parflow-subsetter 1.0.0
A set of tools for clipping ParFlow model inputs and outputs
Requires Python: >=3.6

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# 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/project/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:

`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

1. .pfb
2. .tif
3. .sa