Merge pull request #793 from htwangtw/gifti_improve_io

NF: GiftiImage method agg_data to return usable data arrays

Author: effigies

nibabel/gifti/gifti.py

@@ -678,6 +678,141 @@ def get_arrays_from_intent(self, intent):
         it = intent_codes.code[intent]
         return [x for x in self.darrays if x.intent == it]
 
+    def agg_data(self, intent_code=None):
+        """
+        Aggregate GIFTI data arrays into an ndarray or tuple of ndarray
+
+        In the general case, the numpy data array is extracted from each ``GiftiDataArray``
+        object and returned in a ``tuple``, in the order they are found in the GIFTI image.
+
+        If all ``GiftiDataArray`` s have ``intent`` of 2001 (``NIFTI_INTENT_TIME_SERIES``),
+        then the data arrays are concatenated as columns, producing a vertex-by-time array.
+        If an ``intent_code`` is passed, data arrays are filtered by the selected intents,
+        before being aggregated.
+        This may be useful for images containing several intents, or ensuring an expected
+        data type in an image of uncertain provenance.
+        If ``intent_code`` is a ``tuple``, then a ``tuple`` will be returned with the result of
+        ``agg_data`` for each element, in order.
+        This may be useful for ensuring that expected data arrives in a consistent order.
+
+        Parameters
+        ----------
+        intent_code : None, string, integer or tuple of strings or integers, optional
+            code(s) specifying nifti intent
+
+        Returns
+        -------
+        tuple of ndarrays or ndarray
+            If the input is a tuple, the returned tuple will match the order.
+
+        Examples
+        --------
+
+        Consider a surface GIFTI file:
+
+        >>> import nibabel as nib
+        >>> from nibabel.testing import test_data
+        >>> surf_img = nib.load(test_data('gifti', 'ascii.gii'))
+
+        The coordinate data, which is indicated by the ``NIFTI_INTENT_POINTSET``
+        intent code, may be retrieved using any of the following equivalent
+        calls:
+
+        >>> coords = surf_img.agg_data('NIFTI_INTENT_POINTSET')
+        >>> coords_2 = surf_img.agg_data('pointset')
+        >>> coords_3 = surf_img.agg_data(1008)  # Numeric code for pointset
+        >>> print(np.array2string(coords, precision=3))
+        [[-16.072 -66.188  21.267]
+         [-16.706 -66.054  21.233]
+         [-17.614 -65.402  21.071]]
+        >>> np.array_equal(coords, coords_2)
+        True
+        >>> np.array_equal(coords, coords_3)
+        True
+
+        Similarly, the triangle mesh can be retrieved using various intent
+        specifiers:
+
+        >>> triangles = surf_img.agg_data('NIFTI_INTENT_TRIANGLE')
+        >>> triangles_2 = surf_img.agg_data('triangle')
+        >>> triangles_3 = surf_img.agg_data(1009)  # Numeric code for pointset
+        >>> print(np.array2string(triangles))
+        [0 1 2]
+        >>> np.array_equal(triangles, triangles_2)
+        True
+        >>> np.array_equal(triangles, triangles_3)
+        True
+
+        All arrays can be retrieved as a ``tuple`` by omitting the intent
+        code:
+
+        >>> coords_4, triangles_4 = surf_img.agg_data()
+        >>> np.array_equal(coords, coords_4)
+        True
+        >>> np.array_equal(triangles, triangles_4)
+        True
+
+        Finally, a tuple of intent codes may be passed in order to select
+        the arrays in a specific order:
+
+        >>> triangles_5, coords_5 = surf_img.agg_data(('triangle', 'pointset'))
+        >>> np.array_equal(triangles, triangles_5)
+        True
+        >>> np.array_equal(coords, coords_5)
+        True
+
+        The following image is a GIFTI file with ten (10) data arrays of the same
+        size, and with intent code 2001 (``NIFTI_INTENT_TIME_SERIES``):
+
+        >>> func_img = nib.load(test_data('gifti', 'task.func.gii'))
+
+        When aggregating time series data, these arrays are concatenated into
+        a single, vertex-by-timestep array:
+
+        >>> series = func_img.agg_data()
+        >>> series.shape
+        (642, 10)
+
+        In the case of a GIFTI file with unknown data arrays, it may be preferable
+        to specify the intent code, so that a time series array is always returned:
+
+        >>> series_2 = func_img.agg_data('NIFTI_INTENT_TIME_SERIES')
+        >>> series_3 = func_img.agg_data('time series')
+        >>> series_4 = func_img.agg_data(2001)
+        >>> np.array_equal(series, series_2)
+        True
+        >>> np.array_equal(series, series_3)
+        True
+        >>> np.array_equal(series, series_4)
+        True
+
+        Requesting a data array from a GIFTI file with no matching intent codes
+        will result in an empty tuple:
+
+        >>> surf_img.agg_data('time series')
+        ()
+        >>> func_img.agg_data('triangle')
+        ()
+        """
+
+        # Allow multiple intents to specify the order
+        # e.g., agg_data(('pointset', 'triangle')) ensures consistent order
+
+        if isinstance(intent_code, tuple):
+            return tuple(self.agg_data(intent_code=code) for code in intent_code)
+
+        darrays = self.darrays if intent_code is None else self.get_arrays_from_intent(intent_code)
+        all_data = tuple(da.data for da in darrays)
+        all_intent = {intent_codes.niistring[da.intent] for da in darrays}
+
+        if all_intent == {'NIFTI_INTENT_TIME_SERIES'}:  # stack when the gifti is a timeseries
+            return np.column_stack(all_data)
+
+        if len(all_data) == 1:
+            all_data = all_data[0]
+
+        return all_data
+
     @deprecate_with_version(
         'getArraysFromIntent method deprecated. '
         "Use get_arrays_from_intent instead.",