PR for pspec_graduation

.gitignore

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+# compiled code
+*.pyc
+*__pycache__/
+
+# build
+build/
+env/
+dist/
+eggs/
+*.eggs/
+
+

.travis.yml

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+language: python
+python:
+  # We don't actually use the Travis Python, but this keeps it organized.
+  - "2.7"
+install:
+  # ensure that we have the full tag information available for version.py
+  - git fetch --tags
+  - sudo apt-get update
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda install -q conda=4.3.25
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+  # create environment and install dependencies
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy nose pip matplotlib coverage
+  - source activate test-environment
+  - conda install -c conda-forge aipy
+  - pip install coveralls
+  - pip install git+https://github.com/HERA-Team/pyuvdata.git
+  - pip install git+https://github.com/HERA-Team/omnical.git
+  - pip install git+https://github.com/HERA-Team/hera_cal.git
+  - pip install git+https://github.com/HERA-Team/linsolve.git
+  - python setup.py install
+
+before_script:
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
+  - sleep 3
+
+script: nosetests hera_pspec --with-coverage --cover-package=hera_pspec
+
+after_success:
+  - coveralls

LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2017, Hydrogen Epoch of Reionization Array (HERA)
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

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+include *.md
+include LICENSE
+include hera_pspec/VERSION
+include hera_pspec/GIT_INFO
+

README.md

@@ -1 +1,28 @@
-# hera_pspec
+# hera_pspec
+
+[![Build Status](https://travis-ci.org/HERA-Team/hera_pspec.svg?branch=master)](https://travis-ci.org/HERA-Team/hera_pspec)
+
+**hera_pspec description**
+
+## Installation
+
+### Code Dependencies
+
+* numpy >= 1.10
+* pyuvdata (`pip install pyuvdata` or use https://github.com/HERA-Team/pyuvdata.git)
+* aipy (```conda install -c conda-forge aipy```)
+* scipy >= 0.19
+* astropy >= 2.0
+
+For anaconda users, we suggest using conda to install astropy, numpy and scipy.
+
+### Installing hera_pspec
+Clone the repo using
+`git clone https://github.com/HERA-Team/hera_pspec.git`
+
+Navigate into the directory and run `python setup.py install`.
+
+## Package Details and Usage
+
+
+

hera_pspec/VERSION

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+0.0.0

hera_pspec/__init__.py

@@ -1 +1,9 @@
-import pspec
+"""
+__init__.py file for hera_pspec
+"""
+import version
+import conversions
+from dataset import DataSet
+import pspec as legacy # XXX: This will eventually be deprecated
+
+__version__ = version.version

hera_pspec/conversions.py

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+"""
+conversions.py
+--------
+
+Cosmological and instrumental
+conversion functions for hera_pspec
+
+
+"""
+import numpy as np
+from scipy import integrate
+try:
+    from astropy.cosmology import LambdaCDM
+    _astropy = True
+except:
+    print("could not import astropy")
+    _astropy = False
+
+
+class units:
+    """
+    fundamental constants and conversion constants
+    in ** SI ** units
+
+    c : speed of light m s-1
+    ckm : speed of light in km s-1
+    kb : boltzmann constant 2 kg s-2 K-1
+    hp : planck constant m2 kg s-1
+    sb : stefan-boltzmann constant W m-2 K-4
+    f21 : 21cm frequency in Hz
+    w21 : 21cm wavelength in meters
+    """
+    c = 2.99792458e8  # speed of light in m s-1
+    ckm = c / 1e3  # speed of light in km s-1
+    G = 6.67408e-11  # Newton constant m3 kg-1 s-2
+    kb = 1.38064852e-23  # boltzmann constant m2 kg s-2 K-1
+    hp = 6.62607004e-34  # planck constant m2 kg s-1
+    sb = 5.670367e-8  # stefan boltzmann constant W m-2 K-4
+    f21 = 1.420405751e9  # frequency of 21cm transition in Hz
+    w21 = 0.211061140542  # 21cm wavelength in meters
+    H0_to_SI = 3.24078e-20 # km s-1 Mpc-1 to s-1
+
+class Cosmo_Conversions(object):
+    """
+    Cosmo_Conversions class for mathematical conversion functions,
+    some of which require a cosmological model, others of which
+    do not require a predefined cosmology.
+
+    Default parameter values are Planck 2015 TT,TE,EE+lowP.
+    (Table 4 of https://doi.org/10.1051/0004-6361/201525830)
+
+    Distance measures come from:
+    Hogg 1999 (astro-ph/9905116)
+    Furlanetto 2006 (2006PhR...433..181F)
+
+    Note that all distance measures are by default in h-1 Mpc,
+    because the default H0 = 100 km / sec / Mpc. If the user
+    changes the input H0, distance measures are in Mpc.
+    """
+    # astropy load attribute
+    _astropy = _astropy
+
+    def __init__(self, Om_L=0.68440, Om_b=0.04911, Om_c=0.26442, H0=100.0,
+                 Om_M=None, Om_k=None):
+        """
+
+
+        Default parameter values are Planck 2015 TT,TE,EE+lowP.
+        (Table 4 of https://doi.org/10.1051/0004-6361/201525830)
+
+        Parameters:
+        -----------
+        Om_L : float, Omega Lambda naught, default=0.68440
+            cosmological constant energy density fraction at z=0
+
+        Om_b : float, Omega baryon naught, default=0.04911
+            baryon energy density fraction at z=0
+
+        Om_c : float, Omega cold dark matter naught, default=0.26442
+            cdm energy density fraction at z=0
+
+        H0 : float, Hubble constant, default=67.31 km s-1 Mpc-1
+
+        Om_M : float, Omega matter naught, default=None [optional]
+            matter energy density faction at z=0
+
+        Om_k : float, Omega curvature naught, default=None [optional]
+            curvature energy density at z=0
+
+        Notes:
+        ------
+        Note that all distance measures are by default in h-1 Mpc,
+        because the default H0 = 100 km / sec / Mpc. If the user
+        changes the input H0, the distance measures are in Mpc.
+        """
+        # Setup parameters
+        if Om_M is not None:
+            if np.isclose(Om_b + Om_c, Om_M, atol=1e-5) is False:
+                Om_b = Om_M * 0.156635
+                Om_c = Om_M * 0.843364
+        else:
+            Om_M = Om_b + Om_c
+
+        if Om_k is None:
+            Om_k = 1 - Om_L - Om_M
+
+        ### TODO add radiation component to class and to distance functions
+        self.Om_L = Om_L
+        self.Om_b = Om_b
+        self.Om_c = Om_c
+        self.Om_M = Om_M
+        self.Om_k = Om_k
+        self.H0 = H0
+        self.h = self.H0 / 100.0
+
+        if _astropy:
+            self.lcdm = LambdaCDM(H0=self.H0, Om0=self.Om_M, Ode0=self.Om_L)
+
+    def f2z(self, freq, ghz=False):
+        """
+        convert frequency to redshift for 21cm line
+
+        Parameters:
+        -----------
+        freq : frequency in Hz, type=float
+
+        ghz : boolean, if True: assume freq is GHz
+
+        Output:
+        -------
+        z : float
+            redshift
+        """
+        if ghz:
+            freq = freq * 1e9
+
+        return (units.f21 / freq - 1)
+
+    def z2f(self, z, ghz=False):
+        """
+        convert redshift to frequency in Hz for 21cm line
+
+        Parameters:
+        -----------
+        z : redshift, type=float
+
+        ghz: boolean, if True: convert to GHz
+
+        Output:
+        -------
+        freq : float
+            frequency in Hz
+        """
+        freq = units.f21 / (z + 1)
+        if ghz:
+            freq /= 1e9
+
+        return freq
+
+    def E(self, z):
+        """
+        ratio of hubble parameters: H(z) / H(z=0)
+        Hogg99 Eqn. 14
+
+        Parameters:
+        -----------
+        z : redshift, type=float
+        """
+        return np.sqrt(self.Om_M*(1+z)**3 + self.Om_k*(1+z)**2 + self.Om_L)
+
+    def DC(self, z):
+        """
+        line-of-sight comoving distance in Mpc
+        Hogg99 Eqn. 15
+
+        Parameters:
+        -----------
+        z : redshift, type=float
+        """
+        return integrate.quad(lambda z: 1/self.E(z), 0, z)[0] * units.ckm / self.H0 
+
+    def DM(self, z):
+        """
+        transverse comoving distance in Mpc
+        Hogg99 Eqn. 16
+
+        Parameters:
+        -----------
+        z : redshift, type=float
+        """
+        DH = units.ckm / self.H0
+        if self.Om_k > 0:
+            DM = DH * np.sinh(np.sqrt(self.Om_k) * self.DC(z) / DH) / np.sqrt(self.Om_k)
+        elif self.Om_k < 0:
+            DM = DH * np.sin(np.sqrt(np.abs(self.Om_k)) * self.DC(z) / DH) / np.sqrt(np.abs(self.Om_k))
+        else:
+            DM = self.DC(z)
+
+        return DM
+
+    def DA(self, z):
+        """
+        angular diameter (proper) distance in Mpc
+        Hogg99 Eqn. 18
+
+        Parameters:
+        -----------
+        z : redshift, type=float
+        """
+        return self.DM(z) / (1 + z)
+
+    def dRperp_dtheta(self, z):
+        """
+        conversion factor from angular size (radian) to transverse
+        comoving distance (Mpc) at a specific redshift: [Mpc / radians]
+
+        Parameters:
+        -----------
+        z : float, redshift
+        """
+        return self.DM(z) 
+
+    def dRpara_df(self, z, ghz=False):
+        """
+        conversion from frequency bandwidth to radial
+        comoving distance at a specific redshift: [Mpc / Hz]
+
+        Parameters:
+        -----------
+        z : float, redshift
+        ghz : convert output to [Mpc / GHz]
+        """
+        y = (1 + z)**2.0 / self.E(z) * units.ckm / self.H0 / units.f21
+        if ghz:
+            return y * 1e9
+        else:
+            return y
+
+    def X2Y(self, z):
+        """
+        Conversion from radians^2 Hz -> Mpc^3
+        at a specific redshift.
+
+        Parameters:
+        -----------
+        z : float, redshift
+
+        Notes:
+        ------
+        Calls Cosmo_Conversions.dRperp_dtheta() and Cosmo_Conversions.dRpara_df().
+        """
+        return self.dRperp_dtheta(z)**2 * self.dRpara_df(z)
+
+
+
+

hera_pspec/data/__init__.py

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+"""init file for hera_pspec/data/"""
+DATA_PATH = __path__[0]