Source code for climada.entity.exposures.litpop.nightlight

This file is part of CLIMADA.

Copyright (C) 2017 ETH Zurich, CLIMADA contributors listed in AUTHORS.

CLIMADA is free software: you can redistribute it and/or modify it under the
terms of the GNU General Public License as published by the Free
Software Foundation, version 3.

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PARTICULAR PURPOSE.  See the GNU General Public License for more details.

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with CLIMADA. If not, see <>.


Define nightlight reader and cutting functions.
import glob
import shutil
import tarfile
import gzip
import pickle
import logging
from pathlib import Path
import rasterio

import numpy as np
import scipy.sparse as sparse
import matplotlib.pyplot as plt
from osgeo import gdal
from PIL import Image
from shapefile import Shape

from climada.util import ureg
from climada.util.constants import SYSTEM_DIR
from climada.util.files_handler import download_file
from import save
from climada import CONFIG


LOGGER = logging.getLogger(__name__)

NOAA_RESOLUTION_DEG = (30 * ureg.arc_second).to(ureg.deg).magnitude
"""NOAA nightlights coordinates resolution in degrees."""

NASA_RESOLUTION_DEG = (15 * ureg.arc_second).to(ureg.deg).magnitude
"""NASA nightlights coordinates resolution in degrees."""

NASA_TILE_SIZE = (21600, 21600)
"""NASA nightlights tile resolution."""

NOAA_BORDER = (-180, -65, 180, 75)
"""NOAA nightlights border (min_lon, min_lat, max_lon, max_lat)"""

BM_FILENAMES = ['BlackMarble_%i_A1_geo_gray.tif',
"""Nightlight NASA files which generate the whole earth when put together."""

[docs] def load_nasa_nl_shape(geometry, year, data_dir=SYSTEM_DIR, dtype='float32'): """Read nightlight data from NASA BlackMarble tiles cropped to given shape(s) and combine arrays from each tile. 1) check and download required blackmarble files 2) read and crop data from each file required in a bounding box around the given `geometry`. 3) combine data from all input files into one array. this array then contains all data in the geographic bounding box around `geometry`. 4) return array with nightlight data Parameters ---------- geometry : shape(s) to crop data to in degree lon/lat. for example shapely.geometry.(Multi)Polygon or shapefile.Shape. from polygon defined in a shapefile. The object should have attribute 'bounds' or 'points' year : int target year for nightlight data, e.g. 2016. Closest availble year is selected. data_dir : Path (optional) Path to directory with BlackMarble data. The default is SYSTEM_DIR. dtype : dtype data type for output default 'float32', required for LitPop, choose 'int8' for integer. Returns ------- results_array : numpy array extracted and combined nightlight data for bounding box around shape meta : dict rasterio meta data for results_array """ if isinstance(geometry, Shape): bounds = geometry.bbox else: bounds = geometry.bounds # get years available in BlackMarble data from CONFIG and convert to array: years_available = [ for year in \ CONFIG.exposures.litpop.nightlights.blackmarble_years.list() ] # get year closest to year with BlackMarble data available: year = min(years_available, key=lambda x: abs(x - year)) # determin black marble tiles with coordinates containing the bounds: req_files = get_required_nl_files(bounds) # check wether required files exist locally: files_exist = check_nl_local_file_exists(required_files=req_files, check_path=data_dir, year=year) # download data that is missing: download_nl_files(req_files, files_exist, data_dir, year) # convert `req_files` to sorted list of indices: req_files = np.where(req_files ==1)[0] # init empty lists for tiles depending on position in global grid: results_array_north = list() # tiles A1, B1, C1, D1 (Nothern Hemisphere) results_array_south = list() # tiles A2, B2, C2, D2 (Southern Hemisphere) # loop through required files, load and crop data for each: for idx, i_file in enumerate(req_files): # read cropped data from source file (src) to np.ndarray: out_image, meta_tmp = load_nasa_nl_shape_single_tile(geometry, data_dir / (BM_FILENAMES[i_file] %(year))) # sort indicies to northenr and southern hemisphere: if i_file in [0,2,4,6]: # indicies of northern hemisphere files results_array_north.append(out_image) elif i_file in [1,3,5,7]: # indicies of southern hemisphere files results_array_south.append(out_image) # from first (top left) of tiles, meta is initiated, incl. origin: if idx == 0: meta = meta_tmp # set correct CRS from local tile's CRS to global WGS 84: meta.update({"crs":, "dtype": dtype}) if len(req_files) == 1: # only one tile required: return np.array(out_image, dtype=dtype), meta # Else, combine data from multiple input files (BlackMarble tiles) - # concatenate arrays from west to east and from north to south: del out_image if results_array_north: # northern hemisphere west to east results_array_north = np.concatenate(results_array_north, axis=1) if results_array_south: # southern hemisphere west to east results_array_south = np.concatenate(results_array_south, axis=1) if isinstance(results_array_north, np.ndarray) and isinstance(results_array_south, np.ndarray): # north to south if both hemispheres are involved results_array_north = np.concatenate([results_array_north, results_array_south], axis=0) elif isinstance(results_array_south, np.ndarray): # only southern hemisphere results_array_north = results_array_south del results_array_south # update number of elements per axis in meta dictionary: meta.update({"height": results_array_north.shape[0], "width": results_array_north.shape[1], "dtype": dtype}) return np.array(results_array_north, dtype=dtype), meta
[docs] def get_required_nl_files(bounds): """Determines which of the satellite pictures are necessary for a certain bounding box (e.g. country) Parameters ---------- bounds : 1x4 tuple bounding box from shape (min_lon, min_lat, max_lon, max_lat). Raises ------ ValueError invalid `bounds` Returns ------- req_files : numpy array Array indicating the required files for the current operation with a boolean value (1: file is required, 0: file is not required). """ # check if bounds are valid: if (np.size(bounds) != 4) or (bounds[0] > bounds[2]) or (bounds[1] > bounds[3]): raise ValueError('Invalid bounds supplied. `bounds` must be tuple'+ ' with (min_lon, min_lat, max_lon, max_lat).') min_lon, min_lat, max_lon, max_lat = bounds # longitude first. The width of all tiles is 90 degrees tile_width = 90 req_files = np.zeros(np.count_nonzero(BM_FILENAMES),) # determine the staring tile first_tile_lon = min(np.floor((min_lon - (-180)) / tile_width), 3) # "normalise" to zero last_tile_lon = min(np.floor((max_lon - (-180)) / tile_width), 3) # Now latitude. The height of all tiles is the same as the height. # Note that for this analysis returns an index which follows from North to South oritentation. first_tile_lat = min(np.floor(-(min_lat - 90) / tile_width), 1) last_tile_lat = min(np.floor(-(max_lat - 90) / tile_width), 1) for i_lon in range(0, int(len(req_files) / 2)): if first_tile_lon <= i_lon <= last_tile_lon: if first_tile_lat == 0 or last_tile_lat == 0: req_files[(i_lon) * 2] = 1 if first_tile_lat == 1 or last_tile_lat == 1: req_files[(i_lon) * 2 + 1] = 1 else: continue return req_files
[docs] def check_nl_local_file_exists(required_files=None, check_path=SYSTEM_DIR, year=2016): """Checks if BM Satellite files are avaialbe and returns a vector denoting the missing files. Parameters ---------- required_files : numpy array, optional boolean array of dimension (8,) with which some files can be skipped. Only files with value 1 are checked, with value zero are skipped. The default is np.ones(len(BM_FILENAMES),) check_path : str or Path absolute path where files are stored. Default: SYSTEM_DIR year : int year of the image, e.g. 2016 Returns ------- files_exist : numpy array Boolean array that denotes if the required files exist. """ if required_files is None: required_files = np.ones(len(BM_FILENAMES),) if np.size(required_files) < np.count_nonzero(BM_FILENAMES): required_files = np.ones(np.count_nonzero(BM_FILENAMES),) LOGGER.warning('The parameter \'required_files\' was too short and ' 'is ignored.') if isinstance(check_path, str): check_path = Path(check_path) if not check_path.is_dir(): raise ValueError(f'The given path does not exist: {check_path}') files_exist = np.zeros(np.count_nonzero(BM_FILENAMES),) for num_check, name_check in enumerate(BM_FILENAMES): if required_files[num_check] == 0: continue curr_file = check_path.joinpath(name_check %(year)) if curr_file.is_file(): files_exist[num_check] = 1 if sum(files_exist) == sum(required_files): LOGGER.debug('Found all required satellite data (%s files) in folder %s', int(sum(required_files)), check_path) elif sum(files_exist) == 0:'No satellite files found locally in %s', check_path) else: LOGGER.debug('Not all satellite files available. ' 'Found %d out of %d required files in %s', int(sum(files_exist)), int(sum(required_files)), check_path) return files_exist
[docs] def download_nl_files(req_files=np.ones(len(BM_FILENAMES),), files_exist=np.zeros(len(BM_FILENAMES),), dwnl_path=SYSTEM_DIR, year=2016): """Attempts to download nightlight files from NASA webpage. Parameters ---------- req_files : numpy array, optional Boolean array which indicates the files required (0-> skip, 1-> download). The default is np.ones(len(BM_FILENAMES),). files_exist : numpy array, optional Boolean array which indicates if the files already exist locally and should not be downloaded (0-> download, 1-> skip). The default is np.zeros(len(BM_FILENAMES),). dwnl_path : str or path, optional Download directory path. The default is SYSTEM_DIR. year : int, optional Data year to be downloaded. The default is 2016. Raises ------ ValueError RuntimeError Returns ------- dwnl_path : str or path Download directory path. """ if (len(req_files) != len(files_exist)) or (len(req_files) != len(BM_FILENAMES)): raise ValueError('The given arguments are invalid. req_files and ' 'files_exist must both be as long as there are files to download' ' (' + str(len(BM_FILENAMES)) + ').') if not Path(dwnl_path).is_dir(): raise ValueError(f'The folder {dwnl_path} does not exist. Operation aborted.') if np.all(req_files == files_exist): LOGGER.debug('All required files already exist. No downloads necessary.') return dwnl_path try: for num_files in range(0, np.count_nonzero(BM_FILENAMES)): if req_files[num_files] == 0 or files_exist[num_files] == 1: continue # file already available or not required path_check = False # loop through different possible URLs defined in CONFIG: value_err = None for url in CONFIG.exposures.litpop.nightlights.nasa_sites.list(): try: # control for ValueError due to wrong URL curr_file = url.str() + BM_FILENAMES[num_files] %(year)'Attempting to download file from %s', curr_file) path_check = download_file(curr_file, download_dir=dwnl_path) break # leave loop if sucessful except ValueError as err: value_err = err if path_check: # download succesful continue if value_err: raise ValueError("Download failed," " check URLs inCONFIG.exposures.litpop.nightlights.nasa_sites!\n" f" Last error message:\n {value_err.args[0]}") else: raise ValueError("Download failed, file not found and no nasa sites configured," " check URLs in CONFIG.exposures.litpop.nightlights.nasa_sites!") except Exception as exc: raise RuntimeError('Download failed. Please check the network ' 'connection and whether filenames are still valid.') from exc return dwnl_path
[docs] def load_nasa_nl_shape_single_tile(geometry, path, layer=0): """Read nightlight data from single NASA BlackMarble tile and crop to given shape. Parameters ---------- geometry : shape or geometry object shape(s) to crop data to in degree lon/lat. for example shapely.geometry.Polygon object or from polygon defined in a shapefile. path : Path or str full path to BlackMarble tif (including filename) layer : int, optional TIFF-layer to be returned. The default is 0. BlackMarble usually comes with 3 layers. Returns ------- out_image[layer,:,:] : 2D numpy ndarray 2d array with data cropped to bounding box of shape meta : dict rasterio meta """ # open tif source file with raterio: with, 'r') as src: # read cropped data from source file (src) to np.ndarray: out_image, transform = rasterio.mask.mask(src, [geometry], crop=True) LOGGER.debug('Read cropped %s as np.ndarray.', if out_image.shape[0] < layer: raise IndexError(f"{} has only {out_image.shape[0]} layers," f" layer {layer} can't be accessed.") meta = src.meta meta.update({"driver": "GTiff", "height": out_image.shape[1], "width": out_image.shape[2], "transform": transform}) return out_image[layer,:,:], meta
[docs] def load_nightlight_nasa(bounds, req_files, year): """Get nightlight from NASA repository that contain input boundary. Note: Legacy for BlackMarble, not required for litpop module Parameters ---------- bounds : tuple min_lon, min_lat, max_lon, max_lat req_files : np.array array with flags for NASA files needed year : int nightlight year Returns ------- nightlight : sparse.csr_matrix coord_nl : np.array """ # TODO: argument req_files is not used in this function coord_min = np.array([-90, -180]) + NASA_RESOLUTION_DEG / 2 coord_h = np.full((2,), NASA_RESOLUTION_DEG) min_lon, min_lat, max_lon, max_lat = bounds bounds_mat = np.array([[min_lat, min_lon], [max_lat, max_lon]]) global_idx = (bounds_mat - coord_min[None]) / coord_h[None] global_idx[0, :] = np.floor(global_idx[0, :]) global_idx[1, :] = np.ceil(global_idx[1, :]) tile_size = np.array(NASA_TILE_SIZE) nightlight = [] for idx, fname in enumerate(BM_FILENAMES): tile_coord = np.array([1 - idx % 2, idx // 2]) extent = global_idx - (tile_coord * tile_size)[None] if np.any(extent[1, :] < 0) or np.any(extent[0, :] >= NASA_TILE_SIZE): # this tile does not intersect the specified bounds continue extent = np.int64(np.clip(extent, 0, tile_size[None] - 1)) # pylint: disable=unsubscriptable-object im_nl, _ = read_bm_file(SYSTEM_DIR, fname %(year)) im_nl = np.flipud(im_nl) im_nl = im_nl = im_nl[extent[0, 0]:extent[1, 0] + 1, extent[0, 1]:extent[1, 1] + 1] nightlight.append((tile_coord, im_nl)) tile_coords = np.array([n[0] for n in nightlight]) shape = tile_coords.max(axis=0) - tile_coords.min(axis=0) + 1 nightlight = np.array([n[1] for n in nightlight]).reshape(shape, order='F') nightlight = sparse.bmat(np.flipud(nightlight), format='csr') coord_nl = np.vstack([coord_min, coord_h]).T coord_nl[:, 0] += global_idx[0, :] * coord_h[:] return nightlight, coord_nl
[docs] def read_bm_file(bm_path, filename): """Reads a single NASA BlackMarble GeoTiff and returns the data. Run all required checks first. Note: Legacy for BlackMarble, not required for litpop module Parameters ---------- bm_path : str absolute path where files are stored. filename : str filename of the file to be read. Returns ------- arr1 : array Raw BM data curr_file : gdal GeoTiff File Additional info from which coordinates can be calculated. """ path = Path(bm_path, filename) LOGGER.debug('Importing%s.', path) if not path.exists(): raise FileNotFoundError('Invalid path: check that the path to BlackMarble file is correct.') curr_file = gdal.Open(str(path)) arr1 = curr_file.GetRasterBand(1).ReadAsArray() return arr1, curr_file
[docs] def unzip_tif_to_py(file_gz): """Unzip image file, read it, flip the x axis, save values as pickle and remove tif. Parameters ---------- file_gz : str file fith .gz format to unzip Returns ------- fname : str file_name of unzipped file nightlight : sparse.csr_matrix """"Unzipping file %s.", file_gz) file_name = Path(Path(file_gz).stem) with, 'rb') as f_in: with'wb') as f_out: shutil.copyfileobj(f_in, f_out) nightlight = sparse.csc_matrix(plt.imread(file_name)) # flip X axis nightlight.indices = -nightlight.indices + nightlight.shape[0] - 1 nightlight = nightlight.tocsr() file_name.unlink() file_path = SYSTEM_DIR.joinpath(file_name.stem + ".p") save(file_path, nightlight) return file_name, nightlight
[docs] def untar_noaa_stable_nightlight(f_tar_ini): """Move input tar file to SYSTEM_DIR and extract stable light file. Returns absolute path of stable light file in format tif.gz. Parameters ---------- f_tar_ini : str absolute path of file Returns ------- f_tif_gz : str path of stable light file """ # move to SYSTEM_DIR f_tar_dest = SYSTEM_DIR.joinpath(Path(f_tar_ini).name) shutil.move(f_tar_ini, f_tar_dest) # extract stable_lights.avg_vis.tif with as tar_file: extract_name = [name for name in tar_file.getnames() if name.endswith('stable_lights.avg_vis.tif.gz')] if len(extract_name) == 0: raise ValueError('No stable light intensities for selected year and satellite ' f'in file {f_tar_ini}') if len(extract_name) > 1: LOGGER.warning('found more than one potential intensity file in %s %s', f_tar_ini, extract_name) tar_file.extract(extract_name[0], SYSTEM_DIR) return SYSTEM_DIR.joinpath(extract_name[0])
[docs] def load_nightlight_noaa(ref_year=2013, sat_name=None): """Get nightlight luminosites. Nightlight matrix, lat and lon ordered such that nightlight[1][0] corresponds to lat[1], lon[0] point (the image has been flipped). Parameters ---------- ref_year : int, optional reference year. The default is 2013. sat_name : str, optional satellite provider (e.g. 'F10', 'F18', ...) Returns ------- nightlight : sparse.csr_matrix coord_nl : np.array fn_light : str """ # NOAA's URL used to retrieve nightlight satellite images: noaa_url = CONFIG.exposures.litpop.nightlights.noaa_url.str() if sat_name is None: fn_light = str(SYSTEM_DIR.joinpath('*' + str(ref_year) + '*.stable_lights.avg_vis')) else: fn_light = str(SYSTEM_DIR.joinpath(sat_name + str(ref_year) + '*.stable_lights.avg_vis')) # check if file exists in SYSTEM_DIR, download if not if glob.glob(fn_light + ".p"): fn_light = sorted(glob.glob(fn_light + ".p"))[0] with open(fn_light, 'rb') as f_nl: nightlight = pickle.load(f_nl) elif glob.glob(fn_light + ".tif.gz"): fn_light = sorted(glob.glob(fn_light + ".tif.gz"))[0] fn_light, nightlight = unzip_tif_to_py(fn_light) else: # iterate over all satellites if no satellite name provided if sat_name is None: ini_pre, end_pre = 18, 9 for pre_i in np.arange(ini_pre, end_pre, -1): url = noaa_url + 'F' + str(pre_i) + str(ref_year) + '.v4.tar' try: file_down = download_file(url, download_dir=SYSTEM_DIR) break except ValueError: pass if 'file_down' not in locals(): raise ValueError(f'Nightlight for reference year {ref_year} not available. ' 'Try a different year.') else: url = noaa_url + sat_name + str(ref_year) + '.v4.tar' try: file_down = download_file(url, download_dir=SYSTEM_DIR) except ValueError as err: raise ValueError(f'Nightlight intensities for year {ref_year} and satellite' f' {sat_name} do not exist.') from err fn_light = untar_noaa_stable_nightlight(file_down) fn_light, nightlight = unzip_tif_to_py(fn_light) # first point and step coord_nl = np.empty((2, 2)) coord_nl[0, :] = [NOAA_BORDER[1], NOAA_RESOLUTION_DEG] coord_nl[1, :] = [NOAA_BORDER[0], NOAA_RESOLUTION_DEG] return nightlight, coord_nl, fn_light