def generate_artist(self, *args, **kywds):
# print 'entering fig_grp:: generate_artist'
for name, child in self.get_children():
if child._suppress:
child.del_artist(delall=True)
else:
child.generate_artist(*args, **kywds)
ax = self.get_figaxes()
c = self.get_container()
if self.isempty():
a = Rectangle((0, 0),
1,
1,
facecolor='none',
fill=False,
edgecolor='none',
alpha=0)
a.figobj = self
a.figobj_hl = []
self._artists = [a]
c.patches.append(a)
if ax is not None and ax.get_3d():
import mpl_toolkits.mplot3d.art3d as art3d
art3d.patch_2d_to_3d(a)
figure = self.get_figpage()._artists[0]
a.set_figure(figure)
if self.get_figaxes() is not None:
if len(self.get_figaxes()._artists) != 0:
a.axes = self.get_figaxes()._artists[0]
def generate_artist(self, *args, **kywds):
# print 'entering fig_grp:: generate_artist'
for name, child in self.get_children():
if child._suppress:
child.del_artist(delall=True)
else:
child.generate_artist(*args, **kywds)
ax = self.get_figaxes()
c = self.get_container()
if self.isempty():
a = Rectangle((0,0), 1, 1, facecolor='none', fill=False,
edgecolor='none', alpha=0)
a.figobj=self
a.figobj_hl=[]
self._artists = [a]
c.patches.append(a)
if ax is not None and ax.get_3d():
import mpl_toolkits.mplot3d.art3d as art3d
art3d.patch_2d_to_3d(a)
figure = self.get_figpage()._artists[0]
a.set_figure(figure)
if self.get_figaxes() is not None:
if len(self.get_figaxes()._artists) != 0:
a.axes = self.get_figaxes()._artists[0]
def draw_bool_plume(plume, ax=None):
"""Note: tried to add ells to Pathcollection and then plot that, but kept having a ValueError
Also tried using an EclipseCollection but the patchcollection_2d_to_3d function does not work on it
# xy is actually the yz plane
# val headers: [u'x_position', u'z_position', u'small_radius', u'y_position']
"""
if plume.condition in 'controlControlCONTROL':
print "No plume in ", plume.condition
return
ells = [Ellipse(xy=(val[3], val[1]),
width=2 * val[2],
height=2 * val[2] * 3,
angle=0,
# linestyle='dotted',
facecolor='none',
alpha=0.05,
edgecolor='r')
for i, val in plume.data.iterrows()]
for i, val in plume.data['x_position'].iteritems():
ell = ells[i]
ax.add_patch(ell)
art3d.patch_2d_to_3d(ell, z=val, zdir="x")
# art3d.patch_collection_2d_to_3d(ells)
plt.show()
def draw():
try:
fig = plt.figure()
ax = fig.gca(projection='3d')
# Define theta
theta = np.linspace(0, 2 * np.pi, 50)
# cone
z = np.linspace(0, 10, 50)
theta_cone, z_cone = np.meshgrid(theta, z)
x_cone = (z_cone / 2) * np.cos(theta_cone)
y_cone = (z_cone / 2) * np.sin(theta_cone)
ax.plot_surface(x_cone, y_cone, z_cone)
# Cylinder
zc = np.linspace(0, 10, 50)
theta_cylinder, z_cylinder = np.meshgrid(theta, zc)
x_cylinder = 5 * np.cos(theta_cylinder)
y_cylinder = 5 * np.sin(theta_cylinder)
ax.plot_surface(x_cylinder, y_cylinder, z_cylinder, alpha=0.5)
# Flat
p = Circle((0, 0), 5, alpha=0.5)
ax.add_patch(p)
art3d.patch_2d_to_3d(p, z=0, zdir='z')
ax.set_zlim(0, 10)
ax.zaxis.set_major_locator(LinearLocator(10))
ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))
plt.show()
except Exception as err:
print(err)
def test_patch_modification():
fig = plt.figure()
ax = fig.add_subplot(projection="3d")
circle = Circle((0, 0))
ax.add_patch(circle)
art3d.patch_2d_to_3d(circle)
circle.set_facecolor((1.0, 0.0, 0.0, 1))
assert mcolors.same_color(circle.get_facecolor(), (1, 0, 0, 1))
fig.canvas.draw()
assert mcolors.same_color(circle.get_facecolor(), (1, 0, 0, 1))
def plot_response(
p,
response,
bar_width=1,
source_loc=None,
fig=None,
offset=(0.0, 0.0),
color="#00ceaa",
draw_extras=True,
ax=None,
label=None,
set_zlim=True,
):
if fig is None:
fig = plt.gcf()
if source_loc is None:
source_loc = p.source.R
dx, dy = offset
detector_locs = np.array([i.R for i in p.detectors])
if ax is None:
ax = fig.add_subplot(111, projection='3d')
ax.bar3d(detector_locs[:, 0] + dx,
detector_locs[:, 1] + dy,
np.zeros_like(response),
bar_width,
bar_width,
response,
color=color,
edgecolor=color)
if draw_extras:
ax.scatter([source_loc[0]], [source_loc[1]],
marker='*',
color="red",
label="Source")
ax.scatter(*detector_locs.T, label="Detector")
patches = build_patches(p, alpha=0.3)
for patch in patches:
ax.add_patch(patch)
art3d.patch_2d_to_3d(patch)
set_bounds(p, ax=ax)
if set_zlim:
ax.set_zlim([0, 1.1 * max(response)])
return (fig, ax)
def mplArt_from_shape( shapes, in3d=False, z=0.0, zdir='z' ) :
"""
can be made an Arc with:
matplotlib.patches.Arc(xy, width, height, angle=0.0, theta1=0.0, theta2=360.0, **kwargs)
for circle width=height=R
"""
"""
> dictionary with keys 'dashed' (for edge drawing) and 'solid' (for the geometry)
> shape has type ( 'arc' or 'segment' ), and relevent details
"""
Art = []
for style in [ 'solid', 'dashed' ] :
if not style in shapes : continue
shape = shapes[style]
if shape.type == 'arc' :
piece = mpl.patches.Arc( shape.center, 2*shape.radius, 2*shape.radius,
angle = 0.0,
theta1 = 180.0 * shape.theta1 / np.pi,
theta2 = 180.0 * shape.theta2 / np.pi,
linestyle=style, color='b' )
if in3d : piece = art3d.patch_2d_to_3d( piece, z=z, zdir=zdir )
elif shape.type == 'segment' :
piece = mpl.lines.Line2D( shape.xdata, shape.ydata, linestyle=style )
if in3d : piece = art3d.line_2d_to_3d( piece, zs=z, zdir=zdir )
Art.append(piece)
return Art
def art_convert3d( art, z=0.0, zdir='z' ) :
""" doesn't effing work """
if isinstance( art, mpl.lines.Line2D ) :
new_art = art3d.line_2d_to_3d( art, zs=z, zdir=zdir )
elif isinstance( art, mpl.patches.Patch ) :
new_art = art3d.patch_2d_to_3d( art, z=z, zdir=zdir )
else : raise Exception('not a valid type of art')
return new_art
def mplArt_from_shape( shapes, in3d=False, z=0.0, zdir='z' ) :
Art = []
for style in [ 'solid', 'dashed' ] :
if not style in shapes : continue
shape = shapes[style]
if shape.type == 'arc' :
piece = mpl.patches.Arc( shape.center, 2*shape.radius, 2*shape.radius,
angle = 0.0,
theta1 = 180.0 * shape.theta1 / np.pi,
theta2 = 180.0 * shape.theta2 / np.pi,
linestyle=style, color='b' )
if in3d : piece = art3d.patch_2d_to_3d( piece, z=z, zdir=zdir )
elif shape.type == 'segment' :
piece = mpl.lines.Line2D( shape.xdata, shape.ydata, linestyle=style )
if in3d : piece = art3d.line_2d_to_3d( piece, zs=z, zdir=zdir )
Art.append(piece)
return Art
def add_rhabdomeres(ax,
x0,
y0,
z0,
x1,
y1,
z1,
mirror_lr=False,
mirror_bf=False,
scale=0.015,
camerapos=None,
**kwargs):
'''
Add rhabdomeres R1-R7/8 patches to a 3D plot.
ax : object
Matplotlib Axes object to add attach the patches onto
x0,y0,z0 : float
Coordinates of the rhabdomeres center point (R6/R7)
x1,y1,z1 : float
Vector pointing the direction of R6R3 line
mirror_lr, mirror_bf : True, False (or auto for bf)
Wheter to mirror this rhabdomere or not (left/right, back/front)
scale : float
Scale of the rhabdemeres
**kwargs : dict
To matplotlib.patches.CirclePolygon
Returns a list of matplotlib 3d patches
'''
if camerapos and is_behind_sphere(*camerapos, (x0, y0, z0)):
return None
#v = np.asarray([x0,y0,z0])
#uv = v / np.linalg.norm(v)
try:
phi = math.asin(z0)
except:
phi = math.pi / 2
try:
theta = math.atan(x0 / y0)
except:
theta = math.pi / 2
if y0 < 0:
theta = theta + math.pi
# Calculate rhabdomere rotation to match x1,y1,z1 by transforming
# point [1,0,0] to the x0,y0,z0 point and calculating angle of
# transformed ux and x1,y1,z1
ux = np.array([1, 0, 0])
ux = get_rotation_matrix('x', phi) @ ux
ux = get_rotation_matrix('z', -theta) @ ux
rot = np.arccos(
np.inner(ux, [x1, y1, z1]) /
(np.linalg.norm(ux) * np.linalg.norm([x1, y1, z1])))
if z1 < 0:
rot = -rot
patches = []
if mirror_bf == 'auto' and z0 > 0:
mirror_bf = True
elif mirror_bf is not True:
mirror_bf = False
for diameter, location in zip(RHABDOMERE_DIAMETERS, RHABDOMERE_LOCATIONS):
patch = CirclePolygon((location[0] * scale, location[1] * scale),
diameter / 2 * scale, **kwargs)
patches.append(patch)
ax.add_patch(patch)
art3d.patch_2d_to_3d(patch)
#if mirror_lr:
# patch._segment3d = [get_rotation_matrix('y', math.pi) @ p for p in patch._segment3d]
# Rotate according to the vector (x1,y1,z1)
# First z rotation to set initial rotation
patch._segment3d = [
get_rotation_matrix('z', RHABDOMERE_R3R6_ROTATION) @ p
for p in patch._segment3d
]
#if not mirror_lr and not mirror_bf:
# pass
if mirror_lr and not mirror_bf:
patch._segment3d = [
get_rotation_matrix('x', math.pi) @ p for p in patch._segment3d
]
if not mirror_lr and mirror_bf:
patch._segment3d = [
get_rotation_matrix('x', math.pi) @ p for p in patch._segment3d
]
#patch._segment3d = [get_rotation_matrix('z', math.pi) @ p for p in patch._segment3d]
#if not mirror_lr and mirror_bf:
# patch._segment3d = [get_rotation_matrix('x', math.pi) @ p for p in patch._segment3d]
# patch._segment3d = [get_rotation_matrix('z', math.pi) @ p for p in patch._segment3d]
#if mirror_lr and mirror_bf:
# patch._segment3d = [get_rotation_matrix('z', math.pi) @ p for p in patch._segment3d]
patch._segment3d = [
get_rotation_matrix('z', rot) @ p for p in patch._segment3d
]
patch._segment3d = [
get_rotation_matrix('x', math.pi / 2) @ p for p in patch._segment3d
]
patch._segment3d = [
get_rotation_matrix('x', phi) @ p for p in patch._segment3d
]
patch._segment3d = [
get_rotation_matrix('z', -theta) @ p for p in patch._segment3d
]
# Translate
patch._segment3d = [(x + x0, y + y0, z + z0)
for x, y, z in patch._segment3d]
return patches
def _draw_rectangle(self, *args, z: float = 0, **kwargs):
artist = super()._draw_rectangle(*args, **kwargs)
art3d.patch_2d_to_3d(artist, z=z)
return artist
ax.set_ylim([0, ARENA_SIZE])
ax.set_zlim([(-ARENA_SIZE * 2 / 3), 0])
ax.set_xlabel('X', fontsize=30)
ax.set_ylabel('Y', fontsize=30)
ax.set_zlabel('Z', fontsize=30)
ax.xaxis.set_ticklabels([])
ax.yaxis.set_ticklabels([])
ax.zaxis.set_ticklabels([])
for spot_detail in zip(SPOT_POSITIONS, SPOT_COLOURS):
spot = mpl.patches.Circle(spot_detail[0],
SPOT_RADIUS,
color=spot_detail[1],
zorder=0)
ax.add_patch(spot)
art3d.patch_2d_to_3d(spot, z=0)
# Read files
arrow_magnitudes = np.zeros((16, 3))
arrow_positions = np.zeros((16, 3))
arrows = None # for now
first_file_activity = ''
first_file_datetime = ''
first_file_filename = ''
for file in files:
# pylint: disable=invalid-sequence-index
summary = mflog_utils.summarise_file(file)
# The location of arena files is set to "x,y" where x and y are integers between 0 and 3
locx, locy = summary['location'].split(',', 1)