def _add_lineageid(poly_embryo, input_file_lineageId):
''' enrich embryo VTP with lineageid arrays '''
if not input_file_lineageId:
return
df_cell = pd.read_csv(input_file_lineageId)
nb_levels = 5
l_parentid = []
l_l_levels = []
for ix_row, row_i in df_cell.iterrows():
l_name_lineage = re.findall("\d", str(row_i.name_lineage))
l_name_lineage_levels = []
for ix_level in range(0, nb_levels):
l_name_lineage_levels.append(
l_name_lineage[ix_level] if ix_level < len(l_name_lineage) else '0')
l_l_levels.append(l_name_lineage_levels)
l_parentid.append(row_i.parentIndex)
a_levels = np.transpose(np.char.array(l_l_levels))
for ix_level in range(0, nb_levels):
a_lineage_cum = a_lineage_cum + \
a_levels[ix_level] if ix_level > 0 else a_levels[ix_level]
add_array_with_mapper(poly_embryo, 'parentIndex', f'lineageid{ix_level}', {k: int(v) for k, v in zip(l_parentid, a_lineage_cum)})
return
def _add_canonical_contactid(poly_embryo, d_parentid_canonical):
if not d_parentid_canonical:
return
add_array_with_mapper(poly_embryo, 'contactid',
'contactidCanonical', d_parentid_canonical)
return
def _add_canonical_parentid(poly_embryo, df_canonical_parentid):
if df_canonical_parentid.empty:
return
d_cellname_canonical_parentid = {k: get_canonical_parentid(
k, df_canonical_parentid) for k in d_parentid_cellname.values()}
add_array_with_mapper(poly_embryo, 'cellName', 'parentIndexCanonical',
d_cellname_canonical_parentid, default=999)
d_parentid_canonical = {
i: d_cellname_canonical_parentid[j] for i, j in d_parentid_cellname.items()}
write_mapper_cellname_csv(d_cellname_canonical_parentid)
return d_parentid_canonical
def _add_parentid(poly_embryo, d_parentid_cellname):
add_array_with_mapper(poly_embryo, 'parentIndex', 'cellName',
d_parentid_cellname, default='Unidentified')
return
engage_cd_counter(mysim, cells, h_eff,
CD_cell_cell) # Must be after last remesh
mysim.run_until(mysim.get_time() + dtg)
vtkWriter.VTKSerialWriter(data=cells('triangles'),
filename=str(output_folder / "Seeding"),
select_all=True,
start_index=get_latest_file()[1] +
1).execute()
log_chronology_txt("After final runtime : engaging contactdetection")
# read in clean VTP to fix indices
poly_embryo = read_vtp_file(output_folder / get_latest_file()[0])
d_oldix_newix, _ = get_map_oldix_newix(type='triangles')
add_array_with_mapper(poly_embryo,
name_array_source='contact_index',
name_array_dest='contact_index',
mapper=d_oldix_newix,
field_type="CELL")
d_oldix_newix, _ = get_map_oldix_newix(type='nodes')
add_array_with_mapper(poly_embryo,
name_array_source='vertexIndices',
name_array_dest='vertexIndices',
mapper=d_oldix_newix,
field_type="CELL")
write_vtp_file(poly_embryo, output_folder / get_latest_file()[0])
log_chronology_txt(
"After final runtime : fixing indices due to remeshing => end of simulation"
)
#save centroids
np.savetxt(str(output_folder / "cell_centroids.csv"),