Changeset 1505

Timestamp:

09/28/08 13:28:45 (2 months ago)

Author:

pierregm

Message:

tstables
* fixed tabulate to allow the processing of standard ndarrays
* add support for readCoordinates
* add support for append

Files:

• trunk/timeseries/scikits/timeseries/lib/tests/test_tstables.py (modified) (2 diffs)
• trunk/timeseries/scikits/timeseries/lib/tstables.py (modified) (10 diffs)

trunk/timeseries/scikits/timeseries/lib/tests/test_tstables.py

@@ -9 +9 @@
-import numpy.ma as ma
-import numpy.ma.mrecords as mr
-
+MaskedArray, 
-
-import scikits.timeseries as ts
+from scikits.timeseries import TimeSeries
-
-from numpy.testing import *
@@ -339 +340 @@
-        assert_equal(test._hardmask, data._hardmask)
-
+
+class TestTableRead(TestCase):
+    #
+    def __init__(self, *args, **kwds):
+        TestCase.__init__(self, *args, **kwds)
+        series = ts.time_series(zip(np.random.rand(10),
+                                    np.arange(10)),
+                                start_date=ts.now('M'),
+                                dtype=[('a',float),('b',int)])
+        series.mask[0] = (0,1)
+        series.mask[-1] = (1,0)
+        self.tseries = series
+        self.marray = series._series
+        self.file = tempfile.mktemp(".hdf5")
+        self.h5file = tables.openFile(self.file,'a')
+        self.populate()
+    #
+    def tearDown(self):
+        if self.h5file.isopen:
+            self.h5file.close()
+        os.remove(self.file)
+    #
+    def populate(self):
+        h5file = self.h5file
+        table = h5file.createMaskedTable('/', 'marray', self.marray, "")
+        h5file.flush()
+        table = h5file.createTimeSeriesTable('/', 'tseries', self.tseries, "")
+        h5file.flush()
+    #
+    def test_tseries_read(self):
+        "Test reading specific elements of a TimeSeriesTable"
+        table = self.h5file.root.tseries
+        series = self.tseries
+        #
+        test = table.read()
+        assert(isinstance(test, TimeSeries))
+        assert_equal_records(test, series)
+        #
+        test = table.read(field='a')
+        assert(isinstance(test, TimeSeries))
+        assert_equal(test, series['a'])
+        #
+        test = table.read(step=2)
+        assert(isinstance(test, TimeSeries))
+        assert_equal(test, series[::2])
+        #
+        test = table.readCoordinates([1,2,3])
+        assert(isinstance(test, TimeSeries))
+        assert_equal(test, series[[1,2,3]])
+        #
+        test = table.readCoordinates([1,2,3], field='a')
+        assert(isinstance(test, TimeSeries))
+        assert_equal(test, series['a'][[1,2,3]])
+    #
+    def test_marray_read(self):
+        "Test reading specific elements of a MaskedTable"
+        table = self.h5file.root.marray
+        data = self.marray
+        #
+        test = table.read()
+        assert(isinstance(test, MaskedArray))
+        assert_equal_records(test, data)
+        #
+        test = table.read(field='a')
+        assert(isinstance(test, MaskedArray))
+        assert_equal(test, data['a'])
+        #
+        test = table.read(step=2)
+        assert(isinstance(test, MaskedArray))
+        assert_equal(test, data[::2])
+        #
+        test = table.readCoordinates([1,2,3])
+        assert(isinstance(test, MaskedArray))
+        assert_equal(test, data[[1,2,3]])
+        #
+        test = table.readCoordinates([1,2,3], field='a')
+        assert(isinstance(test, MaskedArray))
+        assert_equal(test, data['a'][[1,2,3]])
+
-###############################################################################
-#------------------------------------------------------------------------------

trunk/timeseries/scikits/timeseries/lib/tstables.py

@@ -144 +144 @@
-
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+_doc_parameters = dict(
+mareturn="""
+    Depending on the value of the ``field`` parameter, the method returns either
+    * a ndarray, if ``field=='_data'`` or if ``field=='_mask'``;
+    * a :class:`~numpy.ma.MaskedArray`, if ``field`` is None or a valid field.
+""",
+tsreturn="""
+    Depending on the value of the ``field`` parameter, the method returns:
+    
+    * a :class:`~scikits.timeseries.TimeSeries`, if ``field`` is None or a valid
+      field;
+    * a :class:`~scikits.timeseries.DateArray`, if ``field=='_dates'``;
+    * a ndarray, if ``field=='_data'`` or if ``field=='_mask'``;
+    * a :class:`~numpy.ma.MaskedArray`, if ``field=='_series'``.
+""",
+readinput="""
+    start : {None, int}, optional
+        Index of the first record to read.
+        If None, records will be read starting from the very first one.
+    stop : {None, int}, optional
+        Index of the last record to read.
+        If None, records will be read until the very last one.
+    step : {None, int}, optional
+        Increment between succesive records to read.
+        If None, all the records between ``start`` and ``stop`` will be read.
+    field : {None, str}, optional
+        Name of the field to read.
+        If None, all the fields from each record are read.
+""",
+readcoordinateinput="""
+    coords : sequence
+        A sequence of integers, corresponding to the indices of the rows to
+        retrieve
+    field : {None, str}, optional
+        Name of the field to read.
+        If None, all the fields from each record are read.
+""",
+)
+
-
-
@@ -160 +199 @@
-        else:
-            pseudodtype = [('_data',basedtype),('_mask',bool)]
-a.filled(
+ma.filled(a
-    else:
-        pseudodtype = [(fname,[('_data',ftype), ('_mask',bool)])
-                       for (fname,ftype) in basedtype.descr]
-        fields = [a[f] for f in basenames]
-f.filled(
+ma.filled(f
-                                 for f in fields])
-    return np.fromiter(pseudo, dtype=pseudodtype)
@@ -223 +262 @@
-        A ndarray with flexible dtype.
-    """
+    a = np.asanyarray(a)
-    if isinstance(a, TimeSeries):
-        return _tabulate_time_series(a)
@@ -279 +319 @@
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-        special_attrs = getattr(self.attrs, 'special_attrs', {})
-        fill_value = special_attrs.get('_fill_value', None)
@@ -314 +330 @@
-        ndtype = self._get_dtype()
-        field_names = ndtype.names
+        field = kwargs.get('field', None)
-        #
-        if field in ['_data','_mask']:
@@ -341 +358 @@
-
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+    def read(self, start=None, stop=None, step=None, field=None):
+        """
+    Reads the current :class:`MaskedTable`.
+    
+    Returns
+    -------
+    %(mareturn)s
+    
+    Parameters
+    ----------
+    %(readinput)s
+        """
+        args = ()
+        kwargs = dict(field=field, start=start, stop=stop, step=step)
+        return self._reader(Table.read, *args, **kwargs)
+    read.__doc__ = ((read.__doc__ or '') % _doc_parameters) or None
+
+
+    def readCoordinates(self, coords, field=None):
+        """
+    Reads a set of rows given their coordinates.
+
+    Parameters
+    ----------
+    %(readcoordinateinput)s
+    
+    Returns
+    -------
+    %(mareturn)s
+        """
+        args = (coords,)
+        kwargs = dict(field=field)
+        return self._reader(Table.readCoordinates, *args, **kwargs)
+    readCoordinates.__doc__ = ((readCoordinates.__doc__ or '') % _doc_parameters) or None
+
+    def append(self, rows):
+        """
+        """
+        rows = tabulate(rows)
+        Table.append(self, rows)
+
+
-class TimeSeriesTable(MaskedTable):
-    """
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-        special_attrs = getattr(self.attrs, 'special_attrs', {})
-        fill_value = special_attrs.get('_fill_value', None)
-        baseclass = special_attrs.get('_baseclass', np.ndarray)
-
-
-
+
-        ndtype = self._get_dtype()
-        field_names = ndtype.names
-        
+        field = kwargs.get('field', None)
-        # Case 1. : Global read .................
-        if field is None:
-Table.read(self, **position_keyword
+meth(self, *args, **kwarg
-            dates = DateArray(data['_dates'],
-                              freq=special_attrs.get('freq','U'))
@@ -452 +584 @@
-        # Case 2. Partial reads..................
-        elif field in ['_dates','_data','_mask']:
-Table.read(self, field=field, **position_keyword
+meth(self, *args, **kwarg
-        # Case 3. The series as a masked array
-        elif field == '_series':
-            # Special case: read the table, but keep it as MaskedArray
-
+
+
-            if field_names is None:
-                output = ma.array(data['_data'], mask=data['_mask'])
@@ -471 +604 @@
-        # Case 4. Field read ....................
-        elif field in field_names:
-
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-            dates = DateArray(dates, freq=special_attrs.get('freq','U'))
-            # Get the data part
@@ -488 +622 @@
-
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+    def readCoordinates(self, coords, field=None):
+        """
+    Reads a set of rows given their coordinates.
+
+    Parameters
+    ----------
+    %(readcoordinateinput)s
+    
+    Returns
+    -------
+    %(tsreturn)s
+        """
+        args = (coords,)
+        kwargs = dict(field=field)
+        return self._reader(Table.readCoordinates, *args, **kwargs)
+    readCoordinates.__doc__ = ((readCoordinates.__doc__ or '') % _doc_parameters) or None
+
+
+    def read(self, start=None, stop=None, step=None, field=None):
+        """
+    Reads the current :class:`TimeSeriesTable`.
+    
+    Returns
+    -------
+    %(tsreturn)s
+    
+    Parameters
+    ----------
+    %(readcoordinateinput)s
+        """
+        args = ()
+        kwargs = dict(field=field, start=start, stop=stop, step=step)
+        return self._reader(Table.read, *args, **kwargs)
+    read.__doc__ = ((read.__doc__ or '') % _doc_parameters) or None
+
+
-#-- File extensions -----------------------------------------------------------                       
-