Merge remote-tracking branch 'upstream/master' into gifti-loadsave

Author: Ben Cipollini

nibabel/fileslice.py

@@ -767,9 +767,15 @@ def strided_scalar(shape, scalar=0.):
     strided_arr : array
         Array of shape `shape` for which all values == `scalar`, built by
         setting all strides of `strided_arr` to 0, so the scalar is broadcast
-        out to the full array `shape`.
+        out to the full array `shape`. `strided_arr` is flagged as not
+        `writeable`.
+
+        The array is set read-only to avoid a numpy error when broadcasting -
+        see https://github.com/numpy/numpy/issues/6491
     """
     shape = tuple(shape)
     scalar = np.array(scalar)
     strides = [0] * len(shape)
-    return np.lib.stride_tricks.as_strided(scalar, shape, strides)
+    strided_scalar = np.lib.stride_tricks.as_strided(scalar, shape, strides)
+    strided_scalar.flags.writeable = False
+    return strided_scalar

nibabel/gifti/gifti.py

@@ -12,11 +12,11 @@
 
 import numpy as np
 
+from .util import (array_index_order_codes, gifti_encoding_codes,
+                   gifti_endian_codes, KIND2FMT)
 from .. import xmlutils as xml
 from ..filebasedimages import FileBasedHeader, FileBasedImage
 from ..nifti1 import data_type_codes, xform_codes, intent_codes
-from .util import (array_index_order_codes, gifti_encoding_codes,
-                   gifti_endian_codes, KIND2FMT)
 
 # {en,de}codestring in deprecated in Python3, but
 # {en,de}codebytes not available in Python2.
@@ -40,7 +40,12 @@ def from_dict(klass, data_dict):
             meda.data.append(nv)
         return meda
 
+    @np.deprecate_with_doc("Use the metadata property instead.")
     def get_metadata(self):
+        return self.metadata
+
+    @property
+    def metadata(self):
         """ Returns metadata as dictionary """
         self.data_as_dict = {}
         for ele in self.data:
@@ -58,7 +63,7 @@ def _to_xml_element(self):
         return metadata
 
     def print_summary(self):
-        print(self.get_metadata())
+        print(self.metadata)
 
 
 class GiftiNVPairs(object):
@@ -118,10 +123,28 @@ def __init__(self, key=0, label='', red=None, green=None, blue=None,
         self.blue = blue
         self.alpha = alpha
 
+    @np.deprecate_with_doc("Use the rgba property instead.")
     def get_rgba(self):
+        return self.rgba
+
+    @property
+    def rgba(self):
         """ Returns RGBA as tuple """
         return (self.red, self.green, self.blue, self.alpha)
 
+    @rgba.setter
+    def rgba(self, rgba):
+        """ Set RGBA via tuple
+
+        Parameters
+        ----------
+        rgba : tuple (red, green, blue, alpha)
+
+        """
+        if len(rgba) != 4:
+            raise ValueError('rgba must be length 4.')
+        self.red, self.green, self.blue, self.alpha = rgba
+
 
 def _arr2txt(arr, elem_fmt):
     arr = np.asarray(arr)
@@ -163,6 +186,17 @@ def print_summary(self):
         print('Affine Transformation Matrix: \n', self.xform)
 
 
+@np.deprecate_with_doc("This is an internal API that will be discontinued.")
+def data_tag(dataarray, encoding, datatype, ordering):
+    class DataTag(xml.XmlSerializable):
+        def __init__(self, *args):
+            self.args = args
+        def _to_xml_element(self):
+            return _data_tag_element(*self.args)
+
+    return DataTag(dataarray, encoding, datatype, ordering).to_xml()
+
+
 def _data_tag_element(dataarray, encoding, datatype, ordering):
     """ Creates the data tag depending on the required encoding,
     returns as XML element"""
@@ -297,6 +331,34 @@ def _to_xml_element(self):
 
         return data_array
 
+    @np.deprecate_with_doc("Use the to_xml() function instead.")
+    def to_xml_open(self):
+        out = """<DataArray Intent="%s"
+\tDataType="%s"
+\tArrayIndexingOrder="%s"
+\tDimensionality="%s"
+%s\tEncoding="%s"
+\tEndian="%s"
+\tExternalFileName="%s"
+\tExternalFileOffset="%s">\n"""
+        di = ""
+        for i, n in enumerate(self.dims):
+            di = di + '\tDim%s=\"%s\"\n' % (str(i), str(n))
+        return out % (intent_codes.niistring[self.intent],
+                      data_type_codes.niistring[self.datatype],
+                      array_index_order_codes.label[self.ind_ord],
+                      str(self.num_dim),
+                      str(di),
+                      gifti_encoding_codes.specs[self.encoding],
+                      gifti_endian_codes.specs[self.endian],
+                      self.ext_fname,
+                      self.ext_offset,
+                      )
+
+    @np.deprecate_with_doc("Use the to_xml() function instead.")
+    def to_xml_close(self):
+        return "</DataArray>\n"
+
     def print_summary(self):
         print('Intent: ', intent_codes.niistring[self.intent])
         print('DataType: ', data_type_codes.niistring[self.datatype])
@@ -313,13 +375,15 @@ def print_summary(self):
             print('Coordinate System:')
             print(self.coordsys.print_summary())
 
+    @np.deprecate_with_doc("Use the metadata property instead.")
     def get_metadata(self):
-        """ Returns metadata as dictionary """
-        return self.meta.get_metadata()
+        return self.meta.metadata
 
+    @property
+    def metadata(self):
+        """ Returns metadata as dictionary """
+        return self.meta.metadata
 
-class GiftiHeader(FileBasedHeader):
-    pass
 
 class GiftiImage(FileBasedImage, xml.XmlSerializable):
     valid_exts = ('.gii',)
@@ -332,38 +396,52 @@ def __init__(self, header=None, extra=None, file_map=None, meta=None,
 
         if darrays is None:
             darrays = []
-        self.darrays = darrays
         if meta is None:
-            self.meta = GiftiMetaData()
-        else:
-            self.meta = meta
+            meta = GiftiMetaData()
         if labeltable is None:
-            self.labeltable = GiftiLabelTable()
-        else:
-            self.labeltable = labeltable
-        self.numDA = len(self.darrays)
+            labeltable = GiftiLabelTable()
+
+        self._labeltable = labeltable
+        self._meta = meta
+
+        self.darrays = darrays
         self.version = version
 
-    def get_labeltable(self):
-        return self.labeltable
+    @property
+    def numDA(self):
+        return len(self.darrays)
 
-    def set_labeltable(self, labeltable):
+    @property
+    def labeltable(self):
+        return self._labeltable
+
+    @labeltable.setter
+    def labeltable(self, labeltable):
         """ Set the labeltable for this GiftiImage
 
         Parameters
         ----------
         labeltable : GiftiLabelTable
 
         """
-        if isinstance(labeltable, GiftiLabelTable):
-            self.labeltable = labeltable
-        else:
-            print("Not a valid GiftiLabelTable instance")
+        if not isinstance(labeltable, GiftiLabelTable):
+            raise TypeError("Not a valid GiftiLabelTable instance")
+        self._labeltable = labeltable
 
-    def get_metadata(self):
-        return self.meta
+    @np.deprecate_with_doc("Use the gifti_img.labeltable property instead.")
+    def set_labeltable(self, labeltable):
+        self.labeltable = labeltable
 
-    def set_metadata(self, meta):
+    @np.deprecate_with_doc("Use the gifti_img.labeltable property instead.")
+    def get_labeltable(self):
+        return self.labeltable
+
+    @property
+    def meta(self):
+        return self._meta
+
+    @meta.setter
+    def meta(self, meta):
         """ Set the metadata for this GiftiImage
 
         Parameters
@@ -374,12 +452,17 @@ def set_metadata(self, meta):
         -------
         None
         """
-        if isinstance(meta, GiftiMetaData):
-            self.meta = meta
-            print("New Metadata set. Be aware of changing "
-                  "coordinate transformation!")
-        else:
-            print("Not a valid GiftiMetaData instance")
+        if not isinstance(meta, GiftiMetaData):
+            raise TypeError("Not a valid GiftiMetaData instance")
+        self._meta = meta
+
+    @np.deprecate_with_doc("Use the gifti_img.labeltable property instead.")
+    def set_metadata(self, meta):
+        self.meta = meta
+
+    @np.deprecate_with_doc("Use the gifti_img.labeltable property instead.")
+    def get_meta(self):
+        return self.meta
 
     def add_gifti_data_array(self, dataarr):
         """ Adds a data array to the GiftiImage
@@ -388,24 +471,20 @@ def add_gifti_data_array(self, dataarr):
         ----------
         dataarr : GiftiDataArray
         """
-        if isinstance(dataarr, GiftiDataArray):
-            self.darrays.append(dataarr)
-            self.numDA += 1
-        else:
-            print("dataarr paramater must be of tzpe GiftiDataArray")
+        if not isinstance(dataarr, GiftiDataArray):
+            raise TypeError("Not a valid GiftiDataArray instance")
+        self.darrays.append(dataarr)
 
     def remove_gifti_data_array(self, ith):
         """ Removes the ith data array element from the GiftiImage """
         self.darrays.pop(ith)
-        self.numDA -= 1
 
     def remove_gifti_data_array_by_intent(self, intent):
         """ Removes all the data arrays with the given intent type """
         intent2remove = intent_codes.code[intent]
         for dele in self.darrays:
             if dele.intent == intent2remove:
                 self.darrays.remove(dele)
-                self.numDA -= 1
 
     def get_arrays_from_intent(self, intent):
         """ Returns a a list of GiftiDataArray elements matching
@@ -438,7 +517,6 @@ def print_summary(self):
             print(da.print_summary())
         print('----end----')
 
-
     def _to_xml_element(self):
         GIFTI = xml.Element('GIFTI', attrib={
             'Version': self.version,

nibabel/gifti/giftiio.py

@@ -0,0 +1,84 @@
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+# General Gifti Input - Output to and from the filesystem
+# Stephan Gerhard, Oktober 2010
+##############
+
+import os
+import codecs
+
+from .parse_gifti_fast import parse_gifti_file
+
+
+def read(filename):
+    """ Load a Gifti image from a file
+
+    Parameters
+    ----------
+    filename : string
+        The Gifti file to open, it has usually ending .gii
+
+    Returns
+    -------
+    img : GiftiImage
+        Returns a GiftiImage
+     """
+    if not os.path.isfile(filename):
+        raise IOError("No such file or directory: '%s'" % filename)
+    return parse_gifti_file(filename)
+
+
+def write(image, filename):
+    """ Save the current image to a new file
+
+    Parameters
+    ----------
+    image : GiftiImage
+        A GiftiImage instance to store
+    filename : string
+        Filename to store the Gifti file to
+
+    Returns
+    -------
+    None
+
+    Notes
+    -----
+    We write all files with utf-8 encoding, and specify this at the top of the
+    XML file with the ``encoding`` attribute.
+
+    The Gifti spec suggests using the following suffixes to your
+    filename when saving each specific type of data:
+
+    .gii
+        Generic GIFTI File
+    .coord.gii
+        Coordinates
+    .func.gii
+        Functional
+    .label.gii
+        Labels
+    .rgba.gii
+        RGB or RGBA
+    .shape.gii
+        Shape
+    .surf.gii
+        Surface
+    .tensor.gii
+        Tensors
+    .time.gii
+        Time Series
+    .topo.gii
+        Topology
+
+    The Gifti file is stored in endian convention of the current machine.
+    """
+    # Our giftis are always utf-8 encoded - see GiftiImage.to_xml
+    with open(filename, 'wb') as f:
+        f.write(image.to_xml())