def rdmb_povray_color(file_base,
time_point=2000,
width=800, height=600,
rotx=0, roty=0, rotz=0,
angle=14,
mode="C"):
"""Render and save RD results using Pov-Ray (color)
Render and save RD results using Pov-Ray
with color indicating parameter values
Args:
file_base:
time_point:
width, height:
rotx, roty, rotz:
angle:
mode:
"""
vs, ucs, As, Cs = load_rd_mb(file_base)
file_png = file_base + "_color_{:05}.png".format(time_point)
tempfile = file_png[:-4] + "__temp__" + ".pov"
camera = Camera('location', [0, 0, -25],
'look_at', [0, 0, 0],
'angle', angle,
'right x*image_width/image_height')
light = LightSource([-3, 2, -6],
'color', [1.0, 1.0, 1.0], 'parallel')
light2 = LightSource([2, -2, -6],
'color', [0.2, 0.2, 0.2], 'parallel')
background = Background('color', [1, 1, 1, 1])
spheres = []
spheres += sph(vs, ucs, As, Cs,
0, 0, 0,
rotx=rotx, roty=roty, rotz=rotz,
mode=mode)
objects = [light, light2, background] + spheres
scene = Scene(camera, objects=objects)
scene.render(file_png,
width=width, height=height,
tempfile=tempfile,
output_alpha=True, antialiasing=0.001)
return file_png
def main():
lookfrom = (13 / 1.5, 2 / 1.5, -5 / 1.5)
lookat = (0, 0, 0)
# dist_to_focus = 10.0
# aperture = 0.1
step = 1
# camera
camera = Camera('location', lookfrom, 'look_at', lookat)
# background
light = LightSource((0, 20, 0), 'color', (1, 1, 1))
bg = Background('color', (0.5, 0.7, 1.0))
base = Sphere((0, -1000, 0), 1000,
Texture(Pigment('color', (0.5, 0.5, 0.5))))
htlist = [bg, base, light]
for a in range(-11, 11, step):
for b in range(-11, 11, step):
choose_mat = random.random()
center = (a + 0.9 * random.random(),
0.2, b + 0.9 * random.random())
if distance(center, (4, 0.2, 0)) < 0.9:
continue
if choose_mat < 0.8:
# diffuse
color = (random.random() * random.random(),
random.random() * random.random(),
random.random() * random.random())
htlist.append(
Sphere(center, 0.2, Texture(Finish('diffuse', 1), Pigment('color', color))))
elif choose_mat < 0.95:
# metal
color = (0.5 * (1 + random.random()),
0.5 * (1 + random.random()),
0.5 * (1 + random.random()))
# p1 = 0.5 * random.random()
htlist.append(
Sphere(center, 0.2, Texture(Finish('Metal'), Pigment('color', color))))
else:
# glass
htlist.append(Sphere(center, 0.2, Material('M_Glass')))
# main 3 sphere
htlist.append(
Sphere((0, 1, 0), 1.0, Material('M_Glass')))
htlist.append(
Sphere((-4, 1, 0), 1.0, Texture(Finish('diffuse', 1), Pigment('color', (0.4, 0.2, 0.2)))))
htlist.append(Sphere((4, 1, 0), 1.0, Texture('Chrome_Texture')))
scene = Scene(camera, objects=htlist, included=[
'metals.inc', 'glass.inc', 'textures.inc', 'colors.inc'])
with open("where-next.pov", "w") as ofp:
print(str(scene), file=ofp)
scene.render('where-next.png', width=800, height=600,
antialiasing=0.1, quality=10)
def rdmb_povray_save(out_file,
vs,
ucs, vcs,
width=800, height=600,
rotx=0, roty=0, rotz=0,
angle=14):
"""Render and save RD results using Pov-Ray
Render and save RD results using Pov-Ray
Args:
out_file: output file
vs: vertices
ucs, vcs: u/v conc.
width, height: width and height of output image
rotx, roty, rotz: rotation angle
angle: camera angle
"""
ucmax = 6.0
ucs = ucs / ucmax
ucs[ucs > 1.0] = 1.0
# ucs = ucs / np.max(ucs)
rot1 = [rotx, 0, 0]
rot2 = [0, roty, 0]
rot3 = [0, 0, rotz]
camera = Camera('location', [0, 0, -25],
'look_at', [0, 0, 0],
'angle', angle,
'right x*image_width/image_height')
light = LightSource([-3, 2, -6], 'color', [1.0, 1.0, 1.0], 'parallel')
light2 = LightSource([2, -2, -6], 'color', [0.6, 0.6, 0.6], 'parallel')
background = Background('color', [1, 1, 1, 1])
spheres = [Sphere(v, 0.02,
Finish('ambient', 0.2, 'diffuse', 0.8, 'phong', 1.0),
Texture(Pigment('color',
[0.3+uc*0.7, 0.2+uc*0.8, 0.2+uc*0.8])),
'rotate', rot1,
'rotate', rot2,
'rotate', rot3) for v, uc in zip(vs, ucs)]
objects = [light, light2, background] + spheres
scene = Scene(camera, objects=objects)
scene.render(out_file, width=width, height=height,
output_alpha=True, antialiasing=0.001,
tempfile=out_file+"__temp__.pov")
def render_povray_mb(mbs, rotx=0, roty=0, rotz=0,
width=400, height=400, angle=14):
"""Render metaballs using Pov-Ray (Vapory)
Render metaballs using Pov-Ray (Vapory)
Args:
mbs: Metaballs
width, height:
Returns:
rendered_scene:
"""
rot1 = [rotx, 0, 0]
rot2 = [0, roty, 0]
rot3 = [0, 0, rotz]
camera = Camera('location', [0, 0, -25],
'look_at', [0, 0, 0],
'angle', angle,
'right x*image_width/image_height')
light = LightSource([-3, 2, -6], 'color', [1.0, 1.0, 1.0], 'parallel')
# light2 = LightSource([2, -2, -6], 'color', [0.6, 0.6, 0.6], 'parallel')
background = Background('color', [1, 1, 1, 1])
mbs_function = mbs.to_povray_func()
isosurface = Isosurface(Function(mbs_function),
ContainedBy(Box(-5, 5)),
'max_gradient', 1.8,
Pigment('color', [1.0, 0.15, 0.3]),
Finish('phong', 0.7,
'specular', 0.2,
'diffuse', 0.9,
'ambient', 0.1),
'rotate', rot1,
'rotate', rot2,
'rotate', rot3,
'translate', [0, 0, 0],
'no_shadow')
objects = [light, background] + [isosurface]
scene = Scene(camera, objects=objects)
return scene.render('ipython', width=width, height=height)
def frame(step):
""" """
# Feedback to user in terminal about render status
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
# Calculates the total frames
n_frames = eval(SETTINGS.NumberFrames)
full_circle = 2 * pi # One full circle equals exactly 2 times pi
# obtain molecules from function
create_molecules()
# Creation of RNA molecule
if step in range(0, n_frames // 5 * 2):
GUANINE.move_to([10, 0, 0])
ADENINE.move_to([-10, 0, 0])
CYTOSINE.move_to([0, 10, 0])
URACIL.move_to([0, -10, 0])
# # Sphere covering the RNA molecule
# if step in range(n_frames // 5 * 2, n_frames // 5 * 3):
#
# # RNA division
# if step in range(n_frames // 5 * 3, n_frames // 5 * 4):
#
# # Sphere division
# if step in range(n_frames // 5 * 4, n_frames):
# Return the Scene object for rendering
return Scene(models.floor_camera,
objects=[models.default_light] + GUANINE.povray_molecule)
def frame(step):
""" Returns the scene at step number (1 step per frame) """
# Show some information about how far we are with rendering
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
# Getting the total number of frames, see the configuration file
nframes = eval(SETTINGS.NumberFrames)
style = Texture(Pigment('color', [0.80, 0.00, 1.00], 'filter', 0.7),
Finish('phong', 0.6, 'reflection', 0.4))
cylinder = Cylinder([-6, -1, 4], [-6, 7, 4], 3, style)
sphere = Sphere([6, 2, -2], 3, style)
leg = legend([-15, 0, 0], 5)
radius = 25
z_start = 0
x_start = 0
#werkt allbei
# alpha = (-pi/2) + (step * 2 * pi / nframes)
alpha = pi / (nframes / 2) * step + 1
x_coord = radius * cos(alpha)
z_coord = radius * sin(alpha)
x = x_start + x_coord
z = z_start - z_coord
return Scene(
Camera('location', [x, 8, z], 'look_at', [0, 0, 0]),
objects=[
models.checkered_ground, models.default_light, cylinder, sphere
] + leg)
def frame(step):
""" Creates a Lightsource a default Camera and calls the Shape function and places this in a scene """
lichtje = LightSource([2, 8, -5], 5.0)
default_camera = Camera('location', [-5, 8, -20], 'look_at', [-5, 0, -5])
shapes = legend([-15, 0, 0], 5)
# Return the Scene object for rendering
return Scene(default_camera, objects=[lichtje] + shapes)
def frame(step):
""" Returns the scene at step number (1 step per frame) """
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
nframes = eval(SETTINGS.NumberFrames)
style = Texture(Pigment('color', [0.80, 0.00, 1.00], 'filter', 0.7),
Finish('phong', 0.6, 'reflection', 0.4))
cylinder = Cylinder([-6, -1, 4], [-6, 7, 4], 3, style)
sphere = Sphere([6, 2, -2], 3, style)
leg = legend([-15, 0, 0], 5)
radius = 25
z_start = 0
x_start = 0
alpha = (-pi / 2) + (step * 2 * pi / nframes)
# For each step, de difference in the x and z positions is equal to the radius time the sin and cos of alpha.
x_coord = radius * cos(alpha)
z_coord = radius * sin(alpha)
# Adding or subtracting the difference of the position for each step from the original camera position.
x = x_start + x_coord
z = z_start - z_coord
return Scene(
Camera('location', [x, 8, z], 'look_at', [0, 0, 0]),
objects=[
models.checkered_ground, models.default_light, cylinder, sphere
] + leg)
def frame(step):
""" Creates a frame of 4 cones, 4 boxes, 1 sphere and a legend """
# Define textures for different models
sphere_model = Texture(Pigment('color', [1, 0, 1], ), Finish('reflection', 0.5))
box_model = Texture(Pigment('color', [0, 1, 1], ), Finish('reflection', 0))
cone_model = Texture(Pigment('color', [1, 0, 1], ), Finish('reflection', 0))
# Create objects
sphere = Sphere([0, 0, 0], 3, sphere_model)
box_1 = Box([-5, -5, -4], [-3, 5, 4], box_model)
box_2 = Box([3, -5, -4], [5, 5, 4], box_model)
box_3 = Box([-5, 4, -4], [5, 6, 4], box_model)
box_4 = Box([-5, -5, -4], [5, -3, 4], box_model)
cone_1 = Cone([0, 6, 0], 3, [0, 10, 0], 0, cone_model)
cone_2 = Cone([0, -6, 0], 3, [0, -10, 0], 0, cone_model)
cone_3 = Cone([-5, 0, 0], 3, [-9, 0, 0], 0, cone_model)
cone_4 = Cone([5, 0, 0], 3, [9, 0, 0], 0, cone_model)
light_1 = LightSource([0, 10, -25], 'color', [1, 1, 1])
light_2 = LightSource([0, 8, -7], 'color', [1, 1, 1])
xyz_legend = legend([-15, 0, 0], 5)
camera = Camera('location', [0, 7, -30], 'look_at', [0, 2, 1])
# Return the Scene object for rendering
return Scene(camera,
objects=[sphere, box_1, box_2, box_3, box_4,
cone_1, cone_2, cone_3, cone_4, light_1, light_2] + xyz_legend)
def frame(step):
""" Renders an Ethanol molecule centered in the scene """
# Dit is een beetje dubbel maar zonder gaat er opnieuw iets mis met self.atom
ETHANOL = pdb.PDBMolecule('{}/pdb/ethanol.pdb'.format(
SETTINGS.AppLocation),
center=True)
camera = Camera('location', [10, 0, 0], 'look_at', [0, 0, 0])
nframes = eval(SETTINGS.NumberFrames)
hele_rotatie = 2 * math.pi
# When step is below or equal to 40, the ethanol molecule is devided into 2 parts.
if step <= (nframes / 2):
y_ass = (1 / (nframes / 2)) * step
splitsing = ETHANOL.divide([7, 8], 'ethanol', offset=[0, y_ass, 0])
else:
# In the second half of the program, last 40 frames we rotate the molecules 360 degrees.
y_ass = (1 / (nframes / 2)) * 40
splitsing = ETHANOL.divide([7, 8], 'ethanol', offset=[0, y_ass, 0])
step = step - 40
rotatie_per_step = (hele_rotatie / nframes) * step
ETHANOL.rotate([1, 0, 0], rotatie_per_step)
splitsing.rotate([1, 0, 0], rotatie_per_step)
# Return the Scene object for rendering.
return Scene(camera,
objects=[models.default_light] + ETHANOL.povray_molecule +
splitsing.povray_molecule,
included=['colors.inc'])
def frame(step):
camera = Camera('location', [0, 7, -30], 'look_at', [0, 2, 1])
xyz_legend = legend([-15, 0, 0], 5)
light = LightSource([0, 10, -25], 'color', [1, 1, 1])
return Scene(camera, objects=[light] + xyz_legend)
def frame(step):
""" Creates a frame of a given frame (step) number. """
# Show some information about how far we are with rendering
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
# Getting the total number of frames, see the configuration file
nframes = eval(SETTINGS.NumberFrames)
# Calculates rotation positions
angle_per_frame = math.pi * 2 / nframes # Calculates how much the angle needs to move per frame
angle = angle_per_frame * step # Calculates the angle of the frame
# Gets locations
x = math.cos(angle) * 20
z = math.sin(angle) * 20
# Create objects
sphere = Sphere([6, 2, -2], 3, models.default_sphere_model)
cylinder = Cylinder([-6, -1, 4], [-6, 7, 4], 3, models.default_sphere_model)
legend_1 = legend([-15, 0, 0], 5)
camera = Camera('location', [x, 8, z], 'look_at', [0, 0, 0])
# Return the Scene object containing all objects for rendering
return Scene(camera,
objects=[sphere, models.default_light, models.checkered_ground, cylinder] + legend_1)
def s2_cell_zoom(step):
""" This scene has the camera moving closer towards the cell and entering it """
cell_sphere = Sphere([0, 0, 0], 25, models.cell_model)
dpf = get_added_distance(TP_START[2], TP_DUR[2], [0, 0, 49.7], step)
camera_scene2 = Camera('location', [0, 0, -75], 'look_at', [0, 0, 0],
'translate', [dpf[0], dpf[1], dpf[2]])
return Scene(camera_scene2, objects=[cell_sphere] + models.lights_scene1)
def frame(step):
""" Makes an image/frame """
time_point = (step / TOTAL_FRAMES) * SETTINGS.Duration
logger.info(" @Time: %.4fs, Step: %d", time_point, step)
# Declaration of the end times of the scenes
global TP_END
TP_END = [4, 8, 11, 15, 18, 26, 32, 38, 44, 50, 58, 64]
# scene 0 1 2 3 4 5 6 7 8 9 10, 11
# Globals that change per frame
global TP_START, TP_DUR, TWITCH1, TWITCH2
TP_START, TP_DUR = get_time_point_data(TP_END)
TWITCH1, TWITCH2 = make_random_int()
if time_point < TP_END[0]:
scene = s0_intro_text()
elif time_point < TP_END[1]:
scene = s1_cell_overview()
elif time_point < TP_END[2]:
scene = s2_cell_zoom(step)
elif time_point < TP_END[3]:
scene = s3_in_cell()
elif time_point < TP_END[4]:
scene = s4_zoom_to_mrna(step)
elif time_point < TP_END[11]:
scene = scenes_mrna(step, time_point)
else:
text = Text('ttf', '"timrom.ttf"', '"Uh-oh, this ain\'t right"', 0, 0,
'translate', [-4, 0, 0], 'scale', [2, 2, 0],
models.text_model)
scene = Scene(models.default_camera,
objects=[models.default_light, text])
return scene
def frame(step):
""" Returns the scene at step number (1 step per frame) """
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
nframes = eval(SETTINGS.NumberFrames)
n_frames_loop = nframes / 5 # 16 frames per wave
stylebox = Texture(Pigment('color', [0.80, 0.00, 1.00], 'filter', 0.7),
Finish('phong', 0.6, 'reflection', 0.4))
x_start = -10
x_end = 10
x_distance = x_end - x_start
distance_per_frame = x_distance / nframes
y_start = 0
y_end = 4
y_distance = y_end - y_start
y_distance_per_frame = y_distance / n_frames_loop
iteratie = step // n_frames_loop
x_coord = x_start + step * distance_per_frame
correctie = iteratie * n_frames_loop
print(iteratie)
step = step - correctie
if step <= (n_frames_loop / 2):
y_coord = y_start + step * y_distance_per_frame
else:
y_coord = y_end - step * y_distance_per_frame
box = Box([x_coord, y_coord, 0], [x_coord + 2, y_coord + 2, 2], stylebox)
return Scene(models.default_camera,
objects=[box, models.default_ground, models.default_light])
def frame(step):
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
nframes = eval(SETTINGS.NumberFrames)
style = Texture(Pigment('color', [0.80, 0.00, 1.00], 'filter', 0.7),
Finish('phong', 0.6, 'reflection', 0.4))
cylinder = Cylinder([-6, -1, 4], [-6, 7, 4], 3, style)
sphere = Sphere([6, 2, -2], 3, style)
leg = legend([-15, 0, 0], 5)
radius = 25
z_start = -25
x_start = 0
alpha = (-pi / 2) + (step * 2 * pi / nframes)
x_coord = radius * cos(alpha)
z_coord = radius * sin(alpha)
x = x_start + x_coord
z = z_start - z_coord
camera_x = 0
camera_z = -25
# x gaat links en rechts en z verder de diepte in en terug -25?
camera = Camera('location', [camera_x, 8, camera_z], 'look_at', [0, 0, 0])
return Scene(
camera,
objects=[
cylinder, sphere, models.default_light, models.checkered_ground
] + shapes,
included=['colors.inc'])
def scene(step):
''' Returns the scene at step number (1 step per frame) '''
A = np.array([-10, 8, 0])
B = np.array([5, 2, -20])
# Find a point with distance 3 from A
BA = B-A # Vector B->A
d = math.sqrt(sum(np.power(BA, 2))) # distance
BA = BA / d # Normalize by its length; BA / ||BA||
scale = 4
N = A + scale * BA # Scale and add to A
l = Cylinder(A, B, 0.05, Pigment('color', [0, 1, 0]))
s1 = Sphere(N, 0.5, Texture(Pigment('color', [0.9, 0.05, 0.05])))
scale = 15
N = A + scale * BA # Scale and add to A
s2 = Sphere(N, 0.5, Texture(Pigment('color', [0.9, 0.05, 0.05])))
scale = 24
N = A + scale * BA # Scale and add to A
s3 = Sphere(N, 0.5, Texture(Pigment('color', [0.9, 0.05, 0.05])))
return Scene(povray.floor_camera,
objects=[povray.default_light, povray.checkered_ground,
l, s1, s2, s3],
included=['colors.inc'])
def frame(step):
""" Creates a sphere and 4 boxes, places this in a scene """
lichtje = LightSource([2, 8, -5], 5.0)
default_camera = Camera('location', [0, 4, -40], 'look_at', [0, 2, -5])
stylebox = Texture(Pigment('color', [0.80, 0.00, 1.00], 'filter', 0.7),
Finish('phong', 0.6, 'reflection', 0.4))
boxright = Box([3, -2, -3], [5, 6, 4], stylebox)
boxleft = Box([-5, -2, -3], [-3, 6, 4], stylebox)
boxupper = Box([-5, 6, -3], [5, 8, 4], stylebox)
boxbottom = Box([-5, -4, -3], [5, -2, 4], stylebox)
styleball = Texture(Pigment('color', [0.80, 0.00, 1.00], 'filter', 0.7))
centerball = Sphere([0, 2, 0], 3, styleball)
conetop = Cone([0, 8, 0], 3, [0, 12, 0], 0, stylebox)
conebottom = Cone([0, -4, 0], 3, [0, -8, 0], 0, stylebox)
coneleft = Cone([-5, 2, 0], 3, [-11, 2, 0], 0, stylebox)
coneright = Cone([5, 2, 0], 3, [11, 2, 0], 0, stylebox)
# Return the Scene object for rendering
return Scene(default_camera,
objects=[
lichtje, centerball, boxright, boxleft, boxupper,
boxbottom, conetop, conebottom, coneleft, coneright
])
def frame(step):
""" Returns the scene at step number (1 step per frame) """
# Show some information about how far we are with rendering
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
# Getting the total number of frames, see the configuration file
nframes = eval(SETTINGS.NumberFrames)
# Start- and end-points
x_start = -10
x_end = 10
distance = x_end - x_start
# Calculate distance to move at each step
distance_per_frame = (distance / nframes) * 2
# Calculate new x-coordinate
if step < (nframes / 2):
# Move from left to right (starting at x = -10)
x_coord = x_start + step * distance_per_frame
else:
# Move from right to left (starting at x = 10)
x_coord = x_end - (step - (nframes / 2)) * distance_per_frame
# Create sphere at calculated x-coordinate using default model
sphere = Sphere([x_coord, 0, 0], 2, models.default_sphere_model)
# Return the Scene object containing all objects for rendering
return Scene(models.default_camera,
objects=[sphere, models.default_ground, models.default_light])
def frame(step):
''' Renders an molecule centered in the scene '''
camera = Camera('location', [10, 0, 0], 'look_at', [0, 0, 0])
# Return the Scene object for rendering
return Scene(camera,
objects=[models.default_light] +
Molecule_name.povray_molecule,
included=['colors.inc'])
def s0_intro_text():
""" This show the title of the animation with our names """
title = Text('ttf', '"timrom.ttf"', '"RNA Splicing"', 0, 0, 'translate',
[-2.85, 0.9, -0], 'scale', [5, 5, 1], models.text_model)
names = Text('ttf', '"timrom.ttf"', '"Reindert Visser and Vincent Talen"',
0, 0, 'translate', [-7.2, -0.5, -0], 'scale', [3, 3, 1],
models.text_model)
return Scene(models.camera_scene0,
objects=[title, names] + models.lights_scene1)
def render_povray(vs, rotx=0, roty=0, rotz=0,
width=400, height=400, angle=14, antialiasing=0.001):
"""Render vertices using Pov-Ray (Vapory)
Render vertices using Pov-Ray (Vapory)
Args:
vs: vertices
rotx, roty, rotz: rotation angle
width, height:
angle: camera angle
Returns:
rendered_scene:
"""
rot1 = [rotx, 0, 0]
rot2 = [0, roty, 0]
rot3 = [0, 0, rotz]
camera = Camera('location', [0, 0, -25],
'look_at', [0, 0, 0],
'angle', angle,
'right x*image_width/image_height')
light = LightSource([-3, 2, -6], 'color', [1.0, 1.0, 1.0], 'parallel')
light2 = LightSource([2, -2, -6], 'color', [0.6, 0.6, 0.6], 'parallel')
background = Background('color', [1, 1, 1])
spheres = [Sphere(v, 0.05,
Finish('ambient', 0.2, 'diffuse', 0.8, 'phong', 1.0),
Texture(Pigment('color', [1.0, 1.0, 1.0])),
'rotate', rot1,
'rotate', rot2,
'rotate', rot3) for v in vs]
objects = [light, light2, background] + spheres
scene = Scene(camera, objects=objects)
return scene.render('ipython',
width=width, height=height,
antialiasing=antialiasing)
def frame(step):
""" Returns a scene at a step number in which a sphere is visualised. """
# Feedback to user in terminal about render status
curr_time = step / eval(SETTINGS.NumberFrames) * eval(SETTINGS.FrameTime)
logger.info(" @Time: %.3fs, Step: %d", curr_time, step)
# Calculates the total frames
n_frames = eval(SETTINGS.NumberFrames)
# Calculate the frames per wave
repeats = 5
n_frames_wave = n_frames / repeats # amount of frames per wave
# Calculates starting coordinates of the sphere
increase = 4 # amount of increase per wave
x_start = -10
x_end = x_start + increase
y_start = -4
y_end = 4
# Calculates total distance and distance per frame
x_distance = x_end - x_start
y_distance = y_end - y_start
x_distance_per_frame = (x_distance / (n_frames_wave / 2))
y_distance_per_frame = (y_distance / (n_frames_wave / 2))
# Determine in which wave this step is
if step // n_frames_wave == 0:
wave = 0
else:
wave = step // n_frames_wave
# Step has to reset for every wave, so subtract frames of previous wave(s)
frame_in_wave = step - (wave * n_frames_wave)
# If it is in the first part of the wave
if frame_in_wave <= (n_frames_wave / 2):
x_coord = x_start + (
wave * increase
) + frame_in_wave * x_distance_per_frame # Increases linear
y_coord = y_start + frame_in_wave * y_distance_per_frame # Increases linear
# Second part of the wave
else:
x_coord = x_end + (wave * increase
) # Stays constant and increases 4 for every wave
y_coord = y_end - (
frame_in_wave -
(n_frames_wave / 2)) * y_distance_per_frame # Decreases linear
# Makes a sphere at given x- and Y-coordinates with the default style
sphere = Sphere([x_coord, y_coord, 0], 0.5, models.default_sphere_model)
# Returns the objects of the scene using the default camera settings
return Scene(models.default_camera,
objects=[sphere, models.default_ground, models.default_light])
def save_frame_image(self, path):
meshes = [Background("color", [self.bk_r, self.bk_g, self.bk_b])]
tex = Texture(Pigment('color', [self.cc_r, self.cc_g, self.cc_b]),
Finish('specular', self.specular))
texo = Texture(Pigment('color', [self.cco_r, self.cco_g, self.cco_b]),
Finish('specular', self.specularo))
for i in xrange(-1, self.expert.nr_obstacles_c()):
vss, nss, iss = self.save_frame_mesh(i)
meshes += [ClothMesh(vss, iss, nss, tex if i == -1 else texo)]
#render
scene = Scene(Camera('location', [self.cx, self.cy, self.cz], 'sky',
[self.ux, self.uy, self.uz], 'look_at',
[self.fx, self.fy, self.fz], 'right', [1, 0, 0],
'up', [0, -1, 0], 'angle', self.fovy),
objects=self.lights + meshes)
scene.render(path,
width=self.w,
height=self.h,
antialiasing=self.aa if hasattr(self, "aa") else 0.0)
def scene(step):
''' Returns the scene at step number (1 step per frame) '''
ATP.rotate([0, 1, 0], [0, RAD_PER_SCENE, 0])
ATP.show_label(camera=povray.floor_camera, name=True)
# Return a 'Scene' object containing -all- objects to render, i.e. the camera,
# lights and in this case, a molecule with its labels.
return Scene(
povray.floor_camera,
objects=[povray.default_light, FRONT_LIGHT, povray.checkered_ground] +
ATP.povray_molecule,
included=['colors.inc'])
def s4_zoom_to_mrna(step):
""" In this scene the camera moves into the nucleus
to further illustrate that the splicing takes place in the nucleus """
dpf_cam = get_added_distance(TP_START[4], TP_DUR[4], [0, 0, 22.5], step)
camera_scene4 = Camera('location', [0, 0, -40], 'look_at', [0, 0, 0],
'translate', [dpf_cam[0], dpf_cam[1], dpf_cam[2]])
dpf_nuc = get_added_distance(TP_START[4], TP_DUR[4], [-20, -7.5, -9.9],
step)
nucleus = Sphere([20, 7.5, 0], 7.5, models.nucleus_model, 'translate',
[dpf_nuc[0], dpf_nuc[1], dpf_nuc[2]])
return Scene(camera_scene4, objects=[nucleus] + models.spot_lights)
def frame(step):
""" Creates the objects and places this in a scene """
# Creates the lines in each directions
x_cylinder = Cylinder([-15, 0, 0], [-10, 0, 0], 0.1, Texture(Pigment('color', [1, 0, 0]), Finish('reflection', 1)))
y_cylinder = Cylinder([-15, 0, 0], [-15, 5, 0], 0.1, Texture(Pigment('color', [0, 0, 1]), Finish('reflection', 1)))
z_cylinder = Cylinder([-15, 0, 0], [-15, 0, 5], 0.1, Texture(Pigment('color', [0, 1, 0]), Finish('reflection', 1)))
# Creates the arrows of each directions
x_cone = Cone([-10, 0, 0], 0.3, [-9, 0, 0], 0, Texture(Pigment('color', [1, 0, 0]), Finish('reflection', 1)))
y_cone = Cone([-15, 5, 0], 0.3, [-15, 6, 0], 0, Texture(Pigment('color', [0, 0, 1]), Finish('reflection', 1)))
z_cone = Cone([-15, 0, 5], 0.3, [-15, 0, 6], 0, Texture(Pigment('color', [0, 1, 0]), Finish('reflection', 1)))
# Return the Scene object for rendering
return Scene(models.default_camera,
objects=[LightSource([2, 8, -20], 2), x_cylinder, y_cylinder, z_cylinder, x_cone, y_cone, z_cone])
def render_frame(self, step, outn):
particles = []
for i in range(self.sm.NUM_PARTICLES):
clr = speed2color(speed=self.speeds[step][i],
speed_limit=self.maxspeed,
alpha=False)
p = Sphere(
[
self.r_vecs[step][i][1], self.r_vecs[step][i][2],
self.r_vecs[step][i][0]
],
self.sm.RADIUS_PARTICLE,
Texture(Pigment("color", clr)),
)
particles.append(p)
self.scene = Scene(self.camera, objects=self.objects + particles)
self.scene.render(f"{self.sm.png_path}/img{outn:06}.png",
width=600,
height=400)
def s1_cell_overview():
""" This scene is a single cell centered without any movement """
cell_sphere = Sphere([0, 0, 0], 25, models.cell_model)
text = Text('ttf', '"timrom.ttf"',
'"To begin you first need to know that"', 0, 0, 'translate',
[-14.5, -5, -30], 'scale', [2.5, 2.5, 1], models.text_model)
text2 = Text('ttf', '"timrom.ttf"',
'"RNA Splicing takes place in the cell"', 0, 0, 'translate',
[-14.5, -6.25, -30], 'scale', [2.5, 2.5, 1],
models.text_model)
return Scene(models.camera_scene1,
objects=[cell_sphere, text, text2] + models.lights_scene1)
def frame(step):
"""Berekeent de posities van alle elementen van de animatie. En simuleert de animatie.
Args: step: het nummer van het frame.
Return: een Scene"""
global aminomoddel_list
# juiste triplet pakken key en aminozuur bij maken en key verplaatsen
key_nmbr = step // key_cycle # key_nmbr = het nummer van de momentele key cyclus
triplet = triplet_list[key_nmbr] # welk triplet de key moet mee nemen
amino = amino_maker(triplet)
pos = move_key(step, key_cycle, key)
amino.move_to([pos[0], pos[1] + AMINO_AFSTAND, pos[2]])
camera = Camera('location', [0, 8, -140], 'look_at', [0, 0, 0])
light = LightSource([0, 40, -100], 2)
objects = [light]
move_aminozuren(step, key_cycle, key_nmbr,
False) # zet de aminozuren op de juiste positie
move_nucleotides(step, key_cycle, key_nmbr,
False) # zet de nucleotide op de juiste positie
if pos[0] > 0:
if key_nmbr > 0:
# voegt alle amino modellen toe uit de aminomoddel_list
# tot aan het molecuul wat de key momenteel mee neemt
for i in range(key_nmbr):
objects += aminomoddel_list[i].povray_molecule
objects += key.povray_molecule + amino.povray_molecule
elif pos[0] == 0:
# voegt alle amino modellen toe uit de aminomoddel_list
# tot en met aan het molecuul wat de key momenteel mee neemt
for i in range(key_nmbr + 1):
objects += aminomoddel_list[i].povray_molecule
objects += key.povray_molecule
elif pos[0] < 0:
# voegt alle amino modellen toe uit de aminomoddel_list
# tot en met aan het molecuul wat de key momenteel mee neemt
# en verplaatst de nucleotiden en aminozuren
move_aminozuren(step, key_cycle, key_nmbr)
move_nucleotides(step, key_cycle, key_nmbr)
for i in range(key_nmbr + 1):
objects += aminomoddel_list[i].povray_molecule
objects += key.povray_molecule
for element in nucleomoddel_list:
objects += element.povray_molecule
return Scene(camera, objects)