clipping and thresholding for particles; improvements for field

field.py

@@ -214,7 +214,11 @@ class Field3d:
         data = self.data[sl]
         return Field3d(data,origin,spacing,deep=deep)
 
-    def clip(self,position,axis,invert=False,deep=False):
+    def clip(self,position,axis,invert=False,deep=False,is_relative=False):
+        '''Extracts a subfield by clipping with a plane with normal pointing
+           direction specified by 'axis'.'''
+        if is_relative:
+            coord = self.origin[axis] + coord*self.dim(axis=axis)*self.spacing[axis]
         idx_clip = self.nearest_gridpoint(coord,axis=axis,lower=True)
         sl = 3*[slice(None)]
         origin_  = self.origin
@@ -228,21 +232,29 @@ class Field3d:
         return Field3d(data_,origin_,spacing_,deep=deep)
 
     def clip_box(self,bounds,deep=False,is_relative=False):
+        '''Extracts a subfield by clipping with a box.'''
         if is_relative:
             bounds = tuple(self.origin[ii//2] + bounds[ii]*self.dim(ii//2)*self.spacing[ii//2] for ii in range(6))
-            print(bounds)
         idx_lo = self.nearest_gridpoint((bounds[0],bounds[2],bounds[4]),lower=True)
         idx_hi = self.nearest_gridpoint((bounds[1],bounds[3],bounds[5]),lower=True)
-        origin_  = self.origin
-        spacing_ = self.spacing
         idx_lo = tuple(0 if idx_lo[axis]<0 else idx_lo[axis] for axis in range(3))
         idx_hi = tuple(0 if idx_hi[axis]<0 else idx_hi[axis] for axis in range(3))
         sl_ = tuple([slice(idx_lo[0],idx_hi[0]+1),
                      slice(idx_lo[1],idx_hi[1]+1),
                      slice(idx_lo[2],idx_hi[2]+1)])
+        origin_ = tuple(self.origin[axis]+idx_lo[axis]*self.spacing[axis] for axis in range(3))
+        spacing_ = self.spacing
         data_ = self.data[sl_]
         return Field3d(data_,origin_,spacing_,deep=deep)
 
+    def threshold(self,val,invert=False):
+        '''Returns a binary array indicating which grid points are above,
+           or in case of invert=True below, a given threshold.'''
+        if invert:
+            return self.data>=val
+        else:
+            return self.data<val
+
     def coordinate(self,idx,axis=None):
         if axis is None:
             assert len(idx)==3, "If 'axis' is None, 'idx' must be a tuple/list of length 3."

helper.py

@@ -81,4 +81,11 @@ def h5read(file,name='data'):
     f = file if is_open else h5py.File(file,'r')
     data = f[name][:]
     if not is_open: f.close()
-    return data
+    return data
+
+def convert_coordinate_to_absolute(coord,bounds):
+    assert len(coord) in (3,6)
+    if len(coord)==3:
+        return tuple(bounds[2*ii]+(bounds[2*ii+1]-bounds[2*ii])*coord[ii] for ii in range(3))
+    else:
+        return tuple(bounds[2*(ii//2)]+(bounds[2*(ii//2)+1]-bounds[2*(ii//2)])*coord[ii] for ii in range(6))

particle.py

@@ -29,6 +29,7 @@ class Particles:
         self.period = tuple(period)
         self.frame_velocity = np.zeros(3)
         return
+
     @classmethod
     def from_array(cls,pp,col,time,period,select_col=None):
         assert 'id' in col, "Need column 'id' to initialize Particles"
@@ -47,14 +48,14 @@ class Particles:
             if (select_col is None or key in select_col or key in ('id','x','y','z')):
                 attr[key] = pp[col[key],:,0].squeeze()
         return cls(num,time,attr,period)
+
     def __getitem__(self,val):
         if isinstance(val,int):
             lo,hi = val,val+1
             hi = hi if hi!=0 else None
             val = slice(lo,hi)
-        elif not isinstance(val,slice):
-            raise TypeError("Particles can only be sliced by slice objects or integers.")
         return self._slice(val)
+
     def __str__(self):
         str = '{:d} particles with\n'.format(self.num)
         str+= ' time: {}\n'.format(self.time)
@@ -65,17 +66,26 @@ class Particles:
         str+= ' period: {}\n'.format(self.period)
         str+= ' frame velocity: {}'.format(self.frame_velocity)
         return str
-    def _slice(self,slice_part=slice(None)):
+
+    def _slice(self,slice_part=None):
+        assert slice_part is None or \
+               isinstance(slice_part,slice) or \
+               (isinstance(slice_part,np.ndarray) and 
+                slice_part.dtype==bool and 
+                slice_part.shape[0]==self.num),\
+               "Slicing requires int, slice or logical array."
         attr = {}
         for key in self.attr:
             attr[key] = self.attr[key][slice_part]
         num = attr['id'].shape[0]
         return Particles(num,self.time,attr,self.period)
+
     def copy(self):
         attr = {}
         for key in self.attr:
             attr[key] = self.attr[key].copy()
         return Particles(self.num,self.time,attr,self.period)
+
     def add_attribute(self,key,val):
         if isinstance(val,(tuple,list,np.ndarray)):
             assert len(val)==self.num and val.ndim==1, "Invalid 'val'."
@@ -83,10 +93,13 @@ class Particles:
         else:
             self.attr[key] = np.full(self.num,val)
         return
+
     def del_attribute(self,key):
         del self.attr[key]
+
     def get_attribute(self,key):
         return self.attr[key]
+
     def get_position(self,axis=None):
         if axis is None:
             return np.vstack([self.attr[key].copy() for key in ('x','y','z')])
@@ -94,14 +107,17 @@ class Particles:
             assert axis<3, "'axis' must be smaller than 3."
             key = ('x','y','z')[axis]
             return self.attr[key].copy()
+
     def has_attribute(self,key):
         return key in self.attr
+
     def translate(self,translation,axis=0):
         '''Translates particles. Periodicity must be enforced manually.'''
         assert axis<3, "'axis' must be smaller than 3."
         key = ('x','y','z')[axis]
         self.attr[key] += translation
         return
+
     def set_frame_velocity(self,val,axis=0):
         '''Adjust frame of reference by translating particles by
         time*frame_velocity and subtracting frame_velocity from 
@@ -114,6 +130,7 @@ class Particles:
             self.attr[key] -= valdiff
         self.frame_velocity[axis] = val
         return
+
     def enforce_periodicity(self,axis=None):
         if axis is None:
             for ii in range(3):
@@ -123,6 +140,7 @@ class Particles:
                 key = ('x','y','z')[axis]
                 self.attr[key] %= self.period[axis]
         return
+
     def position_with_duplicates(self,ipart,padding=0.0):
         pos  = np.array(
             (self.attr['x'][ipart],
@@ -144,6 +162,7 @@ class Particles:
                         tmp[axis] = tmp[axis]-self.period[axis]
                         posd.append(tmp)
         return posd
+
     def mask_field(self,fld,cval=np.nan,padding=0.0):
         '''Fills grid points which lie inside of solid phase with values.'''
         assert self.has_attribute('r'), "Attribute 'r' required."
@@ -162,6 +181,32 @@ class Particles:
                 dist = (xsf-pos[0])**2 + (ysf-pos[1])**2 + (zsf-pos[2])**2
                 sf.data[dist<=rp*rp] = cval
         return
+
+    def clip(self,position,axis,invert=False):
+        '''Clips particles by a plane with normal pointing
+           direction specified by 'axis'.'''
+        return self.threshold(('x','y','z')[axis],position,invert=(not invert))
+
+    def clip_box(self,bounds,invert=False):
+        '''Extracts particls within a bounding box.'''
+        li = np.logical_and(np.logical_and(
+                np.logical_and(self.attr['x']>=bounds[0],self.attr['x']<=bounds[1]),
+                np.logical_and(self.attr['y']>=bounds[2],self.attr['y']<=bounds[3])),
+                np.logical_and(self.attr['z']>=bounds[4],self.attr['z']<=bounds[5]))
+        if invert:
+            np.logical_not(li,li)
+        return self._slice(li)
+
+    def threshold(self,key,val,invert=False):
+        '''Returns particles for which specified attribute is above,
+           or in case invert=True below, the specified threshold.'''
+        assert key in self.attr, "'key' not found in attr."
+        if invert:
+            li = self.attr[key]<val
+        else:
+            li = self.attr[key]>=val
+        return self._slice(li)
+
     def to_vtk(self,deep=False):
         import pyvista as pv
         position = np.vstack([self.attr[key] for key in ('x','y','z')]).transpose()
@@ -169,6 +214,7 @@ class Particles:
         for key in self.attr:
             mesh[key] = self.attr[key]
         return mesh
+
     def glyph(self,theta_resolution=30,phi_resolution=30,deep=False):
         import pyvista as pv
         assert self.has_attribute('r'), "Attribute 'r' required."