""" ============================= Species distribution dataset ============================= This dataset represents the geographic distribution of species. The dataset is provided by Phillips et. al. (2006). The two species are: - `"Bradypus variegatus" `_ , the Brown-throated Sloth. - `"Microryzomys minutus" `_ , also known as the Forest Small Rice Rat, a rodent that lives in Peru, Colombia, Ecuador, Peru, and Venezuela. References ---------- `"Maximum entropy modeling of species geographic distributions" `_ S. J. Phillips, R. P. Anderson, R. E. Schapire - Ecological Modelling, 190:231-259, 2006. Notes ----- For an example of using this dataset, see :ref:`examples/applications/plot_species_distribution_modeling.py `. """ # Authors: Peter Prettenhofer # Jake Vanderplas # # License: BSD 3 clause from io import BytesIO from os import makedirs, remove from os.path import exists import logging import numpy as np import joblib from . import get_data_home from ._base import _fetch_remote from ._base import RemoteFileMetadata from ..utils import Bunch from ..utils.validation import _deprecate_positional_args from ._base import _pkl_filepath # The original data can be found at: # https://biodiversityinformatics.amnh.org/open_source/maxent/samples.zip SAMPLES = RemoteFileMetadata( filename='samples.zip', url='https://ndownloader.figshare.com/files/5976075', checksum=('abb07ad284ac50d9e6d20f1c4211e0fd' '3c098f7f85955e89d321ee8efe37ac28')) # The original data can be found at: # https://biodiversityinformatics.amnh.org/open_source/maxent/coverages.zip COVERAGES = RemoteFileMetadata( filename='coverages.zip', url='https://ndownloader.figshare.com/files/5976078', checksum=('4d862674d72e79d6cee77e63b98651ec' '7926043ba7d39dcb31329cf3f6073807')) DATA_ARCHIVE_NAME = "species_coverage.pkz" logger = logging.getLogger(__name__) def _load_coverage(F, header_length=6, dtype=np.int16): """Load a coverage file from an open file object. This will return a numpy array of the given dtype """ header = [F.readline() for _ in range(header_length)] make_tuple = lambda t: (t.split()[0], float(t.split()[1])) header = dict([make_tuple(line) for line in header]) M = np.loadtxt(F, dtype=dtype) nodata = int(header[b'NODATA_value']) if nodata != -9999: M[nodata] = -9999 return M def _load_csv(F): """Load csv file. Parameters ---------- F : file object CSV file open in byte mode. Returns ------- rec : np.ndarray record array representing the data """ names = F.readline().decode('ascii').strip().split(',') rec = np.loadtxt(F, skiprows=0, delimiter=',', dtype='a22,f4,f4') rec.dtype.names = names return rec def construct_grids(batch): """Construct the map grid from the batch object Parameters ---------- batch : Batch object The object returned by :func:`fetch_species_distributions` Returns ------- (xgrid, ygrid) : 1-D arrays The grid corresponding to the values in batch.coverages """ # x,y coordinates for corner cells xmin = batch.x_left_lower_corner + batch.grid_size xmax = xmin + (batch.Nx * batch.grid_size) ymin = batch.y_left_lower_corner + batch.grid_size ymax = ymin + (batch.Ny * batch.grid_size) # x coordinates of the grid cells xgrid = np.arange(xmin, xmax, batch.grid_size) # y coordinates of the grid cells ygrid = np.arange(ymin, ymax, batch.grid_size) return (xgrid, ygrid) @_deprecate_positional_args def fetch_species_distributions(*, data_home=None, download_if_missing=True): """Loader for species distribution dataset from Phillips et. al. (2006) Read more in the :ref:`User Guide `. Parameters ---------- data_home : optional, default: None Specify another download and cache folder for the datasets. By default all scikit-learn data is stored in '~/scikit_learn_data' subfolders. download_if_missing : optional, True by default If False, raise a IOError if the data is not locally available instead of trying to download the data from the source site. Returns ------- data : :class:`~sklearn.utils.Bunch` Dictionary-like object, with the following attributes. coverages : array, shape = [14, 1592, 1212] These represent the 14 features measured at each point of the map grid. The latitude/longitude values for the grid are discussed below. Missing data is represented by the value -9999. train : record array, shape = (1624,) The training points for the data. Each point has three fields: - train['species'] is the species name - train['dd long'] is the longitude, in degrees - train['dd lat'] is the latitude, in degrees test : record array, shape = (620,) The test points for the data. Same format as the training data. Nx, Ny : integers The number of longitudes (x) and latitudes (y) in the grid x_left_lower_corner, y_left_lower_corner : floats The (x,y) position of the lower-left corner, in degrees grid_size : float The spacing between points of the grid, in degrees References ---------- * `"Maximum entropy modeling of species geographic distributions" `_ S. J. Phillips, R. P. Anderson, R. E. Schapire - Ecological Modelling, 190:231-259, 2006. Notes ----- This dataset represents the geographic distribution of species. The dataset is provided by Phillips et. al. (2006). The two species are: - `"Bradypus variegatus" `_ , the Brown-throated Sloth. - `"Microryzomys minutus" `_ , also known as the Forest Small Rice Rat, a rodent that lives in Peru, Colombia, Ecuador, Peru, and Venezuela. - For an example of using this dataset with scikit-learn, see :ref:`examples/applications/plot_species_distribution_modeling.py `. """ data_home = get_data_home(data_home) if not exists(data_home): makedirs(data_home) # Define parameters for the data files. These should not be changed # unless the data model changes. They will be saved in the npz file # with the downloaded data. extra_params = dict(x_left_lower_corner=-94.8, Nx=1212, y_left_lower_corner=-56.05, Ny=1592, grid_size=0.05) dtype = np.int16 archive_path = _pkl_filepath(data_home, DATA_ARCHIVE_NAME) if not exists(archive_path): if not download_if_missing: raise IOError("Data not found and `download_if_missing` is False") logger.info('Downloading species data from %s to %s' % ( SAMPLES.url, data_home)) samples_path = _fetch_remote(SAMPLES, dirname=data_home) with np.load(samples_path) as X: # samples.zip is a valid npz for f in X.files: fhandle = BytesIO(X[f]) if 'train' in f: train = _load_csv(fhandle) if 'test' in f: test = _load_csv(fhandle) remove(samples_path) logger.info('Downloading coverage data from %s to %s' % ( COVERAGES.url, data_home)) coverages_path = _fetch_remote(COVERAGES, dirname=data_home) with np.load(coverages_path) as X: # coverages.zip is a valid npz coverages = [] for f in X.files: fhandle = BytesIO(X[f]) logger.debug(' - converting {}'.format(f)) coverages.append(_load_coverage(fhandle)) coverages = np.asarray(coverages, dtype=dtype) remove(coverages_path) bunch = Bunch(coverages=coverages, test=test, train=train, **extra_params) joblib.dump(bunch, archive_path, compress=9) else: bunch = joblib.load(archive_path) return bunch