First draft

Author: MarcCote

nibabel/streamlines/__init__.py

@@ -0,0 +1,24 @@
+from nibabel.openers import Opener
+
+from nibabel.streamlines.utils import detect_format
+
+
+def load(fileobj):
+    ''' Load a file of streamlines, return instance associated to file format
+
+    Parameters
+    ----------
+    fileobj : string or file-like object
+       If string, a filename; otherwise an open file-like object
+       pointing to a streamlines file (and ready to read from the beginning
+       of the streamlines file's header)
+
+    Returns
+    -------
+    obj : instance of ``StreamlineFile``
+       Returns an instance of a ``StreamlineFile`` subclass corresponding to
+       the format of the streamlines file ``fileobj``.
+    '''
+    fileobj = Opener(fileobj)
+    streamlines_file = detect_format(fileobj)
+    return streamlines_file.load(fileobj)

nibabel/streamlines/base_format.py

@@ -0,0 +1,39 @@
+
+class StreamlineFile:
+    @staticmethod
+    def get_magic_number():
+        raise NotImplementedError()
+
+    @staticmethod
+    def is_correct_format(cls, fileobj):
+        raise NotImplementedError()
+
+    def get_header(self):
+        raise NotImplementedError()
+
+    def get_streamlines(self, as_generator=False):
+        raise NotImplementedError()
+
+    def get_scalars(self, as_generator=False):
+        raise NotImplementedError()
+
+    def get_properties(self, as_generator=False):
+        raise NotImplementedError()
+
+    @classmethod
+    def load(cls, fileobj):
+        raise NotImplementedError()
+
+    def save(self, filename):
+        raise NotImplementedError()
+
+    def __iter__(self):
+        raise NotImplementedError()
+
+
+class DynamicStreamlineFile(StreamlineFile):
+    def append(self, streamlines):
+        raise NotImplementedError()
+
+    def __iadd__(self, streamlines):
+        return self.append(streamlines)       

nibabel/streamlines/header.py

@@ -0,0 +1,15 @@
+class Field:
+    NB_STREAMLINES = "nb_streamlines"
+    STEP_SIZE = "step_size"
+    METHOD = "method"
+    NB_SCALARS_PER_POINT = "nb_scalars_per_point"
+    NB_PROPERTIES_PER_STREAMLINE = "nb_properties_per_streamline"
+    NB_POINTS = "nb_points"
+    VOXEL_SIZES = "voxel_sizes"
+    DIMENSIONS = "dimensions"
+    MAGIC_NUMBER = "magic_number"
+    ORIGIN = "origin"
+    VOXEL_TO_WORLD = "voxel_to_world"
+    VOXEL_ORDER = "voxel_order"
+    WORLD_ORDER = "world_order"
+    ENDIAN = "endian"

nibabel/streamlines/tests/__init__.py

@@ -0,0 +1,56 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+from pdb import set_trace as dbg
+
+from os.path import join as pjoin, dirname
+
+from numpy.testing import (assert_equal,
+                           assert_almost_equal,
+                           assert_array_equal,
+                           assert_array_almost_equal,
+                           assert_raises)
+
+DATA_PATH = pjoin(dirname(__file__), 'data')
+
+import nibabel as nib
+from nibabel.streamlines.header import Field
+
+
+def test_load_file():
+    # Test loading empty file
+    # empty_file = pjoin(DATA_PATH, "empty.trk")
+    # empty_trk = nib.streamlines.load(empty_file)
+
+    # hdr = empty_trk.get_header()
+    # points = empty_trk.get_points(as_generator=False)
+    # scalars = empty_trk.get_scalars(as_generator=False)
+    # properties = empty_trk.get_properties(as_generator=False)
+    
+    # assert_equal(hdr[Field.NB_STREAMLINES], 0)
+    # assert_equal(len(points), 0)
+    # assert_equal(len(scalars), 0)
+    # assert_equal(len(properties), 0)
+
+    # for i in empty_trk: pass  # Check if we can iterate through the streamlines.
+
+    # Test loading non-empty file
+    trk_file = pjoin(DATA_PATH, "uncinate.trk")
+    trk = nib.streamlines.load(trk_file)
+
+    hdr = trk.get_header()
+    points = trk.get_points(as_generator=False)
+    1/0
+    scalars = trk.get_scalars(as_generator=False)
+    properties = trk.get_properties(as_generator=False)
+    
+    assert_equal(hdr[Field.NB_STREAMLINES] > 0, True)
+    assert_equal(len(points) > 0, True)
+    #assert_equal(len(scalars), 0)
+    #assert_equal(len(properties), 0)
+
+    for i in trk: pass  # Check if we can iterate through the streamlines.
+    
+
+if __name__ == "__main__":
+    test_load_file()