more pep 8 on oidata and more tests

soif/core.py

@@ -110,7 +110,8 @@
                            'is_angle': False
                            }
                 }
-DATAKEYSLOWER = ['vis2', 't3phi', 't3amp', 'visphi', 'visamp']
+DATAKEYSLOWER = [item.lower() for item in ATTRDATATYPE.keys()]
+DATAKEYSUPPER = [item.upper() for item in ATTRDATATYPE.keys()]
 
 
 def abs2(ar):

soif/oidata.py

@@ -51,7 +51,7 @@ def __init__(self, src, hduidx, datatype, hduwlidx, indices=(),
         hdu = hdus[self._input_hduidx[-1]]
         hduwl = hdus[self._input_hduwlidx[-1]]
 
-        if self.datatype not in core.ATTRDATATYPE.keys():
+        if self.datatype not in core.DATAKEYSUPPER:
             if exc.raiseIt(exc.InvalidDataType,
                            self.raiseError,
                            datatype=self.datatype):

soif/oidataempty.py

@@ -36,7 +36,7 @@ class OidataEmpty(object):
     def __init__(self, datatype, **kwargs):
         self.raiseError = bool(kwargs.pop('raiseError', True))
         self.datatype = str(datatype).upper()
-        if self.datatype not in core.ATTRDATATYPE.keys():
+        if self.datatype not in core.DATAKEYSUPPER:
             if exc.raiseIt(exc.InvalidDataType,
                            self.raiseError,
                            datatype=self.datatype):
@@ -50,8 +50,7 @@ def _info(self):
     def __repr__(self):
         return self._info()
 
-    def __str__(self):
-        return self._info()
+    __str__ = __repr__
 
     @property
     def useit(self):

soif/oigrab.py

@@ -165,59 +165,58 @@ def show_specs(self, ret=False, **kwargs):
         if ret:
             return tgtlist
 
-    def show_filtered(self, tgt=None, mjd=(None, None), hduNums=(),
+    def show_filtered(self, tgt=None, mjd=(None, None), hdus=(),
                       vis2=True, t3phi=True, t3amp=True, visphi=True,
                       visamp=True, verbose=False, **kwargs):
         """
-        Given an oifits file 'src' and filtering parameters on the
-        target name (OI_TARGET table), the instrument name
-        (OI_WAVELENGTH table), the array name (OI_ARRAY table),
-        the observation wavelength (OI_WAVELENGTH table) and the
-        acquisition time [t_min, t_max] (OI_VIS2, OI_VIS, OI_T3
-        tables), this function returns the data indices of the data
-        matching all of these different filters. These lists are used
-        to load the data within an Oidata object.
-
-        Leave input parameter to 'None' to discard filtering on that
+        Give filtering parameters on the target name (OI_TARGET table),
+        the observation wavelength (OI_WAVELENGTH table), the
+        acquisition time [mjd_min, mjd_max], or the hdu index.
+        Returns the data indices of the data matching all of these
+        different filters. These lists are used to load the data within
+        an Oidata object.
+        Leave input parameter to 'None' to discard filtering on this
         particular parameter.
-
-        Returns: VIS2, T3, VIS indices as a tuple of 3 lists
         """
-        hdus = pf.open(self.src)
-        mjd = [float(mjd[0] if mjd[0] is not None else -np.inf),
-               float(mjd[1] if mjd[1] is not None else np.inf)]
+        allhdus = pf.open(self.src)
+        mjd = (float(mjd[0] if mjd[0] is not None else -np.inf),
+               float(mjd[1] if mjd[1] is not None else np.inf))
         datayouwant = {'data': {'VIS2': bool(vis2),
                                 'T3PHI': bool(t3phi),
                                 'T3AMP': bool(t3amp),
                                 'VISPHI': bool(visphi),
                                 'VISAMP': bool(visamp)
                                 }
                        }
-        hduNums = core.aslist(hduNums)
-        for idx, item in enumerate(hdus):
-            if len(hduNums) > 0 and idx not in hduNums:
+        hdus = core.aslist(hdus)
+        for idx, item in enumerate(allhdus):
+            # do we want this hdu?
+            if len(hdus) > 0 and idx not in hdus:
                     continue
+            # is this hdu actual data?
             if core.hduToDataType(item) is not None:
                 mjditem = core.gethduMJD(item)[1].ravel()
                 filt = ((mjditem >= mjd[0]) & (mjditem <= mjd[1]))
                 if tgt is not None:
                     filt = (filt & (item.data.field("TARGET_ID") == int(tgt)))
                 if verbose:
-                    print("{}:\n  {}/{}\n".format(
+                    print("hdu {:d}: {}:\n  {}/{}\n".format(
+                                idx,
                                 core.hduToDataType(item),
                                 filt.sum(),
                                 item.data["TARGET_ID"].size))
-                datayouwant[idx] = np.arange(item.data["TARGET_ID"].size)[filt]
-        hdus.close()
+                if filt.any():
+                    datayouwant[idx] = np.arange(item.data["TARGET_ID"].size)[filt]
+        allhdus.close()
         return datayouwant
 
-    def extract(self, tgt=None, mjd=(None, None), wl=(None, None), hduNums=(),
+    def extract(self, tgt=None, mjd=(None, None), wl=(None, None), hdus=(),
                 vis2=True, t3phi=True, t3amp=True, visphi=True, visamp=True,
                 flatten=False, degree=True, significant_figures=5,
                 erb_sigma=None, sigma_erb=None, systematic_prior=None,
                 systematic_bounds=None, verbose=False, **kwargs):
         datayouwant = self.show_filtered(
-                        tgt=tgt, mjd=mjd, vis2=vis2, hduNums=hduNums,
+                        tgt=tgt, mjd=mjd, vis2=vis2, hdus=hdus,
                         t3phi=t3phi, t3amp=t3amp, visphi=visphi, visamp=visamp,
                         verbose=verbose, **kwargs)
         return Oifits(src=self.src, datafilter=datayouwant, flatten=flatten,

soif/test/test_oidata.py

@@ -35,7 +35,7 @@
 from ..oifits import Oifits
 from .. import oiexception as exc
 
-FILENAME = os.path.dirname(os.path.abspath(__file__)) + '/MWC361.oifits'
+"""FILENAME = os.path.dirname(os.path.abspath(__file__)) + '/MWC361.oifits'
 FILENAME_NOTARGET = os.path.dirname(os.path.abspath(__file__)) + '/MWC361_notarget.oifits'
 FILENAME_NOWL = os.path.dirname(os.path.abspath(__file__)) + '/MWC361_nowl.oifits'
 VALIDHDU = 4
@@ -50,3 +50,4 @@ def test_oigrab():
 @raises(exc.NoTargetTable)
 def test_oigrab_NoTargetTable():
     oig = Oigrab(FILENAME_NOTARGET)
+"""

soif/test/test_oidataempty.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+###############################################################################
+#  
+#  SOIF - Sofware for Optical Interferometry fitting
+#  Copyright (C) 2016  Guillaume Schworer
+#  
+#  This program is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#  
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#  
+#  You should have received a copy of the GNU General Public License
+#  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#  
+#  For any information, bug report, idea, donation, hug, beer, please contact
+#    guillaume.schworer@obspm.fr
+#
+###############################################################################
+
+
+import numpy as np
+import os
+from nose.tools import raises
+
+from ..oidata import Oidata
+from ..oidataempty import OidataEmpty
+from .. import oiexception as exc
+from .. import core
+
+
+
+
+def test_create():
+    for typ in core.DATAKEYSUPPER:
+        oie = OidataEmpty(datatype=typ.lower())
+    assert not oie.useit
+    oie.useit = True
+    assert not oie.useit
+    assert not bool(oie)
+    assert not oie
+    oie._has = True
+    assert oie.useit
+    assert bool(oie)
+    assert oie
+    oie.useit = False
+    assert not oie.useit
+    assert bool(oie)
+    assert oie
+    assert str(oie) == repr(oie)
+
+
+@raises(exc.InvalidDataType)
+def test_InvalidDataType():
+    oie = OidataEmpty(datatype='random')
+
+def test_InvalidDataType_noraise():
+    oie = OidataEmpty(datatype='random', raiseError=False)
+    assert not hasattr(oie, '_has')
+

soif/test/test_oifits.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+###############################################################################
+#  
+#  SOIF - Sofware for Optical Interferometry fitting
+#  Copyright (C) 2016  Guillaume Schworer
+#  
+#  This program is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#  
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#  
+#  You should have received a copy of the GNU General Public License
+#  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#  
+#  For any information, bug report, idea, donation, hug, beer, please contact
+#    guillaume.schworer@obspm.fr
+#
+###############################################################################
+
+
+import numpy as np
+import os
+from nose.tools import raises
+
+from ..oidata import Oidata
+from ..oidataempty import OidataEmpty
+from ..oifits import Oifits
+from ..oigrab import Oigrab
+from .. import oiexception as exc
+
+
+
+
+"""def test_extract():
+    oig = Oigrab(FILENAME)
+    ans1 = oig.extract(tgt=VALIDTGT)
+    filt = np.asarray([item[1] for item in oig.show_specs(ret=True)[VALIDHDU]]) == VALIDTGT
+    ans2 = Oifits(oig.src, datafilter={VALIDHDU: np.arange(DATASETSIZE)[filt]+1})
+    assert np.allclose(ans1.vis2.data, ans2.vis2.data)
+
+"""

soif/test/test_oigrab.py

@@ -40,6 +40,7 @@
 FILENAME_NOWL = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'MWC361_nowl.oifits')
 FILENAME_FULL = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'MWC361_full.oifits')
 VALIDHDU = 4
+T3HDU = 6
 DATASETSIZE = 12
 VALIDTGT = 1
 
@@ -53,38 +54,49 @@ def test():
 def test_NoTargetTable():
     oig = Oigrab(FILENAME_NOTARGET)
 
+def test_NoTargetTable_noraise():
+    oig = Oigrab(FILENAME_NOTARGET, raiseError=False)
+    assert not hasattr(oig, '_targets')
+
 @raises(exc.NoWavelengthTable)
 def test_NoWavelengthTable():
     oig = Oigrab(FILENAME_NOWL)
 
+def test_NoWavelengthTable_noraise():
+    oig = Oigrab(FILENAME_NOWL, raiseError=False)
+
 @raises(exc.ReadOnly)
 def test_NoTargetTable():
     oig = Oigrab(FILENAME)
     oig.targets = []
 
 def test_show_specs():
     oig = Oigrab(FILENAME)
+    ans = oig.show_specs(ret=False)
     ans = oig.show_specs(ret=True)
     for item in range(10):
         if item != VALIDHDU:
             assert ans.get(item) is None
     assert len(ans[VALIDHDU]) == DATASETSIZE
     assert np.allclose(ans[VALIDHDU][0], (0, 0, 57190.4437, 1, 38))
     assert (np.diff([item[2] for item in ans[VALIDHDU]]) >= 0).all()
-
 
 def test_show_filtered():
     oig = Oigrab(FILENAME)
     for item in range(10):
         if item != VALIDHDU:
-            assert oig.show_filtered(tgt=VALIDTGT).get(item) is None
+            assert oig.show_filtered(tgt=VALIDTGT, verbose=True).get(item) is None
         else:
-            assert oig.show_filtered(tgt=VALIDTGT).get(item).tolist() == [ 2,  5,  8, 11]
+            assert oig.show_filtered(tgt=VALIDTGT, verbose=True).get(item).tolist() == [ 2,  5,  8, 11]
     oig = Oigrab(FILENAME_FULL)
-
-def test_extract():
-    oig = Oigrab(FILENAME)
-    ans1 = oig.extract(tgt=VALIDTGT)
-    filt = np.asarray([item[1] for item in oig.show_specs(ret=True)[VALIDHDU]]) == VALIDTGT
-    ans2 = Oifits(oig.src, datafilter={VALIDHDU: np.arange(DATASETSIZE)[filt]+1})
-    assert np.allclose(ans1.vis2.data, ans2.vis2.data)
+    ans = oig.show_filtered(tgt=VALIDTGT, verbose=True)
+    assert len(ans) == 5
+    assert len(ans[VALIDHDU]) == 4
+    assert len(ans[T3HDU]) == 140
+    assert len(oig.show_filtered(tgt=VALIDTGT, hdus=(VALIDHDU,T3HDU), verbose=True)) == 3
+    ans = oig.show_filtered(tgt=VALIDTGT, hdus=(T3HDU), t3amp=False, mjd=(55636.3382228, 55636.3396117), verbose=True)
+    assert len(ans) == 2
+    assert ans['data']['T3AMP'] == False
+    assert ans[T3HDU].min() == 70
+    assert ans[T3HDU].max() == 174
+    assert len(ans[T3HDU]) == 70