mooring_all.pl [Mimi Tzeng]

IDENTIFY

Locate - Unique description

  • What is the software called ?
    • mooring_all.pl: a perl script for preparing Seabird and YSI data files for import into Matlab
  • 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. The perl script should be placed in the same directory as the data files to be processed. It takes the CTD, YSI, and thermistor files after they have been initially processed with the proprietary software that came with the sensors, and creates versions that will auto-open in Matlab, by stripping off the headers (which often have a variable and unpredictable number of lines) and reformatting the data. It also creates a file called moor-timestamps.txt to tell Matlab the input variables of importance, that either came from the stripped off headers (sensor names, starting date, starting time) or are found manually (starting and ending scan numbers for the "good" data).
  • What are general categories (keywords, labels) for this software ?
    • Permanent moored instruments
    • CTD
    • data reformatting
  • 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 ?
      • none
    • What useful features of this software are worth highlighting ?
      • It parses the headers of processed CTD files from Seabird and YSI, Inc. and creates files that can be imported into Matlab.
    • [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, 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 ?
                          • Perl
                        • What Operating Systems can the software run on ?
                          • It will run on anything Perl runs on.
                        • How can one install the software ?
                          • Just put the script in the same directory as the files to be processed.
                        • What other software does the software require to be installed ?
                          • Perl
                        • [OPTIONAL] Are there estimates of how long it takes to run this software on average ?
                          • [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 ?
                              • [OPTIONAL] Are there any specific instructions for testing the software ?

                                DO RESEARCH

                                Experiment - Run with other data

                                • What input files does the software require ?
                                    • File Type: 
                                      Seabird *.cnv or *.asc, YSI EcoWatch *.RPT
                                    • File Id: 
                                      cnv, asc, RPT
                                    • File Type: 
                                      A small text file that contains key information parsed from the headers of the input files, and blank spaces to manually record the beginning and ending scan numbers for the "good" data.
                                    • File Id: 
                                      moor-timestamps.txt
                                • What are the input parameters used for this software?
                                  • None. The script automatically looks for *.cnv, *.asc, and *.RPT.
                                • What output files does the software produce ?
                                    • File Type: 
                                      For Seabird files: these are the same with the headers removed. For EcoWatch, the data are reformatted to comma-delimited text.
                                    • File Id: 
                                      *-matlab.txt
                                • [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?
                                    • Matlab 2010b
                                  • [OPTIONAL] Is this software typically used with other software in a workflow ? (eg: for visualization, preprocessing, postprocessing, etc)
                                      • Workflow Description: 
                                        The perl script is typically step D in this workflow diagram: http://dx.doi.org/10.5281/zenodo.20656.
                                      • Compatible Software: 
                                        Matlab: MOORprocess_all.m

                                  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 ?
                                      • The software is not in active development.
                                    • [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.