Hi John and CF-Metadata list,
Forgot to include the revised CDL (attached) using the scalar approach.
Andrew
----- Original Message -----
From: "andrew walsh" <[email protected]>
To: "John Caron" <[email protected]>
Cc: <[email protected]>; "Luke Callcut" <[email protected]>
Sent: Friday, April 27, 2012 4:03 PM
Subject: Re: [CF-metadata] Ocean CTD data following CF Conventions v1.6
Hi John,
Thanks for your advice.
For a single vertical profile and single valued time, lat, long.
it seems there are two acceptable ways i.e 1 element vector or single valued
scalar.
Quoting from 'section 2.4 Dimensions' of CF standard:
1 element vector:
"Dimensions may be of any size, including unity. When a single value of some
coordinate applies to all the values in a variable, the recommended means of
attaching this information to the variable is by use of a dimension of size
unity with a one-element coordinate variable.
and in the next sentence a scalar:
"It is also acceptable to use a scalar coordinate variable which eliminates
the need for an associated size one dimension in the data variable."
1) ***Vector co-ordinate variables*******
Dimensions:
time=1
pressure=56
lat=1
lon=1
Variables:
time(time)
lat(lat)
lon(lon)
temperature(pressure)
2) **Scalar co-ordinate varaibles****
Dimensions:
pressure =56
Variables:
time
lat
lon
temperature(pressure)
The scalar approach you suggest as in section "H.3.3. Single profile" of the
CF v1.6 standard
is simpler than the vector approach so we will take your advice.
Regards,
Andrew
----- Original Message -----
From: "John Caron" <[email protected]>
To: "andrew walsh" <[email protected]>
Cc: <[email protected]>; "Luke Callcut" <[email protected]>;
<[email protected]>
Sent: Thursday, April 26, 2012 10:48 AM
Subject: Re: [CF-metadata] Ocean CTD data following CF Conventions v1.6
Hi andrew:
The file you sent (20110818T001140Z_M_HI504BEN.nc) appears to be a single
profile. Assuming that, you would use the following template:
http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8363696
note that lat, lon and time coordinates all have to be scalars.
John
On 4/18/2012 8:24 PM, andrew walsh wrote:
Hi John,
We have now constructed a real netCDF file for you to check. QC flag
variables have been added in. The QC flagging method is based on the
proposed IODE scheme in (1) below.
Attached are the sample .nc file, text (ncdump) of same and a document
specifying the CDL.
Thanks and Regards,
Andrew Walsh
Ref.
(1) Konovalov et. al (March 2012), Proposal to adopt a quality flag scheme
standard
for oceanographic and marine meteorological data, Version 1.2.
----- Original Message ----- From: "John Caron" <[email protected]>
To: "andrew walsh" <[email protected]>
Sent: Thursday, April 05, 2012 10:44 AM
Subject: Re: [CF-metadata] Ocean CTD data following CF Conventions v1.6
ok
On 4/4/2012 6:42 PM, andrew walsh wrote:
Hi John,
Thank for your offer to check a sample netCDF CTD data file. At moment we
don't have
some real .nc file but when we do I can send you a file for checking.
Andrew
----- Original Message ----- From: John Caron
To: [email protected]
Sent: Wednesday, April 04, 2012 5:55 AM
Subject: Re: [CF-metadata] Ocean CTD data following CF Conventions v1.6
Hi all:
Lets see, I havent followed the entire conversation, but:
1) Andrew if you can send me a sample file (not just the CDL) I can check
if it works in the CDM with the new 1.6 conventions, and maybe give you
some advice from my POV.
2) Aggregation in the CDM comes in 2 flavors. 1) The original
implementation simply appends multidimensional arrays together, eg
"joinNew " and "joinExisting" NCML aggregation. I call it "syntactic
aggregation" because it doesnt know what its aggregating, and the
homogeneity requirements are strict. 2) "Feature Type collections" (aka
"semantic aggregation") are the more recent development. These understand
the coordinate information of the data, and so can handle variations in
the representation, eg ragged arrays, scalar coordinates, etc. In this
case, the CDM understands a dataset as a collection of "features objects",
which can be stored in a collection of files. The interfaces to these
collections is still under development. Most current and future work in
the CDM is in this category.
John
snip ....
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****CDL representation of QC'ed CTD ocean profile data at RAN METOC Data
Centre*****
The following is a proposed CDL for a netCDF file describing
a quality controlled vertical profile of pressure, temperature and salinity collected
by a CTD instrument. The CDL follows the netCDF CF coventions version 1.6
at ref (2). The CTD data is classed
as featureType 'profile' as per Chapter 9 'Discrete sampling geometries' in
ref (2).
The quality control (QC) flagging scheme follows the 2 level
QC flag scheme proposed by IODE in the ref (1) below. In this QC scheme the
Level 1
flag is the primary QC flag. Level 2 flags are secondary indicating results
of specified QC tests. Level 2 flags use a numerical code i.e 0 (passed),1
(failed) or 2
(unknown) to indicate test status of a specified test.
Refs
(1) Konovalov et. al (March 2012), Proposal to adopt a quality flag scheme
standard
for oceanographic and marine meteorological data, Version 1.2.
(2) http://cf-pcmdi.llnl.gov/documents/cf-conventions
dimensions:
pressure = UNLIMITED ; // (9 currently)
variables:
double time ;
time:standard_name = "time" ;
time:units = "days since 1950-01-01 00:00:00Z" ;
time:axis = "T" ;
time:valid_min = 0 ;
time:valid_max = 999999 ;
byte time_qc_flag;
time_qc_flag:long_name = "quality control flag for time (Level 1
flag)" ;
time_qc_flag:quality_control_convention = "Proposed IODE qc scheme
March 2012" ;
time_qc_flag:valid_min = 1 ;
time_qc_flag:valid_max = 9 ;
time_qc_flag:flag_values = 1b, 2b, 3b, 4b, 9b ;
time_qc_flag:flag_meanings = "good not_evaluated_or_unknown suspect
bad missing" ;
double latitude ;
latitude:standard_name = "latitude" ;
latitude:units = "degrees_north" ;
latitude:axis = "Y" ;
latitude:valid_min = -90 ;
latitude:valid_max = 90 ;
double longitude ;
longitude:standard_name = "longitude" ;
longitude:units = "degrees_east" ;
longitude:axis = "X" ;
longitude:valid_min = -180 ;
longitude:valid_max = 180 ;
byte position_qc_flag;
position_qc_flag:long_name = "quality control flag for position
(Level 1 flag)" ;
position_qc_flag:quality_control_convention = "Proposed IODE qc
scheme March 2012" ;
position_qc_flag:valid_min = 1 ;
position_qc_flag:valid_max = 9 ;
position_qc_flag:flag_values = 1b, 2b, 3b, 4b, 9b ;
position_qc_flag:flag_meanings = "good not_evaluated_or_unknown
suspect bad missing" ;
double pressure(pressure) ;
pressure:standard_name = "sea_water_pressure" ;
pressure:units = "decibars" ;
pressure:axis = "Z" ;
pressure:valid_min = 0 ;
pressure:valid_max = 12000 ;
pressure:positive = "down" ;
double temperature(pressure) ;
temperature:_FillValue = -99.99 ;
temperature:standard_name = "sea_water_temperature" ;
temperature:units = "degrees_C" ;
temperature:valid_min = -2 ;
temperature:valid_max = 40 ;
temperature:ancillary_variables = "temperature_whole_profile_flag
temperature_qc_flag temperature_sd_test" ;
temperature:coordinates = "time latitude longitude pressure" ;
byte temperature_whole_profile_flag ;
temperature_whole_profile_flag:long_name = "qc flag for whole
temperature profile (primary L1 flag)" ;
temperature_whole_profile_flag:quality_control_convention = "IODE qc
scheme March 2012" ;
temperature_whole_profile_flag:valid_min = 1 ;
temperature_whole_profile_flag:valid_max = 9 ;
temperature_whole_profile_flag:flag_values = 1b, 2b, 3b, 4b, 9b
;
temperature_whole_profile_flag:flag_meanings = "good
not_evaluated_or_unknown suspect bad missing" ;
byte temperature_qc_flag(pressure) ;
temperature_qc_flag:long_name = "quality control flag for
temperature (primary Level 1 flag)" ;
temperature_qc_flag:standard_name = "sea_water_temperature
status_flag" ;
temperature_qc_flag:quality_control_convention = "IODE qc scheme
March 2012" ;
temperature_qc_flag:valid_min = 1 ;
temperature_qc_flag:valid_max = 9 ;
temperature_qc_flag:flag_values = 1b, 2b, 3b, 4b, 9b ;
temperature_qc_flag:flag_meanings = "good not_evaluated_or_unknown
suspect bad missing" ;
temperature_qc_flag:coordinates = "time latitude longitude
pressure" ;
byte temperature_sd_test(pressure) ;
temperature_sd_test:long_name = "qc flag for monthly temperature 3
standard deviation test (secondary L2 flag)"
temperature_sd_test:quality_control_convention = "IODE qc scheme
March 2012" ;
temperature_sd_test:valid_min = 0 ;
temperature_sd_test:valid_max = 2 ;
temperature_sd_test:flag_values = 0b, 1b, 2b ;
temperature_sd_test:flag_meanings = "passed failed unknown" ;
temperature_sd_test:coordinates = "time latitude longitude
pressure" ;
double salinity(pressure) ;
salinity:_FillValue = -99.99 ;
salinity:standard_name = "sea_water_salinity" ;
salinity:units = "psu" ;
salinity:valid_min = 0 ;
salinity:valid_max = 45 ;
salinity:ancillary_variables = "salinity_whole_profile_flag salinity_qc_flag salinity_sd_test"
salinity:coordinates = "time latitude longitude pressure" ;
byte salinity_whole_profile_flag ;
salinity_whole_profile_flag:long_name = "qc flag for whole salinity
profile (primary L1 flag)" ;
salinity_whole_profile_flag:quality_control_convention = "IODE qc
scheme March 2012" ;
salinity_whole_profile_flag:valid_min = 1 ;
salinity_whole_profile_flag:valid_max = 9 ;
salinity_whole_profile_flag:flag_values = 1b, 2b, 3b, 4b, 9b ;
salinity_whole_profile_flag:flag_meanings = "good
not_evaluated_or_unknown suspect bad missing" ;
byte salinity_qc_flag(pressure) ;
salinity_qc_flag:long_name = "quality control flag for salinity
(primary Level 1 flag)" ;
salinity_qc_flag:standard_name = "sea_water_salinity
status_flag" ;
salinity_qc_flag:quality_control_convention = "Proposed IODE qc
scheme March 2012" ;
salinity_qc_flag:valid_min = 1 ;
salinity_qc_flag:valid_max = 9 ;
salinity_qc_flag:flag_values = 1b, 2b, 3b, 4b, 9b ;
salinity_qc_flag:flag_meanings = "good not_evaluated_or_unknown
suspect bad missing" ;
salinity_qc_flag:coordinates = "time latitude longitude
pressure" ;
byte salinity_sd_test(pressure) ;
salinity_sd_test:long_name = "qc flag for monthly salinity 3
standard deviation test (secondary L2 flag)"
salinity_sd_test:quality_control_convention = "IODE qc scheme March
2012" ;
salinity_sd_test:valid_min = 0 ;
salinity_sd_test:valid_max = 2 ;
salinity_sd_test:flag_values = 0b, 1b, 2b ;
salinity_sd_test:flag_meanings = "passed failed unknown" ;
salinity_sd_test:coordinates = "time latitude longitude
pressure" ;
int profile ; //Unique integer to identify each profile
profile:long_name = "profile identifier"
profile:cf_role = "profile_id";
// global attributes:
:conventions = "CF-1.6" ;
:featureType = "profile" ;
:cdm_data_type = "Profile" ;
data:
time = 22509.0081018517 ;
time_qc_flag = 1;
latitude = -10.5688 ;
longitude = 142.11713 ;
position_qc_flag = 1;
pressure = 4, 5, 6, 7, 8, 9, 10, 11, 12 ;
temperature = 24.737, 24.737, 24.739, 24.738, 24.737, 24.736, 24.7375,
24.737, 24.735 ;
temperature_whole_profile_flag = 1;
temperature_qc_flag = 1,1,1,1,1,1,1,1,1;
temperature_sd_test = 0,0,0,0,0,0,0,0,0;
salinity = 35.2028, 35.2032, 35.2013, 35.2018, 35.2022, 35.2019, 35.2019,
35.2024, 35.204 ;
salinity_whole_profile_flag = 1;
salinity_qc_flag = 1,1,1,1,1,1,1,1,1;
salinity_sd_test = 0,0,0,0,0,0,0,0,0;
profile = 1234567 ;
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