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readParadoppBinary function now stores Nortek data in arrays of struc…
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…tures instead of trying to concatenate all fields of a structure. Fixes bug with some Nortek files where there are more than 1 head / config/ hardware section.
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@ggalibert
ggalibert committed Jan 4, 2017
1 parent fc6759a commit f79a111
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109 changes: 35 additions & 74 deletions Parser/aquadoppProfilerParse.m
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Original file line number Diff line number Diff line change
Expand Up @@ -68,51 +68,11 @@
% this is a plain profiler velocity data
profilerType = 'Id33';
end
nsamples = length(structures.(profilerType).Id);
ncells = user.NBins;

% preallocate memory for all sample data
time = nan(nsamples, 1);
distance = nan(ncells, 1);
analn1 = nan(nsamples, 1);
battery = nan(nsamples, 1);
analn2 = nan(nsamples, 1);
heading = nan(nsamples, 1);
pitch = nan(nsamples, 1);
roll = nan(nsamples, 1);
status = zeros(nsamples, 8, 'uint8');
pressure = nan(nsamples, 1);
temperature = nan(nsamples, 1);
velocity1 = nan(nsamples, ncells);
velocity2 = nan(nsamples, ncells);
velocity3 = nan(nsamples, ncells);
backscatter1 = nan(nsamples, ncells);
backscatter2 = nan(nsamples, ncells);
backscatter3 = nan(nsamples, ncells);

velocityProcessed = false;
if isfield(structures, 'Id106')
% velocity has been processed
velocityProcessed = true;
nsamplesProc = length(structures.Id106.Sync);
timeProc = nan(nsamplesProc, 1);
velocity1Proc = nan(nsamples, ncells);
velocity2Proc = nan(nsamples, ncells);
velocity3Proc = nan(nsamples, ncells);
sig2noise1 = nan(nsamples, ncells);
sig2noise2 = nan(nsamples, ncells);
sig2noise3 = nan(nsamples, ncells);
stdDev1 = nan(nsamples, ncells);
stdDev2 = nan(nsamples, ncells);
stdDev3 = nan(nsamples, ncells);
errorCode1 = nan(nsamples, ncells);
errorCode2 = nan(nsamples, ncells);
errorCode3 = nan(nsamples, ncells);
speed = nan(nsamples, ncells);
direction = nan(nsamples, ncells);
verticalDist = nan(nsamples, ncells);
profileErrorCode = nan(nsamples, ncells);
qcFlag = nan(nsamples, ncells);
end

%
Expand All @@ -124,6 +84,7 @@
freq = head.Frequency; % this is in KHz
blankDist = user.T2; % counts
cellSize = user.BinLength; % counts
ncells = user.NBins;
factor = 0; % used for conversion

switch freq
Expand All @@ -147,45 +108,45 @@
distance = distance + cellSize;

% retrieve sample data
time = structures.(profilerType).Time';
analn1 = structures.(profilerType).Analn1';
battery = structures.(profilerType).Battery';
analn2 = structures.(profilerType).Analn2';
heading = structures.(profilerType).Heading';
pitch = structures.(profilerType).Pitch';
roll = structures.(profilerType).Roll';
status = structures.(profilerType).Status';
pressure = structures.(profilerType).PressureMSB'*65536 + structures.(profilerType).PressureLSW';
temperature = structures.(profilerType).Temperature';
velocity1 = structures.(profilerType).Vel1';
velocity2 = structures.(profilerType).Vel2';
velocity3 = structures.(profilerType).Vel3';
backscatter1 = structures.(profilerType).Amp1';
backscatter2 = structures.(profilerType).Amp2';
backscatter3 = structures.(profilerType).Amp3';
time = [structures.(profilerType)(:).Time]';
analn1 = [structures.(profilerType)(:).Analn1]';
battery = [structures.(profilerType)(:).Battery]';
analn2 = [structures.(profilerType)(:).Analn2]';
heading = [structures.(profilerType)(:).Heading]';
pitch = [structures.(profilerType)(:).Pitch]';
roll = [structures.(profilerType)(:).Roll]';
status = [structures.(profilerType)(:).Status]';
pressure = [structures.(profilerType)(:).PressureMSB]'*65536 + [structures.(profilerType)(:).PressureLSW]';
temperature = [structures.(profilerType)(:).Temperature]';
velocity1 = [structures.(profilerType)(:).Vel1]';
velocity2 = [structures.(profilerType)(:).Vel2]';
velocity3 = [structures.(profilerType)(:).Vel3]';
backscatter1 = [structures.(profilerType)(:).Amp1]';
backscatter2 = [structures.(profilerType)(:).Amp2]';
backscatter3 = [structures.(profilerType)(:).Amp3]';

if velocityProcessed
% velocity has been processed
timeProc = structures.Id106.Time';
timeProc = [structures.Id106(:).Time]';
iCommonTime = ismember(time, timeProc); % timeProc can be shorter than time

velocity1Proc(iCommonTime, :) = structures.Id106.Vel1'; % tilt effect corrected velocity
velocity2Proc(iCommonTime, :) = structures.Id106.Vel2';
velocity3Proc(iCommonTime, :) = structures.Id106.Vel3';
sig2noise1(iCommonTime, :) = structures.Id106.Snr1';
sig2noise2(iCommonTime, :) = structures.Id106.Snr2';
sig2noise3(iCommonTime, :) = structures.Id106.Snr3';
stdDev1(iCommonTime, :) = structures.Id106.Std1'; % currently not used
stdDev2(iCommonTime, :) = structures.Id106.Std2';
stdDev3(iCommonTime, :) = structures.Id106.Std3';
errorCode1(iCommonTime, :) = structures.Id106.Erc1'; % error codes for each cell in one beam, values between 0 and 4.
errorCode2(iCommonTime, :) = structures.Id106.Erc2';
errorCode3(iCommonTime, :) = structures.Id106.Erc3';
speed(iCommonTime, :) = structures.Id106.speed';
direction(iCommonTime, :) = structures.Id106.direction';
verticalDist(iCommonTime, :) = structures.Id106.verticalDistance'; % ? no idea what this is, always same values between 6000 and 65534 for each profile.
profileErrorCode(iCommonTime, :) = structures.Id106.profileErrorCode'; % error codes for each cell of a velocity profile inferred from the 3 beams. 0=good; otherwise error. See http://www.nortek-as.com/en/knowledge-center/forum/waves/20001875?b_start=0#769595815
qcFlag(iCommonTime, :) = structures.Id106.qcFlag'; % QUARTOD QC result. 0=not eval; 1=bad; 2=questionable; 3=good.
velocity1Proc(iCommonTime, :) = [structures.Id106(:).Vel1]'; % tilt effect corrected velocity
velocity2Proc(iCommonTime, :) = [structures.Id106(:).Vel2]';
velocity3Proc(iCommonTime, :) = [structures.Id106(:).Vel3]';
sig2noise1(iCommonTime, :) = [structures.Id106(:).Snr1]';
sig2noise2(iCommonTime, :) = [structures.Id106(:).Snr2]';
sig2noise3(iCommonTime, :) = [structures.Id106(:).Snr3]';
stdDev1(iCommonTime, :) = [structures.Id106(:).Std1]'; % currently not used
stdDev2(iCommonTime, :) = [structures.Id106(:).Std2]';
stdDev3(iCommonTime, :) = [structures.Id106(:).Std3]';
errorCode1(iCommonTime, :) = [structures.Id106(:).Erc1]'; % error codes for each cell in one beam, values between 0 and 4.
errorCode2(iCommonTime, :) = [structures.Id106(:).Erc2]';
errorCode3(iCommonTime, :) = [structures.Id106(:).Erc3]';
speed(iCommonTime, :) = [structures.Id106(:).speed]';
direction(iCommonTime, :) = [structures.Id106(:).direction]';
verticalDist(iCommonTime, :) = [structures.Id106(:).verticalDistance]'; % ? no idea what this is, always same values between 6000 and 65534 for each profile.
profileErrorCode(iCommonTime, :) = [structures.Id106(:).profileErrorCode]'; % error codes for each cell of a velocity profile inferred from the 3 beams. 0=good; otherwise error. See http://www.nortek-as.com/en/knowledge-center/forum/waves/20001875?b_start=0#769595815
qcFlag(iCommonTime, :) = [structures.Id106(:).qcFlag]'; % QUARTOD QC result. 0=not eval; 1=bad; 2=questionable; 3=good.
end
clear structures;

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51 changes: 16 additions & 35 deletions Parser/aquadoppVelocityParse.m
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Original file line number Diff line number Diff line change
Expand Up @@ -60,26 +60,6 @@

% the rest of the sections are aquadopp velocity data, diagnostic header
% and diagnostic data. We will only keep the velocity data (Id == 1) .
nsamples = length(structures.Id1);
ncells = user.NBins;

% preallocate memory for all sample data
time = zeros(nsamples, 1);
distance = zeros(ncells, 1);
analn1 = zeros(nsamples, 1);
battery = zeros(nsamples, 1);
analn2 = zeros(nsamples, 1);
heading = zeros(nsamples, 1);
pitch = zeros(nsamples, 1);
roll = zeros(nsamples, 1);
pressure = zeros(nsamples, 1);
temperature = zeros(nsamples, 1);
velocity1 = zeros(nsamples, ncells);
velocity2 = zeros(nsamples, ncells);
velocity3 = zeros(nsamples, ncells);
backscatter1 = zeros(nsamples, ncells);
backscatter2 = zeros(nsamples, ncells);
backscatter3 = zeros(nsamples, ncells);

%
% calculate distance values from metadata. See continentalParse.m
Expand All @@ -90,6 +70,7 @@
freq = head.Frequency; % this is in KHz
cellStart = user.T2; % counts
cellLength = user.BinLength; % counts
ncells = user.NBins;
factor = 0; % used for conversion

switch freq
Expand All @@ -112,21 +93,21 @@
distance = distance + cellLength;

% retrieve sample data
time = structures.Id1.Time';
analn1 = structures.Id1.Analn1';
battery = structures.Id1.Battery';
analn2 = structures.Id1.Analn2';
heading = structures.Id1.Heading';
pitch = structures.Id1.Pitch';
roll = structures.Id1.Roll';
pressure = structures.Id1.PressureMSB'*65536 + structures.Id1.PressureLSW';
temperature = structures.Id1.Temperature';
velocity1 = structures.Id1.Vel1';
velocity2 = structures.Id1.Vel2';
velocity3 = structures.Id1.Vel3';
backscatter1 = structures.Id1.Amp1';
backscatter2 = structures.Id1.Amp2';
backscatter3 = structures.Id1.Amp3';
time = [structures.Id1(:).Time]';
analn1 = [structures.Id1(:).Analn1]';
battery = [structures.Id1(:).Battery]';
analn2 = [structures.Id1(:).Analn2]';
heading = [structures.Id1(:).Heading]';
pitch = [structures.Id1(:).Pitch]';
roll = [structures.Id1(:).Roll]';
pressure = [structures.Id1(:).PressureMSB]'*65536 + [structures.Id1(:).PressureLSW]';
temperature = [structures.Id1(:).Temperature]';
velocity1 = [structures.Id1(:).Vel1]';
velocity2 = [structures.Id1(:).Vel2]';
velocity3 = [structures.Id1(:).Vel3]';
backscatter1 = [structures.Id1(:).Amp1]';
backscatter2 = [structures.Id1(:).Amp2]';
backscatter3 = [structures.Id1(:).Amp3]';
clear structures;

% battery / 10.0 (0.1 V -> V)
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109 changes: 35 additions & 74 deletions Parser/awacParse.m
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Original file line number Diff line number Diff line change
Expand Up @@ -72,51 +72,11 @@
user = structures.Id0;

% the rest of the sections are awac data
nsamples = length(structures.Id32);
ncells = user.NBins;

% preallocate memory for all sample data
time = nan(nsamples, 1);
distance = nan(ncells, 1);
analn1 = nan(nsamples, 1);
battery = nan(nsamples, 1);
analn2 = nan(nsamples, 1);
heading = nan(nsamples, 1);
pitch = nan(nsamples, 1);
roll = nan(nsamples, 1);
status = zeros(nsamples, 8, 'uint8');
pressure = nan(nsamples, 1);
temperature = nan(nsamples, 1);
velocity1 = nan(nsamples, ncells);
velocity2 = nan(nsamples, ncells);
velocity3 = nan(nsamples, ncells);
backscatter1 = nan(nsamples, ncells);
backscatter2 = nan(nsamples, ncells);
backscatter3 = nan(nsamples, ncells);

velocityProcessed = false;
if isfield(structures, 'Id106')
% velocity has been processed
velocityProcessed = true;
nsamplesProc = length(structures.Id106.Sync);
timeProc = nan(nsamplesProc, 1);
velocity1Proc = nan(nsamples, ncells);
velocity2Proc = nan(nsamples, ncells);
velocity3Proc = nan(nsamples, ncells);
sig2noise1 = nan(nsamples, ncells);
sig2noise2 = nan(nsamples, ncells);
sig2noise3 = nan(nsamples, ncells);
stdDev1 = nan(nsamples, ncells);
stdDev2 = nan(nsamples, ncells);
stdDev3 = nan(nsamples, ncells);
errorCode1 = nan(nsamples, ncells);
errorCode2 = nan(nsamples, ncells);
errorCode3 = nan(nsamples, ncells);
speed = nan(nsamples, ncells);
direction = nan(nsamples, ncells);
verticalDist = nan(nsamples, ncells);
profileErrorCode = nan(nsamples, ncells);
qcFlag = nan(nsamples, ncells);
end

%
Expand All @@ -128,6 +88,7 @@
freq = head.Frequency; % this is in KHz
blankDist = user.T2; % counts
cellSize = user.BinLength; % counts
ncells = user.NBins;
factor = 0; % used in conversion

switch freq
Expand All @@ -148,45 +109,45 @@
distance = distance + cellSize;

% retrieve sample data
time = structures.Id32.Time';
analn1 = structures.Id32.Analn1';
battery = structures.Id32.Battery';
analn2 = structures.Id32.Analn2';
heading = structures.Id32.Heading';
pitch = structures.Id32.Pitch';
roll = structures.Id32.Roll';
status = structures.Id32.Status';
pressure = structures.Id32.PressureMSB'*65536 + structures.Id32.PressureLSW';
temperature = structures.Id32.Temperature';
velocity1 = structures.Id32.Vel1';
velocity2 = structures.Id32.Vel2';
velocity3 = structures.Id32.Vel3';
backscatter1 = structures.Id32.Amp1';
backscatter2 = structures.Id32.Amp2';
backscatter3 = structures.Id32.Amp3';
time = [structures.Id32(:).Time]';
analn1 = [structures.Id32(:).Analn1]';
battery = [structures.Id32(:).Battery]';
analn2 = [structures.Id32(:).Analn2]';
heading = [structures.Id32(:).Heading]';
pitch = [structures.Id32(:).Pitch]';
roll = [structures.Id32(:).Roll]';
status = [structures.Id32(:).Status]';
pressure = [structures.Id32(:).PressureMSB]'*65536 + [structures.Id32(:).PressureLSW]';
temperature = [structures.Id32(:).Temperature]';
velocity1 = [structures.Id32(:).Vel1]';
velocity2 = [structures.Id32(:).Vel2]';
velocity3 = [structures.Id32(:).Vel3]';
backscatter1 = [structures.Id32(:).Amp1]';
backscatter2 = [structures.Id32(:).Amp2]';
backscatter3 = [structures.Id32(:).Amp3]';

if velocityProcessed
% velocity has been processed
timeProc = structures.Id106.Time';
timeProc = [structures.Id106(:).Time]';
iCommonTime = ismember(time, timeProc); % timeProc can be shorter than time

velocity1Proc(iCommonTime, :) = structures.Id106.Vel1'; % tilt effect corrected velocity
velocity2Proc(iCommonTime, :) = structures.Id106.Vel2';
velocity3Proc(iCommonTime, :) = structures.Id106.Vel3';
sig2noise1(iCommonTime, :) = structures.Id106.Snr1';
sig2noise2(iCommonTime, :) = structures.Id106.Snr2';
sig2noise3(iCommonTime, :) = structures.Id106.Snr3';
stdDev1(iCommonTime, :) = structures.Id106.Std1'; % currently not used
stdDev2(iCommonTime, :) = structures.Id106.Std2';
stdDev3(iCommonTime, :) = structures.Id106.Std3';
errorCode1(iCommonTime, :) = structures.Id106.Erc1'; % error codes for each cell in one beam, values between 0 and 4.
errorCode2(iCommonTime, :) = structures.Id106.Erc2';
errorCode3(iCommonTime, :) = structures.Id106.Erc3';
speed(iCommonTime, :) = structures.Id106.speed';
direction(iCommonTime, :) = structures.Id106.direction';
verticalDist(iCommonTime, :) = structures.Id106.verticalDistance'; % ? no idea what this is, always same values between 6000 and 65534 for each profile.
profileErrorCode(iCommonTime, :) = structures.Id106.profileErrorCode'; % error codes for each cell of a velocity profile inferred from the 3 beams. 0=good; otherwise error. See http://www.nortek-as.com/en/knowledge-center/forum/waves/20001875?b_start=0#769595815
qcFlag(iCommonTime, :) = structures.Id106.qcFlag'; % QUARTOD QC result. 0=not eval; 1=bad; 2=questionable; 3=good.
velocity1Proc(iCommonTime, :) = [structures.Id106(:).Vel1]'; % tilt effect corrected velocity
velocity2Proc(iCommonTime, :) = [structures.Id106(:).Vel2]';
velocity3Proc(iCommonTime, :) = [structures.Id106(:).Vel3]';
sig2noise1(iCommonTime, :) = [structures.Id106(:).Snr1]';
sig2noise2(iCommonTime, :) = [structures.Id106(:).Snr2]';
sig2noise3(iCommonTime, :) = [structures.Id106(:).Snr3]';
stdDev1(iCommonTime, :) = [structures.Id106(:).Std1]'; % currently not used
stdDev2(iCommonTime, :) = [structures.Id106(:).Std2]';
stdDev3(iCommonTime, :) = [structures.Id106(:).Std3]';
errorCode1(iCommonTime, :) = [structures.Id106(:).Erc1]'; % error codes for each cell in one beam, values between 0 and 4.
errorCode2(iCommonTime, :) = [structures.Id106(:).Erc2]';
errorCode3(iCommonTime, :) = [structures.Id106(:).Erc3]';
speed(iCommonTime, :) = [structures.Id106(:).speed]';
direction(iCommonTime, :) = [structures.Id106(:).direction]';
verticalDist(iCommonTime, :) = [structures.Id106(:).verticalDistance]'; % ? no idea what this is, always same values between 6000 and 65534 for each profile.
profileErrorCode(iCommonTime, :) = [structures.Id106(:).profileErrorCode]'; % error codes for each cell of a velocity profile inferred from the 3 beams. 0=good; otherwise error. See http://www.nortek-as.com/en/knowledge-center/forum/waves/20001875?b_start=0#769595815
qcFlag(iCommonTime, :) = [structures.Id106(:).qcFlag]'; % QUARTOD QC result. 0=not eval; 1=bad; 2=questionable; 3=good.
end
clear structures;

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