From 7d7c631c6e2d1947b7ac64f2c30ad6680bb56060 Mon Sep 17 00:00:00 2001
From: Jordan Mirocha <mirochaj@gmail.com>
Date: Fri, 3 May 2013 13:33:37 -0600
Subject: [PATCH 1/4] Now using urllib for SDSS data retrieval, added routines
 to fetch ALFALFA catalog and spectra.

---
 astroquery/alfa/__init__.py        |   8 +
 astroquery/alfa/core.py            | 225 +++++++++++++++++++++++++++++
 astroquery/alfa/tests/__init__.py  |   0
 astroquery/alfa/tests/test_alfa.py |  16 ++
 4 files changed, 249 insertions(+)
 create mode 100644 astroquery/alfa/__init__.py
 create mode 100644 astroquery/alfa/core.py
 create mode 100644 astroquery/alfa/tests/__init__.py
 create mode 100644 astroquery/alfa/tests/test_alfa.py

diff --git a/astroquery/alfa/__init__.py b/astroquery/alfa/__init__.py
new file mode 100644
index 0000000000..23d87084a8
--- /dev/null
+++ b/astroquery/alfa/__init__.py
@@ -0,0 +1,8 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+"""
+ALFALFA Spectra Archive Query Tool
+-----------------------------------
+
+:Author: Jordan Mirocha (mirochaj@gmail.com)
+"""
+from .core import *
\ No newline at end of file
diff --git a/astroquery/alfa/core.py b/astroquery/alfa/core.py
new file mode 100644
index 0000000000..1abb843407
--- /dev/null
+++ b/astroquery/alfa/core.py
@@ -0,0 +1,225 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+"""
+
+core.py
+
+Author: Jordan Mirocha
+Affiliation: University of Colorado at Boulder
+Created on: Fri May  3 09:45:13 2013
+
+Description: 
+
+"""
+
+import urllib
+import numpy as np
+import numpy.ma as ma
+from astropy.io import fits
+from astropy import coordinates as coord
+
+ascii_prefix = "http://arecibo.tc.cornell.edu/hiarchive/alfalfa/spectraASCII"
+fits_prefix = "http://arecibo.tc.cornell.edu/hiarchive/alfalfa/spectraFITS"
+propert_path = "http://egg.astro.cornell.edu/alfalfa/data/a40files/a40.datafile1.csv"
+
+placeholder = -999999
+
+def get_catalog():
+    """
+    Download catalog of ALFALFA source properties.
+    
+    Returns
+    -------
+    Dictionary of results, each element is a masked array.
+    
+    """
+    
+    f = urllib.urlopen(propert_path)
+
+    # Read header
+    cols = f.readline().rstrip('\n').split(',')
+
+    catalog = {}
+    for col in cols:
+        catalog[col] = []
+
+    # Parse result
+    for line in f:
+        l = line.rstrip('\n').split(',')
+        for i, col in enumerate(cols):
+            item = l[i].strip()
+            if item == '\"\"':
+                catalog[col].append(placeholder)
+            elif item.isdigit():
+                catalog[col].append(int(item))
+            elif item.replace('.', '').isdigit():
+                catalog[col].append(float(item))
+            else:
+                catalog[col].append(item)
+        
+    # Mask out blank elements    
+    for col in cols:
+        mask = np.zeros(len(catalog[col]))
+        mask[np.array(catalog[col]) == placeholder] = 1
+        catalog[col] = ma.array(catalog[col], mask=mask)    
+        
+    # Make this globally available so we don't have to re-download it 
+    # again in this session 
+    global ALFALFACAT
+    ALFALFACAT = catalog
+    
+    return catalog
+    
+def get_spectrum(agc=None, ra=None, dec=None, unit=None, counterpart=False, 
+    ascii=False):
+    """
+    Download spectrum from ALFALFA catalogue.
+    
+    Parameters
+    ----------
+    agc : int
+        Identification number for object in ALFALFA catalog.
+    ra : float
+        Right ascension (degrees).
+    dec : float
+        Declination (degrees).
+    ascii : bool
+        Download spectrum from remote server in ASCII or FITS format?
+    counterpart : bool
+        Do supplied ra and dec refer to HI source or optical counterpart?
+        
+    Returns
+    -------
+    If ascii == False, returns Spectrum instance, which contains FITS hdulist
+    and properties for x and y axes. If ascii == True, returns a tuple of 4
+    arrays: velocity [km/s], frequency [MHz], flux density [mJy], and baseline 
+    fit [mJy], respectively.
+    
+    """
+        
+    if agc is not None: 
+        agc = str(agc).zfill(6)
+    else:
+        if ra is None and dec is None:
+            raise ValueError('Must supply ra and dec if agc=None!')
+        
+        try:
+            cat = ALFALFACAT
+        except NameError:
+            cat = get_catalog()    
+            
+        if not isinstance(ra, coord.angles.RA):
+            ra = coord.RA(ra, unit=unit)
+        if not isinstance(ra, coord.angles.Dec):    
+            dec = coord.Dec(dec, unit=unit)    
+        
+        # Use RA and DEC to find appropriate AGC
+        if counterpart:
+            ra_ref = cat['RAdeg_OC']
+            dec_ref = cat['DECdeg_OC']
+        else:
+            ra_ref = cat['RAdeg_HI']
+            dec_ref = cat['Decdeg_HI']
+        
+        dra = np.abs(ra_ref - ra.degrees) \
+            * np.cos(dec.degrees * np.pi / 180.)
+        ddec = np.abs(dec_ref - dec.degrees)
+        dr = np.sqrt(dra**2 + ddec**2)
+        
+        agc = cat['AGCNr'][np.argmin(dr)]
+                
+        print 'Found HI source %i %g arcseconds from supplied position.' \
+            % (agc, dr.min() * 3600.)        
+            
+    if ascii:
+        link = "%s/A%s.txt" % (ascii_prefix, agc)
+        f = urllib.urlopen(link)
+    
+        vel = []
+        freq = []
+        flux = []
+        baseline = [] 
+        for i, line in enumerate(f):
+            if i <= 30: continue
+            
+            data = line.split()
+            
+            vel.append(float(data[0]))
+            freq.append(float(data[1]))
+            flux.append(float(data[2]))
+            baseline.append(float(data[3]))
+        
+        f.close()
+            
+        return np.array(vel), np.array(freq), np.array(flux), np.array(baseline)
+      
+    link = "%s/A%s.fits" % (fits_prefix, agc)    
+    hdulist = fits.open(urllib.urlopen(link).url, ignore_missing_end=True)
+    return Spectrum(hdulist)    
+    
+def match_object(ra, dec, ra_ref, dec_ref):
+    """
+    Assumes everything is in degrees.  Supply ra and dec of single object being considered, as well as reference
+    arrays of RA and DEC for some sample.  Returns index of match in reference arrays.
+    """    
+            
+    
+    if min(dr) < maxsep: 
+        return np.argmin(dr)                      
+    else:
+        return placeholder        
+    
+
+class Spectrum:
+    def __init__(self, hdulist):
+        self.hdulist = hdulist
+        
+    @property
+    def hdr(self):
+        if not hasattr(self, '_hdr'):
+            for item in self.hdulist:
+                if item.name == 'PRIMARY':
+                    continue
+                break    
+            
+            self._hdr = {}  
+            for key in item.header.keys(): 
+                self._hdr[key] = self.header.get(key)
+                            
+        return self._hdr
+    
+    @property
+    def header(self):
+        return self.hdulist[0].header    
+        
+    @property
+    def xarr(self):
+        """ Return xarr in units of MHz. """
+        if not hasattr(self, '_xarr'):
+            for item in self.hdulist:
+                if item.name == 'PRIMARY':
+                    continue
+                break    
+                    
+            for i, col in enumerate(item.columns):
+                if col.name == 'FREQ':
+                    self._xarr = item.data[0][i]
+                    break
+            
+        return self._xarr
+        
+    @property
+    def data(self):
+        if not hasattr(self, '_data'):
+            for item in self.hdulist:
+                if item.name == 'PRIMARY':
+                    continue
+                break    
+                    
+            for i, col in enumerate(item.columns):
+                if col.name == 'FLUXDENS':
+                    self._data = item.data[0][i]
+                    break
+                    
+        return self._data
+        
+  
\ No newline at end of file
diff --git a/astroquery/alfa/tests/__init__.py b/astroquery/alfa/tests/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/astroquery/alfa/tests/test_alfa.py b/astroquery/alfa/tests/test_alfa.py
new file mode 100644
index 0000000000..1066553250
--- /dev/null
+++ b/astroquery/alfa/tests/test_alfa.py
@@ -0,0 +1,16 @@
+from astroquery import alfa
+
+# Test Case: A Seyfert 1 galaxy
+RA = '0h8m05.63s'
+DEC = '14d50m23.3s'
+
+def test_alfa_catalog():
+    cat = alfa.get_catalog()
+
+def test_alfa_spectrum():
+    sp = alfa.get_spectrum(ra=RA, dec=DEC, counterpart=True)
+
+if __name__ == '__main__':
+    test_alfa_catalog()
+    test_alfa_spectrum()
+    
\ No newline at end of file

From 94dc0325f0dce35b2e13cf65a8f68ea34d01b3aa Mon Sep 17 00:00:00 2001
From: Jordan Mirocha <mirochaj@gmail.com>
Date: Sat, 25 May 2013 15:01:07 -0600
Subject: [PATCH 2/4] Added to alfa docstring.

---
 astroquery/alfa/core.py            | 43 +++++++++++++++++++++---
 astroquery/sdss/__init__.py        |  2 +-
 astroquery/sdss/core.py            | 54 ++++++------------------------
 astroquery/sdss/tests/test_sdss.py |  4 +++
 4 files changed, 54 insertions(+), 49 deletions(-)

diff --git a/astroquery/alfa/core.py b/astroquery/alfa/core.py
index 1abb843407..9ed1d70f1d 100644
--- a/astroquery/alfa/core.py
+++ b/astroquery/alfa/core.py
@@ -27,12 +27,20 @@ def get_catalog():
     """
     Download catalog of ALFALFA source properties.
     
+    Notes
+    -----
+    This catalog has ~15,000 entries, so after it's downloaded, it is made
+    global to save some time later.
+    
     Returns
     -------
     Dictionary of results, each element is a masked array.
     
     """
     
+    if 'ALFALFACAT' in globals():
+        return ALFALFACAT
+    
     f = urllib.urlopen(propert_path)
 
     # Read header
@@ -87,6 +95,11 @@ def get_spectrum(agc=None, ra=None, dec=None, unit=None, counterpart=False,
     counterpart : bool
         Do supplied ra and dec refer to HI source or optical counterpart?
         
+    Notes
+    -----
+    If AGC number is not supplied, will download entire ALFALFA catalog and
+    do a cross-ID with supplied RA and DEC.     
+        
     Returns
     -------
     If ascii == False, returns Spectrum instance, which contains FITS hdulist
@@ -94,6 +107,10 @@ def get_spectrum(agc=None, ra=None, dec=None, unit=None, counterpart=False,
     arrays: velocity [km/s], frequency [MHz], flux density [mJy], and baseline 
     fit [mJy], respectively.
     
+    See Also
+    --------
+    get_catalog : method that downloads ALFALFA catalog
+    
     """
         
     if agc is not None: 
@@ -127,7 +144,7 @@ def get_spectrum(agc=None, ra=None, dec=None, unit=None, counterpart=False,
         
         agc = cat['AGCNr'][np.argmin(dr)]
                 
-        print 'Found HI source %i %g arcseconds from supplied position.' \
+        print 'Found HI source AGC #%i %g arcseconds from supplied position.' \
             % (agc, dr.min() * 3600.)        
             
     if ascii:
@@ -192,9 +209,9 @@ def header(self):
         return self.hdulist[0].header    
         
     @property
-    def xarr(self):
+    def freq(self):
         """ Return xarr in units of MHz. """
-        if not hasattr(self, '_xarr'):
+        if not hasattr(self, '_freq'):
             for item in self.hdulist:
                 if item.name == 'PRIMARY':
                     continue
@@ -202,10 +219,26 @@ def xarr(self):
                     
             for i, col in enumerate(item.columns):
                 if col.name == 'FREQ':
-                    self._xarr = item.data[0][i]
+                    self._freq = item.data[0][i]
+                    break
+            
+        return self._freq
+    
+    @property
+    def varr(self):
+        """ Return xarr in units of helio-centric velocity (km/s). """
+        if not hasattr(self, '_varr'):
+            for item in self.hdulist:
+                if item.name == 'PRIMARY':
+                    continue
+                break    
+                    
+            for i, col in enumerate(item.columns):
+                if col.name == 'VHELIO':
+                    self._varr = item.data[0][i]
                     break
             
-        return self._xarr
+        return self._varr
         
     @property
     def data(self):
diff --git a/astroquery/sdss/__init__.py b/astroquery/sdss/__init__.py
index 311403c6db..fe3bd70c93 100644
--- a/astroquery/sdss/__init__.py
+++ b/astroquery/sdss/__init__.py
@@ -5,4 +5,4 @@
 
 :Author: Jordan Mirocha (mirochaj@gmail.com)
 """
-from core import *
+from .core import *
diff --git a/astroquery/sdss/core.py b/astroquery/sdss/core.py
index 8cee6b366b..998cb0ec6b 100644
--- a/astroquery/sdss/core.py
+++ b/astroquery/sdss/core.py
@@ -15,8 +15,8 @@
 
 import numpy as np
 import astropy.wcs as wcs
-import os, re, sqlcl, math
 from astropy.io import fits
+import re, sqlcl, math, urllib
 from astropy import coordinates as coord
 
 # Default photometric and spectroscopic quantities to retrieve.
@@ -35,7 +35,7 @@
      'qso_bright': 32 
      }
 
-# Some website prefixes we need          
+# Some website prefixes we need
 spectro1d_prefix = 'http://das.sdss.org/spectro/1d_26'
 images_prefix = 'http://das.sdss.org/www/cgi-bin/drC'
 template_prefix = 'http://www.sdss.org/dr5/algorithms/spectemplates/spDR2'
@@ -161,10 +161,6 @@ def get_spectrum(crossID=None, plate=None, fiberID=None, mjd=None):
     well as the FITS header in dictionary form.
     """
     
-    safe_to_rm = True
-    if os.path.exists('spectro'):
-        safe_to_rm = False
-    
     if crossID is not None:
         plate = crossID['plate']
         fiberID = crossID['fiberID']
@@ -173,17 +169,11 @@ def get_spectrum(crossID=None, plate=None, fiberID=None, mjd=None):
     plate = str(plate).zfill(4)
     fiber = str(fiberID).zfill(3)
     mjd = str(mjd)        
-    web = '%s/%s/1d/spSpec-%s-%s-%s.fit' % (spectro1d_prefix, plate, mjd, 
+    link = '%s/%s/1d/spSpec-%s-%s-%s.fit' % (spectro1d_prefix, plate, mjd, 
         plate, fiber)
-    
-    os.system('wget -x -nH -nv -q %s' % web)
-    
-    hdulist = fits.open('spectro/1d_26/%s/1d/spSpec-%s-%s-%s.fit' % (plate, 
-        mjd, plate, fiber), ignore_missing_end=True)
-          
-    if safe_to_rm:        
-        os.system('rm -rf spectro')
-    
+              
+    hdulist = fits.open(urllib.urlopen(link).url, ignore_missing_end=True)
+
     return Spectrum(hdulist)
             
 def get_image(crossID=None, run=None, rerun=None, camcol=None, 
@@ -221,10 +211,6 @@ def get_image(crossID=None, run=None, rerun=None, camcol=None,
     header in dictionary form.
     """   
     
-    safe_to_rm = True
-    if os.path.exists('imaging') or os.path.exists('www'):
-        safe_to_rm = False
-            
     if crossID is not None:
         run = crossID['run']
         rerun = crossID['rerun']
@@ -238,18 +224,9 @@ def get_image(crossID=None, run=None, rerun=None, camcol=None,
     # Download and read in image data
     link = '%s?RUN=%i&RERUN=%i&CAMCOL=%i&FIELD=%s&FILTER=%s' % (images_prefix, 
         run, rerun, camcol, field, band)            
-    path_to_img = 'www/cgi-bin/drC?RUN=%i&RERUN=%i&CAMCOL=%i&FIELD=%s&FILTER=%s' % (run, 
-        rerun, camcol, field, band)
-                
-    os.system('wget -x -nH -nv -q \'%s\'' % link)
-    
-    hdulist = fits.open(path_to_img, ignore_missing_end=True) 
- 
-    # Erase download directory tree   
-    if safe_to_rm: 
-        os.system('rm -rf www')    
-        os.system('rm -rf imaging')    
-    
+
+    hdulist = fits.open(urllib.urlopen(link).url, ignore_missing_end=True)
+     
     return Image(hdulist)
     
 def get_spectral_template(kind='qso'):
@@ -283,13 +260,8 @@ def get_spectral_template(kind='qso'):
     available for some spectral types.
     """   
     
-    safe_to_rm = True
-    if os.path.exists('dr5'):
-        safe_to_rm = False
-    
     if kind == 'all':
         indices = list(np.arange(33))
-    
     else:    
         indices = spec_templates[kind]
         if type(indices) is not list:
@@ -298,15 +270,11 @@ def get_spectral_template(kind='qso'):
     spectra = []
     for index in indices:
         name = str(index).zfill(3)
-        web = '%s-%s.fit' % (template_prefix, name)        
-        os.system('wget -x -nH -nv -q %s' % web)
-        hdulist = fits.open('dr5/algorithms/spectemplates/spDR2-%s.fit' % name) 
+        link = '%s-%s.fit' % (template_prefix, name)        
+        hdulist = fits.open(urllib.urlopen(link).url, ignore_missing_end=True)
         spectra.append(Spectrum(hdulist)) 
         del hdulist
                 
-    if safe_to_rm:
-        os.system('rm -rf dr5')
-    
     return spectra
     
 class Spectrum:
diff --git a/astroquery/sdss/tests/test_sdss.py b/astroquery/sdss/tests/test_sdss.py
index 4ed08b52af..751ad484b0 100644
--- a/astroquery/sdss/tests/test_sdss.py
+++ b/astroquery/sdss/tests/test_sdss.py
@@ -12,7 +12,11 @@ def test_sdss_image():
     xid = sdss.crossID(ra=RA, dec=DEC)
     img = sdss.get_image(crossID=xid[0])
     
+def test_sdss_template():
+    template = sdss.get_spectral_template('qso')
+    
 if __name__ == '__main__':
     test_sdss_spectrum()
     test_sdss_image()
+    test_sdss_template()
     
\ No newline at end of file

From fde9fc1ca50cc25a57d73cf38eae9845bbc00c08 Mon Sep 17 00:00:00 2001
From: Jordan Mirocha <mirochaj@gmail.com>
Date: Fri, 3 May 2013 13:33:37 -0600
Subject: [PATCH 3/4] Now using urllib for SDSS data retrieval, added routines
 to fetch ALFALFA catalog and spectra.

---
 astroquery/alfa/__init__.py        |   8 +
 astroquery/alfa/core.py            | 225 +++++++++++++++++++++++++++++
 astroquery/alfa/tests/__init__.py  |   0
 astroquery/alfa/tests/test_alfa.py |  16 ++
 4 files changed, 249 insertions(+)
 create mode 100644 astroquery/alfa/__init__.py
 create mode 100644 astroquery/alfa/core.py
 create mode 100644 astroquery/alfa/tests/__init__.py
 create mode 100644 astroquery/alfa/tests/test_alfa.py

diff --git a/astroquery/alfa/__init__.py b/astroquery/alfa/__init__.py
new file mode 100644
index 0000000000..23d87084a8
--- /dev/null
+++ b/astroquery/alfa/__init__.py
@@ -0,0 +1,8 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+"""
+ALFALFA Spectra Archive Query Tool
+-----------------------------------
+
+:Author: Jordan Mirocha (mirochaj@gmail.com)
+"""
+from .core import *
\ No newline at end of file
diff --git a/astroquery/alfa/core.py b/astroquery/alfa/core.py
new file mode 100644
index 0000000000..1abb843407
--- /dev/null
+++ b/astroquery/alfa/core.py
@@ -0,0 +1,225 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+"""
+
+core.py
+
+Author: Jordan Mirocha
+Affiliation: University of Colorado at Boulder
+Created on: Fri May  3 09:45:13 2013
+
+Description: 
+
+"""
+
+import urllib
+import numpy as np
+import numpy.ma as ma
+from astropy.io import fits
+from astropy import coordinates as coord
+
+ascii_prefix = "http://arecibo.tc.cornell.edu/hiarchive/alfalfa/spectraASCII"
+fits_prefix = "http://arecibo.tc.cornell.edu/hiarchive/alfalfa/spectraFITS"
+propert_path = "http://egg.astro.cornell.edu/alfalfa/data/a40files/a40.datafile1.csv"
+
+placeholder = -999999
+
+def get_catalog():
+    """
+    Download catalog of ALFALFA source properties.
+    
+    Returns
+    -------
+    Dictionary of results, each element is a masked array.
+    
+    """
+    
+    f = urllib.urlopen(propert_path)
+
+    # Read header
+    cols = f.readline().rstrip('\n').split(',')
+
+    catalog = {}
+    for col in cols:
+        catalog[col] = []
+
+    # Parse result
+    for line in f:
+        l = line.rstrip('\n').split(',')
+        for i, col in enumerate(cols):
+            item = l[i].strip()
+            if item == '\"\"':
+                catalog[col].append(placeholder)
+            elif item.isdigit():
+                catalog[col].append(int(item))
+            elif item.replace('.', '').isdigit():
+                catalog[col].append(float(item))
+            else:
+                catalog[col].append(item)
+        
+    # Mask out blank elements    
+    for col in cols:
+        mask = np.zeros(len(catalog[col]))
+        mask[np.array(catalog[col]) == placeholder] = 1
+        catalog[col] = ma.array(catalog[col], mask=mask)    
+        
+    # Make this globally available so we don't have to re-download it 
+    # again in this session 
+    global ALFALFACAT
+    ALFALFACAT = catalog
+    
+    return catalog
+    
+def get_spectrum(agc=None, ra=None, dec=None, unit=None, counterpart=False, 
+    ascii=False):
+    """
+    Download spectrum from ALFALFA catalogue.
+    
+    Parameters
+    ----------
+    agc : int
+        Identification number for object in ALFALFA catalog.
+    ra : float
+        Right ascension (degrees).
+    dec : float
+        Declination (degrees).
+    ascii : bool
+        Download spectrum from remote server in ASCII or FITS format?
+    counterpart : bool
+        Do supplied ra and dec refer to HI source or optical counterpart?
+        
+    Returns
+    -------
+    If ascii == False, returns Spectrum instance, which contains FITS hdulist
+    and properties for x and y axes. If ascii == True, returns a tuple of 4
+    arrays: velocity [km/s], frequency [MHz], flux density [mJy], and baseline 
+    fit [mJy], respectively.
+    
+    """
+        
+    if agc is not None: 
+        agc = str(agc).zfill(6)
+    else:
+        if ra is None and dec is None:
+            raise ValueError('Must supply ra and dec if agc=None!')
+        
+        try:
+            cat = ALFALFACAT
+        except NameError:
+            cat = get_catalog()    
+            
+        if not isinstance(ra, coord.angles.RA):
+            ra = coord.RA(ra, unit=unit)
+        if not isinstance(ra, coord.angles.Dec):    
+            dec = coord.Dec(dec, unit=unit)    
+        
+        # Use RA and DEC to find appropriate AGC
+        if counterpart:
+            ra_ref = cat['RAdeg_OC']
+            dec_ref = cat['DECdeg_OC']
+        else:
+            ra_ref = cat['RAdeg_HI']
+            dec_ref = cat['Decdeg_HI']
+        
+        dra = np.abs(ra_ref - ra.degrees) \
+            * np.cos(dec.degrees * np.pi / 180.)
+        ddec = np.abs(dec_ref - dec.degrees)
+        dr = np.sqrt(dra**2 + ddec**2)
+        
+        agc = cat['AGCNr'][np.argmin(dr)]
+                
+        print 'Found HI source %i %g arcseconds from supplied position.' \
+            % (agc, dr.min() * 3600.)        
+            
+    if ascii:
+        link = "%s/A%s.txt" % (ascii_prefix, agc)
+        f = urllib.urlopen(link)
+    
+        vel = []
+        freq = []
+        flux = []
+        baseline = [] 
+        for i, line in enumerate(f):
+            if i <= 30: continue
+            
+            data = line.split()
+            
+            vel.append(float(data[0]))
+            freq.append(float(data[1]))
+            flux.append(float(data[2]))
+            baseline.append(float(data[3]))
+        
+        f.close()
+            
+        return np.array(vel), np.array(freq), np.array(flux), np.array(baseline)
+      
+    link = "%s/A%s.fits" % (fits_prefix, agc)    
+    hdulist = fits.open(urllib.urlopen(link).url, ignore_missing_end=True)
+    return Spectrum(hdulist)    
+    
+def match_object(ra, dec, ra_ref, dec_ref):
+    """
+    Assumes everything is in degrees.  Supply ra and dec of single object being considered, as well as reference
+    arrays of RA and DEC for some sample.  Returns index of match in reference arrays.
+    """    
+            
+    
+    if min(dr) < maxsep: 
+        return np.argmin(dr)                      
+    else:
+        return placeholder        
+    
+
+class Spectrum:
+    def __init__(self, hdulist):
+        self.hdulist = hdulist
+        
+    @property
+    def hdr(self):
+        if not hasattr(self, '_hdr'):
+            for item in self.hdulist:
+                if item.name == 'PRIMARY':
+                    continue
+                break    
+            
+            self._hdr = {}  
+            for key in item.header.keys(): 
+                self._hdr[key] = self.header.get(key)
+                            
+        return self._hdr
+    
+    @property
+    def header(self):
+        return self.hdulist[0].header    
+        
+    @property
+    def xarr(self):
+        """ Return xarr in units of MHz. """
+        if not hasattr(self, '_xarr'):
+            for item in self.hdulist:
+                if item.name == 'PRIMARY':
+                    continue
+                break    
+                    
+            for i, col in enumerate(item.columns):
+                if col.name == 'FREQ':
+                    self._xarr = item.data[0][i]
+                    break
+            
+        return self._xarr
+        
+    @property
+    def data(self):
+        if not hasattr(self, '_data'):
+            for item in self.hdulist:
+                if item.name == 'PRIMARY':
+                    continue
+                break    
+                    
+            for i, col in enumerate(item.columns):
+                if col.name == 'FLUXDENS':
+                    self._data = item.data[0][i]
+                    break
+                    
+        return self._data
+        
+  
\ No newline at end of file
diff --git a/astroquery/alfa/tests/__init__.py b/astroquery/alfa/tests/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/astroquery/alfa/tests/test_alfa.py b/astroquery/alfa/tests/test_alfa.py
new file mode 100644
index 0000000000..1066553250
--- /dev/null
+++ b/astroquery/alfa/tests/test_alfa.py
@@ -0,0 +1,16 @@
+from astroquery import alfa
+
+# Test Case: A Seyfert 1 galaxy
+RA = '0h8m05.63s'
+DEC = '14d50m23.3s'
+
+def test_alfa_catalog():
+    cat = alfa.get_catalog()
+
+def test_alfa_spectrum():
+    sp = alfa.get_spectrum(ra=RA, dec=DEC, counterpart=True)
+
+if __name__ == '__main__':
+    test_alfa_catalog()
+    test_alfa_spectrum()
+    
\ No newline at end of file

From f9717c3a15ffec78184bb0cae1f8d3e16957d7b2 Mon Sep 17 00:00:00 2001
From: Jordan Mirocha <mirochaj@gmail.com>
Date: Sat, 25 May 2013 15:01:07 -0600
Subject: [PATCH 4/4] Added to alfa docstring.

---
 astroquery/alfa/core.py            | 43 +++++++++++++++++++++---
 astroquery/sdss/__init__.py        |  2 +-
 astroquery/sdss/core.py            | 53 +++++++-----------------------
 astroquery/sdss/tests/test_sdss.py |  4 +++
 4 files changed, 54 insertions(+), 48 deletions(-)

diff --git a/astroquery/alfa/core.py b/astroquery/alfa/core.py
index 1abb843407..9ed1d70f1d 100644
--- a/astroquery/alfa/core.py
+++ b/astroquery/alfa/core.py
@@ -27,12 +27,20 @@ def get_catalog():
     """
     Download catalog of ALFALFA source properties.
     
+    Notes
+    -----
+    This catalog has ~15,000 entries, so after it's downloaded, it is made
+    global to save some time later.
+    
     Returns
     -------
     Dictionary of results, each element is a masked array.
     
     """
     
+    if 'ALFALFACAT' in globals():
+        return ALFALFACAT
+    
     f = urllib.urlopen(propert_path)
 
     # Read header
@@ -87,6 +95,11 @@ def get_spectrum(agc=None, ra=None, dec=None, unit=None, counterpart=False,
     counterpart : bool
         Do supplied ra and dec refer to HI source or optical counterpart?
         
+    Notes
+    -----
+    If AGC number is not supplied, will download entire ALFALFA catalog and
+    do a cross-ID with supplied RA and DEC.     
+        
     Returns
     -------
     If ascii == False, returns Spectrum instance, which contains FITS hdulist
@@ -94,6 +107,10 @@ def get_spectrum(agc=None, ra=None, dec=None, unit=None, counterpart=False,
     arrays: velocity [km/s], frequency [MHz], flux density [mJy], and baseline 
     fit [mJy], respectively.
     
+    See Also
+    --------
+    get_catalog : method that downloads ALFALFA catalog
+    
     """
         
     if agc is not None: 
@@ -127,7 +144,7 @@ def get_spectrum(agc=None, ra=None, dec=None, unit=None, counterpart=False,
         
         agc = cat['AGCNr'][np.argmin(dr)]
                 
-        print 'Found HI source %i %g arcseconds from supplied position.' \
+        print 'Found HI source AGC #%i %g arcseconds from supplied position.' \
             % (agc, dr.min() * 3600.)        
             
     if ascii:
@@ -192,9 +209,9 @@ def header(self):
         return self.hdulist[0].header    
         
     @property
-    def xarr(self):
+    def freq(self):
         """ Return xarr in units of MHz. """
-        if not hasattr(self, '_xarr'):
+        if not hasattr(self, '_freq'):
             for item in self.hdulist:
                 if item.name == 'PRIMARY':
                     continue
@@ -202,10 +219,26 @@ def xarr(self):
                     
             for i, col in enumerate(item.columns):
                 if col.name == 'FREQ':
-                    self._xarr = item.data[0][i]
+                    self._freq = item.data[0][i]
+                    break
+            
+        return self._freq
+    
+    @property
+    def varr(self):
+        """ Return xarr in units of helio-centric velocity (km/s). """
+        if not hasattr(self, '_varr'):
+            for item in self.hdulist:
+                if item.name == 'PRIMARY':
+                    continue
+                break    
+                    
+            for i, col in enumerate(item.columns):
+                if col.name == 'VHELIO':
+                    self._varr = item.data[0][i]
                     break
             
-        return self._xarr
+        return self._varr
         
     @property
     def data(self):
diff --git a/astroquery/sdss/__init__.py b/astroquery/sdss/__init__.py
index 311403c6db..fe3bd70c93 100644
--- a/astroquery/sdss/__init__.py
+++ b/astroquery/sdss/__init__.py
@@ -5,4 +5,4 @@
 
 :Author: Jordan Mirocha (mirochaj@gmail.com)
 """
-from core import *
+from .core import *
diff --git a/astroquery/sdss/core.py b/astroquery/sdss/core.py
index dedfeba286..68295e233b 100644
--- a/astroquery/sdss/core.py
+++ b/astroquery/sdss/core.py
@@ -17,6 +17,7 @@
 import astropy.wcs as wcs
 import os, re, math
 from astropy.io import fits
+import re, sqlcl, math, urllib
 from astropy import coordinates as coord
 from . import sqlcl
 
@@ -36,7 +37,7 @@
      'qso_bright': 32 
      }
 
-# Some website prefixes we need          
+# Some website prefixes we need
 spectro1d_prefix = 'http://das.sdss.org/spectro/1d_26'
 images_prefix = 'http://das.sdss.org/www/cgi-bin/drC'
 template_prefix = 'http://www.sdss.org/dr5/algorithms/spectemplates/spDR2'
@@ -162,10 +163,6 @@ def get_spectrum(crossID=None, plate=None, fiberID=None, mjd=None):
     well as the FITS header in dictionary form.
     """
     
-    safe_to_rm = True
-    if os.path.exists('spectro'):
-        safe_to_rm = False
-    
     if crossID is not None:
         plate = crossID['plate']
         fiberID = crossID['fiberID']
@@ -174,17 +171,11 @@ def get_spectrum(crossID=None, plate=None, fiberID=None, mjd=None):
     plate = str(plate).zfill(4)
     fiber = str(fiberID).zfill(3)
     mjd = str(mjd)        
-    web = '%s/%s/1d/spSpec-%s-%s-%s.fit' % (spectro1d_prefix, plate, mjd, 
+    link = '%s/%s/1d/spSpec-%s-%s-%s.fit' % (spectro1d_prefix, plate, mjd, 
         plate, fiber)
-    
-    os.system('wget -x -nH -nv -q %s' % web)
-    
-    hdulist = fits.open('spectro/1d_26/%s/1d/spSpec-%s-%s-%s.fit' % (plate, 
-        mjd, plate, fiber), ignore_missing_end=True)
-          
-    if safe_to_rm:        
-        os.system('rm -rf spectro')
-    
+              
+    hdulist = fits.open(urllib.urlopen(link).url, ignore_missing_end=True)
+
     return Spectrum(hdulist)
             
 def get_image(crossID=None, run=None, rerun=None, camcol=None, 
@@ -222,10 +213,6 @@ def get_image(crossID=None, run=None, rerun=None, camcol=None,
     header in dictionary form.
     """   
     
-    safe_to_rm = True
-    if os.path.exists('imaging') or os.path.exists('www'):
-        safe_to_rm = False
-            
     if crossID is not None:
         run = crossID['run']
         rerun = crossID['rerun']
@@ -239,18 +226,9 @@ def get_image(crossID=None, run=None, rerun=None, camcol=None,
     # Download and read in image data
     link = '%s?RUN=%i&RERUN=%i&CAMCOL=%i&FIELD=%s&FILTER=%s' % (images_prefix, 
         run, rerun, camcol, field, band)            
-    path_to_img = 'www/cgi-bin/drC?RUN=%i&RERUN=%i&CAMCOL=%i&FIELD=%s&FILTER=%s' % (run, 
-        rerun, camcol, field, band)
-                
-    os.system('wget -x -nH -nv -q \'%s\'' % link)
-    
-    hdulist = fits.open(path_to_img, ignore_missing_end=True) 
- 
-    # Erase download directory tree   
-    if safe_to_rm: 
-        os.system('rm -rf www')    
-        os.system('rm -rf imaging')    
-    
+
+    hdulist = fits.open(urllib.urlopen(link).url, ignore_missing_end=True)
+     
     return Image(hdulist)
     
 def get_spectral_template(kind='qso'):
@@ -284,13 +262,8 @@ def get_spectral_template(kind='qso'):
     available for some spectral types.
     """   
     
-    safe_to_rm = True
-    if os.path.exists('dr5'):
-        safe_to_rm = False
-    
     if kind == 'all':
         indices = list(np.arange(33))
-    
     else:    
         indices = spec_templates[kind]
         if type(indices) is not list:
@@ -299,15 +272,11 @@ def get_spectral_template(kind='qso'):
     spectra = []
     for index in indices:
         name = str(index).zfill(3)
-        web = '%s-%s.fit' % (template_prefix, name)        
-        os.system('wget -x -nH -nv -q %s' % web)
-        hdulist = fits.open('dr5/algorithms/spectemplates/spDR2-%s.fit' % name) 
+        link = '%s-%s.fit' % (template_prefix, name)        
+        hdulist = fits.open(urllib.urlopen(link).url, ignore_missing_end=True)
         spectra.append(Spectrum(hdulist)) 
         del hdulist
                 
-    if safe_to_rm:
-        os.system('rm -rf dr5')
-    
     return spectra
     
 class Spectrum:
diff --git a/astroquery/sdss/tests/test_sdss.py b/astroquery/sdss/tests/test_sdss.py
index 4ed08b52af..751ad484b0 100644
--- a/astroquery/sdss/tests/test_sdss.py
+++ b/astroquery/sdss/tests/test_sdss.py
@@ -12,7 +12,11 @@ def test_sdss_image():
     xid = sdss.crossID(ra=RA, dec=DEC)
     img = sdss.get_image(crossID=xid[0])
     
+def test_sdss_template():
+    template = sdss.get_spectral_template('qso')
+    
 if __name__ == '__main__':
     test_sdss_spectrum()
     test_sdss_image()
+    test_sdss_template()
     
\ No newline at end of file