Bathymetry

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# Bathymetry

This repository holds the software for the batheymetry data editing software used by [David Sandwell](http://topex.ucsd.edu/sandwell/)
and his students, working in collaboration with [Yoav Freund](https://cseweb.ucsd.edu/~yfreund/) and his students.

## Organization of the software

The raw data is in `.cm` files. There is a master index file called `sid_filelist.txt`

### Initial filtering software

This software is called CM_EDIT. It takes as input a file corresponding to a single cruise. Display the data visually using apple xcode and lets the user flag (9999) the noisy measurements.

### Assemble the information from a geographic area.

The information from the edited raw data is windowed and then used to create a full image using interpolation. This is performed by the following software:

`maketile` script runs the following steps.
1. GMT/block-median: remove outliers using a median filter.
2. GMT/grd_track: removes a model depth from the data (computes residual)
3. GMT/surface: Interpolation of the residual generates a grid of image. (`netcdf` files)
4. GMT/grdmath: Add the residual grid back the current map.
5. GMT/landmask: creates a grid of land masks. (is it land or ocean).
6. GMT/grdmath: Combines topography and bathymetry based on the land mask.
7. GMT/create the map: produce the geotiff.

### Stereo toolkit from NASA
Takes as input the geotiff and produces a pyrmidal representation that can be used in google maps (`kml` files)

## Human correction
A human goes through the google map and marks polygons at the places that are judged incorrect.

Software that takes the polygons and marks (9999) those locations in the measurements (`cm` files)

### Machine Learning Software.

## Organization of the repository.

## databse
### organization    
| organization  | PRIMARY KEY(organization_id) |
| ------------- | ------------- |
| organization_id  | int  |
| name  | varchar(255)  |
| access_method  | varchar(255)  |

### file_paths
| file_paths  | |
| ------------- | ------------- |
| source_id  | int4  |
| file_path  | varchar|

### pings
| pings  | PRIMARY KEY(ping_id) |
| ------------- | ------------- |
| ping_id  | int  |
| time  | int4  |
| longitude  | float8 |
| latitude  | float8 |
| depth  | float8 |
| sigma_h  | float8 |
| sigma_d  | float8 |
| source_id  | int4 |
| predicted_depth  | float8 |
| predicted_bad  | float8 |
| organization_id  | int |

Indexes:<br>
-    "pings_pkey" PRIMARY KEY, btree (ping_id) 
-    "pings__depth_btree_index" btree (depth) 
-    "pings__source_id_btree_index" btree (source_id)
-    "pings_organization_id_btree_index" btree (organization_id)
-    "pings_predicted_bad_btree_index" btree (predicted_bad)
-    "pings_latitude_btree_index" btree (latitude)
-    "pings_longitude_btree_index" btree (longitude)

# Human editing software

## dev environment installation
First install the Anaconda Python distribution:
    
    https://www.anaconda.com/download/#all
 
 Then in a terminal run:
 
    conda create --name pycmeditor
    source activate pycmeditor
    conda install -c clinicalgraphics vtk
    conda install python.app=1.2
    conda install wxpython=4.0.1
    conda install folium

To run the app use:
    
    pythonw Py-CMeditor.py

The there is a demo .cm file to load in the human_editing branch.

## Notes
Dev branch is called: human_editing

Once software is completed, a pip package will be created for distributing.

Bathymetry

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