enbid-ananke 0.3.0__cp310-cp310-manylinux_2_39_x86_64.whl

enbid_ananke/__init__.py

@@ -0,0 +1,318 @@
+#!/usr/bin/env python
+"""
+enbid_ananke
+======
+
+Provides a set of utilities to run the kernel density estimator EnBiD
+(`Sharma & Steinmetz 2011 <http://ascl.net/1109.012>`).
+
+How to use
+----------
+
+EnBiD comes with the function enbid, please refer to its documentation
+for further help.
+"""
+from typing import Any, Optional, Union, Tuple, Dict
+from numpy.typing import ArrayLike, NDArray
+import pathlib
+import warnings
+import hashlib
+import numpy as np
+import pandas as pd
+from sklearn import neighbors as nghb
+
+from .__metadata__ import *
+from ._constants import *
+from ._templates import *
+from ._defaults import *
+from .utils import execute
+
+__all__ = ['enbid']
+
+
+def __make_path_of_name(name : Optional[Union[str, pathlib.Path]] = None) -> pathlib.Path:
+    """
+        Generate the folders structure representing a given name as a path,
+        or generate a temporary one.
+
+        Call signature::
+
+            path = run_enbid(name=None)
+        
+        Parameters
+        ----------
+        name : string
+            Path representing a folders structure. Default to None.
+        
+        Returns
+        ----------
+        path : pathlib.Path
+            Path corresponding to given name, or to new temporary one.
+    """
+    if name is None:
+        raise NotImplementedError("name is None")  # TODO https://pypi.org/project/temppathlib/
+    else:
+        path = pathlib.Path(name)
+        path.mkdir(parents=True, exist_ok=True)
+    return path
+
+
+def write_for_enbid(points: ArrayLike, name : Optional[Union[str, pathlib.Path]] = None,
+                    caching : bool = False) -> pathlib.Path:
+    """
+        Writes the input files for EnBiD given the input particles 3D
+        coordinates.
+
+        Call signature::
+
+            path = write_for_enbid(points, name=None, caching=False)
+        
+        Parameters
+        ----------
+        points : array_like
+            Contains 3D coordinates of the input particles, must be of shape
+            (N,3) for any given N integer.
+        
+        name : string
+            Name of folder where to place EnBiD input files. Default to None.
+        
+        caching : bool
+            If True, check if EnBiD input file already exists and ignore
+            writing if it does. Default to False.
+        
+        Returns
+        ----------
+        path : pathlib.Path
+            Path of folder where EnBiD input files are located.
+    """
+    path: pathlib.Path = __make_path_of_name(name)
+    enbid_inputfile: pathlib.Path = path / DEFAULT_FOR_PARAMFILE[TTAGS.fname]
+    enbid_inputhashfile: pathlib.Path = enbid_inputfile.with_suffix(f".{HASH_EXT}")
+    points: NDArray = np.asarray(points)
+    inputhash = bytes(hashlib.sha256(points).hexdigest(), HASH_ENCODING)
+    if ((enbid_inputhashfile.read_bytes() != inputhash # proceed if hashes don't match,
+         if (enbid_inputfile.exists() and              # only if enbid_inputfile exists,
+             enbid_inputhashfile.exists())             # and enbid_inputhashfile exists,
+         else True)                                    # otherwise proceed if both don't exist
+        if caching else True):                         # -> proceed anyway if caching is False
+        assert points.ndim == 2 and points.shape[-1] == 3, 'Array-like input must be of shape (X, 3)'
+        # depreciating that warning
+        # temp = np.max(np.abs(np.average(points, axis=0)/np.std(points, axis=0)))
+        # if temp>1: warnings.warn("Input points may be not centered, which may cause EnBiD to run into a SegmentationFault")
+        # center frame on most clustered structure using NN distances
+        NN = nghb.NearestNeighbors(n_neighbors=2)
+        NN.fit(points)
+        NN_distances: NDArray = NN.kneighbors(points)[0][:,1]
+        most_clustered_structure: NDArray = points[NN_distances < np.median(NN_distances)]
+        most_clustered_structure_center: NDArray = np.average(most_clustered_structure, axis=0)
+        #
+        coordinates: NDArray = points - most_clustered_structure_center
+        np.savetxt(enbid_inputfile, coordinates, delimiter=' ')
+        enbid_inputhashfile.write_bytes(inputhash)
+    return path
+
+
+def run_enbid(name: Optional[Union[str, pathlib.Path]] = None, ngb: int = DEFAULT_NGB,
+              verbose: bool = True, caching: bool = False, **kwargs: Dict[str, Any]) -> pathlib.Path:
+    """
+        Run EnBiD using input files in name.
+
+        Call signature::
+
+            path = run_enbid(name=None, ngb=64, verbose=True,
+                             caching=False, **kwargs)
+        
+        Parameters
+        ----------
+        name : string
+            Name of folder where EnBiD input files are located. Default to
+            None.
+
+        ngb : int
+            Number of neighbouring particles EnBiD should consider in the
+            smoothing for the density estimation. Default to {DEFAULT_NGB}.
+
+        verbose : bool
+            Verbose boolean flag to allow EnBiD to print what it's doing to
+            stdout. Default to True.
+
+        caching : bool
+            If True, check if EnBiD paramfile and usedvalues files already
+            exist, and ignore running if parameters from the previous run are
+            the same. Default to False.
+        
+        spatial_scale : float
+            Scaling between position and velocity space where the scaling goes
+            as velocity = position/spatial_scale if spatial_scale is set
+            strictly positive, or velocity = position/std(position) if
+            spatial_scale is set to 0 (with std representing the standard
+            deviation for each coordinate). Default to 1 - TODO currently not
+            implemented.
+        
+        part_bounday : int
+            Minimum number of particles which a node must contain to have a
+            boundary correction applied to its surfaces during tree generation.
+            Optimum choice should be whichever the higher between 7 or d+1
+            where d is the dimensionality of the space considered.
+            Default to 7.
+        
+        node_splitting_criterion : int (0, 1)
+            Flag to allow for the node splitting to always split in priority
+            the dimension with lowest Shannon entropy. If set to 0, the
+            criteria splits each dimension alternately. Default to 1.
+        
+        cubic_cells : int (0, 1)
+            Flag to allow the node splitting to use position or velocity
+            subspaces rather than individual dimensions when generating cells.
+            Only work for 3 & 6 dimensional spaces. Default to 0 - TODO
+            currently not implemented.
+        
+        median_splitting_on : int (0, 1)
+            Flag to allow for cell splitting to happen at the mean of data
+            points when building the tree for faster estimates. Default to 0
+            - TODO currently not implemented.
+        
+        type_of_smoothing : int (0, 1, 2, 3, 4, 5)
+            Type of smoothing used:
+                0) None
+                1) FiEstAS
+                2) Normal isotropic spherical kernel
+                3) Adaptive metric spherical kernel
+                4) Normal isotropic product form kernel
+                5) Adaptive metric product form kernel
+            Default to 3.
+        
+        vol_corr : int (0, 1)
+            Flag to enable a correction that avoid underestimating density
+            when the smoothing box extends outside the boundary. Default to 1.
+        
+        type_of_kernel : int (0, 1, 2, 3, 4, 5)
+            Type of the kernel profile used:
+                0) B-spline
+                1) Top hat
+                2) Bi-weight (1-x^2)^2
+                3) Epanechikov
+                4) Cloud in cell
+                5) Triangular shaped cloud
+            Default to 3.
+        
+        kernel_bias_correction : int (0, 1)
+            Flag to enable corrections that displace central data points when
+            computing densities, and reduce bias caused by irregularly
+            distributed data. Default to 1.
+        
+        anisotropy_kernel : int (0, 1)
+            Flag to enable the use of anisotropic kernels which can have both
+            shear and rotation. Kerels become then rotated ellipsoids in the
+            density computation. With it on, type_of_smoothing should be either
+            2 or 3. Default to 0.
+        
+        anisotropy : float
+            Minimum allowable minor to major axis ratio of the kernel smoothing
+            lengths for computational management. Default to 0.
+        
+        ngb_a : int
+            Number of neighbouring particles EnBiD should consider when
+            computing the anisotropic kernel. Default to ngb.
+        
+        type_list_on : int (0, 1)
+            Flag to extend the number of particle types on which EnBiD can
+            run independent density estimations from the default 6 types of
+            GADGET formated data. Default to 0 - TODO currently not
+            implemented.
+        
+        periodic_boundary_on : int (0, 1)
+            Flag to allow periodic boundary conditions. Default to 0 - TODO
+            currently not implemented.
+        
+        Returns
+        ----------
+        path : pathlib.Path
+            Path of folder where EnBiD output files are located.
+    """
+    path: pathlib.Path = __make_path_of_name(name)
+    kwargs[TTAGS.des_num_ngb] = ngb
+    kwargs[TTAGS.des_num_ngb_a] = kwargs.pop('ngb_a', ngb)
+    paramfile_text: str = ENBID_PARAMFILE_TEMPLATE.substitute(DEFAULT_FOR_PARAMFILE, **kwargs)
+    paramfile: pathlib.Path = path / CONSTANTS.enbid_paramfile
+    usedvalfile: pathlib.Path = path / CONSTANTS.usedvalues
+    if ((paramfile.read_text() != paramfile_text # proceed if paramfile_text is not in paramfile,
+         if (paramfile.exists() and              # only if paramfile exist,
+             usedvalfile.exists())               # and usedvalfile exists,
+         else True)                              # otherwise proceed if both don't exist
+        if caching else True):                   # -> proceed anyway if caching is False
+        paramfile.write_text(paramfile_text)
+        execute([CONSTANTS.enbid, CONSTANTS.enbid_paramfile], verbose=verbose, cwd=path)
+    return path
+
+run_enbid.__doc__ = run_enbid.__doc__.format(DEFAULT_NGB=DEFAULT_NGB)
+
+
+def return_enbid(name: Optional[Union[str, pathlib.Path]] = None) -> NDArray:
+    """
+        Read EnBiD output file and returns the associated kernel density
+        estimates after running the EnBiD estimator.
+
+        Call signature::
+
+            rho = return_enbid(name=None)
+        
+        Parameters
+        ----------
+        name : string
+            Name of folder where EnBiD saved its output files. Default to None.
+        
+        Returns
+        ----------
+        rho : array_like
+            Array representing the kernel density estimates output by EnBiD
+    """
+    path: pathlib.Path = __make_path_of_name(name)
+    usedvals = pd.read_table(path / CONSTANTS.usedvalues, header=None, delim_whitespace=True,
+                             index_col=0).T.reset_index(drop=True).to_dict('records')[0]
+    rho: NDArray = np.loadtxt(path / f"{DEFAULT_FOR_PARAMFILE[TTAGS.fname]}{usedvals[SNAPSHOT_FILEBASE]}.{ENBID_OUT_EXT}")
+    return rho
+
+
+def enbid(*args: Tuple[Any], **kwargs: Dict[str, Any]) -> NDArray:
+    """
+        Returns kernel density estimates given a set of particle 3D coordinates.
+
+        Call signature::
+
+            rho = enbid(points, name=None, **kwargs)
+        
+        Parameters
+        ----------
+        points : array_like
+            Contains 3D coordinates of the input particles, must be of shape
+            (N,3) for any given N integer.
+
+        name : string
+            Name of folder where to save the input/output files for the EnBiD
+            estimator. Default to None.
+        
+        caching : bool
+            Only to be used with a given folder under argument name. If True,
+            check if EnBiD had already been used to produce the kernel density
+            estimates. If it hasn't, compute the estimates, otherwise, load
+            the existing data that had previously been cached. Default to
+            False.
+        
+        **kwargs : dict
+            Refer to function run_enbid documentation for additional keyword
+            arguments.
+        
+        Returns
+        ----------
+        rho : array_like
+            Array representing kernel density estimates for the input particles
+    """
+    points = args[0]
+    name = kwargs.pop('name', None)
+    caching = False if name is None else kwargs.pop('caching', False)
+    return return_enbid(run_enbid(write_for_enbid(points, name=name, caching=caching), caching=caching, **kwargs))
+
+
+if __name__ == '__main__':
+    raise NotImplementedError()

enbid_ananke/__license__/LICENSE

@@ -0,0 +1,339 @@
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+    This program 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; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.

enbid_ananke/__license__/__init__.py

@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+"""
+Reading LICENSE file
+"""
+import pathlib
+
+__all__ = ["__license_full__"]
+
+__license_full__ = (pathlib.Path(__file__).parent / 'LICENSE').read_text()