I have a 3d scatter plot in matplotlib, and have set up annotations, inspired by answers here, particularly that by Don Cristobal.
I have some basic event-capturing code set up, but after several days of trying, I still have not managed to achieve my objectives. These are:
(i) Change colour of a point (dot) when selected with left mouse button from blue to e.g. dark blue/green.
(ii) Remove any selected dot selected in (i) after pressing the 'delete' key, including any annotations
(iii) Select multiple points in (i) using a selection rectangle and delete using 'delete' key
I have tried many approaches, including animating the chart to update based on changes in data, manipulating artist parameters, changing data points via e.g. xs, ys, zs = graph._offsets3d (which does not appear to be documented), but to no avail.
I have attempted, within the onpick(event) function, to:
(i) Interact with points via event.ind to change colour using event.artist.set_face_colour()
(ii) Remove points using both artist.remove()
(iii) Remove points using xs, ys, zs = graph._offsets3d , removing the relevant point by index (event.ind[0]) from xs, ys, and zs, and then resetting graph points via graph._offsets3d = xs_new, ys_new, zs_new
(iv) Redrawing the chart, or relevant sections of the chart only (blitting?)
with no success!
My current code is roughly as below. In fact, I have several hundred points, not the 3 in the simplified example below. I would like the graph to update smoothly if possible, although just getting something usable would be great. Most of the code to do this should probably reside within 'onpick', as that is the function that deals with picking events (see event handler). I have retained some of my code attempts, commented out, which I hope may be of some use. The 'forceUpdate' function is meant to update the graph object on an event trigger, but I am not convinced that it currently does anything. function on_key(event) also does not currently seem to work: presumably there must be a setting in order to determine points to delete, e.g. all artists that have a facecolor that has been changed from the default (e.g. delete all points that have colour dark blue/green rather than light blue).
Any help is much appreciated.
The code (below) is called with:
visualize3DData (Y, ids, subindustry)
Some sample data points are below:
#Datapoints
Y = np.array([[ 4.82250000e+01, 1.20276889e-03, 9.14501289e-01], [ 6.17564688e+01, 5.95020883e-02, -1.56770827e+00], [ 4.55139000e+01, 9.13454423e-02, -8.12277299e+00]])
#Annotations
ids = ['a', 'b', 'c']
subindustry = 'example'
My current code is here:
import matplotlib.pyplot as plt, numpy as np
from mpl_toolkits.mplot3d import proj3d
def visualize3DData (X, ids, subindus):
"""Visualize data in 3d plot with popover next to mouse position.
Args:
X (np.array) - array of points, of shape (numPoints, 3)
Returns:
None
"""
fig = plt.figure(figsize = (16,10))
ax = fig.add_subplot(111, projection = '3d')
graph = ax.scatter(X[:, 0], X[:, 1], X[:, 2], depthshade = False, picker = True)
def distance(point, event):
"""Return distance between mouse position and given data point
Args:
point (np.array): np.array of shape (3,), with x,y,z in data coords
event (MouseEvent): mouse event (which contains mouse position in .x and .xdata)
Returns:
distance (np.float64): distance (in screen coords) between mouse pos and data point
"""
assert point.shape == (3,), "distance: point.shape is wrong: %s, must be (3,)" % point.shape
# Project 3d data space to 2d data space
x2, y2, _ = proj3d.proj_transform(point[0], point[1], point[2], plt.gca().get_proj())
# Convert 2d data space to 2d screen space
x3, y3 = ax.transData.transform((x2, y2))
return np.sqrt ((x3 - event.x)**2 + (y3 - event.y)**2)
def calcClosestDatapoint(X, event):
""""Calculate which data point is closest to the mouse position.
Args:
X (np.array) - array of points, of shape (numPoints, 3)
event (MouseEvent) - mouse event (containing mouse position)
Returns:
smallestIndex (int) - the index (into the array of points X) of the element closest to the mouse position
"""
distances = [distance (X[i, 0:3], event) for i in range(X.shape[0])]
return np.argmin(distances)
def annotatePlot(X, index, ids):
"""Create popover label in 3d chart
Args:
X (np.array) - array of points, of shape (numPoints, 3)
index (int) - index (into points array X) of item which should be printed
Returns:
None
"""
# If we have previously displayed another label, remove it first
if hasattr(annotatePlot, 'label'):
annotatePlot.label.remove()
# Get data point from array of points X, at position index
x2, y2, _ = proj3d.proj_transform(X[index, 0], X[index, 1], X[index, 2], ax.get_proj())
annotatePlot.label = plt.annotate( ids[index],
xy = (x2, y2), xytext = (-20, 20), textcoords = 'offset points', ha = 'right', va = 'bottom',
bbox = dict(boxstyle = 'round,pad=0.5', fc = 'yellow', alpha = 0.5),
arrowprops = dict(arrowstyle = '->', connectionstyle = 'arc3,rad=0'))
fig.canvas.draw()
def onMouseMotion(event):
"""Event that is triggered when mouse is moved. Shows text annotation over data point closest to mouse."""
closestIndex = calcClosestDatapoint(X, event)
annotatePlot (X, closestIndex, ids)
def onclick(event):
print('%s click: button=%d, x=%d, y=%d, xdata=%f, ydata=%f' %
('double' if event.dblclick else 'single', event.button,
event.x, event.y, event.xdata, event.ydata))
def on_key(event):
"""
Function to be bound to the key press event
If the key pressed is delete and there is a picked object,
remove that object from the canvas
"""
if event.key == u'delete':
ax = plt.gca()
if ax.picked_object:
ax.picked_object.remove()
ax.picked_object = None
ax.figure.canvas.draw()
def onpick(event):
xmouse, ymouse = event.mouseevent.xdata, event.mouseevent.ydata
artist = event.artist
# print(dir(event.mouseevent))
ind = event.ind
# print('Artist picked:', event.artist)
# # print('{} vertices picked'.format(len(ind)))
print('ind', ind)
# # print('Pick between vertices {} and {}'.format(min(ind), max(ind) + 1))
# print('x, y of mouse: {:.2f},{:.2f}'.format(xmouse, ymouse))
# # print('Data point:', x[ind[0]], y[ind[0]])
#
# # remove = [artist for artist in pickable_artists if artist.contains(event)[0]]
# remove = [artist for artist in X if artist.contains(event)[0]]
#
# if not remove:
# # add a pt
# x, y = ax.transData.inverted().transform_point([event.x, event.y])
# pt, = ax.plot(x, y, 'o', picker=5)
# pickable_artists.append(pt)
# else:
# for artist in remove:
# artist.remove()
# plt.draw()
# plt.draw_idle()
xs, ys, zs = graph._offsets3d
print(xs[ind[0]])
print(ys[ind[0]])
print(zs[ind[0]])
print(dir(artist))
# xs[ind[0]] = 0.5
# ys[ind[0]] = 0.5
# zs[ind[0]] = 0.5
# graph._offsets3d = (xs, ys, zs)
# print(artist.get_facecolor())
# artist.set_facecolor('red')
graph._facecolors[ind, :] = (1, 0, 0, 1)
plt.draw()
def forceUpdate(event):
global graph
graph.changed()
fig.canvas.mpl_connect('motion_notify_event', onMouseMotion) # on mouse motion
fig.canvas.mpl_connect('button_press_event', onclick)
fig.canvas.mpl_connect('pick_event', onpick)
fig.canvas.mpl_connect('draw_event', forceUpdate)
plt.tight_layout()
plt.show()
from Change colour of data points on selection and remove them with key press in matplotlib 3d scatter plot
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