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Included rve statistics in API
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@AHartmaier
AHartmaier committed Mar 24, 2024
1 parent d9010d3 commit 6e6263e
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Showing 2 changed files with 39 additions and 21 deletions.
48 changes: 33 additions & 15 deletions src/kanapy/api.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
from kanapy.packing import packingRoutine
from kanapy.voxelization import voxelizationRoutine
from kanapy.smoothingGB import smoothingRoutine
from kanapy.rve_stats import get_stats_vox, get_stats_part, get_stats_poly
from kanapy.plotting import plot_init_stats, plot_voxels_3D, plot_ellipsoids_3D, \
plot_polygons_3D, plot_output_stats, plot_particles_3D

Expand Down Expand Up @@ -164,7 +165,7 @@ def pack(self, particle_data=None,
if fill_factor is None and self.precipit is not None:
fill_factor = 1.0 # pack to full volume fraction defined in particles
print(f'Sparse particles (precipitates/pores): '
f'Packing up to particle volume fraction of {(100*self.precipit):.1f}%.')
f'Packing up to particle volume fraction of {(100 * self.precipit):.1f}%.')
if self.precipit > 0.65:
print('Overlap of particles will occur since volume fraction > 65%')
self.particles, self.simbox = \
Expand Down Expand Up @@ -206,9 +207,9 @@ def voxelize(self, particles=None, dim=None):
print('Volume fractions of phases in voxel structure:')
vt = 0.
for ip in range(self.nphases):
vf = vox_count[ip]/self.mesh.nvox
vf = vox_count[ip] / self.mesh.nvox
vt += vf
print(f'{ip}: {self.rve.phase_names[ip]} ({(vf*100):.3f}%)')
print(f'{ip}: {self.rve.phase_names[ip]} ({(vf * 100):.3f}%)')
if not np.isclose(vt, 1.0):
logging.warning(f'Volume fractions of phases in voxels do not add up to 1. Value: {vt}')

Expand Down Expand Up @@ -268,7 +269,7 @@ def generate_grains(self):
igr.append(gblist[1])
if len(ind) > 0:
logging.warning(f'{len(ind)} grains are not represented in polyhedral geometry.')
#logging.warning('Consider increasing the number of voxels, as grains appear to be very irregular.')
# logging.warning('Consider increasing the number of voxels, as grains appear to be very irregular.')
"""ind.reverse()
igr.reverse()
for j, i in enumerate(ind):
Expand All @@ -283,7 +284,7 @@ def generate_grains(self):
ph_vol[ip] += grd['Volume']
print('Volume fractions of phases in polyhedral geometry:')
for ip in range(self.nphases):
vf = 100.0*ph_vol[ip]/np.prod(self.rve.size)
vf = 100.0 * ph_vol[ip] / np.prod(self.rve.size)
print(f'{ip}: {self.rve.phase_names[ip]} ({vf.round(1)}%)')
if empty_vox is not None:
# add removed grain again
Expand Down Expand Up @@ -351,7 +352,7 @@ def generate_orientations(self, data, ang=None, omega=None, Nbase=5000,
'"random" or "unimodal"')
for i, igr in enumerate(self.mesh.grain_dict.keys()):
if self.mesh.grain_phase_dict[igr] == ip:
ind = i - ip*self.ngrains[0]
ind = i - ip * self.ngrains[0]
ori_dict[igr] = ori_rve[ind, :]
self.mesh.grain_ori_dict = ori_dict
return
Expand Down Expand Up @@ -415,7 +416,8 @@ def plot_stats(self, data=None,
gs_data=None, gs_param=None,
ar_data=None, ar_param=None,
particles=True,
save_files=False):
save_files=False,
show_plot=True, verbose=False, ax_max=None):
""" Plots the particle- and grain diameter attributes for statistical
comparison."""
if self.precipit and 0 in self.mesh.grain_dict.keys():
Expand All @@ -424,13 +426,28 @@ def plot_stats(self, data=None,
else:
nphases = self.nphases
if data is None or \
(type(data) is str and data.lower() in ['p', 'part', 'particles']):
if self.rve.particle_data is not None:
# analyse grains w.r.t. statistical descriptors
data = get_stats(self.rve.particle_data, self.geometry, self.rve.units,
nphases, self.mesh.ngrains_phase)
if data is None:
raise ValueError('No microstructure data created yet. Run generate_grains() first.')
(type(data) is str and 'p' in data.lower()):
# analyse particle statistics
if self.particles is None:
logging.error('Particle statistics requested, but no particles defined.')
return
part_stats = get_stats_part(self.particles, show_plot=show_plot,
verbose=verbose, ax_max=ax_max, save_files=save_files)
if data is None or \
(type(data) is str and 'v' in data.lower()):
# analyse voxel statistics
if self.mesh is None:
logging.error('Particle statistics requested, but no particles defined.')
return
vox_stats = get_stats_vox(self.mesh, show_plot=show_plot,
verbose=verbose, ax_max=ax_max, save_files=save_files)

if self.rve.particle_data is not None:
# analyse grains w.r.t. statistical descriptors
data = get_stats(self.rve.particle_data, self.geometry, self.rve.units,
nphases, self.mesh.ngrains_phase)
if data is None:
raise ValueError('No microstructure data created yet. Run generate_grains() first.')
elif type(data) is not list:
data = [data]
if gs_data is None or type(gs_data) is not list:
Expand Down Expand Up @@ -937,6 +954,7 @@ def write_stl(self, data='grains', file=None, path='./'):
None.
"""

def write_facet(nv, pts, ft):
if np.linalg.norm(nv) < 1.e-5:
logging.warning(f'Acute facet detected. Facet: {ft}')
Expand All @@ -955,6 +973,7 @@ def write_facet(nv, pts, ft):
.format(pts[2, 0], pts[2, 1], pts[2, 2]))
f.write(" endloop\n")
f.write(" endfacet\n")

def write_grains():
for ft in self.geometry['Facets']:
pts = self.geometry['Points'][ft]
Expand Down Expand Up @@ -1177,7 +1196,6 @@ def import_particles(self, file, path='./'):
file = os.path.join(path, file)
self.simbox, self.particles = read_dump(file)


"""
-------- legacy methods --------
"""
Expand Down
12 changes: 6 additions & 6 deletions src/kanapy/rve_stats.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -208,7 +208,7 @@ def calc_stats_dict(a, b, c, eqd):
return sd


def get_stats_vox(mesh, minval=1.e-5, show_plot=True, verbose=False, ax_max=None):
def get_stats_vox(mesh, minval=1.e-5, show_plot=True, verbose=False, ax_max=None, save_files=False):
"""
Get statistics about the microstructure from voxels, by fitting a 3D ellipsoid to
each grain.
Expand Down Expand Up @@ -315,12 +315,12 @@ def get_stats_vox(mesh, minval=1.e-5, show_plot=True, verbose=False, ax_max=None
print(f'Standard deviation of equivalent grain diameter: {vox_stats_dict["eqd_sig"]:.4f}')
print('--------------------------------------------------------')
if show_plot:
plot_stats_dict(vox_stats_dict, title='Statistics of voxel structure')
plot_stats_dict(vox_stats_dict, title='Statistics of voxel structure', save_files=save_files)

return vox_stats_dict


def get_stats_poly(grains, minval=1.e-5, show_plot=True, verbose=False, ax_max=None):
def get_stats_poly(grains, minval=1.e-5, show_plot=True, verbose=False, ax_max=None, save_files=False):
""" Extract statistics about the microstructure from polyhedral grains
by fitting a 3D ellipsoid to each polyhedron.
Expand Down Expand Up @@ -394,12 +394,12 @@ def get_stats_poly(grains, minval=1.e-5, show_plot=True, verbose=False, ax_max=N
print('--------------------------------------------------------')
if show_plot:
title = 'Statistics of polyhedral grains'
plot_stats_dict(poly_stats_dict, title=title)
plot_stats_dict(poly_stats_dict, title=title, save_files=save_files)

return poly_stats_dict


def get_stats_part(part, minval=1.e-5, show_plot=True, verbose=False, ax_max=None):
def get_stats_part(part, minval=1.e-5, show_plot=True, verbose=False, ax_max=None, save_files=False):
""" Extract statistics about the microstructure from particles. If inner structure is contained
by fitting a 3D ellipsoid to each structure.
Expand Down Expand Up @@ -483,7 +483,7 @@ def get_stats_part(part, minval=1.e-5, show_plot=True, verbose=False, ax_max=Non
title = 'Particle statistics'
else:
title = 'Statistics of inner particle structures'
plot_stats_dict(part_stats_dict, title=title)
plot_stats_dict(part_stats_dict, title=title, save_files=save_files)

return part_stats_dict

Expand Down

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