def draw_image(self):
if not self.needs_refresh:
return
self.needs_refresh = False
w, h = (self.w, self.h)
clearws()
setwindow(0, self.w, 0, self.h)
setviewport(0, 1, 0, 1)
setbackgroundcolor(1, 1, 1, 0)
vertices, normals = triangulate(data, \
(1.0/64, 1.0/64, 1.0/128), (-0.5, -0.5, -0.5), self.isolevel)
mesh = createmesh(len(vertices)*3, vertices, normals, \
ones(vertices.shape))
drawmesh(mesh, 1, (0,0,0), (0,0,1), (0,1,0), (1,1,1), (1,1,1))
center = spherical_to_cartesian(-2, pi*self.y/self.h+pi/2, pi*self.x/self.w)
up = spherical_to_cartesian(1, pi*self.y/self.h+pi, pi*self.x/self.w)
cameralookat(center[0], center[1], -0.25+center[2], 0, 0, -0.25, up[0], up[1], up[2])
drawimage(0, self.w, 0, self.h, \
self.w, self.h, GR3_Drawable.GR3_DRAWABLE_GKS)
if self.export:
export("mri.html", 800, 800)
print("Saved current isosurface to mri.html")
self.export = False
clear()
deletemesh(c_int(mesh.value))
def draw_image(self):
w, h = (self.w, self.h)
clearws()
setwindow(0, self.w, 0, self.h)
setviewport(0, 1, 0, 1)
setbackgroundcolor(1, 1, 1, 0)
vertices, normals = triangulate(data, \
(1.0/64, 1.0/64, 1.0/128), (-0.5, -0.5, -0.5), self.isolevel)
mesh = createmesh(len(vertices)*3, vertices, normals, \
ones(vertices.shape))
drawmesh(mesh, 1, (0, 0, 0), (0, 0, 1), (0, 1, 0), (1, 1, 1),
(1, 1, 1))
center = spherical_to_cartesian(-2, pi * self.y / self.h + pi / 2,
pi * self.x / self.w)
up = spherical_to_cartesian(1, pi * self.y / self.h + pi,
pi * self.x / self.w)
cameralookat(center[0], center[1], -0.25 + center[2], 0, 0, -0.25,
up[0], up[1], up[2])
drawimage(0, self.w, 0, self.h, \
self.w, self.h, GR3_Drawable.GR3_DRAWABLE_GKS)
if self.export:
export("mri.html", 800, 800)
print("Saved current isosurface to mri.html")
self.export = False
clear()
deletemesh(c_int(mesh.value))
def draw_image(self):
if not self.needs_refresh:
return
self.needs_refresh = False
gr.clearws()
gr.setwindow(0, self.w, 0, self.h)
gr.setviewport(0, 1, 0, 1)
gr3.setbackgroundcolor(1, 1, 1, 0)
vertices, normals = gr3.triangulate(data,
(1.0 / 64, 1.0 / 64, 1.0 / 128),
(-0.5, -0.5, -0.5), self.isolevel)
mesh = gr3.createmesh(
len(vertices) * 3, vertices, normals, np.ones(vertices.shape))
gr3.drawmesh(mesh, 1, (0, 0, 0), (0, 0, 1), (0, 1, 0), (1, 1, 1),
(1, 1, 1))
center = spherical_to_cartesian(-2,
np.pi * self.y / self.h + np.pi / 2,
np.pi * self.x / self.w)
up = spherical_to_cartesian(1, np.pi * self.y / self.h + np.pi,
np.pi * self.x / self.w)
gr3.cameralookat(center[0], center[1], -0.25 + center[2], 0, 0, -0.25,
up[0], up[1], up[2])
gr3.drawimage(0, self.w, 0, self.h, self.w, self.h,
gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
if self.export:
gr3.export("mri.html", 800, 800)
print("Saved current isosurface to mri.html")
self.export = False
gr3.clear()
gr3.deletemesh(c_int(mesh.value))
def save_screenshot(self, file_name, width=3840, height=2160, first=True, last=True):
"""
Save a screenshot in the given resolution.
``first`` and ``last`` can be used to indicate if the first or last screenshot is taken when
multiple images are saved in a loop for example.
"""
if first and self.assigned_opengl_context is not None:
self.assigned_opengl_context.makeCurrent()
gr3.export(file_name, width, height)
if last and self.assigned_opengl_context is not None:
self.assigned_opengl_context.doneCurrent()
def keyboard(key, *args):
if not isinstance(key, str):
key = key.decode('utf-8')
if key == 'p':
gr3.export("test.pov", 0, 0)
elif key == 'j':
gr3.export("test.html", 800, 800)
elif key == 'n':
gr3.export("test.png", 800, 800)
elif key == 'm':
gr3.export("test.jpg", 800, 800)
elif key == ' ':
gr3.terminate()
glutDestroyWindow(window_id)
sys.exit()
elif key == '0':
gr3.setquality(0)
elif key == '1':
gr3.setquality(2)
elif key == '2':
gr3.setquality(4)
elif key == '3':
gr3.setquality(8)
elif key == '4':
gr3.setquality(3)
elif key == '5':
gr3.setquality(5)
elif key == '6':
gr3.setquality(9)
else:
print(key, ord(key))
def keyboard(key, *args):
if key == 'p':
gr3.export("test.pov", 0, 0)
elif key == 'j':
gr3.export("test.html", 800, 800)
elif key == 'n':
gr3.export("test.png", 800, 800)
elif key == 'm':
gr3.export("test.jpg", 800, 800)
elif key == ' ':
gr3.terminate()
sys.exit()
elif key == '0':
gr3.setquality(0)
elif key == '1':
gr3.setquality(2)
elif key == '2':
gr3.setquality(4)
elif key == '3':
gr3.setquality(8)
elif key == '4':
gr3.setquality(3)
elif key == '5':
gr3.setquality(5)
elif key == '6':
gr3.setquality(9)
else:
print key, ord(key)
def keyboard(key, *args):
if key == 'p':
gr3.export("test.pov",0,0)
elif key == 'j':
gr3.export("test.html",800,800)
elif key == 'n':
gr3.export("test.png",800,800)
elif key == 'm':
gr3.export("test.jpg",800,800)
elif key == ' ':
gr3.terminate()
sys.exit()
elif key == '0':
gr3.setquality(0)
elif key == '1':
gr3.setquality(2)
elif key == '2':
gr3.setquality(4)
elif key == '3':
gr3.setquality(8)
elif key == '4':
gr3.setquality(3)
elif key == '5':
gr3.setquality(5)
elif key == '6':
gr3.setquality(9)
else:
print key, ord(key)
def on_export_menu(entry):
if entry == 1:
filename = "scene.pov"
elif entry == 2:
filename = "scene.html"
elif entry == 3:
filename = "scene.jpg"
elif entry == 4:
filename = "scene.png"
else:
return 1
gr3.setquality(export_quality)
gr3.export(filename, 800, 800)
gr3.setquality(0)
return 0
def on_export_menu(entry):
if entry == 1:
filename = "scene.pov"
elif entry == 2:
filename = "scene.html"
elif entry == 3:
filename = "scene.jpg"
elif entry == 4:
filename = "scene.png"
else:
return 1
gr3.setquality(export_quality)
gr3.export(filename,800,800)
gr3.setquality(0)
return 0
def export(molecule,
file_name,
width=500,
height=500,
show_bonds=True,
bonds_method='radii',
bonds_param=None,
camera=None):
"""
Draw the given molecule into a given file. The file type is determined by
the file extension, e.g. '.png' or '.html'. By default, bonds are drawn,
if this is undesired the show_bonds parameter can be set to False.
For information on the bond calculation, see Molecule.calculate_bonds.
If you pass a tuple of camera position, center of view and an up vector to
the camera parameter, the camera will be set accordingly. Otherwise the
molecule will be viewed in the direction of the z axis, with the y axis
pointing upward.
"""
global _camera
molecule.positions -= np.mean(molecule.positions, axis=0)
max_atom_distance = np.max(la.norm(molecule.positions, axis=1))
if show_bonds:
molecule.calculate_bonds(bonds_method, bonds_param)
if camera is None:
if _camera is None:
camera_distance = -max_atom_distance * 2.5
camera = ((0, 0, camera_distance), (0, 0, 0), (0, 1, 0))
else:
camera = _camera
camera = np.array(camera)
_camera = camera
# Create the GR3 scene
gr3.setbackgroundcolor(255, 255, 255, 0)
_set_gr3_camera()
_create_gr3_scene(molecule, show_bonds)
glEnable(GL_DEPTH_TEST)
gr3.setquality(gr3.GR3_Quality.GR3_QUALITY_OPENGL_16X_SSAA)
gr3.export(file_name, width, height)
glBindFramebuffer(GL_FRAMEBUFFER, 0)
glDisable(GL_DEPTH_TEST)
def export(molecule, file_name, width=500, height=500,
show_bonds=True, bonds_method='radii', bonds_param=None,
camera=None):
"""
Draw the given molecule into a given file. The file type is determined by
the file extension, e.g. '.png' or '.html'. By default, bonds are drawn,
if this is undesired the show_bonds parameter can be set to False.
For information on the bond calculation, see Molecule.calculate_bonds.
If you pass a tuple of camera position, center of view and an up vector to
the camera parameter, the camera will be set accordingly. Otherwise the
molecule will be viewed in the direction of the z axis, with the y axis
pointing upward.
"""
global _camera
molecule.positions -= np.mean(molecule.positions, axis=0)
max_atom_distance = np.max(la.norm(molecule.positions, axis=1))
if show_bonds:
molecule.calculate_bonds(bonds_method, bonds_param)
if camera is None:
if _camera is None:
camera_distance = -max_atom_distance*2.5
camera = ((0, 0, camera_distance),
(0, 0, 0),
(0, 1, 0))
else:
camera = _camera
camera = np.array(camera)
_camera = camera
# Create the GR3 scene
gr3.setbackgroundcolor(255, 255, 255, 0)
_set_gr3_camera()
_create_gr3_scene(molecule, show_bonds)
glEnable(GL_DEPTH_TEST)
gr3.export(file_name, width, height)
glBindFramebuffer(GL_FRAMEBUFFER, 0)
glDisable(GL_DEPTH_TEST)
np.save(filename+'.npy', filedata)
print('Done.')
positions = filedata[:, :3].astype(np.int32)
directions = filedata[:, 3:].astype(np.float32)
# define the values used for calculating the isosurface and the isolevel
isovalue = 0
values = directions[:, 2]
# negate the values, as we want negative z to define "inside"
isovalue = -isovalue
values = -values
# transform the values to the range [0, 1]
isovalue -= values.min()
values -= values.min()
isovalue /= values.max()
values /= values.max()
# write them into a contiguous array
nx, ny, nz = positions.max(axis=0)+1
data = np.zeros((nx, ny, nz), np.float32)
ix, iy, iz = positions.T
data[ix, iy, iz] = values
# write out an HTML file
gr3.cameralookat(0, 0, 2, 0, 0, 0, 0, 1, 0)
gr3.drawisosurfacemesh(data, isovalue=isovalue, step=[2.0/(nx-1), 2.0/(ny-1), 2.0/(nz-1)], offset=[-1, -1, -1], position=(0, 0, 0))
gr3.export("output.html", 1024, 1024)
directions = filedata[:, 3:].astype(np.float32)
# define the values used for calculating the isosurface and the isolevel
isovalue = 0
values = directions[:, 2]
# negate the values, as we want negative z to define "inside"
isovalue = -isovalue
values = -values
# transform the values to the range [0, 1]
isovalue -= values.min()
values -= values.min()
isovalue /= values.max()
values /= values.max()
# write them into a contiguous array
nx, ny, nz = positions.max(axis=0) + 1
data = np.zeros((nx, ny, nz), np.float32)
ix, iy, iz = positions.T
data[ix, iy, iz] = values
# write out an HTML file
gr3.cameralookat(0, 0, 2, 0, 0, 0, 0, 1, 0)
gr3.drawisosurfacemesh(data,
isovalue=isovalue,
step=[2.0 / (nx - 1), 2.0 / (ny - 1), 2.0 / (nz - 1)],
offset=[-1, -1, -1],
position=(0, 0, 0))
gr3.export("output.html", 1024, 1024)
