parflow-subsetter 1.0.0

Description:

parflowsubsetter 1.0.0

Subsetter
The subsetter is a suite of tools for clipping ParFlow inputs and outputs. Included are command
line scripts to:

subset the inputs from CONUS1 or CONUS2 domains subset_conus
generate a rasterized mask from a shapefile rasterize_shape
clip data from any number of supported input files bulk_clip

Prerequisites
Packages

parflowio
gdal
numpy
pyyaml
pandas
pftools

Building Solid Files
To build solid files (.pfsol), the following ParFlow tool is required:

pfmask-to-pfsol (included with ParFlow)

Environment Variables
For the SolidFileBuilder to work, it must be able to locate pfmask-to-pfsol

PARFLOW_DIR environment variable must be set
bin/pfmask-to-pfsol must be located directly under PARFLOW_DIR

Setup
It is strongly recommended that you create a clean environment using anaconda or miniconda as it will make
installing the required GDAL package easier.
The easiest way to install the subsetter:
$ pip install parflow-subsetter

Otherwise, you can use the contents of this repository to install the package.
git clone https://github.com/hydroframe/subsetting
cd subsetting
conda env create -f=environment.yml
conda activate pf_subsetter

Input Files
For CONUS1 and CONUS2 domains, local copies of model input files are required.
CONUS1 Files
required_files:
DOMAIN_MASK: Domain_Blank_Mask.tif
SUBSURFACE_DATA: grid3d.v3.pfb
PME: PmE.flux.pfb
SLOPE_X: slopex.pfb
SLOPE_Y: slopey.pfb
CELL_TYPES: Domain_Blank_Mask.tif
optional_files:
LAND_COVER: conus1_landcover.sa
LAT_LON: conus1_Grid_Centers_Short_Deg.format.sa
DEM: CONUS2.0_RawDEM_CONUS1clip.tif

CONUS2 Files
required_files:
DOMAIN_MASK: CONUS2.0.Final1km.SinksAndSelectLakes.Mask.tif
SUBSURFACE_DATA: 3d-grid.v3.tif
PME: PME.tif
SLOPE_X: CONUS2.0.Final1km.slopex.tif
SLOPE_Y: CONUS2.0.Final1km.slopey.tif
CELL_TYPES: CONUS2.0.Final1km.Border.Type.tif
optional_files:
LAND_COVER: 1km_CONUS2_landcover_IGBP.tif
LAT_LON: CONUS2.0.Final.LatLong.sa
DEM: CONUS2.0_RawDEM.tif

Local Filenames
If your local filenames differ from this list, update the local filenames in:
pfsubset/subset/data/conus_manifest.yaml
Or copy the format of the file list above into a new .yaml file and pass it as an argument to subset_conus
script using the --manifest parameter
Testing
Run these tests to do some basic checks to make sure the tools are working correctly after install or update.
chmod +x run_tests.sh
./run_tests.sh

Usage
Create subset from CONUS models from a shapefile
python -m pfsubset.subset.tools.subset_conus --input_path -i INPUT_PATH (--shapefile -s
SHAPEFILE | --watershed -w HUCIDS)
--conus_files -f CONUS_FILES
[--manifest -m MANIFEST_FILE]
[--version -v {1,2}] [--out_dir -o OUT_DIR]
[--out_name -n OUT_NAME] [--clip_clm -c]
[--run_script -r]
[--padding -p Top Right Bottom Left]
[--attribute_ids -a ATTRIBUTE_IDS [ATTRIBUTE_IDS ...]]
[--attribute_name -e ATTRIBUTE_NAME]
[--tif_outs -t]


Example usage:
Create a subset of the CONUS1 domain with CLM inputs based on the shapefile at ~/downloads/shapfiles/WBDHU8.shp and write the .tcl file to run the model
python -m pfsubset.subset.tools.subset_conus -i ~/downloads/shapefiles -s WBDHU8 -f ~/downloads/conus1 -v 1 -r -n watershedA_conus1_clip

Rasterize a shapefile for use as a mask
python -m pfsubset.subset.tools.rasterize_shape -i <path_to_shapefile_parts> -s <shapefile_name> -r <reference_dataset>
-o [path_to_write_outputs=.]
-n [output_filename=shapfile_name]
-p [padding clockwise from top (top,right,bottom,left)=(0,0,0,0)]
-e [shapefile_attribute_name='OBJECTID']
-a [shapefile_attribute_ids=[1]]

Example usage:
Re-project the shapefile at ~/downloads/shapfiles/WBDHU8.shp to the CONUS1 projection and extent
python -m pfsubset.subset.tools.rasterize_shape -i ~/downloads/shapefiles -s WBDHU8 -r ~/conus_inputs/1/Domain_Blank_Mask.tif

Use a mask to clip multiple files to PFB or TIF
assumes all files are identically gridded and same as the mask file. If setting the --tif_outs flag then you
must supply at least one tif with correct projection and transform information as either the mask file,
as a reference dataset with the -r option, or in the list of datafiles to clip
python -m pfsubset.subset.tools.bulk_clipper (--maskfile -m MASK_FILE | --bboxfile -b BBOX_FILE | --inline-bbox -l X1 Y1 NX NY)
(--datafiles -d DATA_FILES [DATA_FILES ...] | --glob -g GLOB_PATTERN)
[--input_path -i INPUT_PATH] [--ref_file -r REF_FILE] [--out_dir -o OUT_DIR]
[--pfb_outs -p] [--tif_outs -t]

Example usage with mask file:
Clip the domain outputs to the bounds of a mask generated from rasterize_shape or subset_conus
python -m pfsubset.subset.tools.bulk_clipper -m ~/outputs/WBDHU8.tif -d ~/outputs/runname.out.press.00001.pfb ~/outputs/runname.out.press.00002.pfb

Example usage with bounding box file:
Clip the domain outputs, starting at x, y, and extending for nx, ny
python -m pfsubset.subset.tools.bulk_clipper -b ~/outputs/bbox.txt -d ~/outputs/runname.out.press.00001.pfb ~/outputs/runname.out.press.00002.pfb

where bbox.txt is a tab-separated text file in the format:



x
y
nx
ny




x_1
y_1
nx
ny



Example bbox.txt clipping only the very first (lower left) cell in a domain:



x
y
nx
ny




1
1
1
1



Example usage with bounding box declared in-line:
Clip the domain outputs, starting at x, y, and extending for nx, ny
python -m pfsubset.subset.tools.bulk_clipper -l 1 1 10 20 -d ~/outputs/runname.out.press.00001.pfb ~/outputs/runname.out.press.00002.pfb

clips a 10 x 20 grid anchored in the lower left from each of the inputs
Optional Arguments Explanation
Many optional arguments are available for subset_conus and rasterize_shape. Below is an explanation of the options.
-n [name for output files=shapfile_name] The name to give the output raster, defaults to shapefile name
-v [conus verson=1] The version of the ParFlow CONUS model to subset from (1 or 2), defaults to version 1
-o [path_to_write_outputs=.] The path to write the output files, defaults to current directory
-c [clip_clim] Whether or not to clip the CLM lat/lon and vegm data. Defaults to False.
-r [run_script] Whether or not to write the ParFlow control file to run the ParFlow model. Defaults to False
-p [padding for mask areas] specified clockwise from top (top, right, bottom, left). Default (0,0,0,0)
-e [shapefile_attribute_name='OBJECTID'] The name of the attribute table column to uniquely ID objects.
-a [shapefile_attribute_ids=[1]] The list of objects in the shapefile to rasterize. Default [1]
-t [tif_outs] Whether or not to write outputs as .tif files. Defaults to False.

Supported File Types

.pfb
.tif
.sa