Pingmapper

What's New

- Ping-wise rectification based on Heading and COG
- Updated sonar tile workflows. [More Info](https://cameronbodine.github.io/PINGMapper/docs/tutorials/SonogramTiles.html)

What's Changed
* Merge dev with main by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/149


**Full Changelog**: https://github.com/CameronBodine/PINGMapper/compare/v4.0...v4.2

New Features
PINGMapper has been turned into a PyPi package. Two additional PyPi packages are also created and are new dependencies: PINGInstaller and PINGWizard. PINGInstaller dramatically improves the installation of PINGMapper, the ping environment, and all dependencies. Another package called PINGWizard now acts as the entry point for PINGMapper and other packages in the [PING ecosystem](https://github.com/PINGEcosystem).

- PINGMapper is a PyPi package
- [)](https://pypi.org/project/pingmapper/)
- [PINGInstaller](https://github.com/CameronBodine/PINGInstaller) - Light-weight application for installing [PING ecosystem](https://github.com/PINGEcosystem) (PINGMapper, etc.)
- [)](https://pypi.org/project/pinginstaller/)
- [PINGWizard](https://github.com/CameronBodine/PINGWizard) - Light-weight interface for running PING ecosystem (PINGMapper, etc.)
- [)](https://pypi.org/project/pingwizard/)

What's Changed
* Update gitignore by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/140
* Pull Dev v4.0.0 into main by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/141


**Full Changelog**: https://github.com/CameronBodine/PINGMapper/compare/v3.0.0...v4.0

New Features

New Features

New Features
**Sonar Log Filtering**
You can now filter a sonar log based on heading deviation over a provided distance, minimum and maximum vessel speed, or based on an Area of Interest (AOI) shapefile. Once filtered, survey transect mosaics are automatically made from contiguous chunks. This enables toggling visibility or layer ordering in a GIS.


**Coverage & Trackline Shapefile**
Option to export sonar coverage polygon and track points to shapefile.

Bug Fixes
**Bankline Shapefile**
Fixed the bankline shapefile export. Previously, the bankline polygon was generated from the sonar mosaic. If the mosaic was very large, this would often result in an OOM error. The new new workflow generates a bankline for each chunk, then merges and dissolves into a final shapefile.



What's Changed

* Sonar log filter, coverage, bankline workflow by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/126


**Full Changelog**: https://github.com/CameronBodine/PINGMapper/compare/v2.0.0...v2.1.0

PINGMapper v2.0.0 adds to existing functionality from v1.0.0 and many bug fixes. The new features will be documented in a forthcoming manuscript. If you encounter any issues, please report them [here](https://github.com/CameronBodine/PINGMapper/issues) with the corresponding logs.

New Features
**Automated Substrate Classification**
Neural network models trained with [Segmentation Gym](https://github.com/Doodleverse/segmentation_gym) have been incorporated into PINGMapper. The models will perform a pixel-wise prediction across 6 different substrate classes [Fines - Rippled, Fines - Flat, Cobble - Boulder, Hard Bottom, Wood, Other]. Plots of the predictions can be optionally exported. Raster and polygon maps can also be exported and overlayed on the sonar mosaics.

_NOTE: Exercise caution when interpreting and using the outputs from the substrate prediction. The models were trained on two river systems in Mississippi. It is currently unknown how well the models will perform on other aquatic systems._

**Image Corrections**
To correct for the impact of attenuation on the sonar imagery, a new feature called Empirical Gain Normalization (EGN) is now available. This process involves calculating the average pixel intensity for each range bin and dividing the raw backscatter by the associated average.

_NOTE: Correcting imagery with EGN does take some time; please be patient._

**Use Matplotlib colormaps on sonar mosaics**
You can now assign one of matplotlibs [many colormaps](https://matplotlib.org/stable/tutorials/colors/colormaps.html) to sonar mosaics.

**GUI**
PINGMapper now includes a simple GUI for passing processing parameters rather then editing the Python script. Run the GUI with `python gui_main.py` or `python gui_main_batchDirectory.py`.

Ready to get started?

**New PINGMapper Users**
Please follow the [installation instructions](https://cameronbodine.github.io/PINGMapper/docs/gettingstarted/InstallationDetailed.html).

**Existing PINGMapper Users**
Update your current installation by following these [instructions](https://cameronbodine.github.io/PINGMapper/docs/gettingstarted/UpdateInstallation.html).

Then check to make sure everything is running as expected by running the [test](https://cameronbodine.github.io/PINGMapper/docs/gettingstarted/Testing.html).

What's Changed
* Pull v1.1.0 bug fixes into dev by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/44
* Remove USE_GPU option and issue with fixNoDat by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/45
* Add explicit pip installation 47 by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/48
* Fix negative values after smoothing w/ instrument depth 43 49 by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/50
* main to dev by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/51
* Change gdal import by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/52
* main to dev by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/53
* Use weights stored in object 54 by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/55
* Pull main changes to dev by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/59
* Pull from main by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/62
* Update sonar tile export options by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/63
* Pull main into dev by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/64
* Merge EGN workflow into dev by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/70
* Add h5py to yml by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/71
* Pulling `cropRange` functionality by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/79
* Pull x/y offset workflow from main to dev by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/82
* Massive mem leak 38 should fix 78 too. Don't return self! by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/86
* Numpy deprecation: use int instead of np.int 85 by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/87
* Merging dev to main for v2.0.0-alpha release by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/89
* Pull main into dev by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/91
* Error in main scripts by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/93
* Merge pull request 93 from CameronBodine/dev by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/94
* Add a simple gui by CameronBodine in https://github.com/CameronBodine/PINGMapper/pull/95
* Add Ubuntu install instructions by mirkix in https://github.com/CameronBodine/PINGMapper/pull/98

New Contributors
* mirkix made their first contribution in https://github.com/CameronBodine/PINGMapper/pull/98

**Full Changelog**: https://github.com/CameronBodine/PINGMapper/compare/v1.1.0...v2.0.0