[med-svn] [python-mne] 340/376: ENH: adding transform_coordinates

[Yaroslav Halchenko]

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yoh pushed a commit to annotated tag v0.1
in repository python-mne.

commit 9caac935b0d25c8a918b68210d600dc11c6a164e
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date:   Tue Aug 16 18:15:59 2011 -0400

    ENH: adding transform_coordinates
---
 mne/__init__.py   |   1 +
 mne/transforms.py | 109 +++++++++++++++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 109 insertions(+), 1 deletion(-)

diff --git a/mne/__init__.py b/mne/__init__.py
index 5a01bf5..92379c9 100644
--- a/mne/__init__.py
+++ b/mne/__init__.py
@@ -12,6 +12,7 @@ from .source_space import read_source_spaces
 from .epochs import Epochs
 from .label import label_time_courses, read_label
 from .misc import parse_config, read_reject_parameters
+from .transforms import transform_coordinates
 import fiff
 import artifacts
 import stats
diff --git a/mne/transforms.py b/mne/transforms.py
index 2b07e49..8908e5a 100644
--- a/mne/transforms.py
+++ b/mne/transforms.py
@@ -2,7 +2,9 @@ import copy
 import numpy as np
 from scipy import linalg
 
-# from .fiff import FIFF
+from .fiff import FIFF
+from .fiff.open import fiff_open
+from .fiff.tag import read_tag
 
 
 def invert_transform(trans):
@@ -53,6 +55,111 @@ def transform_source_space_to(src, dest, trans):
     return res
 
 
+def transform_coordinates(filename, pos, orig, dest):
+    """Transform coordinates between various MRI-related coordinate frames
+
+    Parameters
+    ----------
+    filename: string
+        Name of a fif file containing the coordinate transformations
+        This file can be conveniently created with mne_collect_transforms
+    pos: array of shape N x 3
+        array of locations to transform (in meters)
+    orig: 'meg' | 'mri'
+        Coordinate frame of the above locations.
+        'meg' is MEG head coordinates
+        'mri' surface RAS coordinates
+    dest: 'meg' | 'mri' | 'fs_tal' | 'mni_tal'
+        Coordinate frame of the result.
+        'mni_tal' is MNI Talairach
+        'fs_tal' is FreeSurfer Talairach
+
+    Return
+    ------
+    trans_pos: array of shape N x 3
+        The transformed locations
+
+    Example
+    -------
+    >>> transform_coordinates('all-trans.fif', np.eye(3), 'meg', 'fs_tal')
+    >>> transform_coordinates('all-trans.fif', np.eye(3), 'mri', 'mni_tal')
+    """
+    #   Read the fif file containing all necessary transformations
+    fid, tree, directory = fiff_open(filename)
+
+    coord_names = dict(mri=FIFF.FIFFV_COORD_MRI,
+                       meg=FIFF.FIFFV_COORD_HEAD,
+                       mni_tal=FIFF.FIFFV_MNE_COORD_MNI_TAL,
+                       fs_tal=FIFF.FIFFV_MNE_COORD_FS_TAL)
+
+    orig = coord_names[orig]
+    dest = coord_names[dest]
+
+    T0 = T1 = T2 = T3plus = T3minus = None
+    for d in directory:
+        if d.kind == FIFF.FIFF_COORD_TRANS:
+            tag = read_tag(fid, d.pos)
+            trans = tag.data
+            if (trans['from'] == FIFF.FIFFV_COORD_MRI and
+                trans['to'] == FIFF.FIFFV_COORD_HEAD):
+                T0 = invert_transform(trans)
+            elif (trans['from'] == FIFF.FIFFV_COORD_MRI and
+                  trans['to'] == FIFF.FIFFV_MNE_COORD_RAS):
+                T1 = trans
+            elif (trans['from'] == FIFF.FIFFV_MNE_COORD_RAS and
+                  trans['to'] == FIFF.FIFFV_MNE_COORD_MNI_TAL):
+                T2 = trans
+            elif trans['from'] == FIFF.FIFFV_MNE_COORD_MNI_TAL:
+                if trans['to'] == FIFF.FIFFV_MNE_COORD_FS_TAL_GTZ:
+                    T3plus = trans
+                elif trans['to'] == FIFF.FIFFV_MNE_COORD_FS_TAL_LTZ:
+                    T3minus = trans
+    fid.close()
+    #
+    #   Check we have everything we need
+    #
+    if ((orig == FIFF.FIFFV_COORD_HEAD and T0 is None) or (T1 is None)
+            or (T2 is None) or (dest == FIFF.FIFFV_MNE_COORD_FS_TAL and
+                                ((T3minus is None) or (T3minus is None)))):
+        raise ValueError('All required coordinate transforms not found')
+
+    #
+    #   Go ahead and transform the data
+    #
+    if pos.shape[1] != 3:
+        raise ValueError('Coordinates must be given in a N x 3 array')
+
+    if dest == orig:
+        trans_pos = pos.copy()
+    else:
+        n_points = pos.shape[0]
+        pos = np.c_[pos, np.ones(n_points)].T
+        if orig == FIFF.FIFFV_COORD_HEAD:
+            pos = np.dot(T0['trans'], pos)
+        elif orig != FIFF.FIFFV_COORD_MRI:
+            raise ValueError('Input data must be in MEG head or surface RAS '
+                             'coordinates')
+
+        if dest == FIFF.FIFFV_COORD_HEAD:
+            pos = np.dot(linalg.inv(T0['trans']), pos)
+        elif dest != FIFF.FIFFV_COORD_MRI:
+            pos = np.dot(np.dot(T2['trans'], T1['trans']), pos)
+            if dest != FIFF.FIFFV_MNE_COORD_MNI_TAL:
+                if dest == FIFF.FIFFV_MNE_COORD_FS_TAL:
+                    for k in xrange(n_points):
+                        if pos[2, k] > 0:
+                            pos[:, k] = np.dot(T3plus['trans'], pos[:, k])
+                        else:
+                            pos[:, k] = np.dot(T3minus['trans'], pos[:, k])
+                else:
+                    raise ValueError('Illegal choice for the output '
+                                     'coordinates')
+
+        trans_pos = pos[:3, :].T
+
+    return trans_pos
+
+
 # def transform_meg_chs(chs, trans):
 #     """
 #     %

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