From 608852df839498244e3591ef9170d260f2948b95 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Tue, 12 Feb 2019 10:53:28 +0100
Subject: [PATCH] rotation paper has angle as last component

---
 processing/post/addOrientations.py  |  7 +++++--
 processing/post/rotateData.py       |  3 ++-
 processing/pre/geom_addPrimitive.py |  3 ++-
 python/damask/orientation.py        | 16 ++++++++--------
 4 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/processing/post/addOrientations.py b/processing/post/addOrientations.py
index 8353e0403..c25bfed39 100755
--- a/processing/post/addOrientations.py
+++ b/processing/post/addOrientations.py
@@ -108,8 +108,11 @@ if np.sum(input) != 1: parser.error('needs exactly one input format.')
                          (options.quaternion,representations['quaternion'][1],'quaternion'),
                         ][np.where(input)[0][0]]                                                    # select input label that was requested
 
-r = damask.Rotation.fromAngleAxis(options.crystalrotation,options.degrees)                          # crystal frame rotation
-R = damask.Rotation.fromAngleAxis(options.labrotation,options.degrees)                              #     lab frame rotation
+crystalrotation = np.array(options.crystalrotation[1:4] + (options.crystalrotation[0],))            # Compatibility hack
+labrotation     = np.array(options.labrotation[1:4],    + (options.labrotation[0],))                # Compatibility hack
+r = damask.Rotation.fromAngleAxis(crystalrotation,options.degrees)                                  # crystal frame rotation
+R = damask.Rotation.fromAngleAxis(labrotation,options.degrees)                                      #     lab frame rotation
+
 
 # --- loop over input files ------------------------------------------------------------------------
 
diff --git a/processing/post/rotateData.py b/processing/post/rotateData.py
index 1aafe7eb9..5be38f1e8 100755
--- a/processing/post/rotateData.py
+++ b/processing/post/rotateData.py
@@ -40,7 +40,8 @@ parser.set_defaults(rotation = (0.,1.,0.,0.),
 if options.data is None:
   parser.error('no data column specified.')
 
-r = damask.Rotation.fromAngleAxis(options.rotation,options.degrees,normalise=True)
+rotation = np.array(options.rotation[1:4]+(options.rotation[0],))                                   # Compatibility hack
+r = damask.Rotation.fromAngleAxis(rotation,options.degrees,normalise=True)
 
 # --- loop over input files -------------------------------------------------------------------------
 
diff --git a/processing/pre/geom_addPrimitive.py b/processing/pre/geom_addPrimitive.py
index e0d1094cf..8e512c44d 100755
--- a/processing/pre/geom_addPrimitive.py
+++ b/processing/pre/geom_addPrimitive.py
@@ -63,7 +63,8 @@ parser.set_defaults(center = (.0,.0,.0),
 if options.dimension is None:
   parser.error('no dimension specified.')   
 if options.angleaxis is not None:
-  rotation = damask.Rotation.fromAngleAxis(options.angleaxis,options.degrees,normalise=True)
+  ax = np.array(options.angleaxis[1:4] + (options.angleaxis[0],))   # Compatibility hack
+  rotation = damask.Rotation.fromAngleAxis(ax,options.degrees,normalise=True)
 elif options.quaternion is not None:
   rotation = damask.Rotation.fromQuaternion(options.quaternion)
 else:
diff --git a/python/damask/orientation.py b/python/damask/orientation.py
index 85f3fb173..442a98f6e 100644
--- a/python/damask/orientation.py
+++ b/python/damask/orientation.py
@@ -267,7 +267,7 @@ class Rotation:
                     degrees = False):
                       
       ax = qu2ax(self.quaternion.asArray())
-      if degrees: ax[0] = np.degrees(ax[0])
+      if degrees: ax[3] = np.degrees(ax[3])
       
       return ax
       
@@ -321,13 +321,13 @@ class Rotation:
                       P = -1):
       
       ax = angleAxis if isinstance(angleAxis, np.ndarray) else np.array(angleAxis)
-      if P > 0: ax[1:4] *= -1                                                                       # convert from P=1 to P=-1
-      if degrees:   ax[0] = np.radians(ax[0])
-      if normalise: ax[1:4] /=np.linalg.norm(ax[1:4])
-      if ax[0] < 0.0 or ax[0] > np.pi:
-        raise ValueError('Axis angle rotation angle outside of [0..π].\n'.format(ax[0]))
-      if not np.isclose(np.linalg.norm(ax[1:4]), 1.0):
-        raise ValueError('Axis angle rotation axis is not of unit length.\n{} {} {}'.format(*ax[1:4]))
+      if P > 0: ax[0:3] *= -1                                                                       # convert from P=1 to P=-1
+      if degrees:   ax[3] = np.radians(ax[3])
+      if normalise: ax[0:3] /=np.linalg.norm(ax[0:3])
+      if ax[3] < 0.0 or ax[3] > np.pi:
+        raise ValueError('Axis angle rotation angle outside of [0..π].\n'.format(ax[3]))
+      if not np.isclose(np.linalg.norm(ax[0:3]), 1.0):
+        raise ValueError('Axis angle rotation axis is not of unit length.\n{} {} {}'.format(*ax[0:3]))
       
       return cls(ax2qu(ax))