stoqs_june2011

Parameter-Parameter

Linear regression Free range Samples No stride

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Sampled Parameter Data Access

Click on Sample locations in time-depth plot to get information here

	Apache Parquet binary column format

https://stoqs.mbari.org/stoqs_june2011/api/measuredparameter.parquet?collect=standard_name

	Keyhole Markup Language - click on icon to view in Google Earth

Select a single sampled parameter for data access to view your selection in Google Earth

	Structured Query Language for PostgreSQL

	Matlab - Load data into Matlab structure array

Install this m-file on your system (instructions are in the comments):
https://raw.githubusercontent.com/stoqs/stoqs/master/stoqs/contrib/analysis/dbconn_jdbc_stoqs.m

Then use the 'SQL' in the adjacent tab to load data into Matlab.

	JavaScript Object Notation

https://stoqs.mbari.org/stoqs_june2011/api/sampledparameter.json

	Comma Separated Values

https://stoqs.mbari.org/stoqs_june2011/api/sampledparameter.csv

	Tabbed Separated Values

https://stoqs.mbari.org/stoqs_june2011/api/sampledparameter.tsv

	Hyper Text Markup Language table

https://stoqs.mbari.org/stoqs_june2011/api/sampledparameter.html

Measured Parameter Data Access

	Apache Parquet binary column format

Collect:	standard_name(s) name(s)
Include:	Activity names

	Estimated	Available
RAM (GB)	...	...
Time (min)	...	...
Rows	...
File size (MB)	...

Click "Estimate requirements" button before using this Data Access URL

https://stoqs.mbari.org/stoqs_june2011/api/measuredparameter.parquet?collect=standard_name

In addition to using the above ad hoc .parquet request generation capability you may also script up requests by activity__name, inherently reducing server-side memory and time requirements. Here is an example of reading Dorado data survey-by-survey into a Matlab session:

% File: read_parquet.m
% Read parquet files from STOQS and report the time it takes
campaign_url = "https://stoqs.mbari.org/stoqs_all_dorado";
api_call = "/api/measuredparameter.parquet?collect=name&activity__name__contains=";
surveys = ["Dorado389_2020_006_06_006_06_decim", "Dorado389_2020_035_00_035_00_decim"];
wo = weboptions('CertificateFilename', '', 'Timeout', 300);
for i=1:length(surveys),
    tic;
    disp(strcat("Reading ", surveys(i), " as .parquet"));
    parquet_url = strcat(campaign_url, api_call, surveys(i));
    file = websave(strcat(surveys(i), '.parquet'), parquet_url, wo);
    disp(strcat("Wrote ", file));
    toc;
    tic;
    info = parquetinfo(file);
    T = parquetread(file);
    disp(strcat("Read ", file));
    toc;
end
disp(info.VariableNames)

—————————————————

>> read_parquet
Reading Dorado389_2020_006_06_006_06_decim as .parquet
Wrote /u/mccann/matlab/Dorado389_2020_006_06_006_06_decim.parquet
Elapsed time is 14.278701 seconds.
Read /u/mccann/matlab/Dorado389_2020_006_06_006_06_decim.parquet
Elapsed time is 0.410685 seconds.
Reading Dorado389_2020_035_00_035_00_decim as .parquet
Wrote /u/mccann/matlab/Dorado389_2020_035_00_035_00_decim.parquet
Elapsed time is 14.070438 seconds.
Read /u/mccann/matlab/Dorado389_2020_035_00_035_00_decim.parquet
Elapsed time is 0.097718 seconds.
    Columns 1 through 11

    "adinos"    "altitude"    "bbp420 (m-1)"    "bbp700 (m-1)"    "bg_biolum (ph L^..."    "biolume"    "diatoms"    "fl700_uncorr"    "fluo"    "hdinos"    "intflash (ph s^{..."

    Columns 12 through 19

    "mepCountList (co..."    "nbflash_high (L^..."    "nbflash_low (L^{..."    "nitrate (micromo..."    "oxygen (ml/l)"    "pitch (degree)"    "profile"    "roll (degree)"

    Columns 20 through 30

    "salinity"    "sepCountList (co..."    "sigmat"    "spice"    "temperature (Cel..."    "yaw (degree)"    "platform"    "timevalue"    "depth"    "latitude"    "longitude"

Here is visualize_parquet.ipynb which shows how to read and visualize parquet data in Python.
Here is parquet2csv.py which you can execute at the command line to convert parquet data to a comma separated value file.

	Keyhole Markup Language - click on icon to view in Google Earth

Select a single measured parameter for data access to view your selection in Google Earth

	Structured Query Language for PostgreSQL

	Matlab - Load data into Matlab structure array

Install this m-file on your system (instructions are in the comments):
https://raw.githubusercontent.com/stoqs/stoqs/master/stoqs/contrib/analysis/dbconn_jdbc_stoqs.m

Then use the 'SQL' in the adjacent tab to load data into Matlab.

	JavaScript Object Notation

https://stoqs.mbari.org/stoqs_june2011/api/measuredparameter.json

	Comma Separated Values

https://stoqs.mbari.org/stoqs_june2011/api/measuredparameter.csv

	Tabbed Separated Values

https://stoqs.mbari.org/stoqs_june2011/api/measuredparameter.tsv

	Hyper Text Markup Language table

https://stoqs.mbari.org/stoqs_june2011/api/measuredparameter.html

Click and drag to zoom

Jun 11

Jun 12

Jun 13

Jun 14

Jun 15

Jun 16

Jun 17

Jun 18

Jun 19

Jun 20

Jun 21

Jun 22

Jun 23

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600

Time (gmt)

Depth (m)

Click and drag to zoom

Color by: Platform Activity

Measured Parameters

Parameter-Parameter				Plot Data
X	Y	Z	C	Lines	Color
						Clear Selection
						Longitude
						Latitude
						Depth
						Time
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Parameter Values

Show distribution of parameter values

Attributes

Platforms

	Space	Time
			Check all / Clear

auv

mooring

Dorado389_2011_164_05_164_05_decim.nc	2column	biolume	hist_stats	lopc	nav_adjust	prof_stats
Dorado389_2011_165_00_165_00_decim.nc	2column	biolume	hist_stats	lopc	nav_adjust	prof_stats
Dorado389_2011_166_00_166_00_decim.nc	2column	biolume	hist_stats	lopc	nav_adjust	prof_stats
Dorado389_2011_171_01_171_01_decim.nc	2column	biolume	hist_stats	lopc	nav_adjust	prof_stats
http://dods.mbari.org/opendap/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011164/2011.164.05/lopc.nc (stride=1)
http://dods.mbari.org/opendap/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/lopc.nc (stride=1)
http://dods.mbari.org/opendap/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/lopc.nc (stride=1)
http://dods.mbari.org/opendap/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011171/2011.171.01/lopc.nc (stride=1)

algae		algae_r
amp		amp_r
balance		balance_r
curl		curl_r
deep		deep_r
delta		delta_r
dense		dense_r
diff		diff_r
gray		gray_r
haline		haline_r
ice		ice_r
matter		matter_r
oxy		oxy_r
phase		phase_r
rain		rain_r
solar		solar_r
speed		speed_r
tarn		tarn_r
tempo		tempo_r
thermal		thermal_r
topo		topo_r
turbid		turbid_r

cividis		cividis_r
inferno		inferno_r
magma		magma_r
plasma		plasma_r
viridis		viridis_r

Blues		Blues_r
BuGn		BuGn_r
BuPu		BuPu_r
GnBu		GnBu_r
Greens		Greens_r
Greys		Greys_r
OrRd		OrRd_r
Oranges		Oranges_r
PuBu		PuBu_r
PuBuGn		PuBuGn_r
PuRd		PuRd_r
Purples		Purples_r
RdPu		RdPu_r
Reds		Reds_r
YlGn		YlGn_r
YlGnBu		YlGnBu_r
YlOrBr		YlOrBr_r
YlOrRd		YlOrRd_r

Wistia		Wistia_r
afmhot		afmhot_r
autumn		autumn_r
binary		binary_r
bone		bone_r
cool		cool_r
copper		copper_r
gist_gray		gist_gray_r
gist_heat		gist_heat_r
gist_yarg		gist_yarg_r
gray		gray_r
hot		hot_r
pink		pink_r
spring		spring_r
summer		summer_r
winter		winter_r

Spatial

Measured Parameter

Platforms

Animation

Simulation

Terrain

Metadata: loading...

M1_Mooring

M2_Mooring

dorado

tethys

M1_Mooring

M2_Mooring

dorado

tethys

Parameter-Parameter

Sampled Parameter Data Access

Measured Parameter Data Access

Temporal

Colormaps

Sampled Parameters

Measured Parameters

Parameter Values

Attributes

Platforms

auv

mooring

BrBG		BrBG_r
PRGn		PRGn_r
PiYG		PiYG_r
PuOr		PuOr_r
RdBu		RdBu_r
RdGy		RdGy_r
RdYlBu		RdYlBu_r
RdYlGn		RdYlGn_r
Spectral		Spectral_r
bwr		bwr_r
coolwarm		coolwarm_r
seismic		seismic_r

Accent		Accent_r
Dark2		Dark2_r
Paired		Paired_r
Pastel1		Pastel1_r
Pastel2		Pastel2_r
Set1		Set1_r
Set2		Set2_r
Set3		Set3_r
tab10		tab10_r
tab20		tab20_r
tab20b		tab20b_r
tab20c		tab20c_r

CMRmap		CMRmap_r
brg		brg_r
cubehelix		cubehelix_r
flag		flag_r
gist_earth		gist_earth_r
gist_ncar		gist_ncar_r
gist_rainbow		gist_rainbow_r
gist_stern		gist_stern_r
gnuplot		gnuplot_r
gnuplot2		gnuplot2_r
jet		jet_r
nipy_spectral		nipy_spectral_r
ocean		ocean_r
prism		prism_r
rainbow		rainbow_r
terrain		terrain_r

Restore this database on your system

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Parameter-Parameter Clear Selection

Temporal Clear Selection

Sampled Parameters Clear Selection

Measured Parameters Clear Selection

Parameter Values Clear Selection

Attributes Clear Selection

Platforms Clear Selection

Parameter-Parameter

Temporal

Sampled Parameters

Measured Parameters

Parameter Values

Attributes

Platforms