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| 1 | +#!/usr/bin/env python3 |
| 2 | +import os, argparse, rasterio |
| 3 | +import numpy as np |
| 4 | +import pandas as pd |
| 5 | +from multiprocessing import Pool |
| 6 | + |
| 7 | +from inundation import inundate |
| 8 | +from gms_tools.mosaic_inundation import Mosaic_inundation, __append_id_to_file_name |
| 9 | + |
| 10 | + |
| 11 | +def composite_inundation(fim_dir_ms, fim_dir_fr, huc, flows, composite_output_dir, ouput_name='', |
| 12 | + bin_rast_flag=False, depth_rast_flag=False, clean=True, quiet=True): |
| 13 | + """ |
| 14 | + Run `inundate()` on FIM 3.X mainstem (MS) and full-resolution (FR) outputs and composite results. Assumes that all `fim_run` products |
| 15 | + necessary for `inundate()` are in each huc8 folder. |
| 16 | +
|
| 17 | + Parameters |
| 18 | + ---------- |
| 19 | + fim_dir_ms : str |
| 20 | + Path to MS FIM directory. This should be an output directory from `fim_run.sh`. |
| 21 | + fim_dir_fr : str |
| 22 | + Path to FR FIM directory. This should be an output directory from `fim_run.sh`. |
| 23 | + huc : str |
| 24 | + HUC8 to run `inundate()`. This should be a folder within both `fim_dir_ms` and `fim_dir_fr`. |
| 25 | + flows : str or pandas.DataFrame, can be a single file or a comma-separated list of files |
| 26 | + File path to forecast csv or Pandas DataFrame with correct column names. |
| 27 | + composite_output_dir : str |
| 28 | + Folder path to write outputs. It will be created if it does not exist. |
| 29 | + ouput_name : str, optional |
| 30 | + Name for output raster. If not specified, by default the raster will be named 'inundation_composite_{flows_root}.tif'. |
| 31 | + bin_rast_flag : bool, optional |
| 32 | + Flag to create binary raster as output. If no raster flags are passed, this is the default behavior. |
| 33 | + depth_rast_flag : bool, optional |
| 34 | + Flag to create depth raster as output. |
| 35 | + clean : bool, optional |
| 36 | + If True, intermediate files are deleted. |
| 37 | + quiet : bool, optional |
| 38 | + Quiet output. |
| 39 | +
|
| 40 | + Returns |
| 41 | + ------- |
| 42 | + None |
| 43 | +
|
| 44 | + Raises |
| 45 | + ------ |
| 46 | + TypeError |
| 47 | + Wrong input data types |
| 48 | + AssertionError |
| 49 | + Wrong input data types |
| 50 | +
|
| 51 | + Notes |
| 52 | + ----- |
| 53 | + - Specifying a subset of the domain in rem or catchments to inundate on is achieved by the HUCs file or the forecast file. |
| 54 | +
|
| 55 | + Examples |
| 56 | + -------- |
| 57 | + >>> import composite_ms_fr_inundation |
| 58 | + >>> composite_ms_fr_inundation.composite_inundation( |
| 59 | + '/home/user/fim_ouput_mainstem', |
| 60 | + '/home/user/fim_ouput_fullres', |
| 61 | + '12090301', |
| 62 | + '/home/user/forecast_file.csv', |
| 63 | + '/home/user/fim_inundation_composite', |
| 64 | + True, |
| 65 | + False) |
| 66 | + """ |
| 67 | + # Set inundation raster to True if no output type flags are passed |
| 68 | + if not (bin_rast_flag or depth_rast_flag): |
| 69 | + bin_rast_flag = True |
| 70 | + assert not (bin_rast_flag and depth_rast_flag), 'Output can only be binary or depth grid, not both' |
| 71 | + assert os.path.isdir(fim_dir_ms), f'{fim_dir_ms} is not a directory. Please specify an existing MS FIM directory.' |
| 72 | + assert os.path.isdir(fim_dir_fr), f'{fim_dir_fr} is not a directory. Please specify an existing FR FIM directory.' |
| 73 | + assert os.path.exists(flows), f'{flows} does not exist. Please specify a flow file.' |
| 74 | + |
| 75 | + # Instantiate output variables |
| 76 | + var_keeper = { |
| 77 | + 'ms': { |
| 78 | + 'dir': fim_dir_ms, |
| 79 | + 'outputs': { |
| 80 | + 'inundation_rast': os.path.join(composite_output_dir, f'inundation_ms_{huc}.tif') if bin_rast_flag else None, |
| 81 | + 'depth_rast': os.path.join(composite_output_dir, f'depth_ms_{huc}.tif') if depth_rast_flag else None |
| 82 | + } |
| 83 | + }, |
| 84 | + 'fr': { |
| 85 | + 'dir': fim_dir_fr, |
| 86 | + 'outputs': { |
| 87 | + 'inundation_rast': os.path.join(composite_output_dir, f'inundation_fr_{huc}.tif') if bin_rast_flag else None, |
| 88 | + 'depth_rast': os.path.join(composite_output_dir, f'depth_fr_{huc}.tif') if depth_rast_flag else None |
| 89 | + } |
| 90 | + } |
| 91 | + } |
| 92 | + # Build inputs to inundate() based on the input folders and huc |
| 93 | + if not quiet: print(f"HUC {huc}") |
| 94 | + for extent in var_keeper: |
| 95 | + rem = os.path.join(var_keeper[extent]['dir'], huc, 'rem_zeroed_masked.tif') |
| 96 | + catchments = os.path.join(var_keeper[extent]['dir'], huc, 'gw_catchments_reaches_filtered_addedAttributes.tif') |
| 97 | + catchment_poly = os.path.join(var_keeper[extent]['dir'], huc, 'gw_catchments_reaches_filtered_addedAttributes_crosswalked.gpkg') |
| 98 | + hydro_table = os.path.join(var_keeper[extent]['dir'], huc, 'hydroTable.csv') |
| 99 | + |
| 100 | + # Ensure that all of the required files exist in the huc directory |
| 101 | + for file in (rem, catchments, catchment_poly, hydro_table): |
| 102 | + if not os.path.exists(file): |
| 103 | + raise Exception(f"The following file does not exist within the supplied FIM directory:\n{file}") |
| 104 | + |
| 105 | + # Run inundation() |
| 106 | + extent_friendly = "mainstem (MS)" if extent=="ms" else "full-resolution (FR)" |
| 107 | + if not quiet: print(f" Creating an inundation map for the {extent_friendly} configuration...") |
| 108 | + result = inundate(rem,catchments,catchment_poly,hydro_table,flows,mask_type=None, |
| 109 | + inundation_raster= var_keeper[extent]['outputs']['inundation_rast'], |
| 110 | + depths= var_keeper[extent]['outputs']['depth_rast'], |
| 111 | + quiet= quiet) |
| 112 | + if result != 0: |
| 113 | + raise Exception(f"Failed to inundate {rem} using the provided flows.") |
| 114 | + |
| 115 | + # If no output name supplied, create one using the flows file name |
| 116 | + if not ouput_name: |
| 117 | + flows_root = os.path.splitext(os.path.basename(flows))[0] |
| 118 | + ouput_name = os.path.join(composite_output_dir, f'inundation_composite_{flows_root}.tif') |
| 119 | + else: |
| 120 | + ouput_name = os.path.join(composite_output_dir, ouput_name) |
| 121 | + |
| 122 | + # Composite MS and FR |
| 123 | + inundation_map_file = { |
| 124 | + 'huc8' : [huc] * 2, |
| 125 | + 'branchID' : [None] * 2, |
| 126 | + 'inundation_rasters': [var_keeper['fr']['outputs']['inundation_rast'], |
| 127 | + var_keeper['ms']['outputs']['inundation_rast']], |
| 128 | + 'depths_rasters': [var_keeper['fr']['outputs']['depth_rast'], |
| 129 | + var_keeper['ms']['outputs']['depth_rast']] |
| 130 | + } |
| 131 | + inundation_map_file = pd.DataFrame(inundation_map_file) |
| 132 | + Mosaic_inundation( |
| 133 | + inundation_map_file, |
| 134 | + mosaic_attribute='depths_rasters' if depth_rast_flag else 'inundation_rasters', |
| 135 | + mosaic_output=ouput_name, |
| 136 | + mask=catchment_poly, |
| 137 | + unit_attribute_name='huc8', |
| 138 | + nodata=-9999, |
| 139 | + workers=1, |
| 140 | + remove_inputs=clean, |
| 141 | + subset=None,verbose=not quiet |
| 142 | + ) |
| 143 | + if bin_rast_flag: |
| 144 | + hydroid_to_binary(__append_id_to_file_name(ouput_name, huc)) |
| 145 | + |
| 146 | +def hydroid_to_binary(hydroid_raster_filename): |
| 147 | + '''Converts hydroid positive/negative grid to 1/0''' |
| 148 | + |
| 149 | + #to_bin = lambda x: np.where(x > 0, 1, np.where(x == 0, -9999, 0)) |
| 150 | + to_bin = lambda x: np.where(x > 0, 1, np.where(x != -9999, 0, -9999)) |
| 151 | + hydroid_raster = rasterio.open(hydroid_raster_filename) |
| 152 | + profile = hydroid_raster.profile # get profile for new raster creation later on |
| 153 | + profile['nodata'] = -9999 |
| 154 | + bin_raster = to_bin(hydroid_raster.read(1)) # converts neg/pos to 0/1 |
| 155 | + # Overwrite inundation raster |
| 156 | + with rasterio.open(hydroid_raster_filename, "w", **profile) as out_raster: |
| 157 | + out_raster.write(bin_raster.astype(hydroid_raster.profile['dtype']), 1) |
| 158 | + del hydroid_raster,profile,bin_raster |
| 159 | + |
| 160 | + |
| 161 | +if __name__ == '__main__': |
| 162 | + |
| 163 | + # parse arguments |
| 164 | + parser = argparse.ArgumentParser(description='Inundate FIM 3 full resolution and mainstem outputs using a flow file and composite the results.') |
| 165 | + parser.add_argument('-ms','--fim-dir-ms',help='Directory that contains MS FIM outputs.',required=True) |
| 166 | + parser.add_argument('-fr','--fim-dir-fr',help='Directory that contains FR FIM outputs.',required=True) |
| 167 | + parser.add_argument('-u','--huc',help='HUC within FIM directories to inunundate. Can be a comma-separated list.',required=True) |
| 168 | + parser.add_argument('-f','--flows-file',help='File path of flows csv or comma-separated list of paths if running multiple HUCs',required=True) |
| 169 | + parser.add_argument('-o','--ouput-dir',help='Folder to write Composite Raster output.',required=True) |
| 170 | + parser.add_argument('-n','--ouput-name',help='File name for output(s).',default=None,required=False) |
| 171 | + parser.add_argument('-b','--bin-raster',help='Output raster is a binary wet/dry grid. This is the default if no raster flags are passed.',required=False,default=False,action='store_true') |
| 172 | + parser.add_argument('-d','--depth-raster',help='Output raster is a depth grid.',required=False,default=False,action='store_true') |
| 173 | + parser.add_argument('-j','--num-workers',help='Number of concurrent processesto run.',required=False,default=1,type=int) |
| 174 | + parser.add_argument('-c','--clean',help='If flag used, intermediate rasters are NOT cleaned up.',required=False,default=True,action='store_false') |
| 175 | + parser.add_argument('-q','--quiet',help='Quiet terminal output.',required=False,default=False,action='store_true') |
| 176 | + |
| 177 | + # Extract to dictionary and assign to variables. |
| 178 | + args = vars(parser.parse_args()) |
| 179 | + fim_dir_ms = args['fim_dir_ms'] |
| 180 | + fim_dir_fr = args['fim_dir_fr'] |
| 181 | + hucs = args['huc'].replace(' ', '').split(',') |
| 182 | + flows_files = args['flows_file'].replace(' ', '').split(',') |
| 183 | + num_workers = int(args['num_workers']) |
| 184 | + output_dir = args['ouput_dir'] |
| 185 | + ouput_name = args['ouput_name'] |
| 186 | + bin_raster = bool(args['bin_raster']) |
| 187 | + depth_raster = bool(args['depth_raster']) |
| 188 | + clean = bool(args['clean']) |
| 189 | + quiet = bool(args['quiet']) |
| 190 | + |
| 191 | + assert num_workers >= 1, "Number of workers should be 1 or greater" |
| 192 | + assert len(flows_files) == len(hucs), "Number of hucs must be equal to the number of forecasts provided" |
| 193 | + assert not (bin_raster and depth_raster), "Cannot use both -b and -d flags" |
| 194 | + |
| 195 | + # Create output directory if it does not exist |
| 196 | + if not os.path.isdir(output_dir): |
| 197 | + os.mkdir(output_dir) |
| 198 | + |
| 199 | + # Create nested list for input into multi-threading |
| 200 | + arg_list = [] |
| 201 | + for huc, flows_file in zip(hucs, flows_files): |
| 202 | + arg_list.append((fim_dir_ms, fim_dir_fr, huc, flows_file, output_dir, ouput_name, bin_raster, depth_raster, clean, quiet)) |
| 203 | + |
| 204 | + # Multi-thread for each huc in input hucs |
| 205 | + with Pool(processes=num_workers) as pool: |
| 206 | + # Run composite_inundation() |
| 207 | + pool.starmap(composite_inundation, arg_list) |
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