sophiehcu / interactive-mbes-processing

Tool based on Python and Jupyter Notebook for interactive processing of Kongsberg MBES bathymetry and backscatter data.

Interactive-MBES-processing

Tool based on Python and Jupyter Notebook for interactive processing of Kongsberg MBES bathymetry and backscatter data. Consists of:

• Kongsberg ALL preprocessing module for bathymetry and backscatter
• Jupyter Notebook for processing (filters and corrections) based on Entwine, PDAL and Potree

Important notes:

• To recreate the conda environment two options can be used (:

  • By using the spec-file.txt file → conda command conda create --name myenv --file spec-file.txt
    • myenv should be replaced by the desired environment name
    • Will work only under win-64
  • Or alternatively by using the enironment.yml file → conda command conda env create -f environment.yml

• Hints and troubleshooting:

  • When activating the Hide input all extension, the code cells can be hidden which tiedies the notebook up.
  • Some of the cells are locked with the Freeze extension and have to be unlocked for modification.
  • When the Potree viewer does not update, this is most probably caused by the browser cache. Deactivating or clearing it will help.

interactive-mbes-processing's Issues

Kongsberg_MBES_preprocessing.py: IndexError

Hi.

Thank you for this solution.

I am attempting to process a small dataset from NOAA -> data here (~80MB).

Kongsberg_MBES_preprocessing.py fails.
All I've done is replace line 412 ~bathymetry, backscatter = main('./test/EM122_data.all')
with bathymetry, backscatter = main('./data/0001_20111103_155105_melville.all.mb58').
The distribution format is MBF_EM710RAW -> dataset metadata overview here

Console printout and message:

Decoded 1798 position datagram(s).
Decoded 5098 XYZ datagram(s).
2 ping(s) could not be positioned.
Dataset includes 2201472 soundings.
Traceback (most recent call last):

  File "C:\...\Interactive-MBES-processing-main\software\Kongsberg_MBES_preprocessing.py", line 415, in <module>
    bathymetry, backscatter = main('./data/0001_20111103_155105_melville.all.mb58')

  File "C:\...\Interactive-MBES-processing-main\software\Kongsberg_MBES_preprocessing.py", line 404, in main
    backscatter = decode_raw_backscatter(filename, bathymetry)

  File "C:\...\Interactive-MBES-processing-main\software\Kongsberg_MBES_preprocessing.py", line 371, in decode_raw_backscatter
    reduce(

  File "C:\...\Interactive-MBES-processing-main\software\Kongsberg_MBES_preprocessing.py", line 372, in <lambda>
    lambda acc, beam: acc.update(beam),

  File "C:\...\Interactive-MBES-processing-main\software\Kongsberg_MBES_preprocessing.py", line 275, in update
    nextBeam.samples[nextBeam.centreSampleNumber]*0.1

IndexError: tuple index out of range

I know nothing about bathymetry and less about hydrography.
Your help is appreciated.

Setting path to raw data folder

In the documentation, par 3.1 , when setting the path to the folder containing a set of .all files, it is stated that in this case " basepath could also
be assigned an absolute path such as basepath = 'C:/whatever/comes/in/here' to any other directory" .
Shouldn´t that be Path( 'C:/whatever/comes/in/here') instead? I am having trouble running the code.

BTW, excellent thesis and amazing work.