can plot trajectories now

particle.py

@@ -94,7 +94,8 @@ class Trajectories:
     def __str__(self):
         str = 'Trajectory with\n'
         str+= ' time steps: {:d}\n'.format(self.numtime)
-        str+= ' particles: {:d}'.format(self.numpart)
+        str+= ' particles: {:d}\n'.format(self.numpart)
+        str+= ' unraveled: {}'.format(self.unraveled)
         return str
     def __iadd__(self,other):
         if isinstance(other,Trajectories):
@@ -116,7 +117,7 @@ class Trajectories:
                 sl.append(x)
             else:
                 raise TypeError("Trajectories can only be sliced by slice objects or integers.")
-        return self.get_trajectory(slice_part=sl[0],slice_time=sl[1])
+        return self.get_trajectories(slice_part=sl[0],slice_time=sl[1])
     @classmethod
     def from_mat(cls,file,unraveled=False):
         from .helper import load_mat
@@ -181,7 +182,8 @@ class Trajectories:
         for ii,part in enumerate(self.part):
             time[ii] = part.time
         return time
-    def get_trajectory(self,slice_part=slice(None),slice_time=slice(None)):
+    def get_trajectories(self,slice_part=slice(None),slice_time=slice(None)):
+        '''Get (x,y,z) trajectories in numpy array of dimension (3,npart,ntime).'''
         import numpy
         assert isinstance(slice_part,slice), "'slice_part' must be a slice."
         assert isinstance(slice_time,slice), "'slice_time' must be a slice."
@@ -190,10 +192,48 @@ class Trajectories:
             self.attr['x'][slice_part,slice_time],
             self.attr['y'][slice_part,slice_time],
             self.attr['z'][slice_part,slice_time]],axis=0)
-    def get_segments(self,id=None):
+    def get_trajectories_segmented(self,slice_part=slice(None),slice_time=slice(None),restore_ravel_state=True):
-        #self.unravel()
+        '''Get (x,y,z) segments of trajectories as a tuple (len: npart) of 
-        #if id is None: # npart X ndim X ntime
+        lists (len: nsegments) of numpy arrays (shape: 3 X ntime of the segment)'''
-        return
+        import numpy
+        assert isinstance(slice_part,slice), "'slice_part' must be a slice."
+        assert isinstance(slice_time,slice), "'slice_time' must be a slice."
+        was_unraveled = self.unraveled
+        self.unravel()
+        xyzpath = self.get_trajectories(slice_part=slice_part,slice_time=slice_time)
+        npart = xyzpath.shape[1]
+        ntime = xyzpath.shape[2]
+        # Initialize output and helper arrays
+        out = tuple([] for ii in range(npart))
+        lastJump = numpy.zeros(npart,dtype=numpy.uint)
+        lastPeriod = numpy.zeros((3,npart),dtype=numpy.int)
+        for axis in range(3):
+            if self.period[axis] is not None:
+                lastPeriod[axis,:] = numpy.floor_divide(xyzpath[axis,:,0],self.period[axis])
+        # Construct output tuple
+        for itime in range(1,ntime+1):
+            thisPeriod = numpy.zeros((3,npart),dtype=int)
+            if itime==ntime:
+                hasJumped = numpy.ones(npart,dtype=bool)
+            else:
+                for axis in range(3):
+                    if self.period[axis] is not None:
+                        thisPeriod[axis,:] = numpy.floor_divide(xyzpath[axis,:,itime],self.period[axis])
+                hasJumped = numpy.any(thisPeriod!=lastPeriod,axis=0)
+            for ipart in range(npart):
+                if hasJumped[ipart]:
+                    sl = slice(lastJump[ipart],itime)
+                    segment = xyzpath[:,ipart,sl].copy()
+                    for axis in range(3):
+                        if self.period[axis] is not None:
+                            segment[axis,:] -= lastPeriod[axis,ipart]*self.period[axis] 
+                    out[ipart].append(segment)
+                    lastJump[ipart] = itime
+            lastPeriod = thisPeriod
+        # Restore previous ravel state
+        if restore_ravel_state and not was_unraveled:
+            self.ravel()
+        return out
     def unravel(self):
         import numpy
         if self.unraveled: return

visu.py

@@ -47,6 +47,23 @@ def add_particles(plotter,part,
         opacity=opacity)
     return
 
+def add_trajectories(plotter,traj,
+                        name=None,
+                        color='black',
+                        scalars=None,cmap=None,clim=None,
+                        opacity=1.0):
+    import pyvista
+    segments = traj.get_trajectories_segmented()
+    lines = pyvista.PolyData()
+    for part in segments:
+        for seg in part:
+            lines += pyvista.helpers.lines_from_points(seg.transpose())
+    plotter.add_mesh(lines,name=name,
+            color=color,
+            scalars=scalars,cmap=cmap,clim=clim,
+            opacity=opacity)
+    return
+
 def chunk_to_pvmesh(chunk,gridg):
     import pyvista
     mesh = pyvista.UniformGrid()