Wfmesh

DESCRIPTION

This script will create an object for any Wavefront(.OBJ) mesh file. This is a way to extend the number of objects you can use. Also, you have more control over the coloring, transformations, etc than the CGOs. Although there are a number of these obj files on the web, you can also easily created them with open source tools (OpenFX, Crossroads3D). It takes literally, 2 min to get an object created and then loaded into pymol. Simply open OpenFX Designer, click File->Insert->Model, then choose any of the models (or create your own of course!), then export it as .3ds file. Then open the .3ds file from Crossroads3D and export as Wavefront OBJ.

• createWFMesh - create a mesh object from Wavefront (*.obj) formated file

IMAGES

Star Wars Anyone?

A Torus, as an example shape you could do. Notice polygon normals are being used...need smoothing!

SETUP

Simply "run WFMesh.py"

NOTES / STATUS

• Tested on Pymolv0.97, Windows platform, should work on linux as well.
• Coloring is fixed for grey and sections of mesh are stored, but not used.
• Simple opengl calls; not optimized (display lists, etc) or anything.
• Vertex Normal code is broken, so normals are per polygon right now.
• Post problems in the discussion page, on 'my talk' page or just email me : dwkulp@mail.med.upenn.edu

USAGE

createWFObj file, name [,translate=[0,0,0]] [,flip=0]

EXAMPLES

  createWFObj "ship.obj" "Ship"
  createWFObj "torus.obj" "Torus" flip=1  # Flip = 1, if OBJ created by openFX, crossroads3D combination
  createWFObj "torus.obj" "Torus" translate=[10,10,0] flip=1      
  

REFERENCES

OpenFX Crossroads3D

SCRIPTS (WFMesh.py)

WFMesh.py

###############################################
#  File:          WFObj.py
#  Author:        Dan Kulp
#  Creation Date: 5/13/05
#
#  Notes:
#  Create openGL objects from a wavefront (obj) file
###############################################
 
import os
import re
import math
from pymol.opengl.gl import *
from pymol.callback import Callback
 
 
# Wrapper Function, to create a given WFObj with a specific name (flip = 1 if OpenFX + Crossroads used)
def createWFObj(file, name,translate=[0,0,0],flip=0):
        obj = WFMesh(file,translate,flip)
        cmd.load_callback(obj,name)
 
 
# Class for Wavefront Mesh
class WFMesh(Callback):
 
    verts = []        # list of vertices
    polys = []        # list of poylgons
    pnorms = []       # list of polynomal normals
    vnorms = {}       # dict. of vertex normals
    vavenorms = []    # list of vertex normals, redundant -- I'm far froma python pro.
    sections = {}     # list of sections of mesh
 
    # Read mesh into memory
    def readOBJ(self,file):
        if os.path.exists(file):
            input = open(file,'r')
            for line in input:
                dat = re.split("\s+", line)
 
                # Find vertex line
                if line[0] == 'v' and line[1] != 't' and line[1] != 'n':    self.verts.append([dat[1],dat[2],dat[3]])
 
                # Find polygon line
                if line[0] == 'f':    self.polys.append([dat[1],dat[2],dat[3]])
 
                # Find section line
                if line[0] == 'g':    self.sections[len(self.polys)] = dat[1] 
 
 
    # Compute the normals for each polygon and each vertex              
    def computeNorms(self):
 
        # Compute norms for each polygon
        for p in self.polys:
                v12 = [float(self.verts[int(p[1])-1][0]) - float(self.verts[int(p[0])-1][0]),\
                       float(self.verts[int(p[1])-1][1]) - float(self.verts[int(p[0])-1][1]),\
                       float(self.verts[int(p[1])-1][2]) - float(self.verts[int(p[0])-1][2]) \
                      ]
 
                v13 = [float(self.verts[int(p[2])-1][0]) - float(self.verts[int(p[0])-1][0]),\
                       float(self.verts[int(p[2])-1][1]) - float(self.verts[int(p[0])-1][1]),\
                       float(self.verts[int(p[2])-1][2]) - float(self.verts[int(p[0])-1][2]) \
                      ] 
 
                # Compute poly normal
                polynorm = self.cross(v12,v13) 
                norm = self.normalize(polynorm)
 
 
                # Files created by OpenFX, Crossroads combination need have their normals flipped       
                if self.flip:
                        norm[0] = -norm[0]
                        norm[1] = -norm[1]
                        norm[2] = -norm[2]
 
                # Append poly norm to polygonal norm array
                self.pnorms.append(norm)
 
                # Add norm to each vertexes norm..
                try:
                    self.vnorms[int(p[0])-1] = [float(self.vnorms[int(p[0])-1][0]) + norm[0],
                                            float(self.vnorms[int(p[0])-1][1]) + norm[1],
                                            float(self.vnorms[int(p[0])-1][2]) + norm[2]
                                           ]
                except:
                    self.vnorms[int(p[0])-1] = [norm[0],norm[1],norm[2]]
 
                try:                                       
                    self.vnorms[int(p[1])-1]  = [float(self.vnorms[int(p[1])-1][0]) + norm[0],
                                            float(self.vnorms[int(p[1])-1][1]) + norm[1],
                                            float(self.vnorms[int(p[1])-1][2]) + norm[2]
                                           ]
                except:
                    self.vnorms[int(p[1])-1] = [norm[0],norm[1],norm[2]]
 
                try:
                    self.vnorms[int(p[2])-1]  = [float(self.vnorms[int(p[1])-1][0]) + norm[0],
                                            float(self.vnorms[int(p[1])-1][1]) + norm[1],
                                            float(self.vnorms[int(p[1])-1][2]) + norm[2]
                                           ]
                except:
                    self.vnorms[int(p[2])-1] = [norm[0],norm[1],norm[2]]
 
 
        # Average out each vnorm..
        index = 0
        for v in self.vnorms.values():
                self.vavenorms.append([v[0]/4, v[1]/4, v[2]/4])         
                index += 1
 
    # Utility function to normalize a given vector
    def normalize(self,v):
        mag = v[0]*v[0]+v[1]*v[1]+v[2]*v[2]
        if mag <= 0:
            mag = 1
        else:
            mag = math.sqrt(mag)
 
        return [v[0]/mag, v[1]/mag,v[2]/mag]
 
    # Utility cross product function
    def cross(self,v1,v2):
        x = 0
        y = 1
        z = 2
 
        return [v1[y]*v2[z] - v1[z]*v2[y],\
                v1[z]*v2[x] - v1[x]*v2[z],\
                v1[x]*v2[y] - v1[y]*v2[x]
                ]
 
    # Constructor
    def __init__(self, file,translate=[0,0,0],flip=0):
        self.verts = []
        self.polys = [] 
        self.pnorms = []
        self.vnorms = {}
        self.vavenorms = []
        self.translate = translate
        self.flip      = flip 
 
        print "Read in file: "+str(file)
        self.readOBJ(file)
        print "Done reading in WFMesh, now compute norms"
        self.computeNorms()
        print "Done computing norms, now display WFMesh"
 
    # Draw Function
    def __call__(self):
 
        glColorMaterial(GL_FRONT, GL_DIFFUSE);  
        glEnable(GL_COLOR_MATERIAL);
        glShadeModel(GL_SMOOTH);
 
        # Color Everything grey
        glColor3f(0.5,0.5,0.5);
 
        glPushMatrix()
        glTranslated(self.translate[0],self.translate[1],self.translate[2])
        for index, p in enumerate(self.polys):
                glBegin(GL_POLYGON)
                glNormal3f(float(self.pnorms[index][0]),float(self.pnorms[index][1]),float(self.pnorms[index][2]))
 
                for x in p:
                        glVertex3f(float(self.verts[int(x)-1][0]),float(self.verts[int(x)-1][1]),float(self.verts[int(x)-1][2]))
 
                        # Vertex Normals - not computed correctly, so commented out for now
#                       norm = self.vnorms[int(x)-1]
#                       glNormal3f(float(norm[0]),float(norm[1]),float(norm[2]))
                glEnd()
        glPopMatrix()
 
 
 
 
 
cmd.extend("createWFObj", createWFObj)

ADDITIONAL RESOURCES

Torus.obj Torus.zip