import subprocess
import struct
import sys
from evtk.hl import pointsToVTK
from evtk.hl import unstructuredGridToVTK
from evtk.vtk import VtkTriangle
from evtk.vtk import VtkTetra
import read_write as rw # read_write.py
import utils as ut # utils.py
###########################################################################
# main program
###########################################################################
# NOTE: one-based indexing
print("read basic mesh, write vtu's")
mesh_names = subprocess.check_output("ls 4sim*.bin", shell=True).split()
mesh_names = [s.decode("utf-8") for s in mesh_names] # bytes -> string
for mesh in mesh_names:
fname = mesh.split('.')[0]
print(fname[-4])
sys.stdout.flush()
verts, tris, tets = rw.read_basic_bin(fname)
rw.write_points("nodes_" + fname, verts)
rw.write_tris("surface_" + fname, verts,
tris + 1) # change to one based indexing
rw.write_tets("elements_" + fname, verts, tets + 1) #
###########################################################################
###########################################################################
###################################
IMAGE_SIZE_XY = 1024.0
IMAGE_SIZE_Z = 26.0
ACTUAL_XY = 80.0
ACTUAL_STEP_Z = 2.0
ACTUAL_GLYPH = 3.0
###################
SCALE_X = ACTUAL_XY / IMAGE_SIZE_XY
SCALE_Y = SCALE_X
SCALE_Z = ACTUAL_STEP_Z
###########################################################################
# main program
###########################################################################
fname = 'points'
verts = rw.get_points(fname + '.txt')
print(verts)
verts[:, 0] *= SCALE_X
verts[:, 1] *= SCALE_Y
verts[:, 2] *= SCALE_Z
print(verts)
rw.write_points(fname, verts)
#rw.write_tris("basal_"+fname, lverts[i], ltris[i][btrisi-1]) # has all the verts
#rw.write_tets("elements_"+fname, lverts[i], ltets[i], data={"dfa" : ldfa_tet[i], "dfb" : dfb})
nverts) # get the integer and fractional part of all nverts
# iterate through rvertsi and store the vert that is closest to each (integer) grid point
for i in rvertsi:
dist = np.linalg.norm(ifverts[0][i])
vgridi = (ifverts[1][i]).astype(
int) # grid index is simply the vertex location integer part
if dist > 0.5: # don't bother with grid points that have no close vertex
continue
noise = 0.3 * np.random.ranf(
) # some spatial dithering to break up an aligned visual
dist += noise
# is this vertex closest to the grid point?
if dist < vgrid[vgridi[0]][vgridi[1]][vgridi[2]][0]:
vgrid[vgridi[0]][vgridi[1]][
vgridi[2]][0] = dist # store the new closer distance
vgrid[vgridi[0]][vgridi[1]][
vgridi[2]][1] = i # update the associated vertex index
# extract the close vertex indices
cvi = vgrid[:, :, :, 1]
cvi = np.extract(cvi < toohigh, cvi)
print "Vertex count reduction:", verts.shape[0], "->", cvi.shape[0]
rw.write_points("reduced-nodes_" + fname, verts[cvi.astype(int)])
rw.write_indicies("reduced-indices_" + fname, cvi)
###########################################################################
###########################################################################
print("read mesh, calc dnl/apical/dfa, write nodes/surface/apical")
lsegs = rw.read_lumen()
mesh_names = subprocess.check_output("ls *.msh", shell=True).split()
mesh_names = [s.decode("utf-8") for s in mesh_names] # bytes -> string
for mesh in mesh_names:
fname = mesh.split('.')[0]
print(fname[-4], end='')
sys.stdout.flush()
verts, tris, tets = rw.read_mesh(fname)
dnl = ut.get_dnl(tris, verts, lsegs)
atrisiS, atrisiL = ut.get_apical(tris, dnl, APICAL_SMALL, APICAL_LARGE)
dfa_vert, dfa_tet = ut.get_dfa(atrisiS, tris, verts, tets)
ldfa_vert.append(dfa_vert)
ldfa_tet.append(dfa_tet)
rw.write_points("nodes_" + fname, verts, pdata={"dfa": dfa_vert})
rw.write_tris("surface_" + fname, verts, tris, data={"dnl": dnl})
rw.write_tris("apical_" + fname, verts,
tris[atrisiS - 1]) # has all the verts
lverts.append(verts)
ltris.append(tris)
ltets.append(tets)
latrisiS.append(atrisiS)
latrisiL.append(atrisiL)
print("\ncalc/write common")
ncells = len(mesh_names)
for c1 in range(ncells):
ctrisi = np.empty((3, 0), dtype=int) # common tri indices per cell
for c2 in range(ncells):
if (c1 == c2): continue