def plot_births_and_deaths(config, dataset, keys=None):
if keys is None:
keys = dataset.trajecs.keys()
def make_plot(ax, births, deaths, keys, axis="yz"):
if axis == "yz":
x_births = births[:, [1]]
y_births = births[:, [2]]
x_deaths = deaths[:, [1]]
y_deaths = deaths[:, [2]]
if axis == "xy":
x_births = births[:, [0]]
y_births = births[:, [1]]
x_deaths = deaths[:, [0]]
y_deaths = deaths[:, [1]]
if axis == "xz":
x_births = births[:, [0]]
y_births = births[:, [2]]
x_deaths = deaths[:, [0]]
y_deaths = deaths[:, [2]]
fpl.scatter(
ax, x_births.flatten(), y_births.flatten(), color="green", radius=0.005, alpha=1, use_ellipses=False
)
fpl.scatter(ax, x_deaths.flatten(), y_deaths.flatten(), color="red", radius=0.005, alpha=1, use_ellipses=False)
def collect_births_and_deaths(keys):
births = []
deaths = []
for key in keys:
trajec = dataset.trajecs[key]
births.append(trajec.positions[0])
deaths.append(trajec.positions[-1])
return np.array(births), np.array(deaths)
births, deaths = collect_births_and_deaths(keys)
fig = plt.figure(figsize=(8, 4))
axes = xyz_axis_grid.get_axes(config, fig, figure_padding=[0.15, 0.15, 0.15, 0.15], subplot_padding=0.01)
fig = axes["xy"].figure
make_plot(axes["xy"], births, deaths, keys, axis="xy")
make_plot(axes["xz"], births, deaths, keys, axis="xz")
make_plot(axes["yz"], births, deaths, keys, axis="yz")
xyz_axis_grid.set_spines(config, axes, spines=True)
name = "births_and_deaths.pdf"
path = os.path.join(config.path, FIGURE_PATH)
filename = os.path.join(path, name)
fig.savefig(filename, format="pdf")
def plot_heatmaps(config, dataset, keys=None, zslice="all", xz_axis_z_velocity_range=[-100, 100]):
if keys is None:
keys = dataset.trajecs.keys()
def make_plot(ax, keys, axis="yz"):
n_frames = 0
for key in keys:
trajec = dataset.trajecs[key]
n_frames += trajec.length
binres = 0.003
binsx = np.linspace(config.xlim[0], config.xlim[1], int((config.xlim[1] - config.xlim[0]) / binres))
binsy = np.linspace(config.ylim[0], config.ylim[1], int((config.ylim[1] - config.ylim[0]) / binres))
binsz = np.linspace(config.zlim[0], config.zlim[1], int((config.zlim[1] - config.zlim[0]) / binres))
if axis == "xy":
depth = config.zlim[1] - config.zlim[0]
elif axis == "yz":
depth = config.xlim[1] - config.xlim[0]
elif axis == "xz":
depth = config.ylim[1] - config.ylim[0]
colornorm = [0, 0.0003 * n_frames * depth]
colormap = "hot"
print n_frames
depth_range = [-2, 2]
# get rid of errant walking flies
if axis == "xz":
velocity_range = xz_axis_z_velocity_range
else:
velocity_range = [-100, 100]
img = fap.heatmap(
ax,
dataset,
axis=axis,
keys=keys,
xticks=config.ticks["x"],
yticks=config.ticks["y"],
zticks=config.ticks["z"],
rticks=config.ticks["r"],
colornorm=colornorm,
normalize_for_speed=False,
bins=[binsx, binsy, binsz],
depth_range=depth_range,
colormap=colormap,
return_img=False,
velocity_range=velocity_range,
)
fig = plt.figure(figsize=(8, 5))
axes = xyz_axis_grid.get_axes(config, fig, figure_padding=[0.15, 0.15, 0.15, 0.15], subplot_padding=0.01)
fig = axes["xy"].figure
make_plot(axes["xy"], keys, axis="xy")
make_plot(axes["xz"], keys, axis="xz")
make_plot(axes["yz"], keys, axis="yz")
xyz_axis_grid.set_spines(config, axes, spines=True)
name = "diagnostic_heatmaps.pdf"
path = os.path.join(config.path, FIGURE_PATH)
filename = os.path.join(path, name)
fig.savefig(filename, format="pdf")
