MoorADCP.m [Mimi Tzeng]

IDENTIFY

Locate - Unique description

  • What is the software called ?
    • MoorADCP.m: a Matlab script for processing time-series data from moored ADCPs
  • What is a short description for this software ?
    • This software helps process current velocity 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 script interpolates through data gaps of 4 or fewer missing values, representing 1.5 hours, for u, v, w, velocity error, magnitude, and direction. It creates several types of error flags for data quality, which must be evaluated during later analysis depending on the needs of particular research questions. It aligns by time the ADCP data with 20-minute averaged depth data from a CTD also moored at the bottom. It produces five different types of figures: scatter plots, stick plots, line plots for speed/direction and uv, and color contour plots. It outputs data in space delimited and comma separated text.
  • What are general categories (keywords, labels) for this software ?
    • Permanent moored instruments
    • ADCP
  • 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 ADCP and generates a variety of different figures, post-processed data files, and a *.mat file useful for later 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, current velocity, 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 stickplot.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 ?
                          • MATLAB Mapping Toolbox
                          • stickplot.m
                        • [OPTIONAL] Are there estimates of how long it takes to run this software on average ?
                          • 15 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 ?
                            • [OPTIONAL] Are there any specific instructions for testing the software ?
                              • Make sure endpoints.txt has also been imported. To generate the depth line for the color contour plots, also load the *.mat file from the corresponding Workflow_F_output folder, and clear all variables except ctdburst. (The script will still run without this variable.)

                            DO RESEARCH

                            Experiment - Run with other data

                            • What input files does the software require ?
                                • File Type: 
                                  A Matlab file exported from WinADCP that includes all variables under "Series Data Types", and Pitch, Roll, Heading under "Ancillary Data Types".
                                • File Id: 
                                  *.mat
                                • File Type: 
                                  The variable ctdburst from the Matlab file output by MOORprocess_all.m. Alternately, type "ctdburst = cell(1,1);" into Matlab to create an empty variable for the script to find.
                                • File Id: 
                                  *.mat
                            • What are the input parameters used for this software?
                              • Input parameter (variable name): the scan number of the first good data point (timestart) the scan number for the first blank at the end (datastop) the scan number for the last good data point (timestop) the last good vertical bin closest to the surface (lastbin) These are specified in *endpoints.txt, which should be imported before running the script.
                            • 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: 
                                  ADCP_processed.mat
                                • File Type: 
                                  Four types of figures for each half-meter vertical bin of data: a scatter plot, a stick plot, a uv line plot, and a speed/direction line plot.
                                • File Id: 
                                  PDF
                                • File Type: 
                                  An average of the data for the entire water column. Includes a stickplot, uv plot, speed, and direction.
                                • File Id: 
                                  zavg.PDF
                                • File Type: 
                                  contour color plots of the water column for speed, direction, u, and v.
                                • File Id: 
                                  color.PDF
                                • File Type: 
                                  space delimited text files for u, v, speed, and direction, by individual 0.5 meter vertical bin and averaged over the water column.
                                • File Id: 
                                  *.dat
                                • File Type: 
                                  comma delimited text files for u, v, w (vertical), speed, and direction, by individual 0.5 meter vertical bin and averaged over the water column.
                                • File Id: 
                                  *.csv
                                • File Type: 
                                  A log file for which data points were used, which were discarded, and which data gaps were replaced with interpolation.
                                • File Id: 
                                  worddoc.log
                            • [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?
                                • WinADCP
                              • [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 H2 in this workflow diagram: http://dx.doi.org/10.5281/zenodo.20656
                                  • Compatible Software: 
                                    http://dx.doi.org/10.5281/zenodo.20656

                              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. There is one known bug - the space delimitation for the *.dat files doesn't work quite right.