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refactor: signatureParse
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1. moved functions in +Nortek/ including tests
and description
2. Fix regex in read_header_key.m linked to #758
3. Include Signature100 case and include error message
when the SIgnature is not supported
4. updated signatureParse description as it can read
both .ad2cp and .mat
5. Other clean up
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@evacougnon
evacougnon committed May 11, 2022
1 parent bcb41c7 commit 2dfb513
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Showing 4 changed files with 124 additions and 129 deletions.
58 changes: 58 additions & 0 deletions Parser/+Nortek/read_nortek_header_key.m
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@@ -0,0 +1,58 @@
function [value] = read_nortek_header_key(hstr,mode,key,vtype)
% function value = read_nortek_header_key(hstr,mode,key,vtype)
%
% Read a nortek value from a `key` name
% within a `mode` line from the header string `hstr`.
% The type of the variable is defined by `vtype`.
% See example.
%
% Inputs:
%
% hstr - the header string
% mode- the name of the mode or the first string in the line
% key - the name of the key
% vtype - the textscan type of the value [Optional]
% - default: 'float'
%
%
% Outputs:
%
% value - a single value
%
% Example:
%
% hstr = 'GETAVG1,ABC="CBA",MIAVG=600,ERR=0.00e-10';
% [value] = read_nortek_header_key(hstr,'GETAVG1','MIAVG','int');
% assert(value==600)
% [value] = read_nortek_header_key(hstr,'GETAVG1','ABC','str');
% assert(value=='CBA')
% [value] = read_nortek_header_key(hstr,'GETAVG1','ERR','float');
% assert(value==0.00e-10)
%
% author: [email protected]
%
narginchk(4,4)

if strcmpi(vtype,'float')
mtype = '-?[\d.]+(?:[eE][-?+?\d+]\d+)?';
mfun = @str2double;
elseif strcmpi(vtype,'integer') || strcmpi(vtype,'int')
mtype = '\d+';
mfun = @str2double;
else
mtype = '".*?"';
mfun = @(x) strrep(x,'"','');
end

%header lines always start with command,key0=value0,key1=value1,...
re_match = ['(?<mode>(' mode '))' '(.*?)' key '={1}' '(?<value>(' mtype '))'];
data = regexpi(hstr,re_match,'names');

if ~isempty(data)
value = mfun(data.value);
else
error('Could not find key %s with type %s',key,vtype);
end

end

43 changes: 43 additions & 0 deletions Parser/+Nortek/transfer_matrix.m
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function [Beam2xyz] = transfer_matrix(iA0_Header)
% function [Beam2xyz] = transfer_matrix(iA0_Header)
%
% get transfer function from adcp config command GETXFAVG
%
% Input:
% iA0_Header - the header string
%
% Output:
% Beam2xyz - transfer matrix to use to convert between ENU and beam
%
% Example
%
%
%

narginchk(1,1)

r = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','ROWS','int');
Beam2xyz = zeros(r,r);

Beam2xyz(1,1) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M11','float');
Beam2xyz(1,2) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M12','float');
Beam2xyz(1,3) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M13','float');
Beam2xyz(2,1) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M21','float');
Beam2xyz(2,2) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M22','float');
Beam2xyz(2,3) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M23','float');
Beam2xyz(3,1) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M31','float');
Beam2xyz(3,2) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M32','float');
Beam2xyz(3,3) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M33','float');

if r==4
Beam2xyz(1,4) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M14','float');
Beam2xyz(2,4) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M24','float');
Beam2xyz(3,4) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M34','float');
Beam2xyz(4,1) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M41','float');
Beam2xyz(4,2) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M42','float');
Beam2xyz(4,3) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M43','float');
Beam2xyz(4,4) = Nortek.read_nortek_header_key(iA0_Header,'GETXFAVG','M44','float');
end

end

144 changes: 15 additions & 129 deletions Parser/signatureParse.m
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Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
function sample_data = signatureParse( filename, tMode )
%SIGNATUREPARSE Parses ADCP data from a raw Nortek Signature
% binary (.ad2cp) file.
% binary (.ad2cp) file or a .mat that has extracted from the
% Nortek instrument software(faster).
%
%
% Inputs:
% filename - Cell array containing the name of the raw signature
% file to parse.
% file to parse (either .ad2cp or .mat).
% tMode - Toolbox data type mode.
%
% Outputs:
Expand Down Expand Up @@ -60,9 +61,9 @@
% this is a string data record
if structures.(acquisitionMode{iA0}).Data.Id == 16 || structures.(acquisitionMode{iA0}).Data.Id == 18
iA0_Header = structures.(acquisitionMode{iA0}).Data.String;
instrumentModel = read_header_key(iA0_Header,'ID','STR','string');
magDec = read_header_key(iA0_Header,'GETUSER','DECL','float');
Beam2xyz = TransferMatrix(iA0_Header);
instrumentModel = Nortek.read_nortek_header_key(iA0_Header,'ID','STR','string');
magDec = Nortek.read_nortek_header_key(iA0_Header,'GETUSER','DECL','float');
Beam2xyz = Nortek.transfer_matrix(iA0_Header);
structures = rmfield(structures, acquisitionMode{iA0});
acquisitionMode(iA0) = [];
end
Expand Down Expand Up @@ -342,7 +343,7 @@

data = struct;
nDataset = size(acquisitionMode, 2);
nBeams = 4; % default
nBeams = 4; % default -- WHY IS THIS NEEDED - I don't think it is needed due to l.354 nBeams = blah
for i=1:nDataset
data.(acquisitionMode{1, i}).Time = structures.Data.([acquisitionMode{1, i} 'Time']);

Expand Down Expand Up @@ -634,7 +635,6 @@

diffTimeInSec = diff(data.(acquisitionMode{i}).Time*24*3600);


% look for most frequents modes
Ms = unique(round(diffTimeInSec*100)/100); % unique() sorts in order of most frequent

Expand Down Expand Up @@ -665,13 +665,19 @@
sample_data{i}.meta.beam_angle = 20;
case 'Signature55'
sample_data{i}.meta.beam_angle = 20;
otherwise % Signature500 and Signature1000
case 'Signature100'
sample_data{i}.meta.beam_angle = 20;
case 'Signature500'
sample_data{i}.meta.beam_angle = 25;
case 'Signature1000'
sample_data{i}.meta.beam_angle = 25;
otherwise % send error message
error('Signature not supported');
end
if data.(acquisitionMode{i}).isVelocityData
switch lower(ext)
case '.mat'
sample_data{i}.meta.beam_to_xyz_transform = data.(acquisitionMode{i}).Beam2xyz; % need to find out how to compute this matrix for .ad2cp format. See https://pypkg.com/pypi/nortek/f/nortek/files.py
sample_data{i}.meta.beam_to_xyz_transform = data.(acquisitionMode{i}).Beam2xyz;
case '.ad2cp'
sample_data{i}.meta.beam_to_xyz_transform = Beam2xyz;
end
Expand Down Expand Up @@ -873,123 +879,3 @@
end


%-----------------------------------------------------------------
% get transfer function from adcp config command GETXFAVG
% regexp doesn't like the last parameter on the line as it runs into the
% next line.
% ie M33=-0.3547GETUSER,POFF=9.50,..
%------------------------------------------------------------------
function [Beam2xyz] = TransferMatrix(iA0_Header)
r = read_header_key(iA0_Header,'GETXFAVG','ROWS','int');
Beam2xyz = zeros(r,r);

Beam2xyz(1,1) = read_header_key(iA0_Header,'GETXFAVG','M11','float');
Beam2xyz(1,2) = read_header_key(iA0_Header,'GETXFAVG','M12','float');
Beam2xyz(1,3) = read_header_key(iA0_Header,'GETXFAVG','M13','float');
Beam2xyz(2,1) = read_header_key(iA0_Header,'GETXFAVG','M21','float');
Beam2xyz(2,2) = read_header_key(iA0_Header,'GETXFAVG','M22','float');
Beam2xyz(2,3) = read_header_key(iA0_Header,'GETXFAVG','M23','float');
Beam2xyz(3,1) = read_header_key(iA0_Header,'GETXFAVG','M31','float');
Beam2xyz(3,2) = read_header_key(iA0_Header,'GETXFAVG','M32','float');
if r==3
Beam2xyz(3,3) = read_header_key2(iA0_Header,'M33');
else
Beam2xyz(3,3) = read_header_key(iA0_Header,'GETXFAVG','M33','float');
end

if r==4
Beam2xyz(1,4) = read_header_key(iA0_Header,'GETXFAVG','M14','float');
Beam2xyz(2,4) = read_header_key(iA0_Header,'GETXFAVG','M24','float');
Beam2xyz(3,4) = read_header_key(iA0_Header,'GETXFAVG','M34','float');

Beam2xyz(4,1) = read_header_key(iA0_Header,'GETXFAVG','M41','float');
Beam2xyz(4,2) = read_header_key(iA0_Header,'GETXFAVG','M42','float');
Beam2xyz(4,3) = read_header_key(iA0_Header,'GETXFAVG','M43','float');
Beam2xyz(4,4) = read_header_key2(iA0_Header,'M44');
end
end

%--------------------------------------------------------------
function [x] = read_header_key2(header,key)

mode='GETXFAVG';

mtype = '-?[\d.^\D]+';
re_match = ['(?<mode>(' mode '))' '(.*?)' key '={1}' '(?<value>(' mtype ')),'];
data = regexpi(header,re_match,'names');

% '-0.3547GETUSER,POFF=9.50'
aa = strsplit(data.value, ',');
s = char(aa(1));
ss = '';
for i=1:length(s)
c = s(i);
if c=='-' || c=='.' || ~isempty(str2num(c))
ss = [ss c];
end
end

x = str2double(ss);
end



%----------------------------------------------------------------
function [value] = read_header_key(hstr,mode,key,vtype)
% function value = read_header_key(hstr,mode,key,vtype)
%
% Read a nortek value from a `key` name
% within a `mode` line from the header string `hstr`.
% The type of the variable is defined by `vtype`.
% See example.
%
% Inputs:
%
% hstr - the header string
% mode- the name of the mode or the first string in the line
% key - the name of the key
% vtype - the textscan type of the value [Optional]
% - default: 'float'
%
%
% Outputs:
%
% value - a single value
%
% Example:
%
% hstr = 'GETAVG1,ABC="CBA",MIAVG=600,ERR=0.00e-10';
% [value] = read_nortek_key(hstr,'GETAVG1','MIAVG','int');
% assert(value==600)
% [value] = read_nortek_key(hstr,'GETAVG1','ABC','str');
% assert(value==600)
% [value] = read_nortek_key(hstr,'GETAVG1','ERR','float');
% assert(value==600)
%
% author: [email protected]
%
narginchk(4,4)

if strcmpi(vtype,'float')
mtype = '-?[\d.]+(?:[eE][-?+?\d+]\d+)?';
mfun = @str2double;
elseif strcmpi(vtype,'integer') || strcmpi(vtype,'int')
mtype = '\d+';
mfun = @str2double;
else
mtype = '".*?"';
mfun = @(x) strrep(x,'"','');
end

%header lines always start with command,key0=value0,key1=value1,...
re_match = ['(?<mode>(' mode '))' '(.*?)' key '={1}' '(?<value>(' mtype ')),'];
data = regexpi(hstr,re_match,'names');

if ~isempty(data)
value = mfun(data.value);
else
error('Could not find key %s with type %s',key,vtype);
end

end

8 changes: 8 additions & 0 deletions test/Parser/testSignature.m
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Expand Up @@ -8,6 +8,7 @@

properties (TestParameter)
mode = {'timeSeries'};
% s55_file = files2namestruct(rdir([toolboxRootPath 'data/testfiles/Nortek/signature_55/v000']));
s250_file = files2namestruct(rdir([toolboxRootPath 'data/testfiles/Nortek/signature_250/v000']));
s500_file = files2namestruct(rdir([toolboxRootPath 'data/testfiles/Nortek/signature_500/v000']));
s1000_file = files2namestruct(rdir([toolboxRootPath 'data/testfiles/Nortek/signature_1000/v000']));
Expand All @@ -16,6 +17,13 @@

methods (Test)

% function testReadSignature250(~, s55_file, mode)
% data = signatureParse({s55_file},mode);
% assert(strcmp(data{1}.meta.instrument_model,'Signature55'));
% assert(strcmp(data{1}.meta.instrument_make,'Nortek'));
% assert(data{1}.meta.beam_angle==20);
% end

function testReadSignature250(~, s250_file, mode)
data = signatureParse({s250_file},mode);
assert(strcmp(data{1}.meta.instrument_model,'Signature250'));
Expand Down

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