def apply(ctx_ref, data_size, data, plugin_data):
instance = ctypes.cast(data, ctypes.POINTER(ctypes.c_uint32))[0]
if instance not in Molecule.plugin_instances:
egs.printf("molecule plugin instance not found", egs.WARNING)
else:
Context.call_apply(ctx_ref,
Molecule.plugin_instances[instance].spheres)
Context.call_apply(ctx_ref,
Molecule.plugin_instances[instance].cylinder)
def __init__(self, filename, bonds_param=1.5):
with open(filename, "r") as f:
data = f.read().splitlines()
num_atoms = int(data[0].strip())
positions = np.zeros((num_atoms, 3), np.float)
colors = np.zeros(num_atoms, np.long)
for i, line in enumerate(data[2:]):
atom, x, y, z = line.strip().split()
atom = atom.upper()
if atom not in Molecule.atoms:
print("element not found: {} (at ({}, {}, {}))".format(
atom, x, y, z))
positions[i] = float(x), float(y), float(z)
colors[i] = Molecule.atoms[atom][1]
start = ctypes.POINTER(ctypes.c_float)()
end = ctypes.POINTER(ctypes.c_float)()
bond_lib = ctypes.CDLL(
os.path.join(os.environ.get('EGS_PATH'), 'plugins',
'molecule_plugin', LIB_NAME))
bond_lib.calc_bonds.argtypes = [
ctypes.POINTER(ctypes.c_float),
ctypes.POINTER(ctypes.c_float),
ctypes.POINTER(ctypes.c_float), ctypes.c_int, ctypes.c_float,
ctypes.POINTER(ctypes.POINTER(ctypes.c_float)),
ctypes.POINTER(ctypes.POINTER(ctypes.c_float))
]
bond_lib.calc_bonds.restype = ctypes.c_int
num_bonds = bond_lib.calc_bonds(
(ctypes.c_float * num_atoms)(*positions[:, 0]),
(ctypes.c_float * num_atoms)(*positions[:, 1]),
(ctypes.c_float * num_atoms)(*positions[:, 2]), num_atoms,
bonds_param, ctypes.byref(start), ctypes.byref(end))
bonds_start = np.ctypeslib.as_array(
(ctypes.c_float * 3 * num_bonds).from_address(
ctypes.addressof(start.contents)))
bonds_end = np.ctypeslib.as_array(
(ctypes.c_float * 3 * num_bonds).from_address(
ctypes.addressof(end.contents)))
bonds = [
bonds_start.reshape(num_bonds, 3),
bonds_end.reshape(num_bonds, 3)
]
self._data = PluginWrapper()
self._data.plugin_name = Molecule.plugin_name
self.spheres = Sphere(positions, [0.31] * (len(positions)),
colors).display_list_elem_ref
self.cylinder = Cylinder(bonds[0], bonds[1],
[0.046629] * len(bonds[0]),
0xffffffff).display_list_elem_ref
self._data.data_length = ctypes.sizeof(ctypes.c_uint32)
self._data.data = (ctypes.c_uint8 * self._data.data_length)(
Molecule.plugin_instance_ctr)
Molecule.plugin_instances[Molecule.plugin_instance_ctr] = self
Molecule.plugin_instance_ctr += 1
self._molecule_ref = self._data.get_display_list_elem()
egs.printf("created molecule".encode('utf-8'), egs.DEBUG)
def __init__(self, width, height, rgb_data):
self._data = PluginWrapper()
self._data.plugin_name = Image.plugin_name
self.width = width
self.height = height
self.initialised = False
self.rgb_data = np.array(rgb_data, dtype=np.uint8)
self._data.data_length = ctypes.sizeof(ctypes.c_uint32)
self._data.data = (ctypes.c_uint8 * self._data.data_length)(Image.plugin_instance_ctr)
Image.plugin_instances[Image.plugin_instance_ctr] = self
Image.plugin_instance_ctr += 1
self._image_ref = self._data.get_display_list_elem()
egs.printf("created image", egs.DEBUG)
def from_image_file(filename):
try:
im = PIL.Image.open(filename)
except NameError:
egs.printf("PIL module not loaded.", egs.WARNING)
return Image(width=0, height=0, rgb_data=[])
w, h = im.size
rgba = list(im.getdata())
im.close()
rgb = []
for elem in rgba:
if len(elem) == 3:
rgb += [elem[0], elem[1], elem[2], 255]
else:
rgb += [elem[0], elem[1], elem[2], elem[3]]
return Image(width=w, height=h, rgb_data=rgb)
def apply(ctx_ref, data_size, data, plugin_data):
instance = ctypes.cast(data, ctypes.POINTER(ctypes.c_uint32))[0]
if instance not in Image.plugin_instances:
egs.printf("Plugin instance not found", egs.WARNING)
else:
if not Image.plugin_instances[instance].initialised:
Image.plugin_instances[instance].texture = OpenGL.glGenTextures(1)
OpenGL.glBindTexture(OpenGL.GL_TEXTURE_2D, Image.plugin_instances[instance].texture)
OpenGL.glTexParameterf(OpenGL.GL_TEXTURE_2D, OpenGL.GL_TEXTURE_WRAP_S, OpenGL.GL_REPEAT)
OpenGL.glTexParameterf(OpenGL.GL_TEXTURE_2D, OpenGL.GL_TEXTURE_WRAP_T, OpenGL.GL_CLAMP_TO_EDGE)
OpenGL.glTexParameteri(OpenGL.GL_TEXTURE_2D, OpenGL.GL_TEXTURE_MAG_FILTER, OpenGL.GL_LINEAR)
OpenGL.glTexParameteri(OpenGL.GL_TEXTURE_2D, OpenGL.GL_TEXTURE_MIN_FILTER, OpenGL.GL_LINEAR_MIPMAP_LINEAR)
width = Image.plugin_instances[instance].width
height = Image.plugin_instances[instance].height
OpenGL.glTexImage2D(OpenGL.GL_TEXTURE_2D, 0, OpenGL.GL_RGB, width, height, 0, OpenGL.GL_RGBA,
OpenGL.GL_UNSIGNED_BYTE, Image.plugin_instances[instance].rgb_data)
OpenGL.glGenerateMipmap(OpenGL.GL_TEXTURE_2D)
Image.plugin_instances[instance].initialised = True
OpenGL.glActiveTexture(OpenGL.GL_TEXTURE0)
OpenGL.glBindTexture(OpenGL.GL_TEXTURE_2D, Image.plugin_instances[instance].texture)
def terminate(data_size, data, plugin_data):
instance = ctypes.cast(data, ctypes.POINTER(ctypes.c_uint32))[0]
if instance not in Molecule.plugin_instances:
egs.printf("molecule plugin instance not found", egs.WARNING)
else:
egs.printf("molecule destructor: calling sphere destructor",
egs.DEBUG)
Context.call_terminate(Molecule.plugin_instances[instance].spheres)
egs.printf("molecule destructor: calling cylinder destructor",
egs.DEBUG)
Context.call_terminate(
Molecule.plugin_instances[instance].cylinder)
del instance
egs.printf("molecule destructor: done", egs.DEBUG)
def terminate(data_size, data, plugin_data):
egs.printf("image destructor", egs.DEBUG)
def image_plugin_terminate_plugin():
egs.printf("Image plugin terminated")
from __future__ import print_function
import ctypes
import sys
import os
import numpy as np
lib_path = os.path.abspath(os.path.join('..', '..'))
sys.path.append(lib_path)
from egs import DisplayListElem, PluginWrapper, Context, SerializedDisplayListElem
import egs
try:
import PIL.Image
except ImportError:
egs.printf("Could not import PIL.", egs.WARNING)
import egs.glip as OpenGL
class Image:
apply_fun = None
plugin_name = ctypes.c_char_p("image_plugin")
plugin_instances = {}
plugin_instance_ctr = 0
def __init__(self, width, height, rgb_data):
self._data = PluginWrapper()
self._data.plugin_name = Image.plugin_name
self.width = width
self.height = height
self.initialised = False
def molecule_plugin_terminate_plugin():
egs.printf("Molecule plugin terminated")
