Merge pull request #14 from kadrlica/mlab

Replacing mlab.rec_append_field

ugali/analysis/search.py

@@ -14,13 +14,12 @@
 import numpy
 import numpy.lib.recfunctions as recfuncs
 import scipy.ndimage as ndimage
-from matplotlib import mlab
 
 from ugali.utils.shell import mkdir, which
 from ugali.utils.logger import logger
 from ugali.utils.binning import reverseHistogram
 from ugali.utils.projector import Projector,gal2cel,cel2gal,dec2hms,dec2dms,mod2dist
-from ugali.utils import healpix
+from ugali.utils import healpix, mlab
 from ugali.utils.healpix import pix2ang, ang2pix
 from ugali.candidate.associate import SourceCatalog, catalogFactory
 from ugali.utils.config import Config

ugali/observation/catalog.py

@@ -4,7 +4,6 @@
 import numpy as np
 import fitsio
 import copy
-from matplotlib import mlab
 
 import ugali.utils.projector
 
@@ -13,6 +12,7 @@
 from ugali.utils.healpix import ang2pix,superpixel
 from ugali.utils.logger import logger
 from ugali.utils.fileio import load_infiles
+from ugali.utils import mlab
 
 class Catalog:
 

ugali/preprocess/pixelize.py

@@ -14,12 +14,11 @@
 import numpy as np
 import numpy.lib.recfunctions as recfuncs
 import healpy as hp
-from matplotlib import mlab
 
 #import ugali.utils.binning
 #import ugali.utils.skymap
 from ugali.utils.projector import cel2gal, gal2cel
-from ugali.utils import healpix
+from ugali.utils import healpix, mlab
 from ugali.utils.healpix import ang2pix, pix2ang, superpixel
 
 from ugali.utils.shell import mkdir

ugali/simulation/analyzer.py

@@ -12,7 +12,6 @@
 import healpy
 import numpy.lib.recfunctions as recfuncs
 import fitsio
-from matplotlib import mlab
 
 import ugali.observation.catalog
 import ugali.observation.mask
@@ -25,6 +24,7 @@
 from ugali.utils.healpix import ang2pix, pix2ang
 from ugali.utils.logger import logger
 from ugali.utils.config import Config
+from ugali.utils import mlab
 
 class Analyzer(object):
     """

ugali/simulation/simulator.py

@@ -389,7 +389,7 @@ def toy_background(self,mc_source_id=2,seed=None):
         mc_source_id = mc_source_id * np.ones(len(mag_1))
 
         select = (mag_lim_1>mag_1)&(mag_lim_2>mag_2)
-        
+
         hdu = ugali.observation.catalog.makeHDU(self.config,mag_1[select],mag_err_1[select],
                                                 mag_2[select],mag_err_2[select],
                                                 lon[select],lat[select],mc_source_id[select])
@@ -629,7 +629,8 @@ def makeHDU(self, mag_1, mag_err_1, mag_2, mag_err_2, lon, lat, mc_source_id):
         """
         Create a catalog fits file object based on input data.
 
-        ADW: This should be combined with the write_membership function of loglike.
+        ADW: This should be combined with the write_membership
+        function of loglike.
         """
         if self.config['catalog']['coordsys'].lower() == 'cel' \
            and self.config['coords']['coordsys'].lower() == 'gal':

ugali/utils/mlab.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+"""
+Transplanted from matplotlib.mlab
+"""
+
+import six
+import numpy as np
+
+def iterable(obj):
+    """return true if *obj* is iterable"""
+    try:
+        iter(obj)
+    except TypeError:
+        return False
+    return True
+
+def rec_append_fields(rec, names, arrs, dtypes=None):
+    """
+    Return a new record array with field names populated with data
+    from arrays in *arrs*.  If appending a single field, then *names*,
+    *arrs* and *dtypes* do not have to be lists. They can just be the
+    values themselves.
+    """
+    if (not isinstance(names, six.string_types) and iterable(names)
+            and len(names) and isinstance(names[0], six.string_types)):
+        if len(names) != len(arrs):
+            raise ValueError("number of arrays do not match number of names")
+    else:  # we have only 1 name and 1 array
+        names = [names]
+        arrs = [arrs]
+    arrs = list(map(np.asarray, arrs))
+    if dtypes is None:
+        dtypes = [a.dtype for a in arrs]
+    elif not iterable(dtypes):
+        dtypes = [dtypes]
+    if len(arrs) != len(dtypes):
+        if len(dtypes) == 1:
+            dtypes = dtypes * len(arrs)
+        else:
+            raise ValueError("dtypes must be None, a single dtype or a list")
+    old_dtypes = rec.dtype.descr
+    if six.PY2:
+        old_dtypes = [(name.encode('utf-8'), dt) for name, dt in old_dtypes]
+    newdtype = np.dtype(old_dtypes + list(zip(names, dtypes)))
+    newrec = np.recarray(rec.shape, dtype=newdtype)
+    for field in rec.dtype.fields:
+        newrec[field] = rec[field]
+    for name, arr in zip(names, arrs):
+        newrec[name] = arr
+    return newrec
+
+if __name__ == "__main__":
+    import argparse
+    parser = argparse.ArgumentParser(description=__doc__)
+    args = parser.parse_args()

ugali/utils/stats.py

@@ -7,12 +7,12 @@
 
 import numpy as np
 import numpy.lib.recfunctions as recfuncs
-from matplotlib import mlab
 import scipy.special
 import scipy.stats
 
 # These should probably live in this file
 from ugali.utils.bayesian_efficiency import bayesianInterval, binomialInterval
+from ugali.utils import mlab
 
 _alpha   = 0.32
 _nbins   = 300