Merge pull request #38 from weaverba137/firstfield-fix

Firstfield fix

docs/pydl/changes.rst

@@ -5,9 +5,12 @@ PyDL Changelog
 0.6.1 (unreleased)
 ------------------
 
+* Support the ``firstField`` bit in ObjIDs from DR7 and earlier (Issue `#37`_).
 * Change tests of Astropy development version from Python 2 to Python 3.
 * Update to `astropy_helpers`_/v2.0.2.
 
+.. _`#37`: https://github.com/weaverba137/pydl/issues/37.
+
 0.6.0 (2017-09-19)
 ------------------
 

pydl/__init__.py

@@ -29,6 +29,14 @@
     from .uniq import uniq
 
 
+# Workaround: Numpy 1.14.x changes the way arrays are printed.
+try:
+    from numpy import set_printoptions
+    set_printoptions(legacy='1.13')
+except Exception:
+    pass
+
+
 class PydlException(Exception):
     """Base class for exceptions raised in PyDL functions.
     """

pydl/photoop/photoobj.py

@@ -40,8 +40,8 @@ def unwrap_objid(objid):
     Returns
     -------
     :class:`numpy.recarray`
-        A record array with the same length as objid, with the columns
-        'run', 'camcol', 'frame', 'id', 'rerun', 'skyversion'.
+        A record array with the same length as `objid`, with the columns
+        'skyversion', 'rerun', 'run', 'camcol', 'firstfield', 'frame', 'id'.
 
     Notes
     -----
@@ -57,8 +57,8 @@ def unwrap_objid(objid):
     >>> from numpy import array
     >>> from pydl.photoop.photoobj import unwrap_objid
     >>> unwrap_objid(array([1237661382772195474]))
-    rec.array([(2, 301, 3704, 3, 91, 146)],
-          dtype=[('skyversion', '<i4'), ('rerun', '<i4'), ('run', '<i4'), ('camcol', '<i4'), ('frame', '<i4'), ('id', '<i4')])
+    rec.array([(2, 301, 3704, 3, 0, 91, 146)],
+          dtype=[('skyversion', '<i4'), ('rerun', '<i4'), ('run', '<i4'), ('camcol', '<i4'), ('firstfield', '<i4'), ('frame', '<i4'), ('id', '<i4')])
     """
     import numpy as np
     if objid.dtype.type is np.string_ or objid.dtype.type is np.unicode_:
@@ -70,12 +70,13 @@ def unwrap_objid(objid):
     unwrap = np.recarray(objid.shape,
                          dtype=[('skyversion', 'i4'), ('rerun', 'i4'),
                                 ('run', 'i4'), ('camcol', 'i4'),
+                                ('firstfield', 'i4'),
                                 ('frame', 'i4'), ('id', 'i4')])
     unwrap.skyversion = np.bitwise_and(tempobjid >> 59, 2**4 - 1)
     unwrap.rerun = np.bitwise_and(tempobjid >> 48, 2**11 - 1)
     unwrap.run = np.bitwise_and(tempobjid >> 32, 2**16 - 1)
     unwrap.camcol = np.bitwise_and(tempobjid >> 29, 2**3 - 1)
-    # unwrap.firstfield = np.bitwise_and(tempobjid >> 28, 2**1 - 1)
+    unwrap.firstfield = np.bitwise_and(tempobjid >> 28, 2**1 - 1)
     unwrap.frame = np.bitwise_and(tempobjid >> 16, 2**12 - 1)
     unwrap.id = np.bitwise_and(tempobjid, 2**16 - 1)
     return unwrap

pydl/photoop/tests/test_photoop.py

@@ -24,14 +24,24 @@ def test_unwrap_objid(self):
         assert objid.rerun == 301
         assert objid.run == 3704
         assert objid.camcol == 3
+        assert objid.firstfield == 0
         assert objid.frame == 91
         assert objid.id == 146
         objid = unwrap_objid(np.array(['1237661382772195474']))
         assert objid.skyversion == 2
         assert objid.rerun == 301
         assert objid.run == 3704
         assert objid.camcol == 3
+        assert objid.firstfield == 0
         assert objid.frame == 91
         assert objid.id == 146
+        objid = unwrap_objid(np.array([587722984180548043]))
+        assert objid.skyversion == 1
+        assert objid.rerun == 40
+        assert objid.run == 752
+        assert objid.camcol == 5
+        assert objid.firstfield == 1
+        assert objid.frame == 618
+        assert objid.id == 459
         with raises(ValueError):
             objid = unwrap_objid(np.array([3.14159]))

pydl/pydlutils/cooling.py

@@ -35,9 +35,9 @@ def read_ds_cooling(fname, logT=None):
     --------
     >>> from pydl.pydlutils.cooling import read_ds_cooling
     >>> logT, loglambda = read_ds_cooling('m-15.cie')
-    >>> logT[0:5]
+    >>> logT[0:5] # doctest: +NORMALIZE_WHITESPACE
     array([ 4.  ,  4.05,  4.1 ,  4.15,  4.2 ])
-    >>> loglambda[0:5]
+    >>> loglambda[0:5] # doctest: +NORMALIZE_WHITESPACE
     array([-26.  , -24.66, -23.52, -22.62, -22.11])
     """
     from astropy.utils.data import get_pkg_data_contents

pydl/pydlutils/sdss.py

@@ -287,10 +287,11 @@ def sdss_flagval(flagname, bitname):
     return flagvalue
 
 
-def sdss_objid(run, camcol, field, objnum, rerun=301, skyversion=None):
+def sdss_objid(run, camcol, field, objnum, rerun=301, skyversion=None,
+               firstfield=None):
     """Convert SDSS photometric identifiers into CAS-style ObjID.
 
-    Bits are assigned in objid thus:
+    Bits are assigned in ObjID thus:
 
     ===== ========== ===============================================
     Bits  Name       Comment
@@ -300,7 +301,7 @@ def sdss_objid(run, camcol, field, objnum, rerun=301, skyversion=None):
     48-58 rerun      number of pipeline rerun
     32-47 run        run number
     29-31 camcol     camera column (1-6)
-    28    firstField [is this the first field in segment?] 0 for now
+    28    firstField is this the first field in segment? Usually 0.
     16-27 field      field number within run
     0-15  object     object number within field
     ===== ========== ===============================================
@@ -310,8 +311,9 @@ def sdss_objid(run, camcol, field, objnum, rerun=301, skyversion=None):
     run, camcol, field, objnum : :class:`int` or array of int
         Run, camcol, field and object number within field.  If arrays are
         passed, all must have the same length.
-    rerun, skyversion : :class:`int` or array of int, optional
-        Rerun and skyversion usually don't change very much.  If supplied,
+    rerun, skyversion, firstfield : :class:`int` or array of int, optional
+        `rerun`, `skyversion` and `firstfield` usually don't change at all,
+        especially for ObjIDs in DR8 and later.  If supplied,
         make sure the size matches all the other values.
 
     Returns
@@ -327,7 +329,7 @@ def sdss_objid(run, camcol, field, objnum, rerun=301, skyversion=None):
 
     Notes
     -----
-    * ``firstField`` flag never set.
+    * The ``firstField`` flag is never set in ObjIDs from DR8 and later.
     * On 32-bit systems, makes sure to explicitly declare all inputs as
       64-bit integers.
 
@@ -339,6 +341,8 @@ def sdss_objid(run, camcol, field, objnum, rerun=301, skyversion=None):
     """
     if skyversion is None:
         skyversion = default_skyversion()
+    if firstfield is None:
+        firstfield = 0
     if isinstance(run, int):
         run = np.array([run], dtype=np.int64)
     if isinstance(camcol, int):
@@ -357,11 +361,15 @@ def sdss_objid(run, camcol, field, objnum, rerun=301, skyversion=None):
             skyversion = np.zeros(run.shape, dtype=np.int64) + default_skyversion()
         else:
             skyversion = np.array([skyversion], dtype=np.int64)
+    if isinstance(firstfield, int):
+        if firstfield == 0:
+            firstfield = np.zeros(run.shape, dtype=np.int64)
+        else:
+            firstfield = np.array([firstfield], dtype=np.int64)
 
     #
     # Check that all inputs have the same shape.
     #
-    firstfield = np.zeros(run.shape, dtype=np.int64)
     if run.shape != camcol.shape:
         raise ValueError("camcol.shape does not match run.shape!")
     if run.shape != field.shape:
@@ -372,9 +380,13 @@ def sdss_objid(run, camcol, field, objnum, rerun=301, skyversion=None):
         raise ValueError("rerun.shape does not match run.shape!")
     if run.shape != skyversion.shape:
         raise ValueError("skyversion.shape does not match run.shape!")
+    if run.shape != firstfield.shape:
+        raise ValueError("firstfield.shape does not match run.shape!")
     #
     # Check ranges of parameters
     #
+    if ((firstfield < 0) | (firstfield > 1)).any():
+        raise ValueError("firstfield values are out-of-bounds!")
     if ((skyversion < 0) | (skyversion >= 16)).any():
         raise ValueError("skyversion values are out-of-bounds!")
     if ((rerun < 0) | (rerun >= 2**11)).any():

pydl/pydlutils/tests/test_sdss.py

@@ -131,6 +131,8 @@ def test_sdss_objid(self):
         assert (np.array([1237661382772195474, 1237649770790322299],
                          dtype=np.int64) ==
                 sdss_objid(run, camcol, field, obj)).all()
+        assert (sdss_objid(752, 5, 618, 459, rerun=40,
+                           skyversion=1, firstfield=1) == 587722984180548043)
         #
         # Exceptions
         #
@@ -146,10 +148,16 @@ def test_sdss_objid(self):
             objid = sdss_objid(3704, 3, 91, 146, rerun=np.array([137, 301]))
         with raises(ValueError):
             objid = sdss_objid(3704, 3, 91, 146, skyversion=np.array([2, 3]))
+        with raises(ValueError):
+            objid = sdss_objid(3704, 3, 91, 146, firstfield=np.array([0, 1]))
         with raises(ValueError):
             objid = sdss_objid(3704, 3, 91, 146, skyversion=-2)
         with raises(ValueError):
             objid = sdss_objid(3704, 3, 91, 146, skyversion=16)
+        with raises(ValueError):
+            objid = sdss_objid(3704, 3, 91, 146, firstfield=-2)
+        with raises(ValueError):
+            objid = sdss_objid(3704, 3, 91, 146, firstfield=2)
         with raises(ValueError):
             objid = sdss_objid(3704, 3, 91, 146, rerun=-2)
         with raises(ValueError):
@@ -190,6 +198,21 @@ def test_sdss_specobjid(self):
         #
         # Exceptions
         #
+        with raises(ValueError):
+            s = sdss_specobjid(np.array([4055, 4056]), 408, 55359, 'v5_7_0')
+        with raises(ValueError):
+            s = sdss_specobjid(4055, np.array([408, 409]), 55359, 'v5_7_0')
+        with raises(ValueError):
+            s = sdss_specobjid(4055, 408, np.array([55359, 55360]), 'v5_7_0')
+        with raises(ValueError):
+            s = sdss_specobjid(4055, 408, 55359,
+                               np.array(['v5_7_0', 'v5_7_2']))
+        with raises(ValueError):
+            s = sdss_specobjid(4055, 408, 55359, 'v5_7_0',
+                               line=np.array([137, 138]))
+        with raises(ValueError):
+            s = sdss_specobjid(4055, 408, 55359, 'v5_7_0',
+                               index=np.array([137, 138]))
         with raises(ValueError):
             s = sdss_specobjid(4055, 408, 55359, 'v5_7_0', line=137,
                                index=137)

pydl/rebin.py

@@ -44,9 +44,9 @@ def rebin(x, d, sample=False):
     --------
     >>> from numpy import arange, float
     >>> from pydl import rebin
-    >>> rebin(arange(10, dtype=float), (5,))
+    >>> rebin(arange(10, dtype=float), (5,)) # doctest: +NORMALIZE_WHITESPACE
     array([ 0.5,  2.5,  4.5,  6.5,  8.5])
-    >>> rebin(arange(5, dtype=float), (10,))
+    >>> rebin(arange(5, dtype=float), (10,)) # doctest: +NORMALIZE_WHITESPACE
     array([ 0. ,  0.5,  1. ,  1.5,  2. ,  2.5,  3. ,  3.5,  4. ,  4. ])
     """
     from numpy import floor, zeros