Bugfix

src/kanapy/api.py

@@ -55,13 +55,13 @@ class Microstructure(object):
             List of particle objects of class entities containing information object particle geometries
         rve : object of class RVE_creator
             Contains information about the RVE
-            Attributes: dim, size, nphases, nparticles, periodic, units, packing_steps, particle_data,
+            Attributes: dim, size, nparticles, periodic, units, packing_steps, particle_data,
             phase_names, phase_vf, ialloy
         simbox : Object of class Simulation_Box
             Contains information about geometry of simulation box for particle simulation
         mesh : object of class mesh_creator
             Attributes: dim, grain_dict, grain_ori_dict, grain_phase_dict, grains, ngrains_phase. nodes, nodes_smooth,
-                nphases, nvox, phases, prec_vf_voxels, vox_center_dict, voxel_dict
+                nvox, phases, prec_vf_voxels, vox_center_dict, voxel_dict
         geometry : dict
             Dictionary of grain geometries;
             Dict keys: "Ngrains", "Vertices", "Points", "Simplices", "Facets", "Grains", "GBnodes", GBarea" "GBfaces"
@@ -196,7 +196,7 @@ def voxelize(self, particles=None, dim=None):
         self.mesh.create_voxels(self.simbox)
 
         self.mesh = \
-            voxelizationRoutine(particles, self.mesh, prec_vf=self.precipit)
+            voxelizationRoutine(particles, self.mesh, self.nphases, prec_vf=self.precipit)
         if np.any(self.nparticles != self.mesh.ngrains_phase):
             logging.info(f'Number of grains per phase changed from {self.nparticles} to ' +
                          f'{list(self.mesh.ngrains_phase)} during voxelization.')
@@ -243,11 +243,11 @@ def generate_grains(self):
             # in case of precipit, remove irregular grain 0 from analysis
             empty_vox = self.mesh.grain_dict.pop(0)
             grain_store = self.mesh.grain_phase_dict.pop(0)
-            nphases = self.rve.nphases - 1
+            nphases = self.nphases - 1
         else:
             empty_vox = None
             grain_store = None
-            nphases = self.rve.nphases
+            nphases = self.nphases
 
         self.geometry: dict = \
             calc_polygons(self.rve, self.mesh)  # updates RVE_data

src/kanapy/initializations.py

@@ -80,7 +80,6 @@ def __init__(self, stats_dicts, nsteps=1000, from_voxels=False):
 
         Attributes
         ----------
-        self.nphases = len(stats_dicts)  # number of phases in RVE
         self.packing_steps = nsteps  # max number of steps for packing simulation
         self.size = None  #  tuple of lengths along Cartesian axes
         self.dim = None  # tuple of number of voxels along Cartesian axes
@@ -263,7 +262,6 @@ def gen_data_elong(pdict):
         else:
             print('Creating an RVE based on user defined statistics')
         # Extract grain diameter statistics info
-        self.nphases = len(stats_dicts)  # number of phases in RVE
         self.packing_steps = nsteps  # max number of steps for packing simulation
         self.size = None  # tuple of lengths along Cartesian axes
         self.dim = None  # tuple of number of voxels along Cartesian axes

src/kanapy/input_output.py

@@ -444,7 +444,6 @@ def import_voxels(file, path='./'):
     ms.simbox = Simulation_Box(size)
     # initialize voxel structure (= mesh)
     ms.mesh = mesh_creator(sh)
-    ms.mesh.nphases = nphases
     ms.mesh.grains = grains
     ms.mesh.grain_dict = grain_dict
     ms.mesh.grain_ori_dict = grain_ori_dict

src/kanapy/voxelization.py

@@ -315,7 +315,7 @@ def reassign_shared_voxels(cooDict, Ellipsoids, voxel_dict):
     return
 
 
-def voxelizationRoutine(Ellipsoids, mesh, prec_vf=None):
+def voxelizationRoutine(Ellipsoids, mesh, nphases, prec_vf=None):
     """
     The main function that controls the voxelization routine using: :meth:`kanapy.input_output.read_dump`,
     :meth:`create_voxels`, :meth:`assign_voxels_to_ellipsoid`, :meth:`reassign_shared_voxels`
@@ -374,7 +374,7 @@ def voxelizationRoutine(Ellipsoids, mesh, prec_vf=None):
     # empty voxels will get phase number 1 and be assigned to grain with key 0
     ph_arr = -np.ones(mesh.nvox, dtype=int)
     mesh.grain_phase_dict = dict()
-    mesh.ngrains_phase = np.zeros(mesh.nphases, dtype=int)
+    mesh.ngrains_phase = np.zeros(nphases, dtype=int)
     for ih, il in mesh.grain_dict.items():
         il = np.array(il) - 1
         ip = Ellipsoids[ih - 1].phasenum

tests/test_voxelization.py

@@ -209,10 +209,10 @@ def test_voxelizationRoutine():
     sim_box = Simulation_Box(rve.size)
     sim_box.sim_ts = 500
     mesh = mesh_creator(rve.dim)
-    mesh.nphases = 1
+    nphases = 1
     mesh.create_voxels(sim_box)
     Particles = particle_generator([parDict], sim_box, False)
-    mesh = voxelizationRoutine(Particles, mesh)
+    mesh = voxelizationRoutine(Particles, mesh, nphases)
     assert mesh.vox_center_dict[5][0] == 0.9
     assert mesh.voxel_dict[7] == [29, 30, 26, 25, 31, 32, 28, 27]
     assert mesh.grains.shape == (15, 15, 15)