add lots of cross-references

docs/pydl/changes.rst

@@ -15,6 +15,7 @@ pydl Changelog
 * Removed some code that is 100% redundant with astropy (*e.g.* ``angles_to_xyz()``).
 * Fixed bug in :func:`~pydl.pydlutils.mangle.set_use_caps` that was discovered on the IDL side.
 * Updated documentation of :func:`~pydl.pydlutils.mangle.read_fits_polygons`.
+* Added cross-references to classes, functions, etc.
 
 0.3.0 (2015-02-20)
 ------------------

docs/pydl/pydlutils.rst

@@ -31,6 +31,9 @@ API
 .. automodapi:: pydl.pydlutils.mangle
     :no-inheritance-diagram:
 
+.. automodapi:: pydl.pydlutils.math
+    :no-inheritance-diagram:
+
 .. automodapi:: pydl.pydlutils.misc
     :no-inheritance-diagram:
 

pydl/file_lines.py

@@ -12,14 +12,14 @@ def file_lines(path,compress=False):
 
     Parameters
     ----------
-    path : str or list of str
+    path : :class:`str` or :class:`list` of :class:`str`
         Path to a file.  Can be a list of paths.
-    compress : bool, optional
+    compress : :class:`bool`, optional
         If set to ``True``, assumes that all files in `path` are GZIP compressed.
 
     Returns
     -------
-    file_lines : int or list of int
+    file_lines : :class:`int` or :class:`list` of :class:`int`
         The number of lines in `path`.  Returns a list of lengths if a list of
         files is supplied.
 

pydl/pcomp.py

@@ -10,12 +10,12 @@ class pcomp(object):
 
     Parameters
     ----------
-    x : array_like
+    x : array-like
         A 2-D array with N rows and M columns.
-    standardize : bool, optional
+    standardize : :class:`bool`, optional
         If set to ``True``, the input data will have its mean subtracted off
         and will be scaled to unit variance.
-    covariance : bool, optional.
+    covariance : :class:`bool`, optional.
         If set to ``True``, the covariance matrix of the data will be used for
         the computation.  Otherwise the correlation matrix will be used.
 

pydl/pydlutils/bspline/bspline.py

@@ -11,24 +11,39 @@ class bspline(object):
 
     Parameters
     ----------
-    x
-    nord
-    npoly
-    bkpt
-    bkspread
-    verbose
+    x : :class:`numpy.ndarray`
+        The data.
+    nord : :class:`int`, optional
+        To be documented.
+    npoly : :class:`int`, optional
+        To be documented.
+    bkpt : :class:`numpy.ndarray`, optional
+        To be documented.
+    bkspread : :class:`float`, optional
+        To be documented.
+    verbose : :class:`bool`, optional.
+        If ``True`` print extra information.
 
     Attributes
     ----------
     breakpoints
+        To be documented.
     nord
+        To be documented.
     npoly
+        To be documented.
     mask
+        To be documented.
     coeff
+        To be documented.
     icoeff
+        To be documented.
     xmin
+        To be documented.
     xmax
+        To be documented.
     funcname
+        To be documented.
     """
     def __init__(self,x,nord=4,npoly=1,bkpt=None,bkspread=1.0,verbose=False,**kwargs):
         """Init creates an object whose attributes are similar to the
@@ -118,18 +133,18 @@ def fit(self,xdata,ydata,invvar,x2=None):
 
         Parameters
         ----------
-        xdata : ndarray
+        xdata : :class:`numpy.ndarray`
             Independent variable.
-        ydata : ndarray
+        ydata : :class:`numpy.ndarray`
             Dependent variable.
-        invvar : ndarray
+        invvar : :class:`numpy.ndarray`
             Inverse variance of `ydata`.
-        x2 : ndarray, optional
+        x2 : :class:`numpy.ndarray`, optional
             Orthogonal dependent variable for 2d fits.
 
         Returns
         -------
-        fit : tuple
+        fit : :func:`tuple`
             A tuple containing an integer error code, and the evaluation of the
             b-spline at the input values.  An error code of -2 is a failure,
             -1 indicates dropped breakpoints, 0 is success, and positive
@@ -196,14 +211,14 @@ def action(self,x,x2=None):
 
         Parameters
         ----------
-        x : ndarray
+        x : :class:`numpy.ndarray`
             Independent variable.
-        x2 : ndarray, optional
+        x2 : :class:`numpy.ndarray`, optional
             Orthogonal dependent variable for 2d fits.
 
         Returns
         -------
-        action : tuple
+        action : :func:`tuple`
             A tuple containing the b-spline action matrix; the 'lower' parameter,
             a list of pixel positions, each corresponding to the first
             occurence of position greater than breakpoint indx; and 'upper',
@@ -265,12 +280,12 @@ def intrv(self,x):
 
         Parameters
         ----------
-        x : ndarray
+        x : :class:`numpy.ndarray`
             Data values, assumed to be monotonically increasing.
 
         Returns
         -------
-        intrv : ndarray
+        intrv : :class:`numpy.ndarray`
             Position of array elements with respect to breakpoints.
         """
         gb = self.breakpoints[self.mask]
@@ -286,15 +301,19 @@ def intrv(self,x):
     #
     #
     def bsplvn(self,x,ileft):
-        """
+        """To be documented.
+
         Parameters
         ----------
-        x
-        ileft
+        x : :class:`numpy.ndarray`
+            To be documented.
+        ileft : :class:`int`
+            To be documented
 
         Returns
         -------
-        bsplvn
+        bsplvn : :class:`numpy.ndarray`
+            To be documented.
         """
         bkpt = self.breakpoints[self.mask]
         vnikx = np.zeros((x.size,self.nord),dtype=x.dtype)
@@ -323,22 +342,22 @@ def value(self,x,x2=None,action=None,lower=None,upper=None):
 
         Parameters
         ----------
-        x : ndarray
+        x : :class:`numpy.ndarray`
             Independent variable.
-        x2 : ndarray, optional
+        x2 : :class:`numpy.ndarray`, optional
             Orthogonal dependent variable for 2d fits.
-        action : ndarray, optional
+        action : :class:`numpy.ndarray`, optional
             Action matrix to use.  If not supplied it is calculated.
-        lower : ndarray, optional
+        lower : :class:`numpy.ndarray`, optional
             If the action parameter is supplied, this parameter must also
             be supplied.
-        upper : ndarray, optional
+        upper : :class:`numpy.ndarray`, optional
             If the action parameter is supplied, this parameter must also
             be supplied.
 
         Returns
         -------
-        value : tuple
+        value : :func:`tuple`
             A tuple containing the results of the bspline evaluation and a
             mask indicating where the evaluation was good.
         """
@@ -392,12 +411,12 @@ def maskpoints(self,err):
 
         Parameters
         ----------
-        err : ndarray
+        err : :class:`numpy.ndarray`
             The list of indexes returned by the cholesky routines.
 
         Returns
         -------
-        maskpoints : int
+        maskpoints : :class:`int`
             An integer indicating the results of the masking.  -1 indicates
             that the error points were successfully masked.  -2 indicates
             failure; the calculation should be aborted.

pydl/pydlutils/bspline/cholesky_band.py

@@ -7,17 +7,17 @@ def cholesky_band(l,mininf=0.0,verbose=False):
 
     Parameters
     ----------
-    l : ndarray
+    l : :class:`numpy.ndarray`
         A matrix on which to perform the Cholesky decomposition.
-    mininf : float, optional
+    mininf : :class:`float`, optional
         Entries in the `l` matrix are considered negative if they are less
         than this value (default 0.0).
-    verbose : bool, optional
+    verbose : :class:`bool`, optional
         If set to ``True``, print some debugging information.
 
     Returns
     -------
-    cholesky_band : tuple
+    cholesky_band : :func:`tuple`
         If problems were detected, the first item will be the index or
         indexes where the problem was detected, and the second item will simply
         be the input matrix.  If no problems were detected, the first item

pydl/pydlutils/bspline/cholesky_solve.py

@@ -5,14 +5,14 @@ def cholesky_solve(a,bb):
 
     Parameters
     ----------
-    a : ndarray
-        A in Ax=b.
-    bb : ndarray
-        b in Ax=b
+    a : :class:`numpy.ndarray`
+        :math:`A` in :math:`A x = b`.
+    bb : :class:`numpy.ndarray`
+        :math:`b` in :math:`A x = b`.
 
     Returns
     -------
-    cholesky_solve : tuple
+    cholesky_solve : :func:`tuple`
         A tuple containing the status and the result of the solution.  The
         status is always -1.
     """

pydl/pydlutils/bspline/iterfit.py

@@ -7,26 +7,26 @@ def iterfit(xdata,ydata,invvar=None,upper=5,lower=5,x2=None,maxiter=10,**kwargs)
 
     Parameters
     ----------
-    xdata : ndarray
+    xdata : :class:`numpy.ndarray`
         Independent variable.
-    ydata : ndarray
+    ydata : :class:`numpy.ndarray`
         Dependent variable.
-    invvar : ndarray
+    invvar : :class:`numpy.ndarray`
         Inverse variance of `ydata`.  If not set, it will be calculated based
         on the standard deviation.
-    upper : int or float
+    upper : :class:`int` or :class:`float`
         Upper rejection threshold in units of sigma, defaults to 5 sigma.
-    lower : int or float
+    lower : :class:`int` or :class:`float`
         Lower rejection threshold in units of sigma, defaults to 5 sigma.
-    x2 : ndarray, optional
+    x2 : :class:`numpy.ndarray`, optional
         Orthogonal dependent variable for 2d fits.
-    maxiter : int, optional
+    maxiter : :class:`int`, optional
         Maximum number of rejection iterations, default 10.  Set this to
         zero to disable rejection.
 
     Returns
     -------
-    iterfit : tuple
+    iterfit : :func:`tuple`
         A tuple containing the fitted bspline object and an output mask.
     """
     import numpy as np

pydl/pydlutils/cooling/read_ds_cooling.py

@@ -10,13 +10,13 @@ def read_ds_cooling(fname,logT=None):
     ----------
     fname : { 'm-00.cie', 'm-05.cie', 'm+05.cie', 'm-10.cie', 'm-15.cie', 'm-20.cie', 'm-30.cie', 'mzero.cie' }
         Name of the data file to read.
-    logT : ndarray, optional
+    logT : :class:`numpy.ndarray`, optional
         If provided, values will be interpolated to the provided values.  If
         not provided, the values in the data files will be returned.
 
     Returns
     -------
-    read_ds_cooling : tuple
+    read_ds_cooling : :func:`tuple`
         A tuple containing `logT` and `loglambda`, respectively.
 
     Raises

pydl/pydlutils/coord/SDSSMuNu.py

@@ -26,9 +26,9 @@ class SDSSMuNu(BaseCoordinateFrame):
 
     Parameters
     ----------
-    mu : Angle
+    mu : :class:`~astropy.coordinates.Angle`
         Angle corresponding to longitude measured along a stripe.
-    nu : Angle
+    nu : :class:`~astropy.coordinates.Angle`
         Angle corresponding to latitude measured perpendicular to a stripe.
 
     Notes

pydl/pydlutils/coord/munu_to_radec.py

@@ -7,6 +7,16 @@
 @frame_transform_graph.transform(FunctionTransform, SDSSMuNu, ICRS)
 def munu_to_radec(munu,icrs_frame):
     """Convert from SDSS great circle coordinates to equatorial coordinates.
+
+    Parameters
+    ----------
+    munu : :class:`~pydl.pydlutils.coord.SDSSMuNu`
+        SDSS great circle coordinates (mu, nu).
+
+    Returns
+    -------
+    munu_to_radec : :class:`~astropy.coordinates.ICRS`
+        Equatorial coordinates (RA, Dec).
     """
     from astropy import units as u
     import numpy as np

pydl/pydlutils/coord/radec_to_munu.py

@@ -7,6 +7,16 @@
 @frame_transform_graph.transform(FunctionTransform, ICRS, SDSSMuNu)
 def radec_to_munu(icrs_frame,munu):
     """Convert from equatorial coordinates to SDSS great circle coordinates.
+
+    Parameters
+    ----------
+    icrs_frame : :class:`~astropy.coordinates.ICRS`
+        Equatorial coordinates (RA, Dec).
+
+    Returns
+    -------
+    radec_to_munu : :class:`~pydl.pydlutils.coord.SDSSMuNu`
+        SDSS great circle coordinates (mu, nu).
     """
     from astropy import units as u
     import numpy as np

pydl/pydlutils/coord/stripe_to_eta.py

@@ -5,12 +5,12 @@ def stripe_to_eta(stripe):
 
     Parameters
     ----------
-    stripe : int or numpy.ndarray
+    stripe : :class:`int` or :class:`numpy.ndarray`
         SDSS Stripe number.
 
     Returns
     -------
-    stripe_to_eta : float or numpy.ndarray
+    stripe_to_eta : :class:`float` or :class:`numpy.ndarray`
         The eta value in the SDSS (lambda,eta) coordinate system.
     """
     stripe_sep = 2.5

pydl/pydlutils/coord/stripe_to_incl.py

@@ -5,12 +5,12 @@ def stripe_to_incl(stripe):
 
     Parameters
     ----------
-    stripe : int or numpy.ndarray
+    stripe : :class:`int` or :class:`numpy.ndarray`
         SDSS Stripe number.
 
     Returns
     -------
-    stripe_to_incl : float or numpy.ndarray
+    stripe_to_incl : :class:`float` or :class:`numpy.ndarray`
         Inclination of the stripe relative to the equator (Dec = 0).
     """
     from . import stripe_to_eta