B \"@sdZddlmZddlmZmZddlmZddlZddl Z ddl Z ddl m Z ddl mZdd l mZd d lmZdd lmZdd lmZejddkZeddddZeddddZdZe eZde jfddZddZ ddZ!d!dd Z"dS)"a ============================= 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 `. )BytesIO)makedirsremove)existsN) get_data_home) _fetch_remote)RemoteFileMetadata)Bunch) _pkl_filepath)_joblibz samples.zipz.https://ndownloader.figshare.com/files/5976075Z@abb07ad284ac50d9e6d20f1c4211e0fd3c098f7f85955e89d321ee8efe37ac28)filenameurlZchecksumz coverages.zipz.https://ndownloader.figshare.com/files/5976078Z@4d862674d72e79d6cee77e63b98651ec7926043ba7d39dcb31329cf3f6073807zspecies_coverage.pkzcsbfddt|D}ddtfdd|D}tj|d}t|d}|dkr^d||<|S) zjLoad a coverage file from an open file object. This will return a numpy array of the given dtype csg|] }qS)readline).0i)FrElib/python3.7/site-packages/sklearn/datasets/species_distributions.py Usz"_load_coverage..cSs|dt|dfS)Nrr)splitfloat)trrrVsz _load_coverage..csg|] }|qSrr)rline) make_tuplerrrWs)dtypes NODATA_valuei)rangedictnploadtxtint)rZ header_lengthrheaderMZnodatar)rrr_load_coveragePs r'cCsNtr|dd}n|d}tj|dddd}||j_|S)zLoad csv file. Parameters ---------- F : file object CSV file open in byte mode. Returns ------- rec : np.ndarray record array representing the data ascii,rz a22,f4,f4)ZskiprowsZ delimiterr) PY3_OR_LATERrdecodestriprr"r#rnames)rr-Zrecrrr _load_csv`s r.cCs`|j|j}||j|j}|j|j}||j|j}t|||j}t|||j}||fS)a%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_left_lower_corner grid_sizeNxy_left_lower_cornerNyr"Zarange)ZbatchZxminZxmaxZyminZymaxZxgridZygridrrrconstruct_gridsys  r4Tc Cst|}t|st|tdddddd}tj}t|t}t|s~|sPtdt dt j |ft t |d }t|B}x:|jD]0}t||}d |krt|} d |krt|} qWWd QRXt|t d tj |ft t|d } t| T}g} x:|jD]0}t||}t d|| t|qWtj| |d} Wd QRXt| tf| | | d|} tj| |ddn t|} | S)a 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 -------- The data is returned as a Bunch 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 `. g33333WigfffffLi8g?)r/r1r2r3r0z1Data not found and `download_if_missing` is Falsez&Downloading species data from %s to %s)dirnametraintestNz'Downloading coverage data from %s to %sz - converting {})r) coveragesr7r6 )compress)rrrr!r"int16r DATA_ARCHIVE_NAMEIOErrorloggerinfoSAMPLESrrloadfilesrr.r COVERAGESdebugformatappendr'Zasarrayr r dump)Z data_homeZdownload_if_missingZ extra_paramsrZ archive_pathZ samples_pathXfZfhandler6r7Zcoverages_pathr8Zbunchrrrfetch_species_distributionssTI           rJ)NT)#__doc__iorosrros.pathrsysZloggingZnumpyr"baserrr Zutilsr Zsklearn.datasets.baser Z sklearn.utilsr version_infor*r@rCr<Z getLogger__name__r>r;r'r.r4rJrrrr!s8