Metadata-Version: 2.1
Name: parflow-subsetter
Version: 0.99.5
Summary: A set of tools for clipping ParFlow model inputs and outputs
Home-page: https://github.com/hydroframe/Subsetting
Author: HydroFrame Team
Author-email: parflow@parflow.org
License: UNKNOWN
Description: [![Build Status](https://travis-ci.com/hydroframe/Subsetting.svg?branch=master)](https://travis-ci.com/hydroframe/Subsetting)
        
        # Subsetter
        The subsetter is a suite of tools for clipping ParFlow inputs and outputs. Included are command
        line scripts to: 
        
        1. subset the inputs from CONUS1 or CONUS2 domains [subset_conus](#Use_a_mask_to_clip_multiple_files_to_PFB_or_TIF)
        2. generate a rasterized mask from a shapefile [rasterize_shape](#Create_subset_from_CONUS_models_from_a_shapefile)
        3. clip data from any number of supported input files [bulk_clip](#Rasterize_a_shapefile_for_use_as_a_mask)
        
        
        ## Prerequisites
        
        ### Packages
        * [parflowio](https://pypi.org/parflowio/)
        * [gdal](https://gdal.org/download.html)
        * [numpy](https://numpy.org/install/)
        * [pyyaml](https://pypi.org/project/PyYAML/)
        * [pandas](https://pandas.pydata.org/)
        * [pftools](https://pypi.org/project/pftools)
        
        
        #### Building Solid Files
        
        To build solid files (.pfsol), the following ParFlow tool is required:
        * `pfmask-to-pfsol` (included with [ParFlow](https://github.com/parflow/parflow)) 
        
        ##### Environment Variables
        
        For the SolidFileBuilder to work, it must be able to locate `pfmask-to-pfsol`
        
        1. PARFLOW_DIR environment variable must be set 
        2. 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:
        
        `parflow/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 parflow.subset.tools.subset_conus --input_path -i INPUT_PATH --shapefile -s
                                             SHAPEFILE --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]
                                             [--write_tcl -w]
                                             [--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 parflow.subset.tools.subset_conus -i ~/downloads/shapefiles -s WBDHU8 -f ~/downloads/conus1 -v 1 -w -n watershedA_conus1_clip
        ```
        
        #### Rasterize a shapefile for use as a mask
        ```
        python -m parflow.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 parflow.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 parflow.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 parflow.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 parflow.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 parflow.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.
        -w [write_tcl] Whether or not to write the .tcl 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
        
        1. .pfb
        2. .tif
        3. .sa
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
