Merge 1ed0997 into 399a3e8

nbodykit/algorithms/fftpower.py

@@ -54,13 +54,13 @@ def __init__(self, first, mode, Nmesh=None, BoxSize=None, second=None, los=[0, 0
         ----------
         comm : 
             the MPI communicator
-        first : ParticleSource, MeshSource
-            the source for the first field. ParticleSource is automatically converted
+        first : CatalogSource, MeshSource
+            the source for the first field. CatalogSource is automatically converted to MeshSource
         mode : {'1d', '2d'}
             compute either 1d or 2d power spectra
         Nmesh : int
             the number of cells per side in the particle mesh used to paint the source
-        second : ParticleSource, MeshSource; optional
+        second : CatalogSource, MeshSource; optional
             the second source for cross-correlations
         los : array_like ; optional
             the direction to use as the line-of-sight
@@ -86,7 +86,7 @@ def __init__(self, first, mode, Nmesh=None, BoxSize=None, second=None, los=[0, 0
         # grab comm from first source
         self.comm = first.comm 
 
-        # if input is ParticleSource, use defaults to make it into a mesh
+        # if input is CatalogSource, use defaults to make it into a mesh
         if not hasattr(first, 'paint'):
             first = first.to_mesh(BoxSize=BoxSize, Nmesh=Nmesh, dtype='f8', compensated=True)
 
@@ -297,7 +297,7 @@ def _compute_3d_power(self):
 
         Parameters
         ----------
-        sources : list of ParticleSource or MeshSource
+        sources : list of CatalogSource or MeshSource
             the list of sources which the 3D power will be computed
         pm : ParticleMesh
             the particle mesh object that handles the painting and FFTs

nbodykit/algorithms/fibercollisions.py

@@ -1,6 +1,6 @@
 from nbodykit import CurrentMPIComm
-from nbodykit.base.particles import ParticleSource
-from nbodykit.source import Array
+from nbodykit.base.catalog import CatalogSource
+from nbodykit.source import ArrayCatalog
 
 from nbodykit.transform import SkyToUnitSphere
 import numpy
@@ -41,14 +41,14 @@ def __init__(self, ra, dec, collision_radius=62/60./60., seed=None, degrees=True
             the random seed
         """
         # compute the pos
-        ra = ParticleSource.make_column(ra)
-        dec = ParticleSource.make_column(dec)
+        ra = CatalogSource.make_column(ra)
+        dec = CatalogSource.make_column(dec)
         pos = SkyToUnitSphere(ra, dec, degrees=degrees).compute()
 
         # make the source
         dt = numpy.dtype([('Position', (pos.dtype.str, 3))])
         pos = numpy.squeeze(pos.view(dtype=dt))
-        source = Array(pos, BoxSize=numpy.array([2., 2., 2.]))
+        source = ArrayCatalog(pos, BoxSize=numpy.array([2., 2., 2.]))
 
         self.source = source
         self.comm = source.comm
@@ -116,7 +116,7 @@ def run(self):
         for col, x in d: result[col] = x
 
         # make a particle source
-        self.labels = Array(result, comm=self.comm, **self.source.attrs)
+        self.labels = ArrayCatalog(result, comm=self.comm, **self.source.attrs)
 
     def _assign_fibers(self, Label):
         """

nbodykit/algorithms/fof.py

@@ -3,7 +3,7 @@
 import numpy
 import logging
 from mpi4py import MPI
-from nbodykit.source import Array
+from nbodykit.source import ArrayCatalog
 
 class FOF(object):
     """
@@ -25,7 +25,7 @@ def __init__(self, source, linking_length, nmin, absolute=False):
         """
         Parameters
         ----------
-        source : ParticleSource
+        source : CatalogSource
             the source to run the FOF algorithm on; must support 'Position'
         linking_length : float
             the linking length, either in absolute units, or relative
@@ -84,7 +84,7 @@ def find_features(self):
         
         Returns
         -------
-        ParticleSource : 
+        CatalogSource : 
             a source holding the ('Position', 'Velocity', 'Length')
             of each halo
         """        
@@ -94,7 +94,7 @@ def find_features(self):
         # return a Source
         attrs = self._source.attrs.copy()
         attrs.update(self.attrs)
-        return Array(halos, comm=self.comm, **attrs)
+        return ArrayCatalog(halos, comm=self.comm, **attrs)
 
     def to_halos(self, particle_mass, cosmo, redshift, mdef='vir'):
         """
@@ -107,7 +107,7 @@ def to_halos(self, particle_mass, cosmo, redshift, mdef='vir'):
         
         Parameters
         ----------
-        source : ParticleSource
+        source : CatalogSource
             the source containing info about the particles in each halo
         particle_mass : float
             the particle mass, used to compute the number of particles in 
@@ -136,7 +136,7 @@ def to_halos(self, particle_mass, cosmo, redshift, mdef='vir'):
         # the center-of-mass (Position, Velocity, Length) for each halo
         data = fof_catalog(self._source, self.labels, self.comm)
         data = data[data['Length'] > 0]
-        halos = Array(data, **attrs)
+        halos = ArrayCatalog(data, **attrs)
 
         # add the halo mass column
         halos['Mass'] = particle_mass * halos['Length']
@@ -291,7 +291,7 @@ def fof(source, linking_length, comm):
 
     Parameters
     ----------
-    source: ParticleSource
+    source: CatalogSource
         the input source of particles; must support 'Position' column;
         ``source.attrs['BoxSize']`` is also used
     linking_length: float
@@ -345,7 +345,7 @@ def fof_catalog(source, label, comm,
 
     Parameters
     ----------
-    source: ParticleSource
+    source: CatalogSource
         the parent source of particles from which the center-of-mass
         position and velocity are computed for each halo
     label : array_like

nbodykit/tests/test_conv_power.py → nbodykit/algorithms/tests/test_conv_power.py

@@ -17,8 +17,8 @@ def test_selection(comm):
     CurrentMPIComm.set(comm)
     cosmo = cosmology.Planck15
 
-    data = Source.RandomParticles(NDATA, seed=42)
-    randoms = Source.RandomParticles(NDATA*10, seed=84)
+    data = RandomCatalog(NDATA, seed=42)
+    randoms = RandomCatalog(NDATA*10, seed=84)
 
     # add the random columns
     for s in [data, randoms]:
@@ -38,7 +38,7 @@ def test_selection(comm):
         s['Selection'] = (s['z'] > 0.4)&(s['z'] < 0.6)
 
     # the FKP source
-    fkp = Source.FKPCatalog(data, randoms)
+    fkp = FKPCatalog(data, randoms)
     fkp = fkp.to_mesh(Nmesh=128, dtype='f8', nbar='NZ', selection='Selection')
 
     # compute the multipoles
@@ -64,8 +64,8 @@ def test_run(comm):
     CurrentMPIComm.set(comm)
     cosmo = cosmology.Planck15
 
-    data = Source.RandomParticles(NDATA, seed=42)
-    randoms = Source.RandomParticles(NDATA*10, seed=84)
+    data = RandomCatalog(NDATA, seed=42)
+    randoms = RandomCatalog(NDATA*10, seed=84)
 
     # add the random columns
     for s in [data, randoms]:
@@ -86,7 +86,7 @@ def test_run(comm):
         s['Weight'] = (1 + P0*s['NZ'])**2
 
     # the FKP source
-    fkp = Source.FKPCatalog(data, randoms)
+    fkp = FKPCatalog(data, randoms)
     fkp = fkp.to_mesh(Nmesh=128, dtype='f8', nbar='NZ', fkp_weight='FKPWeight', comp_weight='Weight', selection='Selection')
 
     # compute the multipoles
@@ -117,8 +117,8 @@ def test_with_zhist(comm):
     CurrentMPIComm.set(comm)
     cosmo = cosmology.Planck15
 
-    data = Source.RandomParticles(NDATA, seed=42, use_cache=True)
-    randoms = Source.RandomParticles(NDATA*10, seed=84, use_cache=True)
+    data = RandomCatalog(NDATA, seed=42, use_cache=True)
+    randoms = RandomCatalog(NDATA*10, seed=84, use_cache=True)
 
     # add the random columns
     for s in [data, randoms]:
@@ -132,7 +132,7 @@ def test_with_zhist(comm):
         s['Position'] = transform.SkyToCartesion(s['ra'], s['dec'], s['z'], cosmo=cosmo)
 
     # initialize the FKP source
-    fkp = Source.FKPCatalog(data, randoms)
+    fkp = FKPCatalog(data, randoms)
 
     # compute NZ from randoms
     zhist = RedshiftHistogram(fkp.randoms, FSKY, cosmo, redshift='z')

nbodykit/tests/test_fftpower.py → nbodykit/algorithms/tests/test_fftpower.py

@@ -10,7 +10,7 @@
 def test_fftpower_poles(comm):
 
     CurrentMPIComm.set(comm)
-    source = Source.UniformParticles(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
 
     r = FFTPower(source, mode='2d', BoxSize=1024, Nmesh=32, poles=[0,2,4])
     pkmu = r.power['power'].real
@@ -27,7 +27,7 @@ def test_fftpower_poles(comm):
 def test_fftpower_padding(comm):
 
     CurrentMPIComm.set(comm)
-    source = Source.UniformParticles(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
 
     r = FFTPower(source, mode='1d', BoxSize=1024, Nmesh=32)
     assert r.attrs['N1'] != 0
@@ -37,7 +37,7 @@ def test_fftpower_padding(comm):
 def test_fftpower_padding(comm):
 
     CurrentMPIComm.set(comm)
-    source = Source.UniformParticles(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
 
     r = FFTPower(source, mode='1d', BoxSize=1024, Nmesh=32)
     assert r.attrs['N1'] != 0
@@ -47,7 +47,7 @@ def test_fftpower_padding(comm):
 def test_fftpower_save(comm):
 
     CurrentMPIComm.set(comm)
-    source = Source.UniformParticles(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
 
     r = FFTPower(source, mode='2d', Nmesh=32)
     r.save('fftpower-test.json')
@@ -63,7 +63,7 @@ def test_fftpower_save(comm):
 def test_fftpower(comm):
 
     CurrentMPIComm.set(comm)
-    source = Source.UniformParticles(nbar=3e-3, BoxSize=512., seed=42)
+    source = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
 
     r = FFTPower(source, mode='1d', Nmesh=32)
     # the zero mode is cleared
@@ -76,7 +76,7 @@ def test_fftpower_mismatch_boxsize(comm):
     CurrentMPIComm.set(comm)
 
     # input sources
-    source1 = Source.UniformParticles(nbar=3e-3, BoxSize=512., seed=42)
-    source2 = Source.LinearMesh(cosmology.NoWiggleEHPower(cosmo, 0.55), BoxSize=1024, Nmesh=32, seed=33)
+    source1 = UniformCatalog(nbar=3e-3, BoxSize=512., seed=42)
+    source2 = LinearMesh(cosmology.NoWiggleEHPower(cosmo, 0.55), BoxSize=1024, Nmesh=32, seed=33)
 
     r = FFTPower(source1, second=source2, mode='1d', BoxSize=1024, Nmesh=32)

nbodykit/tests/test_fof.py → nbodykit/algorithms/tests/test_fof.py

@@ -12,7 +12,7 @@ def test_fof(comm):
     CurrentMPIComm.set(comm)
 
     # lognormal particles
-    source = Source.LogNormal(Plin=cosmology.EHPower(cosmo, 0.55),
+    source = LogNormalCatalog(Plin=cosmology.EHPower(cosmo, 0.55),
                 nbar=3e-3, BoxSize=512., Nmesh=128, seed=42)
 
     # compute P(k,mu) and multipoles

nbodykit/tests/test_zhist.py → nbodykit/algorithms/tests/test_zhist.py

@@ -16,7 +16,7 @@ def test_save(comm):
     cosmo = cosmology.Planck15
 
     # create the source
-    source = Source.RandomParticles(N, seed=42)
+    source = RandomCatalog(N, seed=42)
     source['z'] = source.rng.normal(loc=0.5, scale=0.1, size=source.size)
 
     # compute the histogram
@@ -43,7 +43,7 @@ def test_unweighted(comm):
     cosmo = cosmology.Planck15
 
     # create the source
-    source = Source.RandomParticles(N, seed=42)
+    source = RandomCatalog(N, seed=42)
     source['z'] = source.rng.normal(loc=0.5, scale=0.1, size=source.size)
 
     # compute the histogram
@@ -62,7 +62,7 @@ def test_weighted(comm):
     cosmo = cosmology.Planck15
 
     # create the source
-    source = Source.RandomParticles(N, seed=42)
+    source = RandomCatalog(N, seed=42)
     source['z'] = source.rng.normal(loc=0.5, scale=0.1, size=source.size)
     source['weight'] = source.rng.uniform(0, high=1., size=source.size)
 

nbodykit/algorithms/threeptcf.py

@@ -19,7 +19,7 @@ def __init__(self, source, poles, edges, BoxSize=None, periodic=True, weight='We
         """
         Parameters
         ----------
-        source : ParticleSource
+        source : CatalogSource
             the input source of particles providing the 'Position' column
         poles : list of int
             the list of multipole numbers to compute

nbodykit/algorithms/zhist.py

@@ -61,7 +61,7 @@ def __init__(self, source, fsky, cosmo, bins=None, redshift='Redshift', weight=N
         """
         Parameters
         ----------
-        source : ParticleSource
+        source : CatalogSource
             the source of particles holding the redshift column to histogram
         fsky : float
             the sky area fraction, which is used in the volume calculation when