MOORprocess_all.m [Mimi Tzeng]

IDENTIFY

Locate - Unique description

  • What is the software called ?
    • MOORprocess_all.m: a Matlab script for processing time-series data from moored CTDs, YSI sondes, and thermistors
  • What is a short description for this software ?
    • This software helps process mooring data collected by Kyeong Park at Dauphin Island Sea Lab, Alabama, for the Fisheries Oceanography in Coastal Alabama (FOCAL) program, which ran from 2006-2012. It calculates density for CTDs and YSIs, interpolates missing values in data gaps, and (along with the function moorburst.m) averages 1-minute data into 20-minute bins. It produces figures for temperature, salinity, density, and depth over the time series, and outputs the data in space-delimited and comma-separated text. It can also process CTD vertical profile data, which includes averaging data into 0.5 meter bins, producing depth profile figures for all measured parameters, and outputting the data and summary data in space-delimited and comma-separated text.
  • What are general categories (keywords, labels) for this software ?
    • Permanent moored instruments
    • CTD
    • bin averaging
    • YSI
  • Is there a project website for the software ?
  • [OPTIONAL] What is the DOI or any other unique identifier for this software (or software version) ?

    UNDERSTAND

    Trust - Quality and ratings

    • Who created this software? (Project, Organization, Person, Initiative, etc.)
      • Mimi Tzeng
    • Are there any additional contributors of note for this software ?
      • Kyeong Park directed the requirements.
    • What useful features of this software are worth highlighting ?
      • It processes data from the vertical array of the mooring and generates a variety of different figures, post-processed data files, and a *.mat file useful for further analysis.
    • [OPTIONAL] Who is the publisher of this software if not the author ?
      • DISL: Dzwonkowski Lab
    • [OPTIONAL] How can a user get support for the software ? (eg. Report bugs, request features and extensions, etc)
      • [OPTIONAL] Has the software been adopted in a project, organization or by a person?
        • [OPTIONAL] Is there any information about uses of this software (papers, research labs, etc) ?
          • [OPTIONAL] Are there any statistics of its use ?
            • [OPTIONAL] Are there any publications where the software is used ?
              • [OPTIONAL] Is there any benchmark information about the software ?
                • [OPTIONAL] What are the funding sources for this software?
                  • Fisheries Oceanography of Coastal Alabama (FOCAL) Program
                  • Dauphin Island Sea Lab
                • [OPTIONAL] What are the ratings for this software?

                  Relate - Domain knowledge

                  • What are domain specific keywords for this software ? (eg: hydrology, climate)
                    • physical oceanography, marine science, remote sensing, permanent moored instruments, coastal ocean observing system, hydrography, oceanographic time series data
                  • [OPTIONAL] Is there any other similar software that you know of ?
                    • [OPTIONAL] What are the recommended uses and assumptions for the software ?
                      • [OPTIONAL] Are there any constraints on use, situations it is not designed for, simplifications ?

                        EXECUTE

                        Access - Download

                        Install - Execution requirements

                        • Is there any on-line documentation about the software ?
                        • What language(s) is the software written in ?
                          • Matlab 2010b
                        • What Operating Systems can the software run on ?
                          • It will run on anything Matlab runs on.
                        • How can one install the software ?
                          • Put the script anywhere, make sure moorburst.m is also present, and use the addpath command in Matlab to point to it.
                        • What other software does the software require to be installed ?
                          • moorburst.m
                        • [OPTIONAL] Are there estimates of how long it takes to run this software on average ?
                          • 30 minutes
                        • [OPTIONAL] Are there any memory requirements for this software ?
                          • [OPTIONAL] Are there any other important details about the implementation of this code (parallelization, special hardware, etc) ?

                            Run - Testing execution

                            • Is there any test data available for the software ?
                                • Test Data Location: 
                                  http://dx.doi.org/10.5281/zenodo.18943
                                • Test Data Description: 
                                  Data files in Workflow_D_input after they have been processed with mooring_all.pl. Use the completed moor-timestamps.txt provided in Workflow_E.
                            • [OPTIONAL] Are there any specific instructions for testing the software ?
                              • Before running the software, be sure to compare the headers of the data files with the code lines of the input variables: YSI: lines 77-95 moored CTDs: lines 251-259 CTD cast: lines 1255-1275 Also make sure moor-timestamps.txt has been imported.

                            DO RESEARCH

                            Experiment - Run with other data

                            • What input files does the software require ?
                                • File Type: 
                                  Space-delimited or comma-delimited plain text files
                                • File Id: 
                                  *-matlab.txt (as generated by mooring_all.pl)
                            • What are the input parameters used for this software?
                              • Input parameters are specified in moor-timestamps.txt (also generated by mooring_all.pl). Blanks in this file should be filled in manually, and the file imported into Matlab, before running MOORprocess_all.m.
                            • What output files does the software produce ?
                                • File Type: 
                                  Matlab file containing post-processing variables that may be useful for future data analysis.
                                • File Id: 
                                  *.mat
                                • File Type: 
                                  A log file of which data points were used and which were discarded for each moored instrument.
                                • File Id: 
                                  docsummary.txt
                                • File Type: 
                                  Figures for temperature, salinity, density, and depth for each moored instrument. Depth profiles for each variable in a CTD cast, and diagnostic figures of depth, salinity, temperature, and density showing which data points were used.
                                • File Id: 
                                  PDF
                                • File Type: 
                                  A space-delimited text file containing all temperature data from all moored instruments, aligned by timestamp.
                                • File Id: 
                                  alltemp.dat
                                • File Type: 
                                  A text file that contains summary data for the CTD cast.
                                • File Id: 
                                  CTDcast.log
                                • File Type: 
                                  A space-delimited text file for each instrument. For the moored CTDs and thermistors, these are 20-minute averages (to match the 20 minute YSI data). For the cast, the data have been averaged into 0.5 meter vertical bins.
                                • File Id: 
                                  *.dat
                                • File Type: 
                                  A comma-delimited text file for each instrument. These are the "good" data between the beginning and ending scan numbers, which have not been averaged.
                                • File Id: 
                                  *goodrange.csv
                                • File Type: 
                                  For each moored Seabird instrument, a comma delimited text file of 20-minute averaged data.
                                • File Id: 
                                  *_est.csv
                                • File Type: 
                                  For the CTD cast, a comma delimited text file of data that have been averaged into 0.5 meter vertical bins.
                                • File Id: 
                                  *CTDcast_binned.csv
                            • [OPTIONAL] Are there any relevant data catalogs that can be used with this software ?

                              Compose - Run with other software

                              • What other software can interoperate with this one?
                                • perl
                              • [OPTIONAL] Is this software typically used with other software in a workflow ? (eg: for visualization, preprocessing, postprocessing, etc)
                                  • Workflow Description: 
                                    This Matlab script is typically Step E2 in this workflow diagram: http://dx.doi.org/10.5281/zenodo.20656
                                  • Compatible Software: 
                                    Perl: mooring_all.pl

                              Cite - Scientific publications

                              • Is there a preferred publication or citation for this software ?

                              GET SUPPORT

                              Discuss - Support and community

                              • What is the e-mail contact for this software?
                                • mtzeng@disl.org
                              • [OPTIONAL] What is the support offered for this software?

                                UPDATE

                                Contribute - Evolution

                                • [OPTIONAL] How is the software being developed or maintained ?
                                  • [OPTIONAL] Are there any on-line resources for accessing the developer community for this software ? (eg. discussion board, wiki, etc)

                                    Track - Versions

                                    • What versions does the software have ?
                                      • There is only one version. It can be modified according to the specific instruments and variables present in the data to be processed.