<reponame>axiom-data-science/GUTILS
#!/usr/bin/env python3

'''
This script contains functions that decodes the pseudogram from
the echometrics data stream. The resultant information can
be:

 - Rendered in time/depth bin plot
 - Rendered in a scatter plot
 - Saved to a CSV file
 - Saved to a netCDF file

The output can be directed to a file or standard output (stdout)
The netCDF may only be saved to a file.  The netCDF may be saved
as separate files for ease of aggregation of similar variables.

Data written as CSV output is in three columns (comma separated
values): Timestamp, Depth, Density.  A metadata desciption
is given below.

Metadata for the netCDF file is pulled from deployment configuration
files: deployment.json and instruments.json; A general template file
is also required for generic metadata.

Image output is controlled by the filename extension provided.
A typical format is PNG.  Use ".png" in the filename to produce
a PNG formatted image.

Metadata
--------
    Here is the metadata description for each of the coloums
    of this dataset (ASCII, spreadsheet):

    +--------------+--------------------------------------------------+
    | Column       | Description                                      |
    +--------------+--------------------------------------------------+
    | Timestamp    | seconds since 01-01-1970 epoch; timezone GMT/UTC |
    +--------------+--------------------------------------------------+
    | Depth        | depth (meters)                                   |
    +--------------+--------------------------------------------------+
    | Density      | Sv (dB)                                          |
    +--------------+--------------------------------------------------+

Command line arguments
----------------------

::

    -h, --help            show this help message and exit
    --inpDir INPDIR       full or relative path to directory with
                          glider data
    --inpFile INPFILE     glider input file; one segment
    --tbdFile TBDFILE     full or relative path with filename
                          to Teledyne glider tbd binary input file
    --sbdFile SBDFILE     full or relative path with filename
                          to Teledyne glider sbd binary input file
    --cacheDir CACHEDIR   Directory with glider cache files;
                          default current directory
    --dbd2asc DBD2ASC     full or relative path with filename
                          to glider dbd2asc binary
    --csvOut CSVOUT       full or relative path with filename
                          to write CSV output or 'stdout'; default None
    --ncDir NCDIR         full or relative path of a directory for
                          writing netCDF file(s); default None
    --ncFormat NCFORMAT   alternate time format for saving netCDF files
    --csvHeader           (flag) include header with CSV output; default False
    --imageOut IMAGEOUT   filename to write image or stdout; default None
    --debug               (flag) show extra debugging for this
                          python script; default False
    --echosounderRange ECHOSOUNDERRANGE
                          Echosounder range; default -60.0 (meters)
                          instrument facing up; positive values
                          instrument facing down
    --title               optional figure title; default None
    --useScatterPlot      (flag) Plot using a scatterplot
                          instead of a time/depth binned
                          (raster image) plot; default False
    --binnedDepthLabels   (flag) Use the original depth bin
                          labels instead of the adjusted depth
                          labels for the time/depth binned plot;
                          default False
    --deploymentDir       full or relative path to deployment and
                          instrument json files; default None
    --templateDir         full or relative path to glider
                          template directory; default None
'''

import os, sys, datetime, glob, json
import argparse

# Teledyne Webb generic python classes
# and functions
import teledyne

# Functions

def printAttributes(myObj):
    '''
    This is a convienence function for printing object attribute
    information for the supplied object.  This function writes
    to standard output and does not print any objects with
    an underscore prefix.  This was mainly used for debugging
    during development.

    Parameters
    ----------
    myObj : :obj:`any`, required

    Returns
    -------
    Prints information to standard output.
    '''

    for att in dir(myObj):
        # Skip __ attributes
        if att.startswith('_'):
            continue
        print("  %s: %s" % (att, getattr(myObj, att)))

def showHelp(parser):
    '''
    This prints the program description and arguments to standard ouptut and exits.
    '''
    parser.print_help()
    sys.exit()

# Main Program

if __name__ == '__main__':

    parser = argparse.ArgumentParser(description='''
Pseudogram decoder: This reads Teledyne Web glider files. The glider files
may include pseudograms from an echosounder. This program can operate
on a single file or a whole deployment of files.
''')

    parser.add_argument("--inpDir", help="full or relative path to glider input files", type=str, default=None)
    parser.add_argument("--inpFile", help="glider input file(s)", type=str, default=None)
    parser.add_argument("--tbdFile", help="full or relative path with filename to glider tbd binary input file", type=str, default=None)
    parser.add_argument("--sbdFile", help="full or relative path with filename to glider sbd binary input file", type=str, default=None)
    parser.add_argument("--cacheDir", help="Directory with glider cache files; default current directory", type=str, default=None)
    parser.add_argument("--dbd2asc", help="full or relative path with filename to glider dbd2asc binary", type=str, default=None)
    parser.add_argument("--csvOut", help="full or relative path with filename to write CSV output or 'stdout'; default None", type=str, default=None)
    parser.add_argument("--csvHeader", help="(flag) include header with CSV output; default False", action="store_true", default=False)
    parser.add_argument("--ncOut", help="full or realative path with filename to write netCDF output; default None", type=str, default=None)
    parser.add_argument("--ncSeparate", help="save tbd, sbd and sv data separately; default False", action="store_true", default=False)
    parser.add_argument("--imageOut", help="filename to write image or stdout; default None", type=str, default=None)
    parser.add_argument("--debug", help="(flag) show extra debugging for this python script; default False", action="store_true", default=False)
    parser.add_argument("--echosounderRange",
            help="Echosounder range; default -60.0 (meters) instrument facing up; positive values instrument facing down", default=-60.0)
    parser.add_argument("--useScatterPlot", help="(flag) Plot using a scatterplot instead of a time/depth binned (raster image) plot; default False", action="store_true", default=False)
    parser.add_argument("--binnedDepthLabels", help="(flag) Use the original depth bin labels instead of the adjusted depth labels for the time/depth binned plot; default False", action="store_true", default=False)
    parser.add_argument("--title", help="optional figure title; default None", type=str)
    parser.add_argument("--deploymentDir", help="full or relative path directory with json files", type=str, default=None)
    parser.add_argument("--template", help="full or relative path to metadata template", type=str, default=None)
    parser.add_argument("--templateDir", help="full or relative path to metadata template directory", type=str, default=None)
    parser.add_argument("--dacOverlay", help="full or relative path to an overlay configuration file", type=str, default=None)

    args = parser.parse_args()
    debugFlag = args.debug

    # Initial arguments
    if debugFlag:
        print("Initial arguments:")
        printAttributes(args)

    # csv and image cannot be both stdout
    if args.csvOut == 'stdout' and args.imageOut == 'stdout':
        print("ERROR: The csvOut and imageOut options cannot both be set to 'stdout'.")
        print("       Run the decoder command separately for csvOut and imageOut using 'stdout'.")
        showHelp(parser)

    '''
    # Check for glider tbd file
    if args.tbdFile is None:
        print("ERROR: A glider tbd file needs to be specified.\n")
        showHelp(parser)

    if not(os.path.isfile(args.tbdFile)):
        print("ERROR: Glider tbd file not found: %s\n" % (args.tbdFile))
        showHelp(parser)

    if args.sbdFile:
        if not(os.path.isfile(args.sbdFile)):
            print("ERROR: Glider sbd file not found: %s\n" % (args.sbdFile))
            showHelp(parser)
    '''

    # Determine glider cache file directory
    if args.cacheDir is None:
        args.cacheDir = os.getcwd()
    else:
       if not(os.path.isdir(args.cacheDir)):
           print("ERROR: Glider cache directory not found: %s\n" % (args.cacheDir))
           showHelp(parser)

    # Make sure the Teledyne Webb linux binary is present
    ''' depricated
    if args.dbd2asc is None:
        print("ERROR: Teledyne Webb linux binary needs to be specified.\n")
        showHelp(parser)
    if not(os.path.isfile(args.dbd2asc)):
        print("ERROR: Teledyne Webb linux binary not found: %s\n" % (args.dbd2asc))
        showHelp(parser)
    '''

    # This will create a class variable "data" which is a
    # dictionary with the following keys that match the
    # file extension of the DBD file.
    glider = teledyne.Glider()

    # Pass the debugFlag immediately
    glider.debugFlag = debugFlag

    # Give all the program arguments to the glider object
    glider.args = args

    # If ncOut is specified, then --deploymentDir and --templateDir must be
    # specified.
    if args.ncOut:
        # If writing netCDF files, the following information is needed
        # Deployment files: deployment.json, instrument.json
        # Metadata/DAC file: slocum_dac.json or some other template
        # Auxillary configuration/DAC file: in the same path as the deployment directory
        glider.loadMetadata()

    # Final arguments
    if debugFlag:
        print("Processed arguments:")
        printAttributes(args)

    # Scan for input files

    # This can be a single file or multiple files by file glob and
    # be relative to args.inpDir.
    if args.inpDir:
        inputFiles = glob.glob(os.path.join(args.inpDir, args.inpFile))
    else:
        inputFiles = glob.glob(os.path.join(args.inpFile))

    if len(inputFiles) == 0:
        print("ERROR: No input files were specified.")
        sys.exit()

    # Process DBD files
    for inputFile in inputFiles:
        if debugFlag:
            print("Processing: %s" % (inputFile))
        glider.readDbd(inputFile=inputFile, cacheDir=args.cacheDir)

    # Now that we have the appropriate cache file metadata, we
    # can now read the pseudogram from tbd data (if available)
    glider.readPseudogram()

    # Code from echoGenNew.py in teledyne.createPseudogramSpreadsheet
    glider.createPseudogramSpreadsheet()
    #glider.stopToDebug()

    # Handle spreadsheet: send to stdout or write to file
    if args.csvOut:
        glider.handleSpreadsheet()

    # Handle image: send to stdout or write to file
    if args.imageOut:
        glider.handleImage()

    # Write netCDF file (if requested)
    if args.ncOut:
        glider.writeNetCDF()

#!/usr/bin/env python3

'''
This script contains functions that decodes the pseudogram from
the echometrics data stream. The resultant information can
be:

 - Rendered in time/depth bin plot
 - Rendered in a scatter plot
 - Saved to a CSV file
 - Saved to a netCDF file

The output can be directed to a file or standard output (stdout)
The netCDF may only be saved to a file.  The netCDF may be saved
as separate files for ease of aggregation of similar variables.

Data written as CSV output is in three columns (comma separated
values): Timestamp, Depth, Density.  A metadata desciption
is given below.

Metadata for the netCDF file is pulled from deployment configuration
files: deployment.json and instruments.json; A general template file
is also required for generic metadata.

Image output is controlled by the filename extension provided.
A typical format is PNG.  Use ".png" in the filename to produce
a PNG formatted image.

Metadata
--------
    Here is the metadata description for each of the coloums
    of this dataset (ASCII, spreadsheet):

    +--------------+--------------------------------------------------+
    | Column       | Description                                      |
    +--------------+--------------------------------------------------+
    | Timestamp    | seconds since 01-01-1970 epoch; timezone GMT/UTC |
    +--------------+--------------------------------------------------+
    | Depth        | depth (meters)                                   |
    +--------------+--------------------------------------------------+
    | Density      | Sv (dB)                                          |
    +--------------+--------------------------------------------------+

Command line arguments
----------------------

::

    -h, --help            show this help message and exit
    --inpDir INPDIR       full or relative path to directory with
                          glider data
    --inpFile INPFILE     glider input file; one segment
    --tbdFile TBDFILE     full or relative path with filename
                          to Teledyne glider tbd binary input file
    --sbdFile SBDFILE     full or relative path with filename
                          to Teledyne glider sbd binary input file
    --cacheDir CACHEDIR   Directory with glider cache files;
                          default current directory
    --dbd2asc DBD2ASC     full or relative path with filename
                          to glider dbd2asc binary
    --csvOut CSVOUT       full or relative path with filename
                          to write CSV output or 'stdout'; default None
    --ncDir NCDIR         full or relative path of a directory for
                          writing netCDF file(s); default None
    --ncFormat NCFORMAT   alternate time format for saving netCDF files
    --csvHeader           (flag) include header with CSV output; default False
    --imageOut IMAGEOUT   filename to write image or stdout; default None
    --debug               (flag) show extra debugging for this
                          python script; default False
    --echosounderRange ECHOSOUNDERRANGE
                          Echosounder range; default -60.0 (meters)
                          instrument facing up; positive values
                          instrument facing down
    --title               optional figure title; default None
    --useScatterPlot      (flag) Plot using a scatterplot
                          instead of a time/depth binned
                          (raster image) plot; default False
    --binnedDepthLabels   (flag) Use the original depth bin
                          labels instead of the adjusted depth
                          labels for the time/depth binned plot;
                          default False
    --deploymentDir       full or relative path to deployment and
                          instrument json files; default None
    --templateDir         full or relative path to glider
                          template directory; default None
'''

import os, sys, datetime, glob, json
import argparse

# Teledyne Webb generic python classes
# and functions
import teledyne

# Functions

def printAttributes(myObj):
    '''
    This is a convienence function for printing object attribute
    information for the supplied object.  This function writes
    to standard output and does not print any objects with
    an underscore prefix.  This was mainly used for debugging
    during development.

    Parameters
    ----------
    myObj : :obj:`any`, required

    Returns
    -------
    Prints information to standard output.
    '''

    for att in dir(myObj):
        # Skip __ attributes
        if att.startswith('_'):
            continue
        print("  %s: %s" % (att, getattr(myObj, att)))

def showHelp(parser):
    '''
    This prints the program description and arguments to standard ouptut and exits.
    '''
    parser.print_help()
    sys.exit()

# Main Program

if __name__ == '__main__':

    parser = argparse.ArgumentParser(description='''
Pseudogram decoder: This reads Teledyne Web glider files. The glider files
may include pseudograms from an echosounder. This program can operate
on a single file or a whole deployment of files.
''')

    parser.add_argument("--inpDir", help="full or relative path to glider input files", type=str, default=None)
    parser.add_argument("--inpFile", help="glider input file(s)", type=str, default=None)
    parser.add_argument("--tbdFile", help="full or relative path with filename to glider tbd binary input file", type=str, default=None)
    parser.add_argument("--sbdFile", help="full or relative path with filename to glider sbd binary input file", type=str, default=None)
    parser.add_argument("--cacheDir", help="Directory with glider cache files; default current directory", type=str, default=None)
    parser.add_argument("--dbd2asc", help="full or relative path with filename to glider dbd2asc binary", type=str, default=None)
    parser.add_argument("--csvOut", help="full or relative path with filename to write CSV output or 'stdout'; default None", type=str, default=None)
    parser.add_argument("--csvHeader", help="(flag) include header with CSV output; default False", action="store_true", default=False)
    parser.add_argument("--ncOut", help="full or realative path with filename to write netCDF output; default None", type=str, default=None)
    parser.add_argument("--ncSeparate", help="save tbd, sbd and sv data separately; default False", action="store_true", default=False)
    parser.add_argument("--imageOut", help="filename to write image or stdout; default None", type=str, default=None)
    parser.add_argument("--debug", help="(flag) show extra debugging for this python script; default False", action="store_true", default=False)
    parser.add_argument("--echosounderRange",
            help="Echosounder range; default -60.0 (meters) instrument facing up; positive values instrument facing down", default=-60.0)
    parser.add_argument("--useScatterPlot", help="(flag) Plot using a scatterplot instead of a time/depth binned (raster image) plot; default False", action="store_true", default=False)
    parser.add_argument("--binnedDepthLabels", help="(flag) Use the original depth bin labels instead of the adjusted depth labels for the time/depth binned plot; default False", action="store_true", default=False)
    parser.add_argument("--title", help="optional figure title; default None", type=str)
    parser.add_argument("--deploymentDir", help="full or relative path directory with json files", type=str, default=None)
    parser.add_argument("--template", help="full or relative path to metadata template", type=str, default=None)
    parser.add_argument("--templateDir", help="full or relative path to metadata template directory", type=str, default=None)
    parser.add_argument("--dacOverlay", help="full or relative path to an overlay configuration file", type=str, default=None)

    args = parser.parse_args()
    debugFlag = args.debug

    # Initial arguments
    if debugFlag:
        print("Initial arguments:")
        printAttributes(args)

    # csv and image cannot be both stdout
    if args.csvOut == 'stdout' and args.imageOut == 'stdout':
        print("ERROR: The csvOut and imageOut options cannot both be set to 'stdout'.")
        print("       Run the decoder command separately for csvOut and imageOut using 'stdout'.")
        showHelp(parser)

    '''
    # Check for glider tbd file
    if args.tbdFile is None:
        print("ERROR: A glider tbd file needs to be specified.\n")
        showHelp(parser)

    if not(os.path.isfile(args.tbdFile)):
        print("ERROR: Glider tbd file not found: %s\n" % (args.tbdFile))
        showHelp(parser)

    if args.sbdFile:
        if not(os.path.isfile(args.sbdFile)):
            print("ERROR: Glider sbd file not found: %s\n" % (args.sbdFile))
            showHelp(parser)
    '''

    # Determine glider cache file directory
    if args.cacheDir is None:
        args.cacheDir = os.getcwd()
    else:
       if not(os.path.isdir(args.cacheDir)):
           print("ERROR: Glider cache directory not found: %s\n" % (args.cacheDir))
           showHelp(parser)

    # Make sure the Teledyne Webb linux binary is present
    ''' depricated
    if args.dbd2asc is None:
        print("ERROR: Teledyne Webb linux binary needs to be specified.\n")
        showHelp(parser)
    if not(os.path.isfile(args.dbd2asc)):
        print("ERROR: Teledyne Webb linux binary not found: %s\n" % (args.dbd2asc))
        showHelp(parser)
    '''

    # This will create a class variable "data" which is a
    # dictionary with the following keys that match the
    # file extension of the DBD file.
    glider = teledyne.Glider()

    # Pass the debugFlag immediately
    glider.debugFlag = debugFlag

    # Give all the program arguments to the glider object
    glider.args = args

    # If ncOut is specified, then --deploymentDir and --templateDir must be
    # specified.
    if args.ncOut:
        # If writing netCDF files, the following information is needed
        # Deployment files: deployment.json, instrument.json
        # Metadata/DAC file: slocum_dac.json or some other template
        # Auxillary configuration/DAC file: in the same path as the deployment directory
        glider.loadMetadata()

    # Final arguments
    if debugFlag:
        print("Processed arguments:")
        printAttributes(args)

    # Scan for input files

    # This can be a single file or multiple files by file glob and
    # be relative to args.inpDir.
    if args.inpDir:
        inputFiles = glob.glob(os.path.join(args.inpDir, args.inpFile))
    else:
        inputFiles = glob.glob(os.path.join(args.inpFile))

    if len(inputFiles) == 0:
        print("ERROR: No input files were specified.")
        sys.exit()

    # Process DBD files
    for inputFile in inputFiles:
        if debugFlag:
            print("Processing: %s" % (inputFile))
        glider.readDbd(inputFile=inputFile, cacheDir=args.cacheDir)

    # Now that we have the appropriate cache file metadata, we
    # can now read the pseudogram from tbd data (if available)
    glider.readPseudogram()

    # Code from echoGenNew.py in teledyne.createPseudogramSpreadsheet
    glider.createPseudogramSpreadsheet()
    #glider.stopToDebug()

    # Handle spreadsheet: send to stdout or write to file
    if args.csvOut:
        glider.handleSpreadsheet()

    # Handle image: send to stdout or write to file
    if args.imageOut:
        glider.handleImage()

    # Write netCDF file (if requested)
    if args.ncOut:
        glider.writeNetCDF()
#!/usr/bin/env python3 This script contains functions that decodes the pseudogram from the echometrics data stream. The resultant information can be:   - Rendered in time/depth bin plot  - Rendered in a scatter plot  - Saved to a CSV file  - Saved to a netCDF file  The output can be directed to a file or standard output (stdout) The netCDF may only be saved to a file.  The netCDF may be saved as separate files for ease of aggregation of similar variables.  Data written as CSV output is in three columns (comma separated values): Timestamp, Depth, Density.  A metadata desciption is given below.  Metadata for the netCDF file is pulled from deployment configuration files: deployment.json and instruments.json; A general template file is also required for generic metadata.  Image output is controlled by the filename extension provided. A typical format is PNG.  Use ".png" in the filename to produce a PNG formatted image.  Metadata --------     Here is the metadata description for each of the coloums     of this dataset (ASCII, spreadsheet):      +--------------+--------------------------------------------------+     | Column       | Description                                      |     +--------------+--------------------------------------------------+     | Timestamp    | seconds since 01-01-1970 epoch; timezone GMT/UTC |     +--------------+--------------------------------------------------+     | Depth        | depth (meters)                                   |     +--------------+--------------------------------------------------+     | Density      | Sv (dB)                                          |     +--------------+--------------------------------------------------+  Command line arguments ----------------------  ::      -h, --help            show this help message and exit     --inpDir INPDIR       full or relative path to directory with                           glider data     --inpFile INPFILE     glider input file; one segment     --tbdFile TBDFILE     full or relative path with filename                           to Teledyne glider tbd binary input file     --sbdFile SBDFILE     full or relative path with filename                           to Teledyne glider sbd binary input file     --cacheDir CACHEDIR   Directory with glider cache files;                           default current directory     --dbd2asc DBD2ASC     full or relative path with filename                           to glider dbd2asc binary     --csvOut CSVOUT       full or relative path with filename                           to write CSV output or 'stdout'; default None     --ncDir NCDIR         full or relative path of a directory for                           writing netCDF file(s); default None     --ncFormat NCFORMAT   alternate time format for saving netCDF files     --csvHeader           (flag) include header with CSV output; default False     --imageOut IMAGEOUT   filename to write image or stdout; default None     --debug               (flag) show extra debugging for this                           python script; default False     --echosounderRange ECHOSOUNDERRANGE                           Echosounder range; default -60.0 (meters)                           instrument facing up; positive values                           instrument facing down     --title               optional figure title; default None     --useScatterPlot      (flag) Plot using a scatterplot                           instead of a time/depth binned                           (raster image) plot; default False     --binnedDepthLabels   (flag) Use the original depth bin                           labels instead of the adjusted depth                           labels for the time/depth binned plot;                           default False     --deploymentDir       full or relative path to deployment and                           instrument json files; default None     --templateDir         full or relative path to glider                           template directory; default None # Teledyne Webb generic python classes # and functions # Functions This is a convienence function for printing object attribute     information for the supplied object.  This function writes     to standard output and does not print any objects with     an underscore prefix.  This was mainly used for debugging     during development.      Parameters     ----------     myObj : :obj:`any`, required      Returns     -------     Prints information to standard output. # Skip __ attributes This prints the program description and arguments to standard ouptut and exits. # Main Program Pseudogram decoder: This reads Teledyne Web glider files. The glider files may include pseudograms from an echosounder. This program can operate on a single file or a whole deployment of files. # Initial arguments # csv and image cannot be both stdout # Check for glider tbd file     if args.tbdFile is None:         print("ERROR: A glider tbd file needs to be specified.\n")         showHelp(parser)      if not(os.path.isfile(args.tbdFile)):         print("ERROR: Glider tbd file not found: %s\n" % (args.tbdFile))         showHelp(parser)      if args.sbdFile:         if not(os.path.isfile(args.sbdFile)):             print("ERROR: Glider sbd file not found: %s\n" % (args.sbdFile))             showHelp(parser) # Determine glider cache file directory # Make sure the Teledyne Webb linux binary is present depricated     if args.dbd2asc is None:         print("ERROR: Teledyne Webb linux binary needs to be specified.\n")         showHelp(parser)     if not(os.path.isfile(args.dbd2asc)):         print("ERROR: Teledyne Webb linux binary not found: %s\n" % (args.dbd2asc))         showHelp(parser) # This will create a class variable "data" which is a # dictionary with the following keys that match the # file extension of the DBD file. # Pass the debugFlag immediately # Give all the program arguments to the glider object # If ncOut is specified, then --deploymentDir and --templateDir must be # specified. # If writing netCDF files, the following information is needed # Deployment files: deployment.json, instrument.json # Metadata/DAC file: slocum_dac.json or some other template # Auxillary configuration/DAC file: in the same path as the deployment directory # Final arguments # Scan for input files # This can be a single file or multiple files by file glob and # be relative to args.inpDir. # Process DBD files # Now that we have the appropriate cache file metadata, we # can now read the pseudogram from tbd data (if available) # Code from echoGenNew.py in teledyne.createPseudogramSpreadsheet #glider.stopToDebug() # Handle spreadsheet: send to stdout or write to file # Handle image: send to stdout or write to file # Write netCDF file (if requested)