Added wrapper to libtrisurf

Samo Penic

2017-09-17 a4f8eb21f85326596a491b39e0330882ee8017f0

Added wrapper to libtrisurf

 trisurf/VTKRendering.py

@@ -4,7 +4,7 @@
    from vtk import *
except:
    print("Vtk rendering works if you manually install vtk7 for python3")
    exit(1)
#    exit(1)

class MultiRender:
    def __init__(self,args,host):

 trisurf/analyses.py

@@ -36,7 +36,7 @@
    from trisurf import VTKRendering as vtk
    import math
    from multiprocessing import Process
    table=trisurf.Statistics(run.Dir.fullpath(),filename='data_tspoststat.csv').getTable()
    table=trisurf.Statistics(run.Dir.fullpath(),filename='poststat.csv').getTable()
    def running_avg(col):
        import numpy as np
        avg=[]    
@@ -66,7 +66,7 @@
# these functions should be wrapped
# -------------------------------
@analysis('plotColumnFromPostProcess')
def plotColumnFromPostProcess(run, filename='data_tspoststat.csv', column='hbar', **kwargs):
def plotColumnFromPostProcess(run, filename='poststat.csv', column='hbar', **kwargs):
    import matplotlib.pyplot as plt

    def smooth(y, box_pts):

 trisurf/wrapper.py

New file
@@ -0,0 +1,203 @@
from ctypes import *

TS_SUCCESS=0
TS_FAIL=1

TS_ID_FILAMENT=1

TS_COORD_CARTESIAN=0
TS_COORD_SPHERICAL=1
TS_COORD_CYLINDRICAL=2


class ts_coord(Structure):
    _fields_=[
        ("e1", c_double),
        ("e2", c_double),
        ("e3", c_double),
        ("coord_type", c_uint)
        ]
class ts_vertex(Structure):
    pass
class ts_bond(Structure):
    pass
class ts_triangle(Structure):
    pass
class ts_cell(Structure):
    pass
class ts_poly(Structure):
    pass
class ts_cluster(Structure):
    pass
ts_vertex._fields_=[
        ('idx',c_uint),
        ('x',c_double),
        ('y',c_double),
        ('z',c_double),
        ('neigh_no',c_uint),
        ('neigh', POINTER(POINTER(ts_vertex))),
        ('bond_length', POINTER(c_double)),
        ('bond_length_dual',POINTER(c_double)),
        ('curvature', c_double),
        ('energy', c_double),
        ('energy_h',c_double),
        ('tristar_no', c_uint),
        ('tristar', POINTER(POINTER(ts_triangle))),
        ('bond_no',c_uint),
        ('bond',POINTER(POINTER(ts_bond))),
        ('cell',POINTER(ts_cell)),
        ('xk',c_double),
        ('c',c_double),
        ('id', c_uint),
        ('projArea',c_double),
        ('relR', c_double),
        ('solAngle', c_double),
        ('grafted_poly', POINTER(ts_poly)),
        ('cluster',POINTER(ts_cluster)),
        ]
class ts_vertex_list(Structure):
    _fields_=[('n',c_uint), ('vtx',POINTER(POINTER(ts_vertex)))]

ts_bond._fields_=[('idx',c_uint),
        ('vtx1', POINTER(ts_vertex)),
        ('vtx2', POINTER(ts_vertex)),
        ('bond_length',c_double),
        ('bond_length_dual',c_double),
        ('tainted', c_char),
        ('energy',c_double),
        ('x',c_double),
        ('y',c_double),
        ('z',c_double),
    ]
class ts_bond_list(Structure):
    _fields_=[('n', c_uint),('bond',POINTER(POINTER(ts_bond)))]

ts_triangle._fields_=[
        ('idx',c_uint),
        ('vertex', POINTER(ts_vertex)*3),
        ('neigh_no',c_uint),
        ('neigh', POINTER(POINTER(ts_triangle))),
        ('xnorm', c_double),
        ('ynorm', c_double),
        ('znorm', c_double),
        ('area', c_double),
        ('volume', c_double),
    ]

class ts_triangle_list(Structure):
    _fields_=[('n',c_uint),('tria', POINTER(POINTER(ts_triangle)))]


ts_cell._fields_=[
    ('idx', c_uint),
    ('vertex', POINTER(POINTER(ts_vertex))),
    ('nvertex', c_uint),
    ]		

class ts_cell_list(Structure):
    _fields_=[
        ('ncmax', c_uint*3),
        ('cellno', c_uint),
        ('cell',POINTER(POINTER(ts_cell))),
        ('dcell', c_double),
        ('shift', c_double),
        ('max_occupancy', c_double),
        ('dmin_interspecies', c_double)
    ]

class ts_spharm(Structure):
    _fields_=[
        ('l',c_uint),
        ('ulm', POINTER(POINTER(c_double))),
    #    ('ulmComplex', POINTER(POINTER(gsl_complex))), #poisci!!!!
        ('ulmComplex', POINTER(POINTER(c_double))), #temporary solution
        ('sumUlm2', POINTER(POINTER(c_double))),
        ('N', c_uint),
        ('co',POINTER(POINTER(c_double))),
        ('Ylmi', POINTER(POINTER(c_double))),
        ]

ts_poly._fields_=[
        ('vlist', POINTER(ts_vertex_list)),
        ('blist', POINTER(ts_bond_list)),
        ('grafted_vtx',POINTER(ts_vertex)),
        ('k', c_double),
    ]

class ts_poly_list(Structure):
    _fields_=[('n',c_uint),('poly',POINTER(POINTER(ts_poly)))]

class ts_tape(Structure):
    _fields_=[
        ('nshell',c_long),
        ('ncxmax',c_long),
        ('ncymax',c_long),
        ('nczmax',c_long),
        ('npoly',c_long),
        ('nmono',c_long),
        ('internal_poly',c_long),
        ('nfil',c_long),
        ('nfono', c_long),
        ('R_nucleus',c_long),
        ('R_nucleusX',c_double),
        ('R_nucleusY',c_double),
        ('R_nucleusZ',c_double),
        ('pswitch',c_long),
        ('constvolswitch',c_long),
        ('constareaswitch',c_long),
        ('constvolprecision',c_double),
        ('multiprocessing',c_char_p),
        ('brezveze0',c_long),
        ('brezveze1',c_long),
        ('brezveze2',c_long),
        ('xk0',c_double),
        ('dmax',c_double),
        ('dmin_interspecies',c_double),
        ('stepsize',c_double),
        ('kspring',c_double),
        ('xi',c_double),
        ('pressure',c_double),
        ('iterations',c_long),
        ('inititer',c_long),
        ('mcsweeps',c_long),
        ('quiet',c_long),
        ('shc',c_long),
        ('number_of_vertice_with_c0',c_long),
        ('c0', c_double),
        ('w', c_double),
        ('F', c_double),
    ]
		

class ts_vesicle(Structure):
    _fields_=[
        ('vlist', POINTER(ts_vertex_list)),
        ('blist', POINTER(ts_bond_list)),
        ('tlist', POINTER(ts_triangle_list)),
        ('clist', POINTER(ts_cell_list)),
        ('nshell', c_uint),
        ('bending_rigidity',c_double),
        ('dmax',c_double),
        ('stepsize',c_double),
        ('cm', c_double*3),
        ('volume', c_double),
        ('sphHarmonics',POINTER(ts_spharm)),
        ('poly_list', POINTER(ts_poly_list)),
        ('filament_list', POINTER(ts_poly_list)),
        ('spring_constant', c_double),
        ('pressure', c_double),
        ('pswitch', c_int),
        ('tape', POINTER(ts_tape)),
        ('R_nucleus', c_double),
        ('R_nucleusX', c_double),
        ('R_nucleusY', c_double),
        ('R_nucleusZ', c_double),
        ('nucleus_center', c_double *3 ),
        ('area', c_double),
    ]

ts_cluster._fields_=[('nvtx',c_uint),('idx',c_uint),('vtx', POINTER(POINTER(ts_vertex)))]

class ts_cluster_list(Structure):
    _fields_=[('n',c_uint),('poly',POINTER(POINTER(ts_cluster)))]