fixed unravel, but still untested. some small improvements

particle.py

@@ -16,11 +16,10 @@ class Particles:
         self.attr = {}
         sortidx = pp[col['id'],:,0].argsort()
         idsorted = pp[col['id'],sortidx,0]
-        #assert numpy.isclose(idsorted[0],1), "Particle IDs do not start at 1."
-        #assert numpy.isclose(idsorted[-1],self.num), "Particle IDs do not end at Np."
-        #assert numpy.all(numpy.diff(idsorted)>0), "Particle IDs are not unique."
         for key in col:
-            if (key!='id') and (select_col is None or key in select_col or key in ('x','y','z')):
+            if key=='id':
+                self.add_attribute(key,pp[col[key],sortidx,0].astype('int'))
+            elif (select_col is None or key in select_col or key in ('x','y','z')):
                 self.add_attribute(key,pp[col[key],sortidx,0])
         self.period = period
         self.time = time
@@ -91,11 +90,6 @@ class Trajectories:
         for key in self.part[0].attr:
             self.attr[key] = [self.part[0].attr[key].view()]
         self.period = self.part[0].period
-        if any([period is not None for period in self.period]):
-            self._crossings = numpy.zeros((6,self.numpart,1),dtype=numpy.bool)
-        else:
-            self._crossings = None
-        return
         self.unraveled = False
     def __str__(self):
         str = 'Trajectory with\n'
@@ -124,7 +118,7 @@ class Trajectories:
                 raise TypeError("Trajectories can only be sliced by slice objects or integers.")
         return self.get_trajectory(slice_part=sl[0],slice_time=sl[1])
     @classmethod
-    def from_mat(cls,file):
+    def from_mat(cls,file,unraveled=False):
         from .helper import load_mat
         pp,col,time,ccinfo = load_mat(file,['pp','colpy','time','ccinfo'])
         period = [None,None,None]
@@ -137,12 +131,14 @@ class Trajectories:
         traj = cls(Particles(pp[:,:,0],col,time[0],period))
         for ii in range(1,ntime):
             traj += Particles(pp[:,:,ii],col,time[ii],period)
+        traj.unraveled = unraveled
         return traj
     def add_particles(self,part):
         import numpy
         # Verify part
         assert part.time>self.part[-1].time, "Time steps must be added in monotonically increasing order."
         assert part.num==self.numpart, "Number of particles is different from previous time steps."
+        assert all(part['id']==self.part[0].attr['id']), "Particle IDs differ or a not in the same order."
         assert all([part.period[ii]==self.period[ii] for ii in range(0,3)]), "Period differs!"
         for key in self.attr:
             assert key in part.attr, "Particles to be added are missing attribute '{}'".format(key)
@@ -185,58 +181,46 @@ class Trajectories:
         for ii,part in enumerate(self.part):
             time[ii] = part.time
         return time
-    def get_trajectory(self,id=None,slice_part=slice(None),slice_time=slice(None)):
-        # WARNING: slice uses array indexing instead of ID
+    def get_trajectory(self,slice_part=slice(None),slice_time=slice(None)):
         import numpy
         assert isinstance(slice_part,slice), "'slice_part' must be a slice."
         assert isinstance(slice_time,slice), "'slice_time' must be a slice."
         self._make_data_array()
-        if id is None: # npart X ndim X ntime
-            return numpy.stack([
-                self.attr['x'][slice_part,slice_time],
-                self.attr['y'][slice_part,slice_time],
-                self.attr['z'][slice_part,slice_time]],axis=0)
-        else:
-            if id<0:
-                id = self.numpart+id+1
-            assert id>=1 and id<=self.numpart, "Particle ID out-of-bounds: {:d}".format(id)
-            id = slice(id-1,id)
-            return numpy.stack([
-                self.attr['x'][id,slice_time],
-                self.attr['y'][id,slice_time],
-                self.attr['z'][id,slice_time]],axis=0)
+        return numpy.stack([
+            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):
+        #self.unravel()
+        #if id is None: # npart X ndim X ntime
         return
     def unravel(self):
+        import numpy
         if self.unraveled: return
-        if self._crossings is None: return
-        self._compute_crossings()
-        # do sth
+        raise NotImplementedError('Implemented but untested!')
+        self._make_data_array()
+        for axis in range(0,3):
+            if self.period[axis] is not None:
+                key = ('x','y','z')[axis]
+                #posdiff = (self.part[ii].attr[key]-self.part[ii-1].attr[key]).squeeze()
+                posdiff = self.attr[key][:,1:]-self.attr[key][:,0:-1]
+                coeff = -numpy.sign(posdiff)*(numpy.abs(posdiff)>0.5*self.period[axis])
+                coeff = numpy.cumsum(coeff,axis=1)
+                self.attr[key][:,1:] += coeff*self.period[axis]
         self.unraveled = True
         return
     def ravel(self):
         if not self.unraveled: return
+        raise NotImplementedError('Implemented but untested!')
+        for axis in range(0,3):
+            if self.period[axis] is not None:
+                key = ('x','y','z')[axis]
+                self.part[ii].attr[key] %= self.period[axis]
         self.unraveled = False
         return
-    def _compute_crossings(self):
-        import numpy
-        if self._crossings is not None: # None means no periodicity
-            num_computed = self._crossings.shape[1]
-            if num_computed==self.numtime:
-                return
-            crossings = numpy.zeros((6,self.numpart,self.numtime),dtype=numpy.bool)
-            crossings[:,:,0:num_computed] = self._crossings
-            for ii in range(num_computed,self.numtime):
-                for axis in range(0,3):
-                    if self.period[axis] is not None:
-                        key = ('x','y','z')[axis]
-                        posdiff = (self.part[ii].attr[key]-self.part[ii-1].attr[key]).squeeze()
-                        doesCross = abs(posdiff)>0.5*self.period[axis]
-                        upCross   = numpy.logical_and(posdiff<0,doesCross)
-                        crossings[2*axis,:,ii] = doesCross
-                        crossings[2*axis+1,:,ii] = upCross
-            self._crossings = crossings
     def _make_data_array(self):
+        '''Transforms self.attr[key] to a numpy array of dimension npart X ntime
+        and updates self.part[itime].attr[key] to views on self.attr[key][:,itime].'''
         import numpy
         #print('DEBUG: _make_data_array')
         if not self._is_data_list: 
@@ -250,6 +234,8 @@ class Trajectories:
         self._is_data_list = False
         return
     def _make_data_list(self):
+        '''Transforms self.attr[key] to a list of length ntime of numpy arrays of 
+        dimension npart and updates self.part[itime].attr[key] to views on self.attr[key][itime].'''
         import numpy
         #print('DEBUG: _make_data_list')
         if self._is_data_list: 
@@ -264,7 +250,6 @@ class Trajectories:
         return
 
 
-
 def sort(pp,col):
     ncol,npart,ntime = pp.shape
     assert('id' in col)