├── .github └── ISSUE_TEMPLATE │ ├── bug-report---general.md │ ├── feature_request.md │ └── sonar-recording-processing-error.md ├── .gitignore ├── LICENSE ├── README.md ├── docs ├── BinaryStructure.md ├── Processing&RawDataExport.md ├── SonarGeorectification.md └── attach │ ├── 1199SonHead.PNG │ ├── Bearing.PNG │ ├── GeorectifiedSon.PNG │ ├── GeorectifiedWithWaterColumn.PNG │ ├── GithubMap.png │ ├── HelixSonHead.PNG │ ├── Hexinator.PNG │ ├── PINGMapper_Logo.png │ ├── PRL_Boulder.PNG │ ├── PRL_Wood.PNG │ ├── SmoothedTrackline.PNG │ └── Suwa_Son.gif ├── error_2025-10-15_1255.txt ├── pingmapper ├── __init__.py ├── __main__.py ├── class_mapSubstrateObj.py ├── class_portstarObj.py ├── class_rectObj.py ├── class_sonObj.py ├── class_sonObj_nadirgaptest.py ├── conda │ └── PINGMapper.yml ├── default_params.json ├── exampleData │ └── FilesHere.txt ├── funcs_common.py ├── funcs_model.py ├── funcs_rectify.py ├── gui_main.py ├── main_mapSubstrate.py ├── main_readFiles.py ├── main_rectify.py ├── procData │ └── OutputsHere.txt ├── processing_scripts │ ├── main_batchDirectory_2024-01-18_0926.py │ └── main_batchDirectory_2024-01-18_0929.py ├── scratch │ ├── funcs_pyhum_correct.py │ ├── main.py │ └── main_batchDirectory.py ├── test_PINGMapper.py ├── test_time.py ├── ubuntu │ ├── README.md │ └── requirements.txt ├── utils │ ├── DRAFT_Workflows │ │ ├── avg_predictions_Mussel_WBL.py │ │ ├── gen_centerline.py │ │ ├── gen_centerline_from_bankline.py │ │ ├── gen_centerline_trkpnts_fitspline_DRAFT.py │ │ └── testEXAMPLE_mosaic_logit.py │ ├── RawEGN_avg_predictions.py │ ├── Substrate_Summaries │ │ ├── 00_substrate_logits_mosaic_transects.py │ │ ├── 00_substrate_shps_mosaic_transects.py │ │ ├── 01_gen_centerline_from_coverage.py │ │ ├── 02_gen_summary_stamp_shps.py │ │ ├── 03_gen_summary_shp.py │ │ ├── 04_combine_summary_shp_csv.py │ │ ├── 05_gen_summary_shp_plots.py │ │ ├── 06_compare_raw-egn_volume.py │ │ ├── 07_summary_stats_notebook.ipynb │ │ ├── 07_summary_stats_notebook_noegn.ipynb │ 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