basinex 0.2.0

Description:

basinex 0.2.0

basinex



The mHM basin extractor. Extract basins for given gauging stations.
Dependencies

numpy v1.14.5 or later
netCDF4
GDAL
pyyaml
C++ compiler (for development version)

Installation
If you have GDAL already installed, basinex can be installed via pip:
pip install basinex

GDAL installation
Getting GDAL installed with pip is allways a bit cumbersome. Therefore we compiled instructions for the main target systems.
Ubuntu
To get a recent version of GDAL, you can use the ppa of ubuntugis:
sudo add-apt-repository ppa:ubuntugis/ppa
sudo apt-get update
sudo apt install gdal-bin libgdal-dev
pip install wheel numpy
pip install GDAL==$(gdal-config --version)

MacOS
GDAL can be installed with homebrew:
brew install gdal
pip install wheel numpy
pip install GDAL==$(gdal-config --version)

Windows
You can use the unoffical wheels of Christoph Gohlke to install GDAL.
The easiest way to do so, is using pipwin:
pip install pipwin
pipwin install gdal

Development version in conda environment
It is best to use basinex with conda to have gdal and NetCDF installed properly.
To use the development version of basinex, download this repository and do the following in your conda environment:
conda install -y gdal netcdf4 pyyaml cxx-compiler
pip install .

Then you can execute basinex in that conda environment.
Documentation
Here is a short introduction about how to use the basin extractor.
Have a look at the example directory or try it out directly with:
basinex -c examples

Usage
A command line script basinex will be installed with this package.
You can execute it in your terminal and it will search for an input.yml file in your current directory.
To get more information about how to use the command line interface, you can have a look at the help message:
$ basinex -h
usage: basinex [-h] [-n LINE] [-i INPUT] [-v] [-c CWD] [--version]

mHM basin extractor

optional arguments:
-h, --help show this help message and exit
-n LINE, --line LINE the gauge to extract, given as its (0-based) line number in the look up table
-i INPUT, --input INPUT
the input yaml file to read (default: 'input.yml')
-v, --verbose give some status output
-c CWD, --cwd CWD the working directory
--version show program's version number and exit

The input file
The main input file input.yml is documented and should (hopefully) give an overview
The default input file looks like this:
outpath: /path/to/output/
flowacc: /path/to/facc.asc
flowdir: /path/to/fdir.asc
gauges: /path/to/lut.txt
matching:
scaling_factor: 0.001
max_distance: 800
max_error: 0.8
mask:
fname: basin.asc
outpath: morph
gauge:
fname: idgauges.asc
outpath: morph
gridfiles:
- fname: /path/to/input/facc.asc
outpath: morph
- fname: /path/to/input/input1.asc
outpath: morph
- fname: /path/to/input/input2.asc
outpath: luse
ncfiles:
- fname: /path/to/input/input1.nc
outpath: meteo
ydim: northing
xdim: easting
y_shift: 0.5
x_shift: 0.5
- fname: /path/to/input/input2.nc
outpath: meteo
ydim: 'y'
xdim: 'x'

Description

outpath: outpath/gauge_id/ - Required: Output location, all data will be writen to outpath/gauge_id/
flowacc: /path/to/facc.asc - Required: flowaccumulation
flowdir: /path/to/fdir.asc - Required: flowdirection
gauges: /path/to/lut.txt - Required: gauging data lookup table
Structure of the table:

A simple text table with seperator ';'
if the basin should be delineated, the following fields are required:

id: an unique gauging station identifier
size: size of the catchment
y: y coordinate of the gauging station
x: x coordinate of the gauging station


if an pre processed basin mask should be used, the following fields are required:

id: an unique basin identifier
path: path to the mask file
varname: name of the mask variable (optional, only needed if the mask is stored in a netcdf file)




latitude-size-correction: False - Optional:
perform a latitude correction for the given basin size (default: False)

AREA = N_cells * res_x * ( cos(LAT) * res_y ) * scaling factor^2


matching: - Required: gauge matching parameters

Note:
The gauge matching is based on the flowaccumulation data. The value for
any given cell in the flowaccumulation grid is interpreted as the size
[in cells] of a river basin drainig into the respective cell.
During gauge matching the flowaccumulation grid is searched for a cell
with a corresponding basin size close to the given gauge basin size. The
search radius will be increased succesively and can be limited to a
maximum size. As soon as a matching cell is found (error between catchment
sizes is smaller than the given maximum error) the search ends.
scaling_factor: .001 - scaling factor to account for the (possible) unit differences between the flowaccumulation and the gauging data. In order to make the data comparable the effective flowaccumulation will be caclulated as:

flowaccumulation_value * (cellsize * scaling_factor)^2


max_distance: 800 - maximum distance [in map units] around a given gauging station location to search for a matching cell
max_error: 0.8 - maximum error, as a fraction of the given basin size


mask: - Optional: Write the delineated basin

fname: basin.asc - Optional: file name of the mask grid (default: mask.asc)
outpath: morph - output subdirectory


gauge: - Optional: Write the gauge basin

fname: idgauges.asc - Optional: file name of the gauge grid (default: idgauges.asc)
outpath: morph - output subdirectory


gridfiles: - Optional: Any number of grid files to extract.

Note:
currently only the formats ArcAscii and GeoTIFF are supported
fname: /path/to/input/facc.asc - flow accumulation and flow direction won't be written unless listed here
outpath: morph - Optional: output subdirectory under outpath/gauge_id


ncfiles: - Optional: Any number of netcdf files to extract.

Note:
In order to extract from netcdf, coordinate values must be given.

Example:
If your data variables depend on the three dimensions time, y, x
your file should also contain the two one-dimensional (!) variables
y (depending solely on the dimension y) and x (depending solely
on the dimension x).
Tools like cdo tend to silently remove variables, so double check, that this information is avaialable


fname: /path/to/input/input1.nc
outpath: meteo - Optional: output subdirectory under outpath/gauge_id
ydim: northing - Required: name of the (1D-) variable holding the y coordinates
xdim: easting - Required: name of the (1D-) variable holding the x coordinates
y_shift: .5 and x_shift: .5 - Optional:
Coordinates of spatial data are definied on a certain location
of the cell they belong to (e.g. upper or lower left corner).
All the supported file formats handle coordinates transparently,
with excpetion of netcdf.
To account for the flexibility the format offers, it is possible
to specify the fraction of a cell the origin is shifted from
the upper left corner in x and y direction.
The bounding box of the dataset (an imaginary box, that contains
exactly the entire spatial domain) is then caclulated as:

ymin = min(y_values) - (cellsize * (1 - y_shift))
ymax = max(y_values) + (cellsize * y_shift)
xmin = min(x_values) - (cellsize * (1 - x_shift))
xmax = max(x_values) + (cellsize * x_shift)
Examples:

Your coordinate values specify the upper left corner of a cell

y_shift: 0
x_shift: 0


Your coordinate values specify the center of a cell:

y_shift: 0.5
x_shift: 0.5


Your coordinate values specify the lower left corner of a cell

y_shift: 1
x_shift: 0




Default: lower left corner, i.e:

y_shift: 1
x_shift: 0







Notes
This package was orginally developed by David Schäfer who also provides a standalone version of the geoarray subpackage.
The netcdf4 and geoarray subpackages have been taken from the jams-python package, that was formerly developed at the CHS department at the UFZ and is now released under the MIT license.
License
LGPLv3