder(e.tr1060_folder);
+% e.tr1060_v000_files = find_valid_test_files(e.tr1060_folder);
 % e.tr1060_v000_param = files2namestruct(e.tr1060_v000_files);
 
 e.tdr2050_folder = fullpath(e.root_folder, 'data/testfiles/RBR/TDR-2050/v000/');
-e.tdr2050_v000_files = FilesInFolder(e.tdr2050_folder);
+e.tdr2050_v000_files = find_valid_test_files(e.tdr2050_folder);
 e.tdr2050_v000_param = files2namestruct(e.tdr2050_v000_files);
 
 e.twr2050_folder = fullpath(e.root_folder, 'data/testfiles/RBR/TWR-2050/v000/');
-e.twr2050_v000_files = FilesInFolder(e.twr2050_folder);
+e.twr2050_v000_files = find_valid_test_files(e.twr2050_folder);
 e.twr2050_v000_param = files2namestruct(e.twr2050_v000_files);
 
 e.xr420_folder = fullpath(e.root_folder, 'data/testfiles/RBR/XR420/v000/');
-e.xr420_v000_files = FilesInFolder(e.xr420_folder);
+e.xr420_v000_files = find_valid_test_files(e.xr420_folder);
 e.xr420_v000_param = files2namestruct(e.xr420_v000_files);
 
 e.xr620_folder = fullpath(e.root_folder, 'data/testfiles/RBR/XR620/v000/');
-e.xr620_v000_files = FilesInFolder(e.xr620_folder);
+e.xr620_v000_files = find_valid_test_files(e.xr620_folder);
 e.xr620_v000_param = files2namestruct(e.xr620_v000_files);
 
 e.sbe19p_folder = fullpath(e.root_folder, 'data/testfiles/Sea_Bird_Scientific/SBE/19plus/v000/');
-e.sbe19p_v000_files = FilesInFolder(e.sbe19p_folder);
+e.sbe19p_v000_files = find_valid_test_files(e.sbe19p_folder);
 e.sbe19p_v000_param = files2namestruct(e.sbe19p_v000_files);
 
 e.sbe25p_folder = fullpath(e.root_folder, 'data/testfiles/Sea_Bird_Scientific/SBE/25plus/v000/');
-e.sbe25p_v000_files = FilesInFolder(e.sbe25p_folder);
+e.sbe25p_v000_files = find_valid_test_files(e.sbe25p_folder);
 e.sbe25p_v000_param = files2namestruct(e.sbe25p_v000_files);
 
 e.sbe9p_folder = fullpath(e.root_folder, 'data/testfiles/Sea_Bird_Scientific/SBE/9plus/v000/');
-e.sbe9p_v000_files = FilesInFolder(e.sbe9p_folder);
+e.sbe9p_v000_files = find_valid_test_files(e.sbe9p_folder);
 e.sbe9p_v000_param = files2namestruct(e.sbe9p_v000_files);
 
 e.wqmraw_folder = fullpath(e.root_folder, 'data/testfiles/Sea_Bird_Scientific/WQM/RAW/v000/');
-e.wqmraw_v000_files = FilesInFolder(e.wqmraw_folder);
+e.wqmraw_v000_files = find_valid_test_files(e.wqmraw_folder);
 e.wqmraw_v000_param = files2namestruct(e.wqmraw_v000_files);
 
 e.wqmdat_folder = fullpath(e.root_folder, 'data/testfiles/Sea_Bird_Scientific/WQM/DAT/v000/');
-e.wqmdat_v000_files = FilesInFolder(e.wqmdat_folder);
+e.wqmdat_v000_files = find_valid_test_files(e.wqmdat_folder);
 e.wqmdat_v000_param = files2namestruct(e.wqmdat_v000_files);
 end
 
diff --git a/test/Parser/testSBE19Parse.m b/test/Parser/testSBE19Parse.m
index 9519fcfb7..1728a040c 100644
--- a/test/Parser/testSBE19Parse.m
+++ b/test/Parser/testSBE19Parse.m
@@ -8,7 +8,7 @@
 
     properties (TestParameter)
         mode = {'timeSeries'};
-        wqm_file = files2namestruct(rdir([toolboxRootPath 'data/testfiles/Sea_Bird_Scientific/SBE']));
+        wqm_file = files2namestruct(filter_extensions(rdir([toolboxRootPath 'data/testfiles/Sea_Bird_Scientific/SBE']),{'.pqc','.mqc','.ppp'}));
         beam_transmission_file = prepend_dir([toolboxRootPath 'data/testfiles/Sea_Bird_Scientific/SBE/19plus/v000'], {'YON20200306CFALDB_with_PAR_and_battery.cnv'});
         strain_pres_file = prepend_dir([toolboxRootPath 'data/testfiles/Sea_Bird_Scientific/SBE/19plus/v000'], {'SBE19plus_parser1.cnv', 'YON20200306CFALDB_with_PAR_and_battery.cnv', 'chla_aquaT3_as_aquaUV.cnv'});
         par_file = prepend_dir([toolboxRootPath 'data/testfiles/Sea_Bird_Scientific/SBE/19plus/v000'], {'SBE19plus_parser1.cnv', 'YON20200306CFALDB_with_PAR_and_battery.cnv', 'chla_aquaT3_as_aquaUV.cnv'});
diff --git a/test/Parser/testworkhorseParse.m b/test/Parser/testworkhorseParse.m
index 5028c03e5..87ad68f5d 100644
--- a/test/Parser/testworkhorseParse.m
+++ b/test/Parser/testworkhorseParse.m
@@ -1,4 +1,4 @@
-classdef testWorkhorse < matlab.unittest.TestCase
+classdef testworkhorseParse < matlab.unittest.TestCase
 
     % Test Reading Workhorse Signature files with the workhorseParse
     % function.
@@ -7,8 +7,8 @@
     %
 
     properties (TestParameter)
-        enu_file = FilesInFolder(fpath('v000/enu'),{'.mat','.ppp','.pqc'});
-        beam_file = FilesInFolder(fpath('v000/beam'),{'.mat','.ppp','.pqc'});
+        enu_file = FilesInFolder(fpath('v000/enu'), {'.mat', '.ppp', '.pqc'});
+        beam_file = FilesInFolder(fpath('v000/beam'), {'.mat', '.ppp', '.pqc'});
 
         quartermaster_file = {fpath('v000/enu/16413000.000'), ...
                             fpath('v000/enu/16923000.000'), ...
@@ -22,7 +22,6 @@
                             };
 
         sentinel_file = {fpath('/v000/enu/16679000.000')};
-
         %TODO: search for dvs files
         %dvs = {};
 
@@ -33,6 +32,35 @@
 
     methods (Test)
 
+        function testReadingENU_version_regression(~)
+            %This test regression/issue #741
+            %https://github.com/aodn/imos-toolbox/issues/741
+            %by comparing UVEL and VVEL in a sentinel file
+            %data loaded with the toolbox version 2.6.9
+
+            sentinel_file = fpath('/v000/enu/16679000.000');
+            sentinel_mat_file = fpath('/v000/mat/16679000.000_v2.6.9.mat');
+
+            previous_data = load(sentinel_mat_file);
+            pvars = IMOS.as_named_struct(previous_data.sample_data.variables);
+
+            new_data = workhorseParse({sentinel_file},'');
+            nvars = IMOS.as_named_struct(new_data.variables);
+
+            p_ucur = pvars.UCUR_MAG.data;
+            n_ucur = nvars.UCUR_MAG.data;
+            assert(isequal_tol(p_ucur,n_ucur)); 
+
+            p_vcur = pvars.VCUR_MAG.data;
+            n_vcur = nvars.VCUR_MAG.data;
+            assert(isequal_tol(p_vcur,n_vcur));
+
+            p_heading = pvars.HEADING_MAG.data;
+            n_heading = nvars.HEADING_MAG.data;
+            assert(isequal_tol(p_heading,n_heading)) % this pass
+
+        end
+
         function testReadingENU(~, enu_file)
             data = workhorseParse({enu_file}, '');
             check_metadata_consistency(data);
@@ -214,31 +242,34 @@ function check_v2d_consistency(data, is_enu_dataset)
 
 function check_vel_names(data, is_enu_dataset)
     vnames = IMOS.get(data.variables, 'name');
-  
+
     enu_with_mag = is_enu_dataset && data.meta.compass_correction_applied ~= 0;
-    enu_without_mag = is_enu_dataset && data.meta.compass_correction_applied ==0;
+    enu_without_mag = is_enu_dataset && data.meta.compass_correction_applied == 0;
 
     if enu_with_mag
-        name0='UCUR';
-        name1='VCUR';
-        name2='WCUR';
-        name3='ECUR';
+        name0 = 'UCUR';
+        name1 = 'VCUR';
+        name2 = 'WCUR';
+        name3 = 'ECUR';
     elseif enu_without_mag
-        name0='UCUR_MAG';
-        name1='VCUR_MAG';
-        name2='WCUR';
-        name3='ECUR';
+        name0 = 'UCUR_MAG';
+        name1 = 'VCUR_MAG';
+        name2 = 'WCUR';
+        name3 = 'ECUR';
     else
-        name0='VEL1';
-        name1='VEL2';
-        name2='VEL3';
-        name3='VEL4';
+        name0 = 'VEL1';
+        name1 = 'VEL2';
+        name2 = 'VEL3';
+        name3 = 'VEL4';
 
     end
+
     assert(inCell(vnames, name0));
     assert(inCell(vnames, name1));
     assert(inCell(vnames, name2));
+
     if data.meta.adcp_info.number_of_beams > 3
         assert(inCell(vnames, name3));
     end
+
 end
diff --git a/test/Preprocessing/testDepthPP.m b/test/Preprocessing/testDepthPP.m
index 46bd73f69..eb3fc1218 100644
--- a/test/Preprocessing/testDepthPP.m
+++ b/test/Preprocessing/testDepthPP.m
@@ -6,10 +6,12 @@
     %
     properties (TestParameter)
         mode = {'profile','timeSeries'};
+        interactive = {ismember('interactive_tests',who('global'))};
     end
 
     methods (Test)
-        function testDepthPPOverwriteDepth(~, mode)
+        function testDepthPPOverwriteDepth(testCase, mode, interactive)
+            testCase.assumeTrue(interactive,'Interactive test skipped')
             d = IMOS.gen_dimensions(mode,1,{'TIME'},{@double},{randn(100,1)});
             parr = 100*ones(100,1);
             darr = randn(100,1);
diff --git a/test/Preprocessing/testadcpWorkhorseBeam2EarthPP.m b/test/Preprocessing/testadcpWorkhorseBeam2EarthPP.m
index 953f9d6f9..1aa8811ae 100644
--- a/test/Preprocessing/testadcpWorkhorseBeam2EarthPP.m
+++ b/test/Preprocessing/testadcpWorkhorseBeam2EarthPP.m
@@ -1,5 +1,5 @@
 classdef testadcpWorkhorseBeam2EarthPP < matlab.unittest.TestCase
-	%
+    %
     % Test rotation of angles from Beam to Earth coordinates
     % Pre processign function.
     %
@@ -14,68 +14,71 @@
     methods (Test)
 
         function testCompareAgainstBecOriginalFile(test)
-	
-			%This mat file is one produced at commit hash 9efcff9b015c121407e3b95da31efe0cddd1da1b 
-			% by calling:
-			%sample_data = workhorseParse(fpath('v000/beam/1759001.000.reduced'));
-			% Note that, despite the original code is supposedly to perform binmapping,
-			% no actual bin mapping is performed, since in the binmap function within
-			% rdiBeam2Earth, there is are reassignments to original data
-			% (see line 180-190) of rdiBeam2Earth.m at the respective commit.
-	        orig_data = load(fpath('v000/beam/1759001.000.reduced.enu_without_binmap.mat'));
+
+            %This mat file is one produced at commit hash 9efcff9b015c121407e3b95da31efe0cddd1da1b
+            % by calling:
+            %sample_data = workhorseParse(fpath('v000/beam/1759001.000.reduced'));
+            % Note that, despite the original code is supposedly to perform binmapping,
+            % no actual bin mapping is performed, since in the binmap function within
+            % rdiBeam2Earth, there is are reassignments to original data
+            % (see line 180-190) of rdiBeam2Earth.m at the respective commit.
+            orig_data = load(fpath('v000/beam/1759001.000.reduced.enu_without_binmap.mat'));
             orig_enu = orig_data.sample_data;
 
             new_data = workhorseParse({test.quartermaster_file{1}}, '');
             new_enu = adcpWorkhorseVelocityBeam2EnuPP({new_data}, '');
-			new_enu = new_enu{1};
-
-			%adcpWorkhorseVelocityBeam2EnuPP works for both non-bin-mapped and bin-mapped variables.
-			dim_names = IMOS.get(new_enu.dimensions,'name');
-			assert(inCell(dim_names,'DIST_ALONG_BEAMS'))
-
-			orig_var = IMOS.as_named_struct(orig_enu.variables);
-			new_var = IMOS.as_named_struct(new_enu.variables);
-			decrange = 3;
-			velocity_vars = {'UCUR_MAG','VCUR_MAG','WCUR','ECUR'};
-			for k=1:numel(velocity_vars)
-				vname = velocity_vars{k};
-				errmsg = sprintf('Variable %s differs by more than 1%',vname);
-				[~,~,p] = isequal_tol(orig_var.(vname).data,new_var.(vname).data,decrange);
-				assert(p>0.99,errmsg);
-
-				assert(contains(new_var.(vname).comment,'adcpWorkhorseVelocityBeam2EnuPP.m'))
-				assert(contains(new_var.(vname).comment,'has been calculated from velocity data in Beams coordinates using'))
-			end
+            new_enu = new_enu{1};
+
+            %adcpWorkhorseVelocityBeam2EnuPP works for both non-bin-mapped and bin-mapped variables.
+            dim_names = IMOS.get(new_enu.dimensions, 'name');
+            assert(inCell(dim_names, 'DIST_ALONG_BEAMS'))
+
+            orig_var = IMOS.as_named_struct(orig_enu.variables);
+            new_var = IMOS.as_named_struct(new_enu.variables);
+            decrange = 3;
+            velocity_vars = {'UCUR_MAG', 'VCUR_MAG', 'WCUR', 'ECUR'};
+
+            for k = 1:numel(velocity_vars)
+                vname = velocity_vars{k};
+                errmsg = sprintf('Variable %s differs by more than 1%', vname);
+                [~, ~, p] = isequal_tol(orig_var.(vname).data, new_var.(vname).data, decrange);
+                assert(p > 0.99, errmsg);
+
+                assert(contains(new_var.(vname).comment, 'adcpWorkhorseVelocityBeam2EnuPP.m'))
+                assert(contains(new_var.(vname).comment, 'has been calculated from velocity data in Beams coordinates using'))
+            end
 
         end
 
-		function testRotationAfterBinMapping(~,quartermaster_file)
+        function testRotationAfterBinMapping(~, quartermaster_file)
             sample_data = workhorseParse({quartermaster_file}, '');
-			original_varnames = IMOS.get(sample_data.variables,'name');
-			assert(isinside(original_varnames,{'VEL1','VEL2','VEL3','VEL4'}));
-			
-			sample_data = adcpBinMappingPP({sample_data},'');
-			assert(isfield(sample_data{1},'history'))
-			assert(contains(sample_data{1}.history,'adcpBinMappingPP.m'))
-		
-			dim_names = IMOS.get(sample_data{1}.dimensions,'name');
-			assert(~inCell(dim_names,'DIST_ALONG_BEAMS'))
-			assert(inCell(dim_names,'HEIGHT_ABOVE_SENSOR'))
-
-			sample_data = adcpWorkhorseVelocityBeam2EnuPP(sample_data,'');
-			sample_data = sample_data{1};
-			assert(isfield(sample_data,'history'))
-			assert(contains(sample_data.history,'adcpWorkhorseVelocityBeam2EnuPP.m'))
-			rotated_varnames = IMOS.get(sample_data.variables,'name');
-
-			if sample_data.meta.compass_correction_applied
-				complete = isinside(rotated_varnames,{'UCUR','VCUR','WCUR','ECUR'});
-			else
-				complete = isinside(rotated_varnames,{'UCUR_MAG','VCUR_MAG','WCUR','ECUR'});
-			end
-			assert(complete)
-	    end
-	end
+            original_varnames = IMOS.get(sample_data.variables, 'name');
+            assert(isinside(original_varnames, {'VEL1', 'VEL2', 'VEL3', 'VEL4'}));
+
+            sample_data = adcpBinMappingPP({sample_data}, '');
+            assert(isfield(sample_data{1}, 'history'))
+            assert(contains(sample_data{1}.history, 'adcpBinMappingPP.m'))
+
+            dim_names = IMOS.get(sample_data{1}.dimensions, 'name');
+            assert(inCell(dim_names, 'DIST_ALONG_BEAMS'))
+            assert(inCell(dim_names, 'HEIGHT_ABOVE_SENSOR'))
+
+            sample_data = adcpWorkhorseVelocityBeam2EnuPP(sample_data, '');
+            sample_data = sample_data{1};
+            assert(isfield(sample_data, 'history'))
+            assert(contains(sample_data.history, 'adcpWorkhorseVelocityBeam2EnuPP.m'))
+            rotated_varnames = IMOS.get(sample_data.variables, 'name');
+
+            if sample_data.meta.compass_correction_applied
+                complete = isinside(rotated_varnames, {'UCUR', 'VCUR', 'WCUR', 'ECUR'});
+            else
+                complete = isinside(rotated_varnames, {'UCUR_MAG', 'VCUR_MAG', 'WCUR', 'ECUR'});
+            end
+
+            assert(complete)
+        end
+
+    end
 
 end
 
diff --git a/test/UI/test_spikePreview.m b/test/UI/test_spikePreview.m
index a5d3e918d..e96320b05 100644
--- a/test/UI/test_spikePreview.m
+++ b/test/UI/test_spikePreview.m
@@ -1,8 +1,13 @@
 classdef test_spikePreview < matlab.unittest.TestCase
 
+    properties (TestParameter)
+        interactive = {ismember('interactive_tests',who('global'))};
+    end
+
     methods (Test)
 
-        function test_abort_is_empty(~)
+        function test_abort_is_empty(testCase,interactive)
+            testCase.assumeTrue(interactive,'Interactive test skipped')
             [postqc_data] = gen_postqc_data;
             spikeqc = struct();
             spikeqc.fun = @imosSpikeClassifierOTSU;
@@ -14,7 +19,8 @@ function test_abort_is_empty(~)
             assert(isempty(fieldnames(z.UserData)))
         end
 
-        function test_otsu_threshold(~)
+        function test_otsu_threshold(testCase,interactive)
+            testCase.assumeTrue(interactive,'Interactive test skipped')
             [postqc_data] = gen_postqc_data;
             spikeqc = struct();
             spikeqc.fun = @imosSpikeClassifierOTSU;
@@ -26,7 +32,8 @@ function test_otsu_threshold(~)
             assert(isequal(z.UserData.args, {50, 0.8, 1}));
         end
 
-        function test_otsu_savgol(~)
+        function test_otsu_savgol(testCase,interactive)
+            testCase.assumeTrue(interactive,'Interactive test skipped')
             [postqc_data] = gen_postqc_data();
             spikeqc = struct();
             spikeqc.fun = @imosSpikeClassifierNonBurstSavGolOTSU;
@@ -38,7 +45,8 @@ function test_otsu_savgol(~)
             assert(isequal(z.UserData.args, {int64(10), 3, int64(3), 0.2}));
         end
 
-        function test_hampel(~)
+        function test_hampel(testCase,interactive)
+            testCase.assumeTrue(interactive,'Interactive test skipped')
             [postqc_data] = gen_postqc_data();
             spikeqc = struct();
             spikeqc.fun = @imosSpikeClassifierHampel;
@@ -50,7 +58,8 @@ function test_hampel(~)
             assert(isequal(z.UserData.args, {2, 1, 0.01}));
         end
 
-        function test_burst_hampel(~)
+        function test_burst_hampel(testCase,interactive)
+            testCase.assumeTrue(interactive,'Interactive test skipped')
             [postqc_data] = gen_burst_data();
             spikeqc = struct();
             spikeqc.fun = @imosSpikeClassifierBurstHampel;
@@ -62,7 +71,8 @@ function test_burst_hampel(~)
             assert(isequal(z.UserData.args, {1, 1, 3, 0.01, 0}));
         end
 
-        function test_burst_runningstats(~)
+        function test_burst_runningstats(testCase,interactive)
+            testCase.assumeTrue(interactive,'Interactive test skipped')
             [postqc_data] = gen_burst_data();
             spikeqc = struct();
             spikeqc.fun = @imosSpikeClassifierBurstRunningStats;
@@ -124,5 +134,5 @@ function test_burst_runningstats(~)
 
 function [postqc_data] = gen_burst_data()
 [bind, time, tsignal] = gen_burst_signal();
-postqc_data = struct('name', 'TEMP', 'data', tsignal, 'time', time,'l',1,'r',length(tsignal),'valid_burst_range',{bind}); 
+postqc_data = struct('name', 'TEMP', 'data', tsignal, 'time', time,'l',1,'r',length(tsignal),'valid_burst_range',{bind});
 end
diff --git a/test/runAllTests.m b/test/runAllTests.m
index 6dbd858eb..c17a55430 100644
--- a/test/runAllTests.m
+++ b/test/runAllTests.m
@@ -15,7 +15,7 @@
 %
 %
 % Example:
-% runAllTests(1);
+% %runAllTests(0);
 %
 % author: hugo.oliveira@utas.edu.au
 %
diff --git a/tmp/.keep b/tmp/.keep
new file mode 100644
index 000000000..e69de29bb