Removed obsolete modules from mock_observables

Author: Andrew Hearin

docs/full_ref_api/halotools_full_api.rst

@@ -16,7 +16,6 @@ Comprehensive Halotools Reference/API
 
 .. automodapi:: halotools.mock_observables
 .. automodapi:: halotools.mock_observables.pair_counters
-.. automodapi:: halotools.mock_observables.pair_counters.cpairs
 .. automodapi:: halotools.mock_observables.pair_counters.marked_cpairs
 
 

halotools/empirical_models/factories/tests/test_hod_mock_factory.py

@@ -6,10 +6,8 @@
 from astropy.config.paths import _find_home 
 
 import numpy as np 
-from copy import copy, deepcopy
-from time import time 
+from copy import deepcopy 
 
-from ....mock_observables import periodic_3d_distance
 from ....mock_observables import return_xyz_formatted_array, tpcf_one_two_halo_decomp
 
 from ....sim_manager import FakeSim, CachedHaloCatalog
@@ -178,7 +176,13 @@ def test_satellite_positions1(self):
         x2 = gals['halo_x']
         y2 = gals['halo_y']
         z2 = gals['halo_z']
-        d = periodic_3d_distance(x1, y1, z1, x2, y2, z2, self.model.mock.Lbox)
+        dx = np.fabs(x1 - x2)
+        dx = np.fmin(dx, self.model.mock.Lbox - dx)
+        dy = np.fabs(y1 - y2)
+        dy = np.fmin(dy, self.model.mock.Lbox - dy)
+        dz = np.fabs(z1 - z2)
+        dz = np.fmin(dz, self.model.mock.Lbox - dz)
+        d = np.sqrt(dx*dx+dy*dy+dz*dz)
         assert np.all(d <= gals['halo_rvir'])
 
     @pytest.mark.slow

halotools/mock_observables/__init__.py

@@ -22,5 +22,5 @@
 from .isolation_criteria import *
 from .void_stats import *
 from .catalog_analysis_helpers import *
-from .distances import *
-from .pair_counters import (npairs_3d, npairs_projected, npairs_xy_z)
+from .pair_counters import (npairs_3d, npairs_projected, npairs_xy_z, 
+    marked_npairs_3d, marked_npairs_xy_z)

halotools/mock_observables/clustering_helpers.py

@@ -517,7 +517,7 @@ def _s_mu_tpcf_process_args(sample1, s_bins, mu_bins, sample2, randoms,
 
     #work with the sine of the angle between s and the LOS.  Only using cosine as the 
     #input because of convention.  sin(theta_los) increases as theta_los increases, which
-    #is required in order to get the pair counter to work.  see note in cpairs s_mu_pairs.
+    #is required in order to get the pair counter to work.  
     theta = np.arccos(mu_bins)
     mu_bins = np.sin(theta)[::-1] #must be increasing, remember to reverse result.
 

halotools/mock_observables/distances.py

@@ -1,24 +1,22 @@
-# -*- coding: utf-8 -*-
-
 """
-functions to assist in error estimation of mock observations.
+Functions to assist in error estimation of mock observations.
 """
 
-from __future__ import (absolute_import, division, print_function, unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
-__all__=['jackknife_covariance_matrix','cuboid_subvolume_labels']
+__all__ = ['jackknife_covariance_matrix','cuboid_subvolume_labels']
 __author__ = ('Duncan Campbell', )
 
 import numpy as np
-from ..utils.array_utils import convert_to_ndarray
-from ..custom_exceptions import HalotoolsError
 from warnings import warn
 
+from ..utils.array_utils import convert_to_ndarray
+from ..custom_exceptions import HalotoolsError
 
 def cuboid_subvolume_labels(sample, Nsub, Lbox):
     """
-    return integer labels indicating which cuboid subvolume of a larger cuboid volume a 
-    set of pionts occupy.
+    Return integer labels indicating which cubical subvolume of a larger cubical volume a 
+    set of points occupy.
     
     Parameters
     ----------
@@ -32,9 +30,9 @@ def cuboid_subvolume_labels(sample, Nsub, Lbox):
         of subvolumes is then given by `numpy.prod(Nsub)`.
     
     Lbox : array_like
-        Lenght-3 numpy array definging the legnths of the sides of the cuboid volume
-        that ``sample`` occupies.  If only one number is specified, the volume is assumed 
-        to cubic with sides given by np.array([Lbox]*3).
+        Lenght-3 numpy array definging the lengths of the sides of the cubical volume
+        that ``sample`` occupies.  If only a single scalar is specified, the volume is assumed 
+        to be a cube with side-length Lbox
     
     Returns
     -------
@@ -124,7 +122,7 @@ def jackknife_covariance_matrix(observations):
     Examples
     --------
     For demonstration purposes we create some random data.  Let's say we have jackknife
-    samples and to estimate the errors on 15 measurements.  e.g. the two point
+    100 samples and to estimate the errors on 15 measurements, e.g. the two point
     correlation function in 15 radial bins.
     
     >>> observations = np.random.random((100,15))
@@ -144,7 +142,7 @@ def jackknife_covariance_matrix(observations):
 
     # raise a warning if N_samples < Nr
     if N_samples < Nr:
-        msg = ("\n the nubumber of samples is smaller than the number of \n"
+        msg = ("\n the number of samples is smaller than the number of \n"
                "observations. It is recommended to increase the number \n"
                "of samples or decrease the number of observations.")
         warn(msg)

halotools/mock_observables/error_estimation_tools.py

@@ -1,29 +1,29 @@
-# -*- coding: utf-8 -*-
-
 """
-galaxy group classes
+Module containing the `~halotools.mock_observables.FoFGroups` class used to 
+identify friends-of-friends groups of points. 
 """
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 import numpy as np
 from scipy.sparse import csgraph, csr_matrix
+
+from .pair_counters.pairwise_distance_xy_z import pairwise_distance_xy_z
+
 from ..custom_exceptions import HalotoolsError
-from .pair_counters.double_tree_pair_matrix import xy_z_pair_matrix
 
 igraph_available=True
-try: import igraph
+try: 
+    import igraph
 except ImportError:
     igraph_available=False
 if igraph_available is True: #there is another package called igraph--need to distinguish.
     if not hasattr(igraph,'Graph'):
         igraph_available is False
 no_igraph_msg = ("igraph package not installed.  Some functions will not be available. \n"
-                 "See http://igraph.org/ and note that there are two packages called \n"
-                 "'igraph'.")
+    "See http://igraph.org/ and note that there are two packages called 'igraph'.")
 
-__all__=['FoFGroups']
+__all__ = ['FoFGroups']
 __author__ = ['Duncan Campbell']
 
 class FoFGroups(object):
@@ -37,34 +37,42 @@ def __init__(self, positions, b_perp, b_para, period=None, Lbox=None, num_thread
         
         The first two dimensions (x, y) define the plane for perpendicular distances. 
         The third dimension (z) is used for line-of-sight distances.  
+        
         See the :ref:`mock_obs_pos_formatting` documentation page for 
         instructions on how to transform your coordinate position arrays into the 
         format accepted by the ``positions`` argument.   
-        See also :ref:`galaxy_catalog_analysis_tutorial5`. 
 
+        See also :ref:`galaxy_catalog_analysis_tutorial5`. 
+        
         Parameters
         ----------
         positions : array_like
             Npts x 3 numpy array containing 3-D positions of galaxies. 
-        
+            Length units assumed to be in Mpc/h, here and throughout Halotools. 
+
         b_perp : float
-            Normalized maximum linking length in the perpendicular direction.
-            Normalized to the mean separation between galaxies. 
+            Maximum linking length in the perpendicular direction, 
+            normalized to the mean separation between galaxies. 
         
         b_para : float
-            Normalized maximum linking length in the parallel direction. 
-            Normalized to the mean separation between galaxies. 
+            Maximum linking length in the parallel direction, 
+            normalized to the mean separation between galaxies. 
         
         period : array_like, optional
-            length 3 array defining periodic boundary conditions.
-        
+            Length-3 sequence defining the periodic boundary conditions 
+            in each dimension. If you instead provide a single scalar, Lbox, 
+            period is assumed to be the same in all Cartesian directions. 
+            Length units assumed to be in Mpc/h, here and throughout Halotools. 
+
         Lbox : array_like, optional
             length 3 array defining boundaries of the simulation box.
         
         num_threads : int, optional
-            number of threads to use in calculation. Default is 1. A string 'max' may be 
-            used to indicate that the pair counters should use all available cores on
-            the machine.
+            Number of threads to use in calculation, where parallelization is performed 
+            using the python ``multiprocessing`` module. Default is 1 for a purely serial 
+            calculation, in which case a multiprocessing Pool object will 
+            never be instantiated. A string 'max' may be used to indicate that 
+            the pair counters should use all available cores on the machine.
         
         Examples
         --------
@@ -73,7 +81,7 @@ def __init__(self, positions, b_perp, b_para, period=None, Lbox=None, num_thread
         
         >>> Npts = 1000
         >>> Lbox = 1.0
-        >>> period = np.array([Lbox,Lbox,Lbox])
+        >>> period = Lbox
         
         >>> x = np.random.random(Npts)
         >>> y = np.random.random(Npts)
@@ -103,11 +111,11 @@ def __init__(self, positions, b_perp, b_para, period=None, Lbox=None, num_thread
             raise ValueError("Lbox and Period cannot be both be None.")
         elif (Lbox is None) & (period is not None):
             Lbox = period
-        elif np.shape(Lbox)==():
-            Lbox = np.array([Lbox]*3)
-        elif np.shape(Lbox)==(1,):
-            Lbox = np.array([Lbox[0]]*3)
-        else: Lbox = np.array(Lbox)
+
+        Lbox = np.atleast_1d(Lbox)
+        if len(Lbox) == 1:
+            Lbox = np.array([period, period, period])
+
         if np.shape(Lbox) != (3,):
             raise ValueError("Lbox must be an array of length 3, or number indicating the\
                               length of one side of a cube")
@@ -123,7 +131,7 @@ def __init__(self, positions, b_perp, b_para, period=None, Lbox=None, num_thread
         self.d_perp = self.b_perp/(self.n_gal**(1.0/3.0))
         self.d_para = self.b_para/(self.n_gal**(1.0/3.0))
 
-        self.m_perp, self.m_para = xy_z_pair_matrix(
+        self.m_perp, self.m_para = pairwise_distance_xy_z(
             self.positions, self.positions, self.d_perp, self.d_para,
             period=self.period,num_threads=num_threads)
 
@@ -171,7 +179,8 @@ def create_graph(self):
         """
         if igraph_available is True:
             self.g = _scipy_to_igraph(self.m, self.positions, directed=False)
-        else: raise HalotoolsError(no_igraph_msg)
+        else: 
+            raise HalotoolsError(no_igraph_msg)
 
     def get_degree(self):
         """
@@ -186,7 +195,8 @@ def get_degree(self):
         if igraph_available is True:
             self.degree = self.g.degree()
             return self.degree
-        else: raise HalotoolsError(no_igraph_msg)
+        else: 
+            raise HalotoolsError(no_igraph_msg)
 
     def get_betweenness(self):
         """
@@ -200,7 +210,8 @@ def get_betweenness(self):
         if igraph_available is True:
             self.betweenness = self.g.betweenness()
             return self.betweenness
-        else: raise HalotoolsError(no_igraph_msg)
+        else: 
+            raise HalotoolsError(no_igraph_msg)
 
     def get_multiplicity(self):
         """
@@ -211,7 +222,8 @@ def get_multiplicity(self):
             mltp = np.array(clusters.sizes())
             self.multiplicity = mltp[self.group_ids]
             return self.multiplicity
-        else: raise HalotoolsError(no_igraph_msg)
+        else: 
+            raise HalotoolsError(no_igraph_msg)
 
     def get_edges(self):
         """

halotools/mock_observables/groups.py

@@ -2,22 +2,17 @@
 
 from __future__ import (absolute_import, division, print_function, unicode_literals)
 
-from .double_tree_pairs import *
-from .double_tree_per_object_pairs import *
-from .marked_double_tree_pairs import *
-from .double_tree import *
-from .double_tree_pair_matrix import *
-from .npairs_3d import npairs_3d
 from .rectangular_mesh import RectangularDoubleMesh
-from .npairs_xy_z import npairs_xy_z
+from .npairs_3d import npairs_3d
 from .npairs_projected import npairs_projected
-from .npairs_s_mu import npairs_s_mu
-from .npairs_jackknife_3d import npairs_jackknife_3d
+from .npairs_xy_z import npairs_xy_z
 from .marked_npairs_3d import marked_npairs_3d
 from .marked_npairs_xy_z import marked_npairs_xy_z
+from .npairs_jackknife_3d import npairs_jackknife_3d
+from .npairs_s_mu import npairs_s_mu
 from .npairs_per_object_3d import npairs_per_object_3d
 from .velocity_marked_npairs_3d import velocity_marked_npairs_3d
-from .velocity_marked_npairs_xy_z import velocity_marked_npairs_xy_z
 from .pairwise_distance_3d import pairwise_distance_3d
 from .pairwise_distance_xy_z import pairwise_distance_xy_z
-
+from .velocity_marked_npairs_3d import velocity_marked_npairs_3d
+from .velocity_marked_npairs_xy_z import velocity_marked_npairs_xy_z

halotools/mock_observables/pair_counters/__init__.py

@@ -24,9 +24,9 @@ All actual distance caclualtions are done using "cdef" functions defined in "dis
 
 Available functions are:
 
-* cpairs : pair counts in bins
+* pair_counting_engines : pair counts in bins
 * pairwise_distances : a matrix of distances between points
-* per_object_cpairs : pair counts in bins per object
+* per_object_npairs : pair counts in bins per object
 
 There are usually two version of these functions, one assuming non-periodic distances, and another that presumes periodic boundary conditions.  However, the functions that assume non-periodic distances can be used for the periodic case if the points have been shifted to account for the periodic boundaries--this is the current approach of the halotools higher level pair counting modules.
 

halotools/mock_observables/pair_counters/cpairs/README.md

@@ -2,8 +2,6 @@
 
 from __future__ import (absolute_import, division, print_function, unicode_literals)
 
-from .cpairs import *
-from .per_object_cpairs import *
 from .pairwise_distances import *
 from .npairs_3d_engine import npairs_3d_engine
 from .npairs_projected_engine import npairs_projected_engine
@@ -15,4 +13,3 @@
 from .cylindrical_isolation_engine import cylindrical_isolation_engine
 from .pairwise_distance_3d_engine import pairwise_distance_3d_engine
 from .pairwise_distance_xy_z_engine import pairwise_distance_xy_z_engine
-