Merge pull request #263 from smash-transport/sass/rename_particle_fun…

…ctions

Sass/rename particle functions

CHANGELOG.md

@@ -28,6 +28,19 @@ Date:
 
 ### Changed
 * Filter: Perform general clean up to reduce code duplications
+* Particle: Rename several methods for a more intuitive naming scheme. Renamed methods are:
+| Old Method Name                     | New Method Name             |
+|-------------------------------------|-----------------------------|
+| momentum_rapidity_Y()               | rapidity()                  |
+| spatial_rapidity()                  | spacetime_rapidity()        |
+| spatial_rapidity_cut()              | spacetime_rapidity_cut()    |
+| pt_abs()                            | pT_abs()                    |
+| pt_cut()                            | pT_cut()                    |
+| compute_mass_from_energy_momentum() | mass_from_energy_momentum() |
+| compute_charge_from_pdg()           | charge_from_pdg()           |
+
+### Added
+* Tests: Add HelperFunctions.py that contains free utility functions used in the tests and add corresponding tests.
 
 ## v1.3.0-Newton
 Date: 2024-07-25

docs/source/classes/Jetscape/index.rst

@@ -17,7 +17,7 @@ Jetscape
 .. automethod:: Jetscape.charged_particles
 .. automethod:: Jetscape.uncharged_particles
 .. automethod:: Jetscape.strange_particles
-.. automethod:: Jetscape.pt_cut
+.. automethod:: Jetscape.pT_cut
 .. automethod:: Jetscape.rapidity_cut
 .. automethod:: Jetscape.pseudorapidity_cut
 .. automethod:: Jetscape.multiplicity_cut

docs/source/classes/Oscar/index.rst

@@ -19,9 +19,9 @@ Oscar
 .. automethod:: Oscar.charged_particles
 .. automethod:: Oscar.uncharged_particles
 .. automethod:: Oscar.strange_particles
-.. automethod:: Oscar.pt_cut
+.. automethod:: Oscar.pT_cut
 .. automethod:: Oscar.rapidity_cut
 .. automethod:: Oscar.pseudorapidity_cut
-.. automethod:: Oscar.spatial_rapidity_cut
+.. automethod:: Oscar.spacetime_rapidity_cut
 .. automethod:: Oscar.multiplicity_cut
 .. automethod:: Oscar.print_particle_lists_to_file

docs/source/classes/Particle/index.rst

@@ -8,15 +8,15 @@ Particle
 
 .. automethod:: Particle.print_particle
 .. automethod:: Particle.angular_momentum
-.. automethod:: Particle.momentum_rapidity_Y
+.. automethod:: Particle.rapidity
 .. automethod:: Particle.p_abs
-.. automethod:: Particle.pt_abs
+.. automethod:: Particle.pT_abs
 .. automethod:: Particle.phi
 .. automethod:: Particle.theta
 .. automethod:: Particle.pseudorapidity
-.. automethod:: Particle.spatial_rapidity
+.. automethod:: Particle.spacetime_rapidity
 .. automethod:: Particle.proper_time
-.. automethod:: Particle.compute_mass_from_energy_momentum
+.. automethod:: Particle.mass_from_energy_momentum
 .. automethod:: Particle.compute_charge_from_pdg
 .. automethod:: Particle.mT
 .. automethod:: Particle.is_meson

src/sparkx/CentralityClasses.py

@@ -177,7 +177,6 @@ def __create_centrality_classes(self) -> None:
 
         MinRecord = int(number_events / 4 * self.centrality_bins_[0] / 100.0)
         for i in range(1, len(self.centrality_bins_)):
-
             MaxRecord = int(
                 number_events / 4 * self.centrality_bins_[i] / 100.0
             )

src/sparkx/EventCharacteristics.py

@@ -630,7 +630,7 @@ def generate_eBQS_densities_Minkowski_from_OSCAR_IC(
                 "n_sigma_x, n_sigma_y, n_sigma_z must be positive float or int"
             )
         if (IC_info is not None) and not isinstance(IC_info, str):
-            warnings.warn("The given IC_info is not a string")
+            raise TypeError("The given IC_info is not a string")
         if not isinstance(output_filename, str):
             raise TypeError("output_filename must be a string")
         if self.has_lattice_:

src/sparkx/Filter.py

@@ -451,7 +451,7 @@ def spacetime_cut(particle_list, dim, cut_value_tuple):
     return updated_particle_list
 
 
-def pt_cut(particle_list, cut_value_tuple):
+def pT_cut(particle_list, cut_value_tuple):
     """
     Apply p_t cut to all events by passing an acceptance range by
     ::code`cut_value_tuple`. All particles outside this range will
@@ -512,8 +512,8 @@ def pt_cut(particle_list, cut_value_tuple):
             elem
             for elem in particle_list[i]
             if (
-                lim_min <= elem.pt_abs() <= lim_max
-                and not np.isnan(elem.pt_abs())
+                lim_min <= elem.pT_abs() <= lim_max
+                and not np.isnan(elem.pT_abs())
             )
         ]
         updated_particle_list.append(particle_list_tmp)
@@ -626,8 +626,8 @@ def rapidity_cut(particle_list, cut_value):
                 elem
                 for elem in particle_list[i]
                 if (
-                    lim_min <= elem.momentum_rapidity_Y() <= lim_max
-                    and not np.isnan(elem.momentum_rapidity_Y())
+                    lim_min <= elem.rapidity() <= lim_max
+                    and not np.isnan(elem.rapidity())
                 )
             ]
             updated_particle_list.append(particle_list_tmp)
@@ -642,8 +642,8 @@ def rapidity_cut(particle_list, cut_value):
                 elem
                 for elem in particle_list[i]
                 if (
-                    -limit <= elem.momentum_rapidity_Y() <= limit
-                    and not np.isnan(elem.momentum_rapidity_Y())
+                    -limit <= elem.rapidity() <= limit
+                    and not np.isnan(elem.rapidity())
                 )
             ]
             updated_particle_list.append(particle_list_tmp)
@@ -726,10 +726,10 @@ def pseudorapidity_cut(particle_list, cut_value):
     return updated_particle_list
 
 
-def spatial_rapidity_cut(particle_list, cut_value):
+def spacetime_rapidity_cut(particle_list, cut_value):
     """
-    Apply spatial rapidity (space-time rapidity) cut to all events and
-    remove all particles with spatial rapidity not complying with cut_value.
+    Apply space-time rapidity cut to all events and remove all particles with
+    space-time rapidity not complying with cut_value.
 
     Parameters
     ----------
@@ -743,7 +743,7 @@ def spatial_rapidity_cut(particle_list, cut_value):
         in [-1.0, 1.0] are kept.
 
     cut_value : tuple
-        To specify an asymmetric acceptance range for the spatial rapidity
+        To specify an asymmetric acceptance range for the space-time rapidity
         of particles, pass a tuple (cut_min, cut_max)
 
     Returns
@@ -764,8 +764,8 @@ def spatial_rapidity_cut(particle_list, cut_value):
                 elem
                 for elem in particle_list[i]
                 if (
-                    lim_min <= elem.spatial_rapidity() <= lim_max
-                    and not np.isnan(elem.spatial_rapidity())
+                    lim_min <= elem.spacetime_rapidity() <= lim_max
+                    and not np.isnan(elem.spacetime_rapidity())
                 )
             ]
             updated_particle_list.append(particle_list_tmp)
@@ -780,8 +780,8 @@ def spatial_rapidity_cut(particle_list, cut_value):
                 elem
                 for elem in particle_list[i]
                 if (
-                    -limit <= elem.spatial_rapidity() <= limit
-                    and not np.isnan(elem.spatial_rapidity())
+                    -limit <= elem.spacetime_rapidity() <= limit
+                    and not np.isnan(elem.spacetime_rapidity())
                 )
             ]
             updated_particle_list.append(particle_list_tmp)

src/sparkx/Histogram.py

@@ -166,7 +166,6 @@ def __init__(self, bin_boundaries):
             self.systematic_error_ = np.asarray([np.zeros(num_bins)])
 
         elif isinstance(bin_boundaries, (list, np.ndarray)):
-
             self.number_of_bins_ = len(bin_boundaries) - 1
             self.bin_edges_ = np.asarray(bin_boundaries)
             self.histograms_ = np.asarray([np.zeros(self.number_of_bins_)])

src/sparkx/Jetscape.py

@@ -107,7 +107,7 @@ class Jetscape:
         Keep strange particles only
     particle_status:
         Keep only particles with a given status flag
-    pt_cut:
+    pT_cut:
         Apply pT cut to all particles
     rapidity_cut:
         Apply rapidity cut to all particles
@@ -402,8 +402,8 @@ def __apply_kwargs_filters(self, event, filters_dict):
                 event = lower_event_energy_cut(
                     event, filters_dict["lower_event_energy_cut"]
                 )
-            elif i == "pt_cut":
-                event = pt_cut(event, filters_dict["pt_cut"])
+            elif i == "pT_cut":
+                event = pT_cut(event, filters_dict["pT_cut"])
             elif i == "mT_cut":
                 event = mT_cut(event, filters_dict["mT_cut"])
             elif i == "rapidity_cut":
@@ -412,9 +412,9 @@ def __apply_kwargs_filters(self, event, filters_dict):
                 event = pseudorapidity_cut(
                     event, filters_dict["pseudorapidity_cut"]
                 )
-            elif i == "spatial_rapidity_cut":
-                event = spatial_rapidity_cut(
-                    event, filters_dict["spatial_rapidity_cut"]
+            elif i == "spacetime_rapidity_cut":
+                event = spacetime_rapidity_cut(
+                    event, filters_dict["spacetime_rapidity_cut"]
                 )
             elif i == "multiplicity_cut":
                 event = multiplicity_cut(
@@ -761,7 +761,7 @@ def lower_event_energy_cut(self, minimum_event_energy):
 
         return self
 
-    def pt_cut(self, cut_value_tuple):
+    def pT_cut(self, cut_value_tuple):
         """
         Apply transverse momentum cut to all events by passing an acceptance
         range by ::code`cut_value_tuple`. All particles outside this range will
@@ -781,7 +781,7 @@ def pt_cut(self, cut_value_tuple):
             Containing only particles complying with the transverse momentum
             cut for all events
         """
-        self.particle_list_ = pt_cut(self.particle_list_, cut_value_tuple)
+        self.particle_list_ = pT_cut(self.particle_list_, cut_value_tuple)
         self.__update_num_output_per_event_after_filter()
 
         return self

src/sparkx/Lattice3D.py

@@ -1231,7 +1231,17 @@ def interpolate_to_lattice_new_extent(
         for i, x in enumerate(x_new):
             for j, y in enumerate(y_new):
                 for k, z in enumerate(z_new):
-                    value = self.interpolate_value(x, y, z)
+                    if (
+                        x < self.x_min_
+                        or x > self.x_max_
+                        or y < self.y_min_
+                        or y > self.y_max_
+                        or z < self.z_min_
+                        or z > self.z_max_
+                    ):
+                        value = 0
+                    else:
+                        value = self.interpolate_value(x, y, z)
                     new_lattice.set_value_by_index(i, j, k, value)
 
         return new_lattice

src/sparkx/MultiParticlePtCorrelations.py

@@ -83,7 +83,6 @@ class MultiParticlePtCorrelations:
     """
 
     def __init__(self, max_order: int) -> None:
-
         self.max_order = max_order
         # Check if max_order is an integer
         if not isinstance(self.max_order, int):
@@ -125,7 +124,7 @@ def _P_W_k(
                 # if particle.weight is np.nan, then set it to 1
                 if np.isnan(particle.weight):
                     particle.weight = 1.0
-                Pk[k] += (particle.weight * particle.pt_abs()) ** (k + 1)
+                Pk[k] += (particle.weight * particle.pT_abs()) ** (k + 1)
                 Wk[k] += particle.weight ** (k + 1)
         return (Pk, Wk)
 

src/sparkx/Oscar.py

@@ -117,14 +117,14 @@ class Oscar:
         Keep strange particles only
     spacetime_cut:
         Apply spacetime cut to all particles
-    pt_cut:
+    pT_cut:
         Apply pT cut to all particles
     rapidity_cut:
         Apply rapidity cut to all particles
     pseudorapidity_cut:
         Apply pseudorapidity cut to all particles
-    spatial_rapidity_cut:
-        Apply spatial rapidity (space-time rapidity) cut to all particles
+    spacetime_rapidity_cut:
+        Apply space-time rapidity cut to all particles
     multiplicity_cut:
         Apply multiplicity cut to all particles
     print_particle_lists_to_file:
@@ -465,8 +465,8 @@ def __apply_kwargs_filters(self, event, filters_dict):
                     filters_dict["spacetime_cut"][0],
                     filters_dict["spacetime_cut"][1],
                 )
-            elif i == "pt_cut":
-                event = pt_cut(event, filters_dict["pt_cut"])
+            elif i == "pT_cut":
+                event = pT_cut(event, filters_dict["pT_cut"])
             elif i == "mT_cut":
                 event = mT_cut(event, filters_dict["mT_cut"])
             elif i == "rapidity_cut":
@@ -475,9 +475,9 @@ def __apply_kwargs_filters(self, event, filters_dict):
                 event = pseudorapidity_cut(
                     event, filters_dict["pseudorapidity_cut"]
                 )
-            elif i == "spatial_rapidity_cut":
-                event = spatial_rapidity_cut(
-                    event, filters_dict["spatial_rapidity_cut"]
+            elif i == "spacetime_rapidity_cut":
+                event = spacetime_rapidity_cut(
+                    event, filters_dict["spacetime_rapidity_cut"]
                 )
             elif i == "multiplicity_cut":
                 event = multiplicity_cut(
@@ -956,7 +956,7 @@ def spacetime_cut(self, dim, cut_value_tuple):
 
         return self
 
-    def pt_cut(self, cut_value_tuple):
+    def pT_cut(self, cut_value_tuple):
         """
         Apply transverse momentum cut to all events by passing an acceptance
         range by ::code`cut_value_tuple`. All particles outside this range will
@@ -977,7 +977,7 @@ def pt_cut(self, cut_value_tuple):
             cut for all events
         """
 
-        self.particle_list_ = pt_cut(self.particle_list_, cut_value_tuple)
+        self.particle_list_ = pT_cut(self.particle_list_, cut_value_tuple)
         self.__update_num_output_per_event_after_filter()
 
         return self
@@ -1066,10 +1066,10 @@ def pseudorapidity_cut(self, cut_value):
 
         return self
 
-    def spatial_rapidity_cut(self, cut_value):
+    def spacetime_rapidity_cut(self, cut_value):
         """
-        Apply spatial rapidity (space-time rapidity) cut to all events and
-        remove all particles with spatial rapidity not complying with cut_value
+        Apply space-time rapidity cut to all events and remove all particles
+        with space-time rapidity not complying with cut_value
 
         Parameters
         ----------
@@ -1086,11 +1086,11 @@ def spatial_rapidity_cut(self, cut_value):
         Returns
         -------
         self : Oscar object
-            Containing only particles complying with the spatial rapidity cut
+            Containing only particles complying with the space-time rapidity cut
             for all events
         """
 
-        self.particle_list_ = spatial_rapidity_cut(
+        self.particle_list_ = spacetime_rapidity_cut(
             self.particle_list_, cut_value
         )
         self.__update_num_output_per_event_after_filter()