MBARI stoqs_february2012
STOQS GitHub

Spatial

 

Select a Measured Parameter for plotting (radio button) to see it in 3D.
Check Platforms to animate their positions.
Open the Terrain section for terrain visualization options.
Navigation hints for X3DOM's Examine mode:
    Rotate: Left mouse
    Translate: Ctrl + left mouse
    Zoom: Alt + left mouse
    Recenter rotation: double click
    Navigation speed: +/-
    Reset viewpoint: R
The button is known to work on iPhone and Android with Firefox.
Experimental: Enter Rift
Measured Parameter
in minute slices (for contour curtain images) Center viewpoint over data
Platforms
Animation
Simulation
Terrain

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Metadata: loading...

Parameter-Parameter

Linear regression Free range Samples No stride 

                                    

                                

                                

                                    

                                        

                                            

                                                 Rotate: Left mouse
Translate: Ctrl + left mouse
Zoom: Alt + left mouse 
                                            

                                            

                                                
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                        Measured Parameter Data Access
                         

                    

                    

                        


                            
                            

                                
                                    
                                        

                                        

                                            

                                                mp-parquet
                                                 Apache Parquet binary column format
                                            

                                        

                                     
                                    
                                        
                                            
                                                

                                                    

                                                        

                                                            

                                                                Collect:
                                                                
                                                                     standard_name(s)
                                                                     name(s)
                                                                
                                                            

                                                                Include:
                                                                
                                                                     Activity names
                                                                
                                                            

                                                            

                                                                
                                                                    
                                                                
                                                            

                                                        

                                                    

                                                    

                                                        

                                                            

                                                                
                                                                Estimated
                                                                Available
                                                            

                                                            

                                                            

                                                                RAM (GB)
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                                                                Time (min)
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                                                                Rows
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                                                                File size (MB)
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Click "Estimate requirements" button before using this Data Access URL

                                                

                                                    

                                                

                                                

                                                    

                                                    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.
                                                

                                            
                                        
                                    
                                

                                
                                    
                                        

                                        

                                            

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

                                        

                                     
                                    
                                        
                                        

                                    
                                

                                
                                    
                                        

                                        

                                            

                                                mp-sql
                                                 Structured Query Language for PostgreSQL
                                            

                                        

                                     
                                    
                                        
                                            

                                        
                                    
                                

                                
                                    
                                        

                                        

                                            

                                                mp-matlab
                                                 Matlab - Load data into Matlab structure array
                                            

                                        

                                     
                                    
                                        
                                            
                                                

                                            
                                        
                                    
                                

                                
                                    
                                        

                                        

                                            

                                                mp-json
                                                 JavaScript Object Notation
                                            

                                        

                                     
                                    
                                        
                                            
                                                

                                            
                                        
                                    
                                

                                
                                    
                                        

                                        

                                            

                                                mp-csv
                                                 Comma Separated Values
                                            

                                        

                                     
                                    
                                        
                                            
                                                

                                            
                                        
                                    
                                

                                
                                    
                                        

                                        

                                            

                                                mp-tsv
                                                 Tabbed Separated Values
                                            

                                        

                                     
                                    
                                        
                                            
                                                

                                            
                                        
                                    
                                

                                
                                    
                                        

                                        

                                            

                                                mp-html
                                                 Hyper Text Markup Language table
                                            

                                        

                                     
                                    
                                        
                                            
                                                

                                            
                                        
                                    
                                

                                            
                            

                            
                        

                    

                


            


        

        
        

            


                

                    

                        

                        Temporal
                        
                        

                    

                    

                        


                            

                            

                                

                                    

                                        

                                            Click and drag to zoom
                                            
                                        

                                        

                                    

                                    

                                        

                                        

                                            

                                            

                                        

                                        

                                            

                                                 
                                                
                                                 
                                            

                                            

                                                
                                                    
                                                
                                            

                                        

                                    

                                

                                

                                    

                                        

                                            

                                                Click and drag to zoom
                                                
                                            

                                            

                                                 
                                            

                                            

                                            

                                        

                                        

                                        

                                            

                                                Color by: 
                                                 Platform
                                                 Activity
                                            

                                        

                                    

                                

                            



                        

                    

                



                




                


                

                    

                        

                        Measured Parameters
                        
                        

                    

                    

                        

                            

                                
                                
                                
                                
                            

                            

                            

                                
                                    

                                        
                                        Plot Data
                                        Filter & Select for data access
                                        
                                    

                                    

                                        
                                        
                                        
                                        
                                        Lines
                                        Color
                                        
                                        
                                        
                                    

                                                             
                                
                                    

                                        
                                        
                                        
                                        
                                        
                                            
                                        
                                        
                                                            
                                            
                                        
                                         
                                        Clear Selection
                                    

                                    
                                    
                                    
                                    
                                
                            

                            

                        

                    

                


                

                    

                        

                        Parameter Values
                         
                        

                        
                    

                    

                        

                            
Show distribution of parameter values

                            

                                

                                    Histogram display: 
                                    
                                    
                                

                            

                            

                            

                        

                    

                


                

                

                    

                        

                        Platforms