A set of utilities for lisflood users. pcr2nc: Convert PCRaster files to netCDF CF 1.6; nc2pcr: Convert netCDF files ot PCRaster format; cutmaps: cut netCDF files;compare: compare two set of netcdf files

Lisflood Utilities

This repository hosts source code of LISFLOOD utilities. Go to Lisflood OS page for more information.

Other useful resources

Project Documentation Source code
Lisflood Model docs https://github.com/ec-jrc/lisflood-code
User guide
Lisvap Docs https://github.com/ec-jrc/lisflood-lisvap
Calibration tool Docs https://github.com/ec-jrc/lisflood-calibration
Lisflood Utilities https://github.com/ec-jrc/lisflood-utilities (this repository)
Lisflood Usecases https://github.com/ec-jrc/lisflood-usecases

Intro

Lisflood Utilities is a set of tools to help LISFLOOD users (or any users of PCRaster/netCDF files) to execute some mundane tasks that are necessary to operate lisflood. Here's a list of utilities you can find in lisflood-utilities package.

• pcr2nc is a tool to convert PCRaster maps to netCDF4 files.

• convert a single map into a NetCDF4 file
• convert a time series of maps into a NetCDF4 mapstack
• support for WGS84 and ETRS89 (LAEA) reference systems
• fine tuning of output files (compression, significant digits, etc.)
• nc2pcr is a tool to convert a netCDF file into PCRaster maps.

• convert 2D variables in single PCRaster maps
• netCDF4 mapstacks are not supported yet
• cutmaps is a tool to cut netcdf files in order to reduce size, using either

• a bounding box of coordinates
• a bounding box of matrix indices
• an existing boolean area mask
• a list of stations and a LDD (in netCDF or PCRaster format) Note: PCRaster must be installed in the conda env
• compare is a package containing a set of simple Python classes that helps to compare netCDF, PCRaster and TSS files.

• waterregions is a package containing two scripts that allow to create and verify a water regions map, respectively.

The package contains convenient classes for reading/writing:

• PCRasterMap
• NetCDFMap
• NetCDFWriter

Installation

Requisites

The easy way is to use conda environment as they incapsulate C dependencies as well, so you wouldn't need to install libraries.

Otherwise, ensure you have properly installed the following software:

• Python 3.5+
• GDAL C library and software
• netCDF4 C library

Install

If you use conda, create a new env (or use an existing one) and install gdal and lisflood-utilities:

conda create --name myenv python=3.7 -c conda-forge
conda activate myenv
conda install -c conda-forge pcraster gdal
pip install lisflood-utilities


If you don't use conda but a straight python3 virtualenv:

source /path/myenv/bin/activate
pip install lisflood-utilities


If GDAL library fails to install, ensure to install the same package version of the C library you have on your system. You may also need to setup paths to gdal headers.

To check which version of GDAL libraries you have installed on your computer, use gdal-config

sudo apt-get install libgdal-dev libgdal
export CPLUS_INCLUDE_PATH=/usr/include/gdal
export C_INCLUDE_PATH=/usr/include/gdal
gdal-config --version  # 3.0.1
pip install GDAL==3.0.1


Note: if you previously installed an older version of the lisflood-utilitiies, it is highly recommended to remove it before installing the newest version:

pip uninstall lisflood-utilities
pip install -e./


pcr2nc

Usage

Note: This guide assumes you have installed the program with pip tool. If you cloned the source code instead, just substitute the executable pcr2nc with python pcr2nc_script.py that is in the root folder of the cloned project.

The tool takes three command line input arguments:

• -i, --input: It can be a path to a single file, a folder or a unix-like widlcard expression like /path/to/files/dis00*
• -o, --output_file: Path to the output nc file
• -m, --metadata: Path to a yaml or json file containing configuration for the NetCDF4 output file.

Unless the input is a single file, the resulting NetCDF4 file will be a mapstack according to a time dimension.

Input as a folder containing PCRaster maps. In this case, the folder must contain ONLY PCraster files and the output will be a mapstack.

pcr2nc -i /path/to/input/ -o /path/to/output/out.nc -m ./nc_metadata.yaml


Input as a path to a single map. In this case, the output won't be a mapstack.

pcr2nc -i /path/to/input/pcr.map -o /path/to/output/out.nc -m ./nc_metadata.yaml


Input as a Unix style pathname pattern expansion. The output will be a mapstack. Note that in this case the input argument must be contained in double quotes!

pcr2nc -i "/path/to/input/pcr00*" -o /path/to/output/out.nc -m ./nc_metadata.json


Format of resulting NetCDF4 file is configured into a metadata configuration file. This file can be written in YAML or JSON format.

An example of a metadata configuration file is the following

variable:
shortname: dis
description: Discharge
longname: discharge
units: m3/s
compression: 9
least_significant_digit: 2
source: JRC Space, Security, Migration
reference: JRC Space, Security, Migration
geographical:
datum: WGS84
time:
calendar: proleptic_gregorian
units: days since 1996-01-01


Variable section

In variable section you can configure metadata for the main variable:

• shortname: A short name for the variable
• longname: The long name version
• description: A description for humans
• units: The units of the variable
• compression: Optional, integer number between 1 and 9, default 0 (no compression). If present the output nc file will be compressed at this level.
• least_significant_digit: Optional, integer number, default 2. From NetCDF4 documentation:

If your data only has a certain number of digits of precision (say for example, it is temperature data that was measured with a precision of 0.1 degrees), you can dramatically improve zlib compression by quantizing (or truncating) the data using the least_significant_digit keyword argument to createVariable. The least significant digit is the power of ten of the smallest decimal place in the data that is a reliable value. For example if the data has a precision of 0.1, then setting least_significant_digit=1 will cause data the data to be quantized using numpy.around(scale*data)/scale, where scale = 2**bits, and bits is determined so that a precision of 0.1 is retained (in this case bits=4). Effectively, this makes the compression 'lossy' instead of 'lossless', that is some precision in the data is sacrificed for the sake of disk space.

Source and reference

source and reference add information for the institution that is providing the NetCDF4 file.

Geographical section

In geographical section the only setting to configure is datum. Currently, pcr2nc supports the following list:

• WGS84
• ETRS89
• GISCO

Time section

This section is optional and is only required if the output file is a mapstack (a timeseries of georeferenced 2D arrays) In this section you have to configure units and calendar.

• units: Can be one of the following strings (replacing placeholders with the actual date):
• hours since YYYY-MM-DD HH:MM:SS
• days since YYYY-MM-DD
• calendar: A recognized calendar identifier, like proleptic_gregorian, gregorian etc.

nc2pcr

This tool converts single maps netCDF (time dimension is not supported yet) to PCRaster format.

Usage

nc2pcr -i /path/to/input/file.nc -o /path/to/output/out.map -c /path/to/clone.map


If input file is a LDD map, you must add the -l flag:

nc2pcr -i /path/to/input/ldd.nc -o /path/to/output/ldd.map -c /path/to/clone.map -l


This tool cut netcdf files, using a mask, a bounding box or a list of stations along with a LDD map.

Usage:

The tool accepts as input:

• a mask map (either PCRaster or netCDF format) or
• alternatively, matrix indices in the form xmini_xmaxi:ymini_ymaxi or
• alternatively, coordinates bounding box in the form xmin_xmax:ymin_ymax
• alternatively, list of stations with coordinates and a LDD map.
• a path to a folder containing netCDF files to cut or a static dataset path like LISFLOOD static files.
• a path to a folder where to write cut files.

The following command will cut all netcdf files inside /workarea/Madeira/lai/ folder and produced files will be writte in current folder. The cookie-cutter that will be used is /workarea/Madeira/maps/MaskMap/Bacia_madeira.nc. This file is a mask (boolean map with 1 only in the area of interest) where cutmaps takes the bounding box from. The mask can also be in PCRaster format.

cutmaps -m /workarea/Madeira/maps/MaskMap/Bacia_madeira.nc -f /workarea/Madeira/lai/ -o ./


Indices can also be passed as an argument (using -c argument instead of -m). Knowing your area of interest from your netCDF files, you can determine indices of the array and you can pass in the form imin imax jmin jmax.

cutmaps -c "150 350 80 180" -f /workarea/Madeira/lai/ -o ./


Example with coordinates and path to EFAS/GloFAS static data (-S option), with -W to allow overwriting existing files in output directory:

cutmaps -S /home/projects/lisflood-eu -c "4078546.12 4463723.85 811206.57 1587655.50" -o /Work/Tunisia/cutmaps -W


Example with stations.txt and LDD

Given a LDD map and a list of stations in a text file, each row having coordinates X/Y or lat/lon and an index, separated by tabs:

4297500	1572500 1
4292500	1557500 2
4237500	1537500 3
4312500	1482500 4
4187500	1492500 5

cutmaps -S /home/projects/lisflood-eu -l ldd.map -N stations.txt -o /Work/Tunisia/cutmaps


If ldd is in netCDF format, LDD will be converted to PCRaster format, first.

cutmaps -S /home/projects/lisflood-eu -l ldd.nc -N stations.txt -o /Work/Tunisia/cutmaps


If you experience problems, you can try to pass a path to a PCRaster clone map.

cutmaps -S /home/projects/lisflood-eu -l ldd.nc -C area.map -N stations.txt -o /Work/Tunisia/cutmaps


You will find the produced mask.map and mask.nc for your area in the same folder of ldd map; you will need it for lisflood/lisvap executions. You will also have outlets.map/outlets.nc based on stations.txt, which let you produce gauges TSS if configured in LISFLOOD.

compare utility

This tool let you compare two netcdf datasets. You can configure it with tolerances (atol, rtol, thresholds for percentage of tolerated different values). You can also set the option to write diff files, so that you can inspect maps and differences with a tool like Panoply

usage: compare [-h] -a DATASET_A -b DATASET_B -m MASKAREA [-M SUBMASKAREA]
[-e] [-s] [-D] [-r RTOL] [-t ATOL] [-p MAX_DIFF_PERCENTAGE]
[-l MAX_LARGEDIFF_PERCENTAGE]

Compare netCDF outputs: 0.12.12

optional arguments:
-h, --help            show this help message and exit
-a DATASET_A, --dataset_a DATASET_A
path to dataset version A
-b DATASET_B, --dataset_b DATASET_B
path to dataset version B
-e, --array-equal     flag to compare files to be identical
-s, --skip-missing    flag to skip missing files in comparison
-D, --save-diffs      flag to save diffs in netcdf files for visual
comparisons. Files are saved in ./diffs folder of
current directory.For each file presenting
differences, you will find files diffs, original A and
B (only for timesteps where differences are found).
-r RTOL, --rtol RTOL  rtol
-t ATOL, --atol ATOL  atol
-p MAX_DIFF_PERCENTAGE, --max-diff-percentage MAX_DIFF_PERCENTAGE
threshold for diffs percentage
-l MAX_LARGEDIFF_PERCENTAGE, --max-largediff-percentage MAX_LARGEDIFF_PERCENTAGE
threshold for large diffs percentage


gfit

Introduction

The tool Gfit2 was created to extract flood warning thresholds from a map stack of daily discharge for several years, given in NetCDF format. It is designed to work with any other variable as well as with different sampling (sub- or super- daily)

The tool is made of three files:

1. Gfit2.sh: the main file, used to run the tool (e.g., ./Gfit2.sh ./settingFile_test.sh)
2. settingFile_test.sh: a setting file, where paths and values of the input variables are defined. It can be renamed, as long as the correct name is called in the script (e.g.: set1.sh --> ./Gfit2.sh ./set1.sh)
3. gfit2.r: the r script that performs the extreme value analysis

Requirements

You need to have installed the following:

• CDO
• R

How to run

The tool operates in a Linux environment (also as a job with qsub). To run the tool you'll need:

• R (the script was tested with R version 3.5.0)
• the following R packages: ncdf4, lmomco, ismev
• CDO (the script was tested with CDO version 1.6.5.1)

What does the tool do

The Gfit2 tool performs the following steps:

• It takes the input file in NetCDF and extract the series of annual maxima. an optional number of warm-up years (\$warmup_yrs) are excluded at the beginning of the data, to remove potential spin-up effect. Also the map of average value is computed
• An extreme value fitting is performed on each pixel of the map, using L-moments and a 2-parameter Gumbel distribution. As option, the user can limit the analysis to a specific number of years. Also, one can use the option to remove from the fitting all values smaller than the long-term average. The fitting is performed only where at least 5 annual maxima are available, otherwise a NA is returned on the output map
• Output return level maps (corresponding to user-selected years of recurrence interval) are saved in a netcdf file (return_levels.nc) and as ascii files. If a clone map in PCRaster format is provided, maps are also saved in PCRaster (return level maps and parameters of the Gumbel distribution)
• After the EV fitting, the tool estimates some further statistics from the long-term input file, including minimum, maximum, and different percentile maps. This part can be commented out if not of interest

Reference

L-Moments: Analysis and Estimation of Distributions Using Linear Combinations of Order Statistics

Hosking, J.R.M., 1990. L-Moments: Analysis and Estimation of Distributions Using Linear Combinations of Order Statistics. J. R. Stat. Soc. Ser. B Methodol. 52, 105124.

waterregions

The modelling of water abstraction for domestic, industrial, energetic, agricoltural and livestock use can require a map of the water regions. The concept of water regions and information for their definition are explained here. Since groundwater and surface water resources demand and abstraction are spatially distributed inside each water region, each model set-up must include all the pixels of the water region. This requirement is crucial for the succes of the calibration of the model. This utility allows the user to meet this requirement. More specifically, this utility can be used to:

1. create a water region map which is consistent with a set of calibration points: this purpose is achieved by using the script define_waterregions.
2. verify the consistency between an existing water region map and an exixting map of calibration catchments: this purpose is achieved by using the script verify_waterregions It is here reminded that when calibrating a catchment which is a subset of a larger computational domain, and the option wateruse is switched on, then the option groudwatersmooth must be switched off. The explanation of this requirement is provided in the chapter Water use of the LISFLOOD documentation.

Requirements

python3, pcraster 4.3. The protocol was tested on Linux.

define_waterregions

This utility allows to create a water region map which is consistent with a set of calibration points. The protocol was created by Ad De Roo (Unit D2, Joint Research Centre).

Input

• List of the coordinates of the calibration points. This list must be provided in a .txt file with three columns: LONGITUDE(or x), LATITUDE(or y), point ID.
• LDD map can be in netcdf format or pcraster format. When using pcraster format, the following condition must be satisfied: PCRASTER_VALUESCALE=VS_LDD.
• Countries map in netcdf format or pcraster format. When using pcraster format, the following condition must be satisfied: PCRASTER_VALUESCALE=VS_NOMINAL. This map shows the political boundaries of the Countries, each Coutry is identified by using a unique ID. This map is used to ensure that the water regions are not split accross different Countries.
• Map of the initial definition of the water regions in netcdf format or pcraster format. When using pcraster format, the following condition must be satisfied: PCRASTER_VALUESCALE=VS_NOMINAL. This map is used to attribute a water region to areas not included in the calibration catchments. In order to create this map, the user can follow the guidelines provided here.
• file .yaml or .json to define the metadata of the output water regions map in netcdf format. An example of the structure of these files is provided here
Input data provided by this utility:

This utility provides three maps of Countries IDs: 1arcmin map of Europe (EFAS computational domain), 0.1 degree and 3arcmin maps of the Globe . ACKNOWLEDGEMENTS: both the rasters were retrieved by upsampling the original of the World Borders Datase provided by http://thematicmapping.org/ (the dataset is available under a Creative Commons Attribution-Share Alike License).

Output

Map of the water regions which is consistent with the calibration catchments. In other words, each water region is entirely included in one calibration catchment. The test to check the consistency between the newly created water regions map and the calibration catchments is implemented internally by the code and the outcome of the test is printed on the screen. In the output map, each water region is identified by a unique ID. The format of the output map can be netcdf or pcraster.

Usage

The following command lines allow to produce a water region map which is consistent with the calibration points (only one commad line is required: each one of the command lines below shows a different combination of input files format):

python define_waterregions.py -p calib_points_test.txt -l ldd_test.map -C countries_id_test.map -w waterregions_initial_test.map -o my_new_waterregions.map

python define_waterregions.py -p calib_points_test.txt -l ldd_test.nc -C countries_id_test.nc -w waterregions_initial_test.nc -o my_new_waterregions.nc -m metadata.test.json

python define_waterregions.py -p calib_points_test.txt -l ldd_test.map -C countries_id_test.nc -w waterregions_initial_test.map -o my_new_waterregions.nc -m metadata.test.yaml

The input maps can be in nectdf format or pcraster format (the same command line can accept a mix of pcraster and netcdf formats).It is imperative to write the file name in full, that is including the extension (which can be either ".nc" or ".map").
The utility can return either a pcraster file or a netcdf file. The users select their preferred format by specifying the extension of the file in the output option (i.e. either ".nc" or ".map").
The metadata file in .yaml format must be provided only if the output file is in netcdf format.

The code internally verifies that the each one of the newly created water regions is entirely included within one calibration catchments. If this condition is satisfied, the follwing message in printed out: “OK! Each water region is completely included inside one calibration catchment”. If the condition is not satisfied, the error message is “ERROR: The water regions WR are included in more than one calibration catchment”. Moreover, the code provides the list of the water regions WR and the calibration catchments that do not meet the requirment. This error highlight a problem in the input data: the user is recommended to check (and correct) the list of calibration points and the input maps.

The input and output arguments are listed below.

usage: define_waterregions.py [-h] -p CALIB_POINTS -l LDD -C COUNTRIES_ID -w
WATERREGIONS_INITIAL -o OUTPUT_WR

Define Water Regions consistent with calibration points: {}

optional arguments:
-h, --help            show this help message and exit
-p CALIB_POINTS, --calib_points CALIB_POINTS
list of calibration points: lon or x, lat or y, point id. File extension: .txt,
-l LDD, --ldd LDD     LDD map, file extension: .nc or .map
-C COUNTRIES_ID, --countries_id COUNTRIES_ID
map of Countries ID, fike extension .nc or .map
-w WATERREGIONS_INITIAL, --waterregions_initial WATERREGIONS_INITIAL
initial map of water regions, file extension: .nc or .map
-o OUTPUT_WR, --output_wr OUTPUT_WR
output map of water regions, file extension: .nc or .map
Path to metadata file for NetCDF, .yaml or .json format


verify_waterregions

This function allows to verify the consistency between a water region map and a map of calibration catchments. This function must be used when the water region map and the map of calibration catchments have been defined in an independent manner (i.e. not using the utility define_waterregions). The function verify_waterregions verifies that each water region map is entirely included in one calibration catchment. If this condition is not satisfied, an error message is printed on the screen.

Input

• Map of calibration catchments in netcdf format.
• Water regions map in netcdf format.

Output

The output is a message on the screen. There are two options:

• 'OK! Each water region is completely included inside one calibration catchment.'
• 'ERROR: The water regions WR are included in more than one calibration catchment’: this message is followed by the list of the water regions and of the catchment that raised the isuue. In case of error message, the user can implement the function define_waterregions.

Usage

The following command line allows to produce a water region map which is consistent with the calibration points:

python verify_waterregions.py -cc calib_catchments_test.nc -wr waterregions_test.nc

The input and output arguments are listed below. All the inputs are required.

usage: verify_waterregions.py [-h] -cc CALIB_CATCHMENTS -wr WATERREGIONS

Verify that the Water Regions map is consistent with the map of the
calibration catchments

optional arguments:
-h, --help            show this help message and exit
-cc CALIB_CATCHMENTS, --calib_catchments CALIB_CATCHMENTS
map of calibration catchments, netcdf format
-wr WATERREGIONS, --waterregions WATERREGIONS
map of water regions, netcdf format


NOTE: The utility pcr2nc can be used to convert a map in pcraster format into netcdf format.

Using lisfloodutilities programmatically TODO

You can use lisflood utilities in your python programs.

lisfloodutilities.cutmaps

from lisfloodutilities.cutmaps.cutlib import mask_from_ldd
from lisfloodutilities.nc2pcr import convert

ldd = 'tests/data/cutmaps/ldd_eu.nc'
clonemap = 'tests/data/cutmaps/area_eu.map'
stations = 'tests/data/cutmaps/stations.txt'

ldd_pcr = convert(ldd, clonemap, 'tests/data/cutmaps/ldd_eu_test.map', is_ldd=True)[0]


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