def do_3d_projection(self, renderer):
xs, ys, zs = self._offsets3d
vxs, vys, vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
self._alpha = None
self.set_facecolors(zalpha(self._facecolor3d, vzs))
self.set_edgecolors(zalpha(self._edgecolor3d, vzs))
PatchCollection.set_offsets(self, zip(vxs, vys))
return min(vzs)
def do_3d_projection(self, renderer):
xs, ys, zs = self._offsets3d
vxs, vys, vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
#FIXME: mpl allows us no way to unset the collection alpha value
self._alpha = None
self.set_facecolors(zalpha(self._facecolor3d, vzs))
self.set_edgecolors(zalpha(self._edgecolor3d, vzs))
PatchCollection.set_offsets(self, zip(vxs, vys))
return min(vzs)
def do_3d_projection(self, renderer):
xs, ys, zs = self._offsets3d
vxs, vys, vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
#FIXME: mpl allows us no way to unset the collection alpha value
self._alpha = None
self.set_facecolors(zalpha(self._facecolor3d, vzs))
self.set_edgecolors(zalpha(self._edgecolor3d, vzs))
PatchCollection.set_offsets(self, list(zip(vxs, vys)))
if vzs.size > 0 :
return min(vzs)
else :
return np.nan
def do_3d_projection(self, renderer):
xs, ys, zs = self._offsets3d
vxs, vys, vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
fcs = zalpha(self._facecolor3d, vzs) if self._depthshade else self._facecolor3d
fcs = mcolors.colorConverter.to_rgba_array(fcs, self._alpha)
self.set_facecolors(fcs)
ecs = zalpha(self._edgecolor3d, vzs) if self._depthshade else self._edgecolor3d
ecs = mcolors.colorConverter.to_rgba_array(ecs, self._alpha)
self.set_edgecolors(ecs)
PatchCollection.set_offsets(self, list(zip(vxs, vys)))
if vzs.size > 0:
return min(vzs)
else:
return np.nan
def do_3d_projection(self, renderer):
xs, ys, zs = self._offsets3d
vxs, vys, vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
fcs = (zalpha(self._facecolor3d, vzs) if self._depthshade else
self._facecolor3d)
fcs = mcolors.colorConverter.to_rgba_array(fcs, self._alpha)
self.set_facecolors(fcs)
ecs = (zalpha(self._edgecolor3d, vzs) if self._depthshade else
self._edgecolor3d)
ecs = mcolors.colorConverter.to_rgba_array(ecs, self._alpha)
self.set_edgecolors(ecs)
PatchCollection.set_offsets(self, list(zip(vxs, vys)))
if vzs.size > 0:
return min(vzs)
else:
return np.nan
def render(self, patch_size=0.5, alpha=1.0, x_offset=100):
'''Draws the legend graphic and saves it to a file.'''
n = len(self.colors)
s = patch_size
# This offset is transformed to "data" coordinates (inches)
left_offset = (-s * 1.5) - (x_offset / self.dpi)
# Create grid to plot the artists
grid = np.concatenate((
np.zeros(n).reshape(n, 1),
np.arange(-n, 1)[1:].reshape(n, 1)
), axis=1)
plt.text(left_offset, 1.1, 'Legend', family='sans-serif',
size=14, weight='bold', color='#ffffff')
patches = []
for i in range(n):
# Add a rectangle
rect = mpatches.Rectangle(grid[i] - [0, 0], s, s, ec='none')
patches.append(rect)
self.__label__(grid[i], self.labels[i], x_offset)
collection = PatchCollection(patches, alpha=alpha)
# Space the patches and the text labels
collection.set_offset_position('data')
collection.set_offsets(np.array([
[left_offset, 0]
]))
collection.set_facecolors(self.colors)
#collection.set_edgecolor('#ffffff') # Draw color for box outlines
self.axis.add_collection(collection)
plt.axis('equal')
plt.axis('off')
plt.savefig(self.file_path, facecolor=self.bg_color, dpi=self.dpi,
pad_inches=0)
return self.file_path
def do_3d_projection(self, renderer):
xs, ys, zs = self._offsets3d
vxs, vys, vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
fcs = (zalpha(self._facecolor, vzs) if self._depthshade else
self._facecolor)
fcs = mcolors.to_rgba_array(fcs, self._alpha)
self.set_facecolor(fcs)
ecs = (zalpha(self._edgecolor, vzs) if self._depthshade else
self._edgecolor)
ecs = mcolors.to_rgba_array(ecs, self._alpha)
self.set_edgecolor(ecs)
PatchCollection.set_offsets(self, np.column_stack([vxs, vys]))
if vzs.size > 0:
return min(vzs)
else:
return np.nan
def animate(x, rs, label=False, lims=(12, 12), cols=[]):
"""
Takes an array of positions with shape = (steps, particle, coordinates) and spot size (r)
and animates their trajectory.
"""
if not plt.get_fignums():
fig, ax = plt.subplots(figsize=(5,5))
else:
ax = plt.gca()
fig = plt.gcf()
x = np.squeeze(x) # if there is one particle
fig.subplots_adjust(left=0.1, right=0.9, bottom=0.1, top=0.9)
# use plt.Circle over ax.scatter since Circle size is in data coordinates, but
# scatter marker sizes are in Figure coordinates.
c = PatchCollection([plt.Circle((0, 0), r) for r in rs])
c.set_offset_position('data')
c.set_offsets(x[0])
if not cols and x.shape[1] > 10:
cols = ['r' if i < lims[0]/2 else 'b' for i in x[0, :, 0]]
elif cols:
pass
else:
cols = ['r' for i in x[0, :]]
c.set_color(cols)
ax.add_collection(c)
def advance(fn):
step = fn % len(x)
c.set_offsets(x[step])
ax.set_title(step)
for l, xy in zip(ls, x[step]):
l.set_x(xy[0])
l.set_y(xy[1])
if label:
ls = [plt.text(*xy, i) for i, xy in enumerate(x[0])]
else:
ls = []
ax.set_xlim((0, lims[0]))
ax.set_ylim((0, lims[0]))
ax.add_collection(c)
fa = animation.FuncAnimation(fig, advance, interval=5e3//len(x))
plt.show()
return fa
def do_3d_projection(self, renderer):
# see _update_scalarmappable docstring for why this must be here
_update_scalarmappable(self)
xs, ys, zs = self._offsets3d
vxs, vys, vzs, vis = proj3d.proj_transform_clip(xs, ys, zs, renderer.M)
fcs = (_zalpha(self._facecolor3d, vzs) if self._depthshade else
self._facecolor3d)
fcs = mcolors.to_rgba_array(fcs, self._alpha)
self.set_facecolors(fcs)
ecs = (_zalpha(self._edgecolor3d, vzs) if self._depthshade else
self._edgecolor3d)
ecs = mcolors.to_rgba_array(ecs, self._alpha)
self.set_edgecolors(ecs)
PatchCollection.set_offsets(self, np.column_stack([vxs, vys]))
if vzs.size > 0:
return min(vzs)
else:
return np.nan
class InstrumentView:
def __init__(self,
scipp_obj=None,
bins=None,
masks=None,
cmap=None,
log=None,
vmin=None,
vmax=None,
aspect=None,
size=1,
projection=None,
nan_color=None,
filename=None,
continuous_update=None,
dim=None):
self.fig2d = None
self.fig3d = None
self.scatter2d = None
self.scatter3d = None
self.outline = None
self.size = size
self.aspect = aspect
self.do_update = None
self.figurewidget = widgets.Output()
self.figure2d = False
self.figure3d = False
self.image = None
self.nan_color = nan_color
self.log = log
self.current_projection = None
self.dim = dim
self.data_arrays = {}
tp = type(scipp_obj)
if tp is sc.Dataset or tp is sc.DatasetProxy:
for key in sorted(scipp_obj.keys()):
var = scipp_obj[key]
if self.dim in var.dims:
self.data_arrays[key] = var
elif tp is sc.DataArray or tp is sc.DataProxy:
self.data_arrays[scipp_obj.name] = scipp_obj
else:
raise RuntimeError("Unknown input type: {}. Allowed inputs "
"are a Dataset or a DataArray (and their "
"respective proxies).".format(tp))
self.globs = {"cmap": cmap, "log": log, "vmin": vmin, "vmax": vmax}
self.params = {}
self.hist_data_array = {}
self.scalar_map = {}
self.minmax = {}
# Find the min/max time-of-flight limits and store them
self.minmax["tof"] = [np.Inf, np.NINF, 1]
for key, data_array in self.data_arrays.items():
bins_here = bins
if data_array.sparse_dim is not None and bins_here is None:
bins_here = True
if bins_here is not None:
dim = None if data_array.sparse_dim is not None else self.dim
spdim = None if data_array.sparse_dim is None else self.dim
var = make_bins(data_array=data_array,
sparse_dim=spdim,
dim=dim,
bins=bins_here,
padding=(data_array.sparse_dim is not None))
else:
var = data_array.coords[self.dim]
self.minmax["tof"][0] = min(self.minmax["tof"][0], var.values[0])
self.minmax["tof"][1] = max(self.minmax["tof"][1], var.values[-1])
self.minmax["tof"][2] = var.shape[0]
# Rebin all DataArrays to common Tof axis
self.rebin_data(np.linspace(*self.minmax["tof"]))
# Create dropdown menu to select the DataArray
keys = list(self.hist_data_array.keys())
self.dropdown = widgets.Dropdown(options=keys,
description="Select entry:",
layout={"width": "initial"})
self.dropdown.observe(self.change_data_array, names="value")
# Store current active data entry (DataArray)
self.key = keys[0]
# Create a Tof slider and its label
self.tof_dim_indx = self.hist_data_array[self.key].dims.index(self.dim)
self.slider = widgets.IntSlider(
value=0,
min=0,
step=1,
description=str(self.dim).replace("Dim.", ""),
max=self.hist_data_array[self.key].shape[self.tof_dim_indx] - 1,
continuous_update=continuous_update,
readout=False)
self.slider.observe(self.update_colors, names="value")
self.label = widgets.Label()
# Add text boxes to change number of bins/bin size
self.nbins = widgets.Text(value=str(
self.hist_data_array[self.key].shape[self.tof_dim_indx]),
description="Number of bins:",
style={"description_width": "initial"})
self.nbins.on_submit(self.update_nbins)
tof_values = self.hist_data_array[self.key].coords[self.dim].values
self.bin_size = widgets.Text(value=str(tof_values[1] - tof_values[0]),
description="Bin size:")
self.bin_size.on_submit(self.update_bin_size)
projections = [
"3D", "Cylindrical X", "Cylindrical Y", "Cylindrical Z",
"Spherical X", "Spherical Y", "Spherical Z"
]
# Create toggle buttons to change projection
self.buttons = {}
for p in projections:
self.buttons[p] = widgets.Button(
description=p,
disabled=False,
button_style=("info" if (p == projection) else ""))
self.buttons[p].on_click(self.change_projection)
items = [self.buttons["3D"]]
for x in "XYZ":
items.append(self.buttons["Cylindrical {}".format(x)])
items.append(self.buttons["Spherical {}".format(x)])
if x != "Z":
items.append(widgets.Label())
self.togglebuttons = widgets.GridBox(
items,
layout=widgets.Layout(grid_template_columns="repeat(3, 150px)"))
# Place widgets in boxes
self.vbox = widgets.VBox([
widgets.HBox([self.dropdown, self.slider, self.label]),
widgets.HBox([self.nbins, self.bin_size]), self.togglebuttons
])
self.box = widgets.VBox([self.figurewidget, self.vbox])
self.box.layout.align_items = "center"
# Protect against uninstalled ipyvolume
if ipv is None and projection == "3D":
print("Warning: 3D projection requires ipyvolume to be "
"installed. Use conda/pip install ipyvolume. Reverting to "
"2D projection.")
self.buttons[projections[1]].button_style = "info"
self.buttons["3D"].button_style = ""
self.buttons["3D"].disabled = True
# Render the plot here instead of at the top level because to capture
# the matplotlib output (if a 2D projection is requested to begin with,
# the output widget needs to be displayed first, before any mpl figure
# is displayed.
render_plot(widgets=self.box, filename=filename, ipv=ipv)
# Get detector positions
self.det_pos = np.array(
sn.position(self.hist_data_array[self.key]).values)
# Find extents of the detectors
for i, x in enumerate("xyz"):
self.minmax[x] = [
np.amin(self.det_pos[:, i]),
np.amax(self.det_pos[:, i])
]
# Update the figure
self.change_projection(self.buttons[projection])
# Create members object
self.members = {
"widgets": {
"sliders": self.slider,
"buttons": self.buttons,
"text": {
"nbins": self.nbins,
"bin_size": self.bin_size
},
"dropdown": self.dropdown
},
"fig2d": self.fig2d,
"fig3d": self.fig3d,
"scatter2d": self.scatter2d,
"scatter3d": self.scatter3d,
"outline": self.outline
}
return
def rebin_data(self, bins):
"""
Rebin the original data to Tof given some bins. This is executed both
on first instrument display and when either the number of bins or the
bin width is changed.
"""
for key, data_array in self.data_arrays.items():
# Histogram the data in the Tof dimension
if data_array.sparse_dim is not None:
self.hist_data_array[key] = histogram_sparse_data(
data_array, data_array.sparse_dim, bins)
else:
self.hist_data_array[key] = sc.rebin(
data_array, self.dim,
make_bins(data_array=data_array,
dim=self.dim,
bins=bins,
padding=False))
# Parse input parameters for colorbar
self.params[key] = parse_params(
globs=self.globs, array=self.hist_data_array[key].values)
cmap = cm.get_cmap(self.params[key]["cmap"])
cmap.set_bad(color=self.nan_color)
self.scalar_map[key] = cm.ScalarMappable(
cmap=cmap, norm=self.params[key]["norm"])
return
def update_colors(self, change):
self.do_update(change)
self.label.value = name_with_unit(
var=self.hist_data_array[self.key].coords[self.dim],
name=value_to_string(self.hist_data_array[self.key].coords[
self.dim].values[change["new"]]))
return
def change_projection(self, owner):
if owner.description == self.current_projection:
owner.button_style = "info"
return
if self.current_projection is not None:
self.buttons[self.current_projection].button_style = ""
# Temporarily disable automatic plotting in notebook
if plt.isinteractive():
plt.ioff()
re_enable_interactive = True
else:
re_enable_interactive = False
update_children = False
if owner.description == "3D":
self.projection_3d()
self.do_update = self.update_colors_3d
else:
if self.current_projection == "3D" or \
self.current_projection is None:
update_children = True
self.projection_2d(owner.description, update_children)
self.do_update = self.update_colors_2d
self.update_colors({"new": self.slider.value})
self.current_projection = owner.description
self.buttons[owner.description].button_style = "info"
# Re-enable automatic plotting in notebook
if re_enable_interactive:
plt.ion()
return
def projection_3d(self):
# Initialise Figure
if not self.figure3d:
self.fig3d = ipv.figure(width=config.plot.width,
height=config.plot.height,
animation=0,
lighting=False)
max_size = 0.0
dx = {"x": 0, "y": 0, "z": 0}
for ax in dx.keys():
dx[ax] = np.ediff1d(self.minmax[ax])
max_size = np.amax(list(dx.values()))
# Make plot outline if aspect ratio is to be conserved
if self.aspect == "equal":
arrays = dict()
for ax, s in dx.items():
diff = max_size - s
arrays[ax] = [
self.minmax[ax][0] - 0.5 * diff,
self.minmax[ax][1] + 0.5 * diff
]
outl_x, outl_y, outl_z = np.meshgrid(arrays["x"],
arrays["y"],
arrays["z"],
indexing="ij")
self.outline = ipv.plot_wireframe(outl_x,
outl_y,
outl_z,
color="black")
# Try to guess marker size
perc_size = 100.0 * self.size / max_size
self.scatter3d = ipv.scatter(x=self.det_pos[:, 0],
y=self.det_pos[:, 1],
z=self.det_pos[:, 2],
marker="square_2d",
size=perc_size)
self.figure3d = True
self.figurewidget.clear_output()
self.box.children = tuple([self.figurewidget, ipv.gcc(), self.vbox])
return
def update_colors_3d(self, change):
arr = self.hist_data_array[self.key][self.dim, change["new"]].values
if self.log:
arr = np.ma.masked_where(arr <= 0, arr)
self.scatter3d.color = self.scalar_map[self.key].to_rgba(arr)
return
def projection_2d(self, projection, update_children):
# Initialise figure if we switched from 3D view, if not re-use current
# figure.
if update_children:
self.box.children = tuple([self.figurewidget, self.vbox])
if not self.figure2d:
self.fig2d, self.ax = plt.subplots(
1,
1,
figsize=(config.plot.width / config.plot.dpi,
config.plot.height / config.plot.dpi))
if update_children:
with self.figurewidget:
disp.display(self.fig2d)
# Compute cylindrical or spherical projections
permutations = {"X": [0, 2, 1], "Y": [1, 0, 2], "Z": [2, 1, 0]}
axis = projection[-1]
theta = np.arctan2(self.det_pos[:, permutations[axis][2]],
self.det_pos[:, permutations[axis][1]])
if projection.startswith("Cylindrical"):
z_or_phi = self.det_pos[:, permutations[axis][0]]
elif projection.startswith("Spherical"):
z_or_phi = np.arcsin(
self.det_pos[:, permutations[axis][0]] /
np.sqrt(self.det_pos[:, 0]**2 + self.det_pos[:, 1]**2 +
self.det_pos[:, 2]**2))
# Create the scatter
if not self.figure2d:
patches = []
for x, y in zip(theta, z_or_phi):
patches.append(
Rectangle((x - 0.5 * self.size, y - 0.5 * self.size),
self.size, self.size))
self.scatter2d = PatchCollection(
patches,
cmap=self.params[self.key]["cmap"],
norm=self.params[self.key]["norm"],
array=self.hist_data_array[self.key][self.dim,
self.slider.value].values)
self.ax.add_collection(self.scatter2d)
self.save_xy = np.array([theta, z_or_phi]).T
if self.params[self.key]["cbar"]:
self.cbar = plt.colorbar(self.scatter2d, ax=self.ax)
self.cbar.ax.set_ylabel(
name_with_unit(var=self.hist_data_array[self.key],
name=""))
self.cbar.ax.yaxis.set_label_coords(-1.1, 0.5)
self.figure2d = True
else:
self.scatter2d.set_offset_position("data")
self.scatter2d.set_offsets(
np.array([theta, z_or_phi]).T - self.save_xy)
self.ax.set_xlim(
[np.amin(theta) - self.size,
np.amax(theta) + self.size])
self.ax.set_ylim(
[np.amin(z_or_phi) - self.size,
np.amax(z_or_phi) + self.size])
return
def update_colors_2d(self, change):
self.scatter2d.set_array(
self.hist_data_array[self.key][self.dim, change["new"]].values)
self.fig2d.canvas.draw_idle()
return
def update_nbins(self, owner):
try:
nbins = int(owner.value)
except ValueError:
print("Warning: could not convert value: {} to an "
"integer.".format(owner.value))
return
# self.rebin_data(nbins, from_nbins_text)
self.rebin_data(
np.linspace(self.minmax["tof"][0], self.minmax["tof"][1],
nbins + 1))
x = self.hist_data_array[self.key].coords[self.dim].values
self.bin_size.value = str(x[1] - x[0])
self.update_slider()
return
def update_bin_size(self, owner):
try:
binw = float(owner.value)
except ValueError:
print("Warning: could not convert value: {} to a "
"float.".format(owner.value))
return
self.rebin_data(
np.arange(self.minmax["tof"][0], self.minmax["tof"][1], binw))
self.nbins.value = str(
self.hist_data_array[self.key].shape[self.tof_dim_indx])
self.update_slider()
return
def update_slider(self):
"""
Try to replace the slider around the same position
"""
# Compute percentage position
perc_pos = self.slider.value / self.slider.max
# Compute new position
nbins = int(self.nbins.value)
new_pos = int(perc_pos * nbins)
# Either place new upper boundary first, or change slider value first
if new_pos > self.slider.max:
self.slider.max = nbins
self.slider.value = new_pos
else:
self.slider.value = new_pos
self.slider.max = nbins
return
def change_data_array(self, change):
self.key = change["new"]
if self.scatter2d is not None:
# Apparently, you have to set norm, clim on PatchCollection and
# clim on the colorbar to get this working. Only setting norm
# seems to work only on the first change.
self.scatter2d.set_norm(self.params[self.key]["norm"])
self.scatter2d.set_clim(vmin=self.params[self.key]["vmin"],
vmax=self.params[self.key]["vmax"])
self.cbar.set_clim(vmin=self.params[self.key]["vmin"],
vmax=self.params[self.key]["vmax"])
self.update_colors({"new": self.slider.value})
