Merge pull request #46 from ChristopherMayes/slice_stats_dev

Add methods for slice_statistics and plotting into ParticleGroup

pmd_beamphysics/labels.py

@@ -36,6 +36,20 @@
  'gamma': r'\gamma',
  'theta': r'\theta',
  'charge': 'Q',
+ 'twiss_alpha_x'     : 'Twiss\ '+r'\alpha_x',
+ 'twiss_beta_x'      : 'Twiss\ '+r'\beta_x',   
+ 'twiss_gamma_x'     : 'Twiss\ '+r'\gamma_x',   
+ 'twiss_eta_x'       : 'Twiss\ '+r'\eta_x',   
+ 'twiss_etap_x'      : 'Twiss\ '+r"\eta'_x",     
+ 'twiss_emit_x'      : 'Twiss\ '+r'\epsilon_{x}',
+ 'twiss_norm_emit_x' : 'Twiss\ '+r'\epsilon_{n, x}',
+ 'twiss_alpha_y'     : 'Twiss\ '+r'\alpha_y',
+ 'twiss_beta_y'      : 'Twiss\ '+r'\beta_y',   
+ 'twiss_gamma_y'     : 'Twiss\ '+r'\gamma_y',   
+ 'twiss_eta_y'       : 'Twiss\ '+r'\eta_y',   
+ 'twiss_etap_y'      : 'Twiss\ '+r"\eta'_y",     
+ 'twiss_emit_y'      : 'Twiss\ '+r'\epsilon_{y}',
+ 'twiss_norm_emit_y' : 'Twiss\ '+r'\epsilon_{n, y}',    
 # 'species_charge',
 # 'weight',
  'average_current': r'I_{av}',

pmd_beamphysics/particles.py

@@ -16,7 +16,7 @@
 from pmd_beamphysics.readers import particle_array, particle_paths
 from pmd_beamphysics.species import charge_of, mass_of
 
-from pmd_beamphysics.statistics import norm_emit_calc, normalized_particle_coordinate, particle_amplitude, particle_twiss_dispersion, matched_particles, resample_particles
+from pmd_beamphysics.statistics import norm_emit_calc, normalized_particle_coordinate, particle_amplitude, particle_twiss_dispersion, matched_particles, resample_particles, slice_statistics
 from pmd_beamphysics.writers import write_pmd_bunch, pmd_init
 
 from h5py import File
@@ -549,30 +549,30 @@ def Jy(self):
 
     def delta(self, key):
         """Attribute (array) relative to its mean"""
-        return getattr(self, key) - self.avg(key)
+        return self[key] - self.avg(key)
 
 
     # Statistical property functions
 
     def min(self, key):
         """Minimum of any key"""
-        return np.min(getattr(self, key))
+        return np.min(self[key]) # was: getattr(self, key)
     def max(self, key):
         """Maximum of any key"""
-        return np.max(getattr(self, key)) 
+        return np.max(self[key]) 
     def ptp(self, key):
         """Peak-to-Peak = max - min of any key"""
-        return np.ptp(getattr(self, key))     
+        return np.ptp(self[key])     
 
     def avg(self, key):
         """Statistical average"""
-        dat = getattr(self, key) # equivalent to self.key for accessing properties above
+        dat = self[key]  # equivalent to self.key for accessing properties above
         if np.isscalar(dat): 
             return dat
         return np.average(dat, weights=self.weight)
     def std(self, key):
         """Standard deviation (actually sample)"""
-        dat = getattr(self, key)
+        dat = self[key]
         if np.isscalar(dat):
             return 0
         avg_dat = self.avg(key)
@@ -586,7 +586,7 @@ def cov(self, *keys):
         P.cov('x', 'px', 'y', 'py')
     
         """
-        dats = np.array([ getattr(self, key) for key in keys ])
+        dats = np.array([ self[key] for key in keys ])
         return np.cov(dats, aweights=self.weight)
 
     def histogramdd(self, *keys, bins=10, range=None):
@@ -604,9 +604,7 @@ def histogramdd(self, *keys, bins=10, range=None):
         H, edges = np.histogramdd(np.array([self[k] for k in list(keys)]).T, weights=self.weight, bins=bins, range=range)
 
         return H, edges
-
-
-
+
 
     # Beam statistics
     @property
@@ -900,27 +898,51 @@ def plot(self, key1='x', key2=None,
         if return_figure:
             return fig
 
-    def slice_plot(self, key='sigma_x', 
+
+
+
+    def slice_statistics(self, *keys,
+                   n_slice=100,
+                   slice_key=None):
+        """
+        Slice statistics
+        
+        """      
+
+        if slice_key is None:
+            if self.in_t_coordinates:
+                slice_key = 'z'
+
+            else:
+                slice_key = 't'  
+
+        if slice_key in ('t', 'delta_t'):
+            density_name = 'current'
+        else:
+            density_name = 'density'
+
+        keys = set(keys)
+        keys.add('mean_'+slice_key)
+        keys.add('ptp_'+slice_key)
+        keys.add('charge')
+        slice_dat = slice_statistics(self, n_slice=n_slice, slice_key=slice_key,
+                                keys=keys)
+
+        slice_dat[density_name] = slice_dat['charge']/ slice_dat['ptp_'+slice_key]
+
+        return slice_dat
+
+    def slice_plot(self, *keys,
                    n_slice=100,
                    slice_key=None,
                    tex=True,
                    nice=True,
                    return_figure=False,
                    xlim=None,
                    ylim=None,
-                   **kwargs):
-        """
-        Slice statistics plot. 
+                   **kwargs):   
 
-        """        
-
-        if not slice_key:
-            if self.in_t_coordinates:
-                slice_key = 'z'
-            else:
-                slice_key = 't'
-
-        fig = slice_plot(self, stat_key=key,
+        fig = slice_plot(self, *keys,
                          n_slice=n_slice,
                          slice_key=slice_key,
                          tex=tex,
@@ -930,7 +952,7 @@ def slice_plot(self, key='sigma_x',
                          **kwargs)
 
         if return_figure:
-            return fig
+            return fig        
 
 
     # New constructors
@@ -1129,7 +1151,7 @@ def split_particles(particle_group, n_chunks = 100, key='z'):
     """
 
     # Sorting
-    zlist = getattr(particle_group, key) 
+    zlist = particle_group[key] 
     iz = np.argsort(zlist)
 
     # Split particles into chunks

pmd_beamphysics/plot.py

@@ -38,9 +38,9 @@ def plt_histogram(a, weights=None, bins=40):
 
 
 def slice_plot(particle_group, 
-               stat_key='sigma_x',
+               *keys,
                n_slice=40,
-               slice_key='z',
+               slice_key=None,
                xlim=None,
                ylim=None,
                tex=True,
@@ -54,63 +54,108 @@ def slice_plot(particle_group,
     particle_group: ParticleGroup
         The object to plot
     
-    stat_key: str, default = 'sigma_x'
-        Key to calculate the statistics
+    keys: iterable of str
+        Keys to calculate the statistics, e.g. `sigma_x`.
         
     n_slice: int, default = 40
         Number of slices 
         
-    slice_key: str, default = 'z'
-        Should be 'z' or 't'
+    slice_key: str, default = None 
+         The dimension to slice in. This is typically `t` or `z`.
+         `delta_t`, etc. are also allowed.
+         If None, `t` or `z` will automatically be determined.
         
     ylim: tuple, default = None
         Manual setting of the y-axis limits. 
         
-    tex: bool, defaul = True
+    tex: bool, default = True
         Use TEX for labels
         
-    
     Returns
     -------
     fig: matplotlib.figure.Figure
 
     """
+
+    # Allow a single key
+    #if isinstance(keys, str):
+   # 
+   #     keys = (keys, )
+
+    if slice_key is None:
+        if particle_group.in_t_coordinates:
+            slice_key = 'z'
+        else:
+            slice_key = 't'  
+
+    # Special case for delta_
+    if slice_key.startswith('delta_'):
+        slice_key = slice_key[6:]
+        has_delta_prefix = True
+    else:
+        has_delta_prefix = False
 
+    # Get all data
     x_key = 'mean_'+slice_key
-    y_key = stat_key
-    slice_dat = slice_statistics(particle_group, n_slice=n_slice, slice_key=slice_key,
-                            keys=[x_key, y_key, 'ptp_'+slice_key, 'charge'])
-
-
+    slice_dat = particle_group.slice_statistics(*keys, n_slice=n_slice, slice_key=slice_key)
     slice_dat['density'] = slice_dat['charge']/ slice_dat['ptp_'+slice_key]
     y2_key = 'density'
+
+    # X-axis
+    x = slice_dat['mean_'+slice_key]  
+    if has_delta_prefix:
+        x -= particle_group['mean_'+slice_key]
+        slice_key = 'delta_'+slice_key # restore        
+
+    x, f1, p1, xmin, xmax = plottable_array(x, nice=nice, lim=xlim)
+    ux = p1+str(particle_group.units(slice_key))
+
+    # Y-axis
+
+    # Units check
+    ulist = [particle_group.units(k).unitSymbol for k in keys]
+    uy = ulist[0]
+    if not all([u==uy for u in ulist] ):
+        raise ValueError(f'Incompatible units: {ulist}')
+
+    ymin = max([slice_dat[k].min() for k in keys])
+    ymax = max([slice_dat[k].max() for k in keys])
+
+    _, f2, p2, ymin, ymax = plottable_array(np.array([ymin, ymax]), nice=nice, lim=ylim)
+    uy = p2 + uy
+
+    # Form Figure
     fig, ax = plt.subplots(**kwargs)
 
-    # Get nice arrays
-    x, f1, prex, xmin, xmax       = plottable_array(slice_dat[x_key], nice=nice, lim=xlim)
-    y, f2, prey, ymin, ymax = plottable_array(slice_dat[y_key], nice=nice, lim=ylim)
+    # Main curves  
+    if len(keys) == 1:
+        color = 'black'
+    else:
+        color = None
+
+    for k in keys:
+        label = mathlabel(k, units=uy, tex=tex)
+        ax.plot(x, slice_dat[k]/f2, label=label, color=color)
+    if len(keys) > 1:
+        ax.legend()      
+
     # Density on r.h.s
     y2, _, prey2, _, _ = plottable_array(slice_dat[y2_key], nice=nice, lim=None)
 
-    x_units = f'{prex}{particle_group.units(x_key)}'
-    y_units = f'{prey}{particle_group.units(y_key)}'    
-
     # Convert to Amps if possible
     y2_units = f'C/{particle_group.units(x_key)}'
     if y2_units == 'C/s':
         y2_units = 'A'
     y2_units = prey2+y2_units 
 
     # Labels
-    labelx = mathlabel(slice_key, units=x_units, tex=tex)
-    labely = mathlabel(y_key, units=y_units, tex=tex)    
+    labelx = mathlabel(slice_key, units=ux, tex=tex)
+    labely = mathlabel(*keys, units=uy, tex=tex)    
     labely2 = mathlabel(y2_key, units=y2_units, tex=tex)        
 
     ax.set_xlabel(labelx)
     ax.set_ylabel(labely)
-
-    # Main plot
-    ax.plot(x, y, color = 'black')
+
 
     # rhs plot
     ax2 = ax.twinx()

pmd_beamphysics/statistics.py

@@ -404,7 +404,7 @@ def normalized_particle_coordinate(particle_group, key, twiss=None, mass_normali
 # ---------------
 # Other utilities
 
-def slice_statistics(particle_group,  keys=['mean_z'], n_slice=40, slice_key='z'):
+def slice_statistics(particle_group,  keys=['mean_z'], n_slice=40, slice_key=None):
     """
     Slices a particle group into n slices and returns statistics from each sliced defined in keys. 
     
@@ -413,12 +413,48 @@ def slice_statistics(particle_group,  keys=['mean_z'], n_slice=40, slice_key='z'
     Any key can be used to slice on. 
     
     """
+
+    if slice_key is None:
+        if particle_group.in_t_coordinates:
+            slice_key = 'z'
+        else:
+            slice_key = 't'   
+
     sdat = {}
+    twiss_planes = set()
+    twiss = {}    
+
+    normal_keys = set()
+
     for k in keys:
         sdat[k] = np.empty(n_slice)
+        if k.startswith('twiss'):
+            if k == 'twiss' or k == 'twiss_xy':
+                twiss_planes.add('x')
+                twiss_planes.add('y')
+            else:
+                plane = k[-1] # 
+                assert plane in ('x', 'y')
+                twiss_planes.add(plane)
+        else:
+            normal_keys.add(k)
+
+    twiss_plane = ''.join(twiss_planes) # flatten
+    assert twiss_plane in ('x', 'y', 'xy', 'yx', '')
+
     for i, pg in enumerate(particle_group.split(n_slice, key=slice_key)):
-        for k in keys:
+        for k in normal_keys:
             sdat[k][i] = pg[k]
+
+        # Handle twiss
+        if twiss_plane:
+            twiss = pg.twiss(plane=twiss_plane)
+            for k in twiss:
+                full_key = f'twiss_{k}'
+                if full_key not in sdat:
+                    sdat[full_key] = np.empty(n_slice)
+                sdat[full_key][i] = twiss[k]
+
 
     return sdat
 

pmd_beamphysics/units.py

@@ -464,6 +464,16 @@ def plottable_array(x, nice=True, lim=None):
     PARTICLEGROUP_UNITS[f'E{component}'] = unit('V/m')
     PARTICLEGROUP_UNITS[f'B{component}'] = unit('T')    
 
+# Twiss
+for plane in ('x', 'y'):
+    for k in ('alpha', 'etap'):
+        PARTICLEGROUP_UNITS[f'twiss_{k}_{plane}'] = unit('1') 
+    for k in ('beta', 'eta', 'emit', 'norm_emit'):
+        PARTICLEGROUP_UNITS[f'twiss_{k}_{plane}'] = unit('m') 
+    for k in ('gamma', ):
+        PARTICLEGROUP_UNITS[f'twiss_{k}_{plane}'] = divide_units(unit('1'), unit('m') )
+
+
 
 
 
@@ -479,7 +489,7 @@ def pg_units(key):
     for prefix in ['sigma_', 'mean_', 'min_', 'max_', 'ptp_', 'delta_']:
         if key.startswith(prefix):
             nkey = key[len(prefix):]
-            return PARTICLEGROUP_UNITS[nkey]
+            return pg_units(nkey)
 
     if key.startswith('cov_'):
         subkeys = key.strip('cov_').split('__')