FAIR ADCP da a wi h OSADCP:
a wo kflow o p ocess ocean
cu en da a om essel-
moun ed ADCPs
Robe Kop e
1
*, Ma ius Becke
1
, Tim Fische
2
, Pe e B and
2,3
,
Ge d K ahmann
2
, Maximilian Be z
4
, Claas Fabe
5
,
Ch is ian Win e
1
, Johannes Ka s ensen
2
and Gau ain Wieme
6
1
Ins i u e o Geosciences, Kiel Uni e si y, Kiel, Ge many,
2
Depa men o Physical Oceanog aphy,
GEOMAR Helmhol z Cen e o Ocean Resea ch Kiel, Kiel, Ge many,
3
Facul y o Ma hema ics and
Na u al Sciences, Kiel Uni e si y, Kiel, Ge many,
4
Compu ing and Da a Cen e, Al ed-Wegene -
Ins i u e o Pola and Ma ine Resea ch, B eme ha en, Ge many,
5
Da a Managemen , GEOMAR
Helmhol z Cen e o Ocean Resea ch Kiel, Kiel, Ge many,
6
Da a Managemen and Digi aliza ion,
Ge man Ma ine Resea ch Alliance (DAM), Be lin, Ge many
This pape p esen s he open-sou ce Py hon so wa e OSADCP de eloped o
he p ocessing o essel-moun ed Acous ic Dopple Cu en P ofile (VMADCP)
da a. A his s age, he oolbox is designed o p ocessing VMADCP
measu emen s om open-ocean applica ions o Teledyne RDI Ocean Su eyo
ADCPs and he da a acquisi ion so wa e VMDAS. Based on he VMDAS ENX
bina y ou pu o ma , he so wa e con ains implemen a ions o cleaning and
ec o -a e aging o single-ping eloci y da a, e ifica ion o he posi ion da a,
and applying misalignmen and ampli ude co ec ions. The p ocedu es o
OSADCP a e desc ibed in de ail o encou age he scien ific communi y o use
i o hei own pu poses. The oolbox is an in eg al pa o a wo kflow
implemen ed on he Ge man ma ine esea ch essels in he amewo k o he
Unde way Resea ch Da a p ojec o he Ge man Ma ine Resea ch Alliance (DAM).
I aims o ensu e s anda dized da a acquisi ion measu es, eliable da a ans e
om he ADCP o sho e bo h nea - eal- ime and in delayed-mode, p ocessing
and quali y con ol, and dissemina ion o he cu a ed da a p oduc in he da a
eposi o y PANGAEA. F om PANGAEA, da a se s a e o wa ded o he Eu opean
ma ine da a hubs Cope nicus Ma ine Se ice and EMODne . The wo kflow ha
o ms he amewo k o OSADCP is desc ibed he e as an example o scien ific
da a managemen ha ollows he FAIR da a guidelines.
KEYWORDS
ADCP, unde way da a, FAIR da a, py hon, ocean cu en s
F on ie s in Ma ine Science on ie sin.o g01
OPEN ACCESS
EDITED BY
Sa ah T. Gille,
Uni e si y o Cali o nia, San Diego,
Uni ed S a es
REVIEWED BY
E ic Fi ing,
Uni e si y o Hawaii a Manoa, Uni ed S a es
An onio No ellino,
ETT SpA, I aly
*CORRESPONDENCE
Robe Kop e
[email p o ec ed]
RECEIVED 29 Ap il 2024
ACCEPTED 02 Augus 2024
PUBLISHED 26 Augus 2024
CITATION
Kop e R, Becke M, Fische T, B and P,
K ahmann G, Be z M, Fabe C, Win e C,
Ka s ensen J and Wieme G (2024) FAIR
ADCP da a wi h OSADCP: a wo kflow
o p ocess ocean cu en da a
om essel-moun ed ADCPs.
F on . Ma . Sci. 11:1425086.
doi: 10.3389/ ma s.2024.1425086
COPYRIGHT
© 2024 Kop e, Becke , Fische , B and ,
K ahmann, Be z, Fabe , Win e , Ka s ensen and
Wieme .Thisisanopen-accessa icle
dis ibu ed unde he e ms o he C ea i e
Commons A ibu ion License (CC BY). The
use, dis ibu ion o ep oduc ion in o he
o ums is pe mi ed, p o ided he o iginal
au ho (s) and he copy igh owne (s) a e
c edi ed and ha he o iginal publica ion in
his jou nal is ci ed, in acco dance wi h
accep ed academic p ac ice. No use,
dis ibu ion o ep oduc ion is pe mi ed
which does no comply wi h hese e ms.
TYPE Technology and Code
PUBLISHED 26 Augus 2024
DOI 10.3389/ ma s.2024.1425086
1 In oduc ion
Ocean cu en measu emen s a e indispensable o
unde s anding he dynamics and ci cula ion pa e ns o ma ine
en i onmen s. Ocean cu en s edis ibu e hea and impac he
su ace ocean momen um flux and hus influence global clima e
pa e ns ha ha e a - eaching e ec s on wea he sys ems
wo ldwide. Addi ionally, ocean cu en s impac he heal h o
ma ine ecosys ems by dispe sing nu ien s, dilu ing pollu an s,
anspo ing plank on and a ec ing he beha io o mobile
species. Unde s anding and moni o ing ocean cu en s is essen ial
o p edic ing clima e change impac s, imp o ing wea he o ecas s,
and ensu ing he sus ainable managemen o ma ine esou ces.
Obse a ions o ocean cu en s se e as suppo ing a iables o he
es ima ion o so-called Essen ial Ocean Va iables (EOVs,
Linds om e al., 2012), which a e he backbone o obse a ional
con ibu ions o bo h he Global Ocean Obse ing Sys em (GOOS)
and he Global Clima e Obse ing Sys em (GCOS).
Acous ic Dopple Cu en P ofile s (ADCPs) a e among he
mos commonly used oceanog aphic ins umen s, as hey e ficien ly
measu e ocean eloci y p ofiles de i ed indi ec ly om he acous ic
echoes o suspended ma e passi ely ad ec ed by he cu en . A
s anda d applica ion in oceanog aphic esea ch is he use o ADCPs
on a mo ing ship, in he ollowing e e ed o as essel-moun ed
ADCPs (VMADCPs). VMADCPs acili a e unde way and quasi-
s a iona y measu emen s o uppe ocean cu en s, co e ing a
measu emen ange o se e al hund ed me e s below he ship.
Beginning wi h he Wo ld Ocean Ci cula ion Expe imen
(WOCE) in he 1990s (King e al., 2001), VMADCPs ha e
become he s anda d ins umen o measu ing ocean cu en s
du ing esea ch c uises. They a e ou inely used o moni o
changes o he e ical s uc u e o he flow along epea ed
sec ions, e.g., in he opical Pacific(Johnson e al., 2002), in he
opical A lan ic (Johns e al., 2014;B and e al., 2014) o ac oss
D ake Passage (Sp in all e al., 2012;Fi ing e al., 2012). In gene al,
VMADCPs assis esea ch ac oss all ma ine science disciplines,
enhancing in e disciplina y p ocess s udies by p o iding eal- ime
in o ma ion abou he ocean cu en benea h he ship. This
capabili y o example suppo s apid-sampling s a egies ha
allow scien is s o s udy ansien phenomena like mesoscale
eddies, on s, wa es and upwelling e en s (e.g., Menkes e al.,
2002;Shche bina e al., 2015;Hummels e al., 2020;L’Hega e
e al., 2023).
To maximize he alue o VMADCP ocean cu en da a
p oduc s o scien ific and moni o ing use, hei cu a ion,
publica ion, accessibili y and p ese a ion is a key ask. Recen
demands in ma ine da a managemen in gene al a e d i en by he
need o high- esolu ion, e en ually eal- ime da a o add ess
complex global issues such as clima e change, biodi e si y loss
and ocean heal h. In his con ex , he lack o s anda dized da a
o ma s and p o ocols emains a pe sis en issue complica ing da a
in eg a ion and in e ope abili y. A in e na ional le el, a ious
g oups and o ganiza ions add ess hese challenges by de eloping
commonly ag eed s anda ds and bes p ac ices, imp o ing
coo dina ion and dialogue ac oss p ac i ione s and use s.
Embedded in he In e go e nmen al Oceanog aphic Commission
(IOC) o he Uni ed Na ions Educa ional, Scien ific and Cul u al
O ganiza ion (UNESCO) is he Obse a ion Coo dina ion G oup
(OGC) o he GOOS ha assembles a ious global obse a ion
pla o m-specific g oups, such as GO-SHIP, which ocuses on da a
om esea ch essels, and A go, which manages da a om p ofiling
floa s. As gene al guidelines o he managemen o scien ific da a,
he FAIR (Findable, Accessible, In e ope able, Reusable) p inciples
(Wilkinson e al., 2016) we e accep ed as a guiding p inciple o
da a managemen , oge he wi h he CARE (Collec i e benefi ,
Au ho i y o con ol, Responsibili y, E hics) p inciples (Ca oll
e al., 2021). E ficien coo dina ion a na ional le el is a
p e equisi e o he ep esen a ion o indi idual coun ies and
cons uc i e coope a ion o suppo he in e na ional e o s. In
Ge many, wo di e en associa ions o ma ine esea ch ins i u ions
enable s a egic ini ia i es and o e a ching discussions,
encompassing he ins i u ional di e si y. These associa ions a e
he Konso ium Deu sche Mee es o schung (KDM), ounded in
2004, and he Ge man Ma ine Resea ch Alliance (DAM). One
ini ia i e, launched by he DAM in 2019, is he Unde way Resea ch
Da a p ojec . The p ojec pools he da a managemen expe ise o
a ious ma ine esea ch ins i u ions o demons a e he sys ema ic
p o ision o FAIR obse a ional da a om he Ge man ma ine
esea ch essels. Following he app oach aken in o he coun ies,
such as he Rolling deck o Reposi o y in he U.S. (R2R, Ca bo e
e al., 2022), wo kflows o ship bo ne scien ific senso s ha e been
es ablished ha add ess ship-specific equi emen s o
configu a ion, (nea -) eal- ime moni o ing, da a access and
quali y assu ance. Wi h his p ojec , DAM also con ibu es o he
ecen ly es ablished Na ional Resea ch Da a In as uc u e (NFDI,
Ha l e al., 2021) as a case s udy on sys ema ic FAIR and open
p o ision o he e ogeneous and ansdisciplina y ma ine da a.
VMADCPs a e among he senso s co e ed by he DAM
Unde way Resea ch Da a p ojec . A e a sho summa y o he
s a e o he a o VMADCP echnology (Sec ion 2), his a icle
desc ibes he wo kflow implemen ed on he la ge ships o he
Ge man Ma ine esea ch flee as an example o scien ific da a
managemen ha ollows FAIR da a guidelines (Sec ion 3). An
essen ial componen o he wo kflow is he pos -p ocessing so wa e
OSADCP (Kop e e al., 2024), w i en in Py hon and designed o
p ocess VMADCP aw da a acqui ed using Teledyne RDI’s Vessel
Moun Da a Acquisi ion So wa e (VMDAS). The handling o
OSADCP is desc ibed in Sec ion 3.3, as a basic amewo k o he
so wa e is made a ailable o he scien ific communi y along wi h
his a icle.
2 Backg ound
2.1 (VM)ADCP echnology
ADCPs in e wa e eloci ies indi ec ly om he acous ic echoes
o suspended ma e , e.g., plank on o suspended sedimen ,
assuming passi e ad ec ion o he sca e e s wi h he cu en .
Hyd oacous ic pulses a e emi ed along na ow, slan ed beams.
The ene gy is abso bed, sca e ed and pa ly eflec ed by he
sca e e s o be ecei ed by he ADCP. As o he Dopple e ec , a
Kop e e al. 10.3389/ ma s.2024.1425086
F on ie s in Ma ine Science on ie sin.o g02
mo emen o sca e e s along he beam axis causes a change o
equency o he ecei ed echo compa ed o he equency o he
emi ed pulse. Wi h indi idual beams o ien ed in di e en
di ec ions, each beam measu es a p ojec ion o he local eloci y
ec o on i s espec i e beam axis. Assuming ho izon ally
homogeneous flow ac oss he a ea co e ed by he slan ed beams,
he beam geome y is aken in o accoun o calcula e he
componen s o he cu en eloci y in ca esian coo dina es (RD
Ins umen s, 2010).
In o iginal ADCP echnology, a single homogeneous acous ic
pulse is emi ed (na owband ping ype). La e , he b oadband ping
ype was de eloped, which sends a con inuous sequence o sub-
pings coded by phase e e sals (Pinkel and Smi h, 1992). The eby
he in o ma ion con en o he e u ning echo is inc eased,
imp o ing he p ecision o he eloci y measu emen s
subs an ially, a he expense o some educ ion in ange
and obus ness.
To de e mine a eloci y p ofile om one acous ic pulse, he
ange along he acous ic pa h is spli in o successi e empo al
segmen s, which co espond o dep h cells a successi ely g ea e
dis ances om he de ice. This p ocess is e e ed o as ange-ga ing
(RD Ins umen s, 2011). In deep-wa e applica ions, VMADCPs
ypically ope a e a equencies be ween 150 kHz and 38 kHz,
esul ing in maximum p ofiling anges be ween 400 m and mo e
han 1000 m, espec i ely. To achie e highe e ical esolu ion a
he expense o p ofiling ange, ADCPs wi h highe equencies, e.g.,
600 kHz o 300 kHz, may be used simul aneously wi h long-
ange ADCPs.
2.2 VMADCP da a acquisi ion sys ems
The mos common acquisi ion sys ems used by he
oceanog aphic communi y a e VMDAS and UHDAS, as desc ibed
and compa ed by Fi ing and Hummon, 2010.VMDAS is a
Windows so wa e p o ided by Teledyne RD Ins umen s
(TRDI), one o he manu ac u e s o ADCPs. UHDAS is a Linux
so wa e de eloped and main ained by he Uni e si y o Hawaii,
U.S (Fi ing e al., 2012;Hummon e al., 2023). UHDAS handles
auxilia y da a s eams mo e obus ly han VMDAS. I p o ides
au oma ic p e-p ocessing and he expo o diagnos ic da a, and can
p ocess da a om se e al VMADCPs a he same ime.
2.3 VMADCP pos -p ocessing solu ions
Se e al s eps o pos -p ocessing a e equi ed o de e mine ocean
cu en s om aw VMADCP da a (Fi ing and Hummon, 2010).
These include coo dina e ans o ma ions, he cleaning o single-
ping da a, me ging o ADCP wi h auxilia y da a, e ifica ion o
posi ioning in o ma ion, ec o -a e aging o single-ping eloci y
da a, and he applica ion o heading misalignmen and eloci y
ampli ude co ec ions. Pos -p ocessing also includes he gene al
assessmen o da a quali y, which may be influenced by
en i onmen al condi ions, e.g., he sea s a e o he occu ence and
he na u e o sca e e s in he wa e column.
Scien ific use s de eloped a numbe o pos -p ocessing ools o
VMADCP da a, ollowing di e en app oaches and enabling
di e en ways o quali y con ol. Mos o hese ools ead ADCP
aw da a in pd0 o ma , he s anda d bina y ou pu o ma o TRDI.
Basic p ocessing solu ions consis o sc ip s, which implemen
essen ial p ocessing s eps and a e easily adap able o specific
equi emen s o use cases. One example is he OSSI MATLAB
oolbox, de eloped a he depa men o Physical Oceanog aphy o
he Ins i u ü Mee eskunde, now GEOMAR Helmhol z Cen e o
Ocean Resea ch Kiel, Ge many (Fische e al., 2003). The OSSI
oolbox was no eleased o ficially, bu is widely used in he Ge man
ADCP use communi y. Ano he example o a sc ip -based
implemen a ion o p ocessing and isualiza ion o essel-moun ed
ADCP da a is con ained in he R package o oceanog aphic
analysis oce (Kelley, 2018). Mo e in eg a ed and au oma ed
me hods a e also a ailable. CASCADE is an open-sou ce
MATLAB p og am de eloped a he F ench Labo a o y o
Physical Oceanog aphy (LOPS, Le Bo e al., 2011). CASCADE
uses a g aphical in e ace and allows he selec ion o h esholds and
c i e ia o da a quali y checks. A widely-used p ocessing
amewo k is CODAS p ocessing, de eloped and main ained by
he UH Cu en s G oup a he Uni e si y o Hawaii, U.S (Fi ing and
Hummon, 2010;Hummon e al., 2023). CODAS p ocessing is used
by he UHDAS acquisi ion so wa e o p o ide online p e-
p ocessing and emo e moni o ing du ing da a acquisi ion.
2.4 VMADCP da a dissemina ion
Following acquisi ion and pos -p ocessing, he alue chain o
VMADCP da a is supposed o yield quali y-con olled and openly
accessible ocean eloci y da a p oduc s, published acco ding o
FAIR p inciples (Wilkinson e al., 2016). VMADCP da a om U.S
na ional c uises bu also om a ious in e na ional p og ams a e
published by he Join A chi e o Shipboa d ADCP (JASADCP),
main ained by he Na ional Cen e s o En i onmen al
In o ma ion(NCEI)incollabo a ion wi h he Uni e si y o
Hawaii. In he E.U., he Cope nicus Ma ine Se ice (CMEMS)
and EMODne a e he main in eg a o s o pla o m-independen
ma ine in-si u da a. They in eg a e da a om na ional
oceanog aphic eposi o ies, e.g., om PANGAEA, he Ge man
node o ea h sys em esea ch da a (Felden e al., 2023).
None heless, due o he he e ogenei y o he da a se s ollowing
di e en me a da a s anda ds and ocabula ies, in eg a ion o en
emains a challenge and e o s a e needed o achie e a highe le el
o ha moniza ion.
3 Wo kflow o essel-moun ed ADCP
da a managemen
The wo kflow (Figu e 1) p esen ed he e aims o map he en i e
alue chain o VMADCP da a and co e s he a eas o da a
acquisi ion (Sec ion 3.1), da a ans e (Sec ion 3.2), da a
p ocessing and quali y con ol (Sec ion 3.3) and dissemina ion o
he final da a p oduc (Sec ion 3.4).
Kop e e al. 10.3389/ ma s.2024.1425086
F on ie s in Ma ine Science on ie sin.o g03
3.1 Da a acquisi ion
The Ge man ma ine esea ch essels R/V Ma ia S. Me ian, R/V
Me eo , and R/V Sonne a e equipped wi h 75-kHz and 38-kHz
Teledyne RDI Ocean Su eyo ADCPs o p ofiling he uppe wa e
column, up o 1200 m dep h. High-quali y, ime-synch onous
posi ion and a i ude da a a e p o ided by Kongsbe g Seapa h
sys ems. Each VMADCP is con olled by a VMDAS ins ance
ins alled on a dedica ed senso PC ha bundles he VMADCP
and na iga ion da a s eams. All aw da a, ha accumula es on he
senso PC is con inuously backed up o he mass da a managemen
(MDM) sys em implemen ed in he IT in as uc u e o each ship in
he amewo k o he Unde way Resea ch Da a p ojec . The MDM
sys em collec s all eco ded esea ch da a in a uni o m, campaign-
based manne and con inuously mi o s i on o sui able anspo
ha d d i es.
FIGURE 1
ADCP da a wo kflow as implemen ed and es ablished on he Ge man esea ch essels R/V Ma ia S. Me ian, R/V Me eo , and R/V Sonne (see Sec ion
3 o de ails).
Kop e e al. 10.3389/ ma s.2024.1425086
F on ie s in Ma ine Science on ie sin.o g04
In he wo kflow’s s anda d se ing o ou ine unde way deep-
wa e p ofiling, VMDAS is configu ed o use na owband single-
ping eco ding wi h bo om- acking disabled. Na owband
measu emen s a e less sensi i e o dis u bances and noise o low
abundances o sca e e s in he wa e column. The p ofile
pa ame e s (numbe o cells/cell size/blanking dis ance) o se he
sampling dep hs a e chosen in he ange o he ecommended
de aul alues p o ided by he manu ac u e o 75 kHz (100/8 m/8
m) and 38 kHz (50/32 m/16 m) sys ems.
VMDAS gene a es h ee, pa ly edundan aw da a o ma s
con aining single-ping da a in pd0 o ma , each ep esen ing a
di e en s a us o in e nally applied coo dina e ans o ma ion and
da a s eam me ging. ENR files con ain eloci ies in beam coo dina es
bu no ex e nal na iga ion da a. ENS files addi ionally con ain
na iga ion da a o each single ping. ENX files con ain eloci y da a
in ea h coo dina es and na iga ion da a. Using ENR o ENS files o
s a pos -p ocessing, he equi ed coo dina e ans o ma ions (RD
Ins umen s, 2010) a e o be conduc ed by he use . In case o ENR
files, he use also me ges he ancilla y da a s eams wi h he ADCP
single-ping da a. S a ing wi h ENR o ENS files allows edi ing o
single-ping da a o indi idual beams and gi es con ol o he use on
how o pe o m he coo dina e ans o ma ion (e.g., using a h ee-
beam-solu ion i one beam is ound mal unc ioning). S a ing wi h
ENX files, he use needs o speci y he senso s in he da a acquisi ion
se up ha a e o be conside ed as a i ude da a sou ces by he
VMDAS in e nal coo dina e ans o ma ion.
In addi ion o being inse ed in o he ENS and ENX files, he
na iga ion da a is logged in sepa a e files. Bina y o ma na iga ion
da a is collec ed in NMS files, while N[1,2,3]R files con ain aw
NMEA messages as configu ed in VMDAS.In hewo kflow’s
s anda d se ing, NMEA posi ion da a (GGA) and NMEA ship
speed da a (VTG) a e collec ed in N1R files, and NMEA a i ude
(heading, pi ch, oll) da a (PRDID) a e collec ed in N2R files.
Addi ionally, PADCP messages wi h he ADCP ensemble numbe
and a imes amp a e con ained in he N[1,2,3]R files. These can be
used o align na iga ion da a wi h he ADCP ime se ies, i he e was
a p oblem wi h eco ding o he na iga ion da a in he ENS o ENX
files. VMDAS elies on he ime se ings o he eco ding PC when
c ea ing imes amps o pings, so i is ad isable o keep he PC ime
synch onized wi h UTC ime. None heless, PADCP messages
p o ided by VMDAS con ain in o ma ion on he di e ence
be ween UTC and PC ime, ha can be used o co ec ping
imes. VMDAS p io i izes inse ing PADCP messages in o he N
[1,2,3]R files, which migh occasionally co up o he NMEA
messages and complica es pa sing du ing pos -p ocessing. Also,
in he pas , whole sec ions o na iga ion da a could be co up ed by
se ial da a o e flows, bu wi h mode n IT in as uc u e his is
no mally no longe a p oblem.
3.2 Da a ans e
3.2.1 Nea eal- ime
Fo sys em diagnos ics and da a quali y checks, incoming
VMADCP aw da a is egula ly sen asho e. A c onjob is
wa ching he di ec o y o VMADCP aw da a on he MDM.
E e y hou , newly c ea ed ENX files (usually 10 MB in size) a e
iden ified, comp essed and sen as a sepa a e e-mail including me a
in o ma ion and a checksum. Asho e, da a a e ecei ed by he O2A
inges se ices o aw da a (Koppe e al., 2015) hos ed a Al ed-
Wegene -Ins i u e (AWI) in B eme ha en, Ge many and s o ed in
he p ojec ’s cen al wo kspace.
3.2.2 Pos -campaign ans e
In he des ina ion po be ween wo campaigns, he dedica ed
anspo ha d disks wi h a comple e copy o he expedi ion da a a e
emo ed om he MDM and sen o AWI as an insu ed shipmen .
In e u n, he ship ecei es emp y ha d d i es o he nex
campaign. A AWI, he en i e da a se is checked o in eg i y
and ed in o he cen al wo kspace using he O2A inges (Koppe
e al., 2015) and is made accessible o delayed-mode p ocessing and
final quali y con ol ia he p ojec ’s cen al wo kspace.
3.3 P ocessing and quali y con ol
using OSADCP
The Py hon-based so wa e OSADCP (Kop e e al., 2024)is
de eloped bo h o he nea - eal- ime moni o ing and o he
delayed-mode p ocessing o he VMADCP aw da a. OSADCP
con ains modules ha include he essen ial p ocessing s eps
(Figu e 2) o coo dina e ans o ma ion, posi ion da a e ifica ion,
eloci y da a cleaning, bo om in e e ence de ec ion, ensemble
a e aging and wa e - ack calib a ion. I configu ed in VMDAS,
also bo om- ack eloci ies can be used o he calcula ion o he
eloci y p ofiles. Cus omized add-on modules ha e been de eloped
o he wo kflow p esen ed he e o au oma e o example he
gene a ion o da a p ocessing epo s, da a isualiza ions, o da a
o ma con e sions o dissemina ion p ocedu es.
3.3.1 Abou OSADCP
OSADCP eme ged om he MATLAB-based OSSI oolbox,
which was de eloped o e many yea s a GEOMAR, Helmhol z
Cen e o Ocean Resea ch Kiel. As pa o he DAM Unde way
Resea ch Da a p ojec , i was edesigned and u he de eloped o
mee he equi emen s o s anda dized and, as a as possible,
au oma ed p ocessing o VMADCP da a om Ge man esea ch
essels. To acili a e access o he whole scien ific communi y,
OSADCP is w i en in Py hon. The so wa e is designed o p ocess
VMADCP aw da a acqui ed wi h Teledyne RDI’s da a acquisi ion
so wa e VMDAS. A basic amewo k o he so wa e is made
a ailable o he scien ific communi y along wi h his a icle (see
Appendix o ins uc ions on he ins alla ion and se up). By de aul ,
OSADCP p ocesses ENX files, which equi es bo h high-quali y and
comple e ADCP aw da a and na iga ion da a. F om ou
expe ience, wo king wi h ENX files is gene ally p e e ed due o
he simplici y o he handling. In he e en ha p oblems a ise wi h
ei he ADCP o na iga ion da a, ha equi e o example edi ing o
beam-wise ADCP eloci ies o he manual me ging o na iga ion
da a, OSADCP has add-on modules p ocessing ei he ENR o ENS
files ha a e no ye made publicly a ailable.
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The gene al p ocedu e o wo king wi h OSADCP is shown in
Figu e 3. To illus a e key aspec s o he p ocessing we use an
example da a se om a 75 kHz Ocean Su eyo ADCP o he R/V
Me eo campaign M189 (Dengle e al., 2023) ha was acqui ed
acco ding o he wo kflow p esen ed he e.
3.3.2 os_se ings.py
A cen al poin o he oolbox is he module os_se ings.py,
which uns a basic GUI (Figu e 4). This GUI is used o c ea e and
modi y a configu a ion json file o he p ocessing. I makes use o
he json dic iona y json/ essel_adcp_lib a y.json, whe e me a-
in o ma ion on essel-specific ADCPs a e s o ed (see Appendix).
The configu a ion file is sa ed o json/OSCONFIG.json. A lis o
files o be p ocessed is sa ed o he chosen p ocessing di ec o y,
along wi h a copy o he configu a ion file o documen a ion
pu pose. Bo h he configu a ion file json/OSCONFIG.json and he
lis o files will be used by all o he OSADCP p ocessing modules
(see Figu e 3).
I is possible o load an exis ing configu a ion ei he om he
wo king di ec o y json/OSCONFIG.json o om any p ocessing
FIGURE 3
Wo kflow o he OSADCP p ocessing oolbox. The main Py hon modules a e depic ed by da k blue boxes. Files s o ing majo p ocessing in o ma ion
a e depic ed in g een boxes, ADCP da a (bina y pd0, in e media e ne CDF files and final ne CDF files) a e ep esen ed by yellow boxes, while files
documen ing he p ocessing a e shown by o ange boxes.
FIGURE 2
Gene al p ocessing chain o essel-moun ed ADCP da a. O ange (g een) colo s ep esen s eps ca ied ou on he single-ping (ensemble-a e age)
da a (see Sec ion 3.3 o de ails).
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di ec o y [p oc_di ]/OSCONFIG_[adcp]_[ essel]_[leg].json, which
is a common s ep when efining a da a se o esuming wo k on an
olde da ase .
An al e na i e way is o manually edi he file json/
OSCONFIG.json di ec ly and hen upda e he lis o files and he
configu a ion copy in he p ocessing di ec o y by execu ing he
Py hon module os_upda e_filelis .py.
3.3.3 os_ ead_enx.py
The Py hon module os_ ead_enx.py is execu ed o loop o e all
files lis ed in [p oc_di ]/OSFILELIST_*. x and ex ac all VMADCP
aw da a and na iga ion da a om he bina y ENX files. Fo each
bina y aw da a file, a co esponding ne CDF file (Unida a, 2021)is
sa ed o he p ocessing di ec o y, con aining all da a on he single-
ping le el (Figu e 3). These files can be accessed o any use -specific
edi ing on single-ping le el no co e ed by he OSADCP s anda d
ea men be o e con inuing on he ensemble-a e age le el.
A majo ask ca ied ou by he module is he e ifica ion o he
na iga ion da a me ged in o he ENX files. Common p oblems include
he occu ence o ze o/ze o posi ions when no eal da a is a ailable due
o p oblems o he na iga ion senso and i egula i ies in he ime
alloca ion such as ime s ops, backwa d ime jumps, ime shi s e c.
A ec ed pings a e flagged acco dingly and igno ed in u he p ocessing.
In he case o e y poo na iga ion da a, he manual inse ion o ex e nal
na iga ion da a on single-ping le el should be conside ed.
3.3.4 os_edi _bo om.py
An impo an aspec o he p ocessing conce ns he scanning o
echo eedback om he g ound, which in oduces spu ious eloci ies
in he a ec ed cell ange. This ask can be au oma ed only o a limi ed
ex en since he echo in ensi y p ofile used o he iden ifica ion is
a ely unambiguous. I can be a ec ed by acous ic in e e ence in he
wa e column o he occu ence o s ong sca e ing laye s, o
example, ha may lead o alse bo om de ec ion. Fu he mo e,
nea he sea bed eloci ies a e po en ially co up ed by sidelobe
in e e ence. Depending on he beam angle qand he dis ance z o
he ADCP ansduce (igno ing pi ch and oll il s), eloci ies in he
ange zshadow =z(1−cos q) abo e he bo om, he so-called shadow
zone, a e hen con amina ed by he sidelobe echo e u ning ea lie o
he ansduce han he slan ed main lobe. The de ec ion and emo al
o spu ious eloci ies benea h he shadow zone is a p e equisi e o
he subsequen wa e - ack calib a ion, especially i he shadow zone
dep h o e laps wi h he e e ence laye chosen o he calib a ion (see
os_wa e ack.py below).
OSADCP p o ides he module os_edi _bo om.py ha loops
h ough all da a files and le s he use decide whe he a bo om
signal is p esen and should be ea ed based on a isual inspec ion
o he ime se ies o he beam-a e aged echo in ensi y (Figu e 5, le
panel). As he co esponding eloci y bias in he shadow zone is
mos ob ious in he along- ack eloci y while he ship is unde way,
i is shown as assis ing in o ma ion in he igh panel o he
in e ac i e plo p o ided by os_edi _bo om.py. To isualize a
po en ial eloci y bias, he median along- ack eloci y is emo ed
o each ping. Using he in o ma ion p o ided in Figu e 5, a line
co esponding o he dep h o bo om influence on he measu ed
eloci ies is picked manually, adjus ed as equi ed and finally sa ed
as a sepa a e ne CDF file wi h a *_bo .nc ex ension added o he file
naming con en ion (Figu e 2).
FIGURE 4
GUI con olling ADCP da a p ocessing in OSADCP. The GUI is execu ed ia os_se ings.py.
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3.3.5 os_wa e ack.py
The p ima y module o he so wa e o de i ing deep-wa e
eloci y p ofiles is called os_wa e ack.py. I ca ies ou impo an
s eps conce ning he de i a ion o ship speed, he cleaning and
a e aging o single-ping da a, and he es ima ion and applica ion o
he eloci y calib a ion (Figu e 2). Fo he ea men o single-ping
da a, he module loops o e all da a files c ea ed by os_ ead_enx.py
du ing he bina y da a con e sion (Figu e 3). A e a e aging each
da a se sepa a ely, he module ca ies ou he wa e - ack
calib a ion and calcula ion o wa e eloci ies based on he
ensemble-a e aged da a o all da a se s as specified
by os_se ings.py.
The ship speed is calcula ed ia cen al di e ences based on he
GNSS posi ion da a, igno ing only pings wi h ques ionable
na iga ion da a as flagged by os_ ead_enx.py. I he configu a ion
file json/OSCONFIG.json con ains le e a m in o ma ion o he
gi en se up o ADCP and GNSS senso , he GNSS posi ions a e
co ec ed p io o he calcula ion o ship speed as ollows:
lonadd = 1
1:11x105mcos (la )( cos (H)(xADCP −xGPS)
+  sin (H)(yADCP −yGPS))
la add = 1
1:11x105m(−sin (H)(xADCP −xGPS) +  cos (H)(yADCP
−yGPS))
wi h Hbeing he ship’s heading, and xADCPjGPS  and yADCPjGPS
being he posi ions o he ADCP ansduce and GNSS an enna
ela i e o he ship’s cen e poin along he mino and majo axes o
he ship, espec i ely (x: s a boa d, y: o wa d). This co ec ion
imp o es cu en eloci ies du ing ship maneu e s when he
heading changes apidly. In he example (Figu e 6), he dis ance
be ween ADCP and GNSS an enna was abou 15 m. Single-ping
da a we e combined in o 1-minu e ensembles and he
app oxima ely 3-hou exce p con ains h ee sec ions wi h ab up
changes o di ec ion o he ship a a ound 06:30, 07:50, and 08:55
UTC (Figu e 6A). Wi hou le e a m co ec ion, he de i ed
di ec ion o he ocean cu en p ofiles du ing hese sec ions is
no ably di e en om he emaining ime, whe e he ship’s heading
is ei he cons an o changes smoo hly (Figu e 6B). Geome ic
co ec ion o he le e a ms hen imp o es he measu ed
di ec ion o ocean cu en s, he e elimina ing bands o e oneous
cu en di ec ion o he h ee sec ions (Figu e 6C).
os_wa e ack.py applies a numbe o au oma ed cleaning
c i e ia o he single-ping eloci y da a:
1. E o eloci y: La ge e o eloci ies indica e a non-
homogeneous flow field o la ge eflec o s like fish, ha
canno be assumed o mo e passi ely wi h he cu en .
Du ing he cleaning all cells a e masked, whe e he de i ed
cell e o eloci y exceeds wice he s anda d de ia ion o
he e o eloci y.
2. Doub ul heading da a: This c i e ion deals wi h un ealis ic
ship heading da a by masking en i e eloci y p ofiles, whe e
he ping- o-ping heading change exceeds 10°.
3. Doub ul cu en eloci ies: Fo his c i e ion, he single-
ping cu en eloci y is app oxima ed by sub ac ing he
ship eloci y componen s om he measu ed eloci ies in
he e e ence laye . Subsequen ly, en i e eloci y p ofiles a e
masked, ei he whe e he ping- o-ping change in ei he
eloci y componen exceeds 2 m s
-1
,o whe eei he
eloci y componen exceeds 5 m s
-1
.
4. Acous ic in e e ence: This is an op ional cleaning c i e ion
ha can be enabled ia os_se ings.py, wi h addi ional
con ol on he dep h ange conside ed o he cleaning
(Figu e 4). To de ec spikes associa ed wi h acous ic
in e e ence, os_wa e ack.py fi s cons uc s an echo
FIGURE 5
In e ac i e plo execu ed by os_edi _bo om.py, o pick he a ea a ec ed by bo om in e e ence. The le panel shows he a e age o he echo
in ensi y measu ed by he ou beams. The igh panel shows he along- ack eloci y componen wi h he median emo ed o each ping. The
along- ack componen is displayed, which mos p ominen ly shows a po en ial eloci y bias caused by bo om in e e ence, in case o da a
collec ed unde way. The echo in ensi y local maximum in he le panel co esponds o he bo om dep h, while he ansi ion owa ds high-biased
along- ack eloci ies in he igh panel ma ks he dep h o sidelobe in e e ence by he bo om e u n echo. The ed line is picked based on he
in o ma ion p o ided by he wo panels. In subsequen p ocessing s eps, cells below he ed line a e igno ed.
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in ensi y anomaly field by sub ac ing he median echo
in ensi y p ofile om each echo in ensi y p ofile con ained
in he da a file. Cells po en ially a ec ed by in e e ence a e
hen de e mined by iden i ying ping- o-ping di e ences
ha ei he exceed o all below +0.7 o -0.7 o he o al
s anda d de ia ion o ping- o-ping di e ences, espec i ely.
The candida e cells a e hen checked i hey a e o single-
ping du a ion and whe he he associa ed in ensi y spikes
ex end o e se e al dep h cells. All cells ha a e iden ified
asbeinga ec edbyacous icin e e encea e
subsequen ly masked.
5. Bo om and sidelobe in e e ence: To mask cells a ec ed by
he bo om e u n echo, os_wa e ack.py eads he
co esponding *_bo .nc files c ea ed by os_edi _bo om.py
and applies he gene a ed bo om in e e ence mask o he
single-ping eloci y da a.
Subsequen ly, single-ping da a along he wa e column is
a e aged in o so-called ensembles, wi h he eloci ies being
ec o -a e aged. Using ensemble a e ages educes he sp ead o
single-ping cu en es ima es, inc easing he p ecision o he
measu emen . In os_wa e ack.py he de aul a e age in e al is
1 minu e.
The wa e - ack calib a ion implemen ed in os_wa e ack.py
add esses wo di e en e o s (Joyce, 1989;Fi ing and
Hummon, 2010):
1. Misalignmen e o : A de ia ion o he ansduce
alignmen wi h espec o he heading e e ence o he
ship in oduces a bias wi h i s main e ec being a spu ious
c oss- ack eloci y componen p opo ional o ship speed.
2. Scaling e o : Small e o s in he beam geome y o a non-
ze o im o he ansduce o ship can cause a sys ema ic
bias a ec ing mos ly he along- ack eloci y componen ,
p opo ional o ship speed.
The calib a ion aims a minimizing hese e o s by de e mining
a misalignmen angle co ec ion aand a scale ac o co ec ion b,
FIGURE 6
E ec o le e a m co ec ion on he cu en di ec ion. The da a se was gene a ed by a 75 kHz Ocean Su eyo ADCP du ing he M189 campaign o
R/V Me eo (Dengle e al., 2023). (A) Ship heading on May 9, 2023. (B) Di ec ion o he uppe -ocean cu en s as 1-minu e ensemble a e ages
wi hou le e a m co ec ion applied, (C) same as (B), bu wi h le e a m co ec ion applied du ing pos -p ocessing. The dis ance be ween he ADCP
ansduce and he GNSS an enna was app oxima ely 15 m along he main axis o he ship.
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Appendix - OSADCP ins alla ion
and se up
OSADCP equi es a wo king and easonably cu en Py hon3
ins alla ion. Depending on he ope a ing sys em, an ins alla ion o
QT5 migh be equi ed. Al hough i is pe ec ly possible o ins all
OSADCP wi hin he sys em’s main Py hon ins alla ion, some kind
o isola ion, such as a i ual en i onmen , is ecommended.
OSADCP is buil p ima ily wi h he ollowing open-sou ce
packages: numpy, scipy, PyQ 5, ma plo lib, ne CDF4 (in o de :
Ha is e al., 2020;Vi anen e al., 2020,Ri e bank Compu ing,
Hun e , 2007;Unida a, 2021).
The OSADCP oolbox is published ia a Gi eposi o y a
h ps://gi .geoma .de/dam/osadcp_ oolbox. I can be downloaded
as zip a chi e and ex ac ed locally. Al e na i ely, i he use has Gi
ins alled, he ollowing command can be used o download he
oolbox: gi clone h ps://gi .geoma .de/dam/osadcp_ oolbox.gi .
Subsequen ly, OSADCP’sdependenciesasspecified in he
equi emen file need o be ins alled ia pip ins all -
equi emen s. x . Please e e o he gi eposi o y o he la es
e sion o he oolbox and o upda ed ins alla ion ins uc ions and
use manuals.
A e se ing up he oolbox, me a-in o ma ion on ADCPs and
essels, such as se ial numbe s, le e a ms e c., can be added o he
json-dic iona y json/ essel_adcp_lib a y.json. This dic iona y
manages ADCP and essel-specific me ada a cen ally and is used
by he p ocessing managemen module (Sec ion 3.3) o e ficien
alloca ion and o wa ding.
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