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Added script to backfill monthly plots for NS10.
Added line in DataProcessor.createPacIOOSPlots() to remove values outside given ranges before plotting. git-svn-id: https://bbl.ancl.hawaii.edu/projects/bbl/trunk@1162 9e959af2-1677-4b95-8350-622619c7fe3b
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| % schedule_MB01XX_001CTDXXXXR00_processing | ||
| % This is a short runtime script that kicks off processing and | ||
| % display of CTD data. It depends on configuration information | ||
| % found in the Configure class, and creates an instance of the | ||
| % CTDProcessor class, and then runs the process() method via a | ||
| % timer object so that the processing regularly recurs. | ||
|
|
||
| % Copyright: 2007 Regents of the University of Hawaii and the | ||
| % School of Ocean and Earth Science and Technology | ||
| % Authors: Christopher Jones | ||
| % | ||
| % $HeadURL: https://bbl.ancl.hawaii.edu/projects/bbl/trunk/src/matlab/schedule_MB01XX_001CTDXXXXR00_processing.m $ | ||
| % $LastChangedDate: 2016-03-08 17:09:19 -1000 (Tue, 08 Mar 2016) $ | ||
| % $LastChangedBy: kilonalu $ | ||
| % $LastChangedRevision: 1160 $ | ||
| % | ||
| % This program is free software; you can redistribute it and/or modify | ||
| % it under the terms of the GNU General Public License as published by | ||
| % the Free Software Foundation; either version 2 of the License, or | ||
| % (at your option) any later version. | ||
| % | ||
| % This program is distributed in the hope that it will be useful, | ||
| % but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| % GNU General Public License for more details. | ||
| % | ||
| % You should have received a copy of the GNU General Public License | ||
| % along with this program; if not, write to the Free Software | ||
| % Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA | ||
| % | ||
|
|
||
| % Create a new Configure instance and set the configuration details | ||
| import edu.hawaii.soest.bbl.configuration.Configure; | ||
| configuration = Configure; | ||
|
|
||
| % Set the processing-specific configuration details for the instrument | ||
|
|
||
| % Set the pertinent directory and file locations (so they're not hard-coded), | ||
| % where: | ||
| % | ||
| % baseDirectory - is the location where the bbl software is installed | ||
| % outputDirectory - is the location where figure image files will be written | ||
| % libraryDirectory - is where 3rd party matlab functions are located | ||
| % convertPath - is the location of the command used to convert figures | ||
| % convertOptions - are the options to be passed to the convert command | ||
| % copyPath - is the location of the 'copy' command for the OS | ||
| % rbnbPath - is the base directory for the DataTurbine installation | ||
| % rbnbLibraryPath - is the library directory for the DataTurbine installation | ||
| % rbnbMatlabPath - is the matlab library directory for the DataTurbine | ||
| set( configuration, ... | ||
| 'baseDirectory' , '/usr/local/bbl/trunk/' , ... | ||
| 'outputDirectory' , '/var/www/html/OE/KiloNalu/Data/CTD/MB01XX_001CTDXXXXR00/' , ... | ||
| 'libraryDirectory' , '/usr/local/bbl/trunk/lib/matlab/' , ... | ||
| 'convertPath' , '/usr/bin/gs' , ... | ||
| 'convertOptions' , [' -q' ... | ||
| ' -dNOPAUSE' ... | ||
| ' -dBATCH' ... | ||
| ' -dSAFER' ... | ||
| ' -dTextAlphaBits=4' ... | ||
| ' -dGraphicsAlphaBits=4' ... | ||
| ' -dJPEGQ=100' ... | ||
| ' -dDEVICEWIDTH=1000' ... | ||
| ' -dDEVICEHEIGHT=800' ... | ||
| ' -sDEVICE=jpeg' ... | ||
| ' -r90x90' ... | ||
| ' -sOutputFile=' ... | ||
| ] , ... | ||
| 'copyPath' , '/bin/cp' , ... | ||
| 'mkdirPath' , '/bin/mkdir' , ... | ||
| 'rbnbPath' , '/usr/local/RBNB/current/' , ... | ||
| 'rbnbLibraryPath' , '/usr/local/RBNB/current/bin/rbnb.jar' , ... | ||
| 'rbnbMatlabPath' , '/usr/local/RBNB/current/Matlab/' ... | ||
| ); | ||
|
|
||
| % Set the pertinent DataTurbine configuration details (so they're not hard-coded) | ||
| % where: | ||
| % | ||
| % rbnbServer - is the IP address or name of the4 DataTurbine server | ||
| % rbnbSinkName - is the name of the sink client to be used when connecting | ||
| % rbnbSource - is the name of the DataTurbine source for the instrument | ||
| % rbnbChannel - is the name of the DataTurbine channel for the instrument | ||
| % archiveDirectory - is the name up the upper level archive directory for | ||
| % the instrument | ||
| % startDate - is the start date (mm-dd-yyyy HH:MM:SS) that the | ||
| % DataTurbine queries will use | ||
| % timeOffset - is the difference in hours between the sensor time and UTC | ||
| % (ie. local timezone) | ||
| % duration - is the duration (in seconds) that DataTurbine queries will use | ||
| % reference - is the channel reference point (get oldest or newest data) | ||
| set( configuration, ... | ||
| 'rbnbServer' , 'bbl.ancl.hawaii.edu' , ... | ||
| 'rbnbSinkName' , 'MatlabMB01XX_001CTDXXXXR00ProcessingSink' , ... | ||
| 'rbnbSource' , 'MB01XX_001CTDXXXXR00' , ... | ||
| 'rbnbChannel' , 'DecimalASCIISampleData' , ... | ||
| 'archiveDirectory' , 'alawai' , ... | ||
| 'dataStartDate' , '07-01-2015 10:00:00' , ... | ||
| 'dataEndDate' , '01-01-2016 00:00:00' , ... | ||
| 'sensorTimeOffset' , -10 , ... | ||
| 'duration' , 'full' , ... | ||
| 'reference' , 'newest' ... | ||
| ); | ||
|
|
||
| % Set the boolean flags that enable or disable which parts of the code run where: | ||
| % | ||
| % createFigures - is a flag to either create or not create figures | ||
| % exportFigures - is a flag to export (to EPS) or not to export figures | ||
| set( configuration, ... | ||
| 'readArchive' , true , ... | ||
| 'createFigures' , false , ... | ||
| 'createPacIOOSFigures', true , ... | ||
| 'exportFigures' , true ... | ||
| ); | ||
|
|
||
| % Set the parsing specific configuration details for the ASCII data being | ||
| % returned from the DataTurbine where: | ||
| % | ||
| % dataFormatString - is the fprintf format string used by textscan() to parse | ||
| % the ASCII data string | ||
| % fieldDelimiter - is the character used to delimit variables in the data | ||
| % numberOfHeaderLines - is the number of header lines found in the data string | ||
| % instrumentSampleRate - is an integer of the approximate per minute sampling rate of the | ||
| % instrument, used by textscan() to allocate buffer memory | ||
| % dataVariableNames - is a cell array of the data variables found in the ASCII data, | ||
| % in the order that each column parsed. These must correspond | ||
| % with the dataFormatString (one variable per format) | ||
| % dataVariableUnits - is a cell array of the data variable units found in the ASCII | ||
| % data, in the order that each column parsed. These must | ||
| % correspond with each of the dataVariableNames. For | ||
| % dates, use the datestr() formats (i.e yyyy mm dd, etc.) | ||
| % These are used for axes labels | ||
| set( configuration, ... | ||
| 'dataFormatString' , '# %f %f %f %f %f %f %s' , ... | ||
| 'fieldDelimiter' , ',' , ... | ||
| 'numberOfHeaderLines' , '0' , ... | ||
| 'instrumentSampleRate', 15 , ... | ||
| 'dataVariableNames' , {'temperature' , ... | ||
| 'conductivity' , ... | ||
| 'pressure' , ... | ||
| 'chlorophyllVolts' , ... | ||
| 'turbidityVolts' , ... | ||
| 'salinity' , ... | ||
| 'datetime' ... | ||
| } , ... | ||
| 'dataVariableUnits' , {'\circC' , ... | ||
| 'S/m' , ... | ||
| 'decibars' , ... | ||
| 'V' , ... | ||
| 'V' , ... | ||
| 'PSU' , ... | ||
| 'dd mmm yyyy HH:MM:SS' ... | ||
| } ... | ||
| ); | ||
|
|
||
| set( configuration, ... | ||
| 'derivedVariableNames', {'serialdate' , ... | ||
| 'depth' , ... | ||
| 'chlorophyll' , ... | ||
| 'turbidity' ... | ||
| } ... | ||
| ); | ||
|
|
||
| % Set the latitude and longitude of the sensor | ||
| set(configuration, ... | ||
| 'sensorLatitude', 21.28009444 , ... | ||
| 'sensorLongitude', -157.71083 ... | ||
| ); | ||
|
|
||
| % set the calibration coefficient name/value pairs. These will be used | ||
| % in the createDerivedVariables() method for specific derivations where: | ||
| % | ||
| % calibrationCoefficientNames - is a cell array of the names of the callibration | ||
| % coefficients that will be used in calculating | ||
| % certain derived variables. For instance, | ||
| % chlorophyllDarkCounts and chlorophyllScaleFactor | ||
| % (and their corresponding values) will be used | ||
| % to derive chlorophyll from the chlorophyllVolts | ||
| % column of the ASCII data. | ||
| % calibrationCoefficientValues - is a cell array of the values of the callibration | ||
| % coefficients that will be used in calculating | ||
| % certain derived variables. these must correspond | ||
| % with the calibrationCoefficientNames array. | ||
| set(configuration, ... | ||
| 'calibrationCoefficientNames' , ... | ||
| { ... | ||
| 'chlorophyllDarkCounts' , ... | ||
| 'chlorophyllScaleFactor' , ... | ||
| 'turbidityDarkCounts' , ... | ||
| 'turbidityScaleFactor' ... | ||
| } , ... | ||
| 'calibrationCoefficientValues' , ... | ||
| { ... | ||
| 0.064 , ... | ||
| 10 , ... | ||
| 0.075 , ... | ||
| 5 ... | ||
| } ... | ||
| ); | ||
|
|
||
| % Set the depth (in meters) of the sensor below average Mean Low Low Water | ||
| % level to correct output to MLLW | ||
| set(configuration, ... | ||
| 'MLLWadjustment', [-1.9 -1.4] , ... | ||
| 'MLLWadjustmentDate', {'10 Sep 2013 12:00:00'} ... | ||
| ); | ||
|
|
||
| % Set title and duration for PaciOOS time series plots | ||
| % PacIOOSFigures = { {figure 1 properties}; {figure 2 properties}; ...} | ||
| % Set properties in order listed below for each figure to be created: | ||
| % | ||
| % Figure Title Prefix : Sensor location and name (string) | ||
| % | ||
| % Figure Duration : Duration of figures in days (string) | ||
| % | ||
| % Output format : Output as .eps and/or .jpg | ||
| % (set as {.eps,.jpg} for both) | ||
|
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||
| set( configuration, ... | ||
| 'PacIOOSFigures', { ... | ||
| % Figure 3 (monthly plot) | ||
| {{'Nearshore Sensor, Maunalua Bay (NS10)'} , ... %Title prefix | ||
| {'monthly'} , ... | ||
| {'.eps'} ... %Output format | ||
| } ... | ||
| } ... | ||
| ) ; | ||
|
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||
| % Set the configuration parameters for the PacIOOS figures that should | ||
| % be generated. PacIOOSFigureProperties is a cell array that includes | ||
| % five sub cell arrays that contain figure properties. | ||
| % For the figures to be generated, the following properties must be included, | ||
| % in the order listed below: | ||
| % | ||
| % 1) cell array of variables to plot (as strings) | ||
| % 2) cell array of axis labels (as strings) | ||
| % 3) cell array of axis locations (positions are 1-8, 1 being topmost-left | ||
| % 8 being bottommost-right | ||
| % 4) cell array of plot colors, each color represented as a 3x1 array | ||
| % 5) cell array containing info for y-axis range and scaling. | ||
| % set 1st parameter to 'dynamic' or 'fixed' | ||
| % if 'dynamic' then 2nd parameter is the multiple used in dynamic scaling | ||
| % if 'fixed' then 2nd parameter is the min/max values | ||
| % if more than 2 values input, will result in step-scaling between the | ||
| % values (upwards if values in numerical order, downwards if in reverse | ||
| % numerical order) | ||
| % 3rd parameter is the number of ticks for the axis (will default to 5 | ||
| % if no value set) | ||
|
|
||
| set(configuration, ... | ||
| 'PacIOOSFigureProperties',{ ... | ||
| { ... %Figure Variables | ||
| 'adjustedDepth' , ... | ||
| 'temperature' , .... | ||
| 'salinity' , ... | ||
| 'turbidity' , ... | ||
| 'chlorophyll' ... | ||
| } , ... | ||
| { ... %Axis Labels | ||
| 'Actual WL (m)' , ... | ||
| 'Temperature (\circC)' , ... | ||
| 'Salinity (PSU)' , ... | ||
| 'Turbidity (NTU)' , ... | ||
| 'Chlorophyll (\mug/L)' ... | ||
| } , ... | ||
| {1 2 3 4 5} , ... %Plot Locations | ||
| { ... %Plot Colors | ||
| [0 0 0 ] , ... %WL | ||
| [1 0 0 ] , ... %Temp | ||
| [0 0 0 ] , ... %Sal | ||
| [0.63 0.4 0.31] , ... %Turb | ||
| [0.1 0.55 0.35] ... %Chlo | ||
| } , ... | ||
| { ... %y-axis ranges | ||
| {'fixed', [-0.4 1.2], 4} , ... %WL | ||
| {'dynamic', 2, 4} , ... %Temp | ||
| {'fixed', [36 31 21 11 1 -4], 5} , ... %Sal | ||
| {'fixed', [0 25]} , ... %Turb | ||
| {'fixed', [0 10 20 30 40 50]} ... %Chlo | ||
| } ... | ||
| } ... | ||
| ) ; | ||
|
|
||
| % Tell the DataProcessor which type of figure to create | ||
| % Either: temperatureSalinity or timeSeries | ||
| set( configuration, 'currentFigureType', 'timeSeries'); | ||
|
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| % Tell the DataProcessor what format to use when exporting TS or timeseries | ||
| % figures | ||
| set( configuration, 'outputFormat', {'.eps' '.jpg'}); | ||
|
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|
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| % Set the timer specific configuration details for periodically running the code | ||
| % where: | ||
| % | ||
| % startTime - the time when the timer should start (in seconds, 0 meaning now) | ||
| % timerInterval - the interval (in minutes) that the timer process should fire | ||
| %set( configuration, ... | ||
| %'startTime' , 0 , ... | ||
| %'timerInterval' , 20 ... | ||
| %); | ||
|
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| % Set up directory paths, and create a new DataProcessor instance | ||
| import edu.hawaii.soest.bbl.processing.DataProcessor; | ||
| javaaddpath(configuration.rbnbLibraryPath); | ||
| addpath(configuration.rbnbMatlabPath); | ||
| addpath(configuration.libraryDirectory); | ||
| NS10ctdProcessor = DataProcessor(configuration); | ||
|
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| NS10ctdProcessor.process() |