From e6d4a78dfefaa48cd66744ec40d2e80979e2c81b Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 14 Sep 2018 13:44:05 -0500
Subject: [PATCH] Added rotate and translate operations to segments
---
mrdna/segmentmodel.py | 68 ++++++++++++++++++++++++++++++++++++++-----
1 file changed, 60 insertions(+), 8 deletions(-)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index b880154..0682714 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -398,11 +398,63 @@ class Segment(ConnectableElement, Group):
def set_splines(self, contours, coords):
tck, u = interpolate.splprep( coords.T, u=contours, s=0, k=1)
- self.position_spline_params = tck
+ self.position_spline_params = (tck,u)
def set_orientation_splines(self, contours, quaternions):
tck, u = interpolate.splprep( quaternions.T, u=contours, s=0, k=1)
- self.quaternion_spline_params = tck
+ self.quaternion_spline_params = (tck,u)
+
+ def get_center(self):
+ tck, u = self.position_spline_params
+ return np.mean(self.contour_to_position(u), axis=0)
+
+ def __filter_contours(contours, positions, position_filter, contour_filter):
+ u = contours
+ r = positions
+
+ ## Filter
+ ids = list(range(len(u)))
+ if contour_filter is not None:
+ ids = list(filter(lambda i: contour_filter(u[i]), ids))
+ if position_filter is not None:
+ ids = list(filter(lambda i: position_filter(r[i,:]), ids))
+ return ids
+
+ def translate(self, translation_vector, about=None, position_filter=None, contour_filter=None):
+ dr = np.array(translation_vector)
+ tck, u = self.position_spline_params
+ r = self.contour_to_position(u)
+
+ ids = Segment.__filter_contours(u, r, position_filter, contour_filter)
+
+ ## Translate
+ r[ids,:] = r[ids,:] + dr[np.newaxis,:]
+ self.set_position_splines(r,u)
+
+ def rotate(self, rotation_matrix, about=None, position_filter=None, contour_filter=None):
+ tck, u = self.position_spline_params
+ r = self.contour_to_position(u)
+
+ ids = Segment.__filter_contours(u, r, position_filter, contour_filter)
+
+ if about is None:
+ ## TODO: do this more efficiently
+ r[ids,:] = np.array([rotation_matrix.dot(r[i,:]) for i in range(r.shape[0])])
+ else:
+ dr = np.array(about)
+ ## TODO: do this more efficiently
+ r[ids,:] = np.array([rotation_matrix.dot(r[i,:]-dr) + dr for i in range(r.shape[0])])
+
+ self.set_position_splines(r,u)
+
+ if self.quaternion_spline_params is not None:
+ ## TODO: performance: don't shift between quaternion and matrix representations so much
+ tck, u = self.quaternion_spline_params
+ orientations = [self.contour_to_orientation(v)) for v in u]
+ for i in ids:
+ orientations[i,:] = rotation_matrix.dot(orientations[i])
+ quats = [quaternion_from_matrix(o) for o in orientations]
+ self.set_orientation_splines(quats,u)
def _set_splines_from_ends(self):
self.quaternion_spline_params = None
@@ -426,12 +478,12 @@ class Segment(ConnectableElement, Group):
return (nt_pos+0.5)/(self.num_nt)
def contour_to_position(self,s):
- p = interpolate.splev( s, self.position_spline_params )
+ p = interpolate.splev( s, self.position_spline_params[0] )
if len(p) > 1: p = np.array(p).T
return p
def contour_to_tangent(self,s):
- t = interpolate.splev( s, self.position_spline_params, der=1 )
+ t = interpolate.splev( s, self.position_spline_params[0], der=1 )
t = (t / np.linalg.norm(t,axis=0))
return t.T
@@ -456,7 +508,7 @@ class Segment(ConnectableElement, Group):
orientation = rotationAboutAxis( axis, self.twist_per_nt*self.contour_to_nt_pos(s), normalizeAxis=False )
orientation = orientation.dot(orientation0)
else:
- q = interpolate.splev( s, self.quaternion_spline_params )
+ q = interpolate.splev( s, self.quaternion_spline_params[0] )
if len(q) > 1: q = np.array(q).T # TODO: is this needed?
orientation = quaternion_to_matrix(q)
@@ -885,7 +937,7 @@ class DoubleStrandedSegment(Segment):
## Set up interpolation for azimuthal angles
a = np.array([self.start_position,self.end_position]).T
tck, u = interpolate.splprep( a, u=[0,1], s=0, k=1)
- self.position_spline_params = tck
+ self.position_spline_params = (tck,u)
## TODO: initialize sensible spline for orientation
@@ -1600,7 +1652,7 @@ class SegmentModel(ArbdModel):
# if ret[2] > 0:
# pdb.set_trace()
- s.position_spline_params = tck
+ s.position_spline_params = (tck,ret[1][0])
""" Get twist """
cb = [e for e in zip(contours,beads) if 'orientation_bead' in e[1].__dict__]
@@ -1634,7 +1686,7 @@ class SegmentModel(ArbdModel):
quats = np.array(quats)
# tck, u = interpolate.splprep( quats.T, u=contours, s=3, k=3 ) ;# cubic spline not as good
tck, u = interpolate.splprep( quats.T, u=contours, s=0, k=1 )
- s.quaternion_spline_params = tck
+ s.quaternion_spline_params = (tck,u)
def _generate_bead_model(self,
max_basepairs_per_bead = 7,
--
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