Custom markers with screen coordinate size in (older) matplotlib - matplotlib

Question

Originally, I was hoping that I could create a sort of a class for a marker in matplotlib, which would be a square with text showing the, say, x coordinate and a label, so I could instantiate it with something like (pseudocode):
plt.plot(..., marker=myMarkerClass(label="X:"), ... )
... but as far as I can see, you cannot do stuff like that.
However, it seems that customization of markers is not available in older matplotlib; so I'd like to reduce my question to: how to get custom (path) markers in older matplotlib, so their sizes are defined in screen coordinates (so markers don't scale upon zoom)? To clarify, here are some examples:
Default (uncustomized) markers
Below is an example with the default matplotlib markers, which works with older matplotlib. Note that I've tried instead of using pyplot.plot(), I'm trying to work with matplotlib.figure.Figure directly (as that is the form usually used with diverse backends), requiring use of "figure manager" (see also matplotlib-devel - Backends object structure):
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.figure
import numpy as np
t = np.arange(0.0,1.5,0.25)
s = np.sin(2*np.pi*t)
mfigure = matplotlib.figure.Figure(figsize=(5,4), dpi=100)
ax = mfigure.add_subplot(111)
ax.plot(t,s, marker='o', color='b', markerfacecolor='orange', markersize=10.0)
fig = plt.figure() # create something (fig num 1) for fig_manager
figman = matplotlib._pylab_helpers.Gcf.get_fig_manager(1)
figman.canvas.figure = mfigure # needed
mfigure.set_canvas(figman.canvas) # needed
plt.show()
If we do an arbitrary zoom rect here, the markers remain the same size:
Customized markers via Path
This is documented in artists (Line2D.set_marker) — Matplotlib 1.2.1 documentation; however, it doesn't work with older matplotlib; here's an example:
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.figure
import matplotlib.path
import numpy as np
print("matplotlib version {0}".format(matplotlib.__version__))
def getCustomSymbol1(inx, iny, sc, yasp):
verts = [
(-0.5, -0.5), # left, bottom
(-0.5, 0.5), # left, top
(0.5, 0.5), # right, top
(0.5, -0.5), # right, bottom
(-0.5, -0.5), # ignored
]
codes = [matplotlib.path.Path.MOVETO,
matplotlib.path.Path.LINETO,
matplotlib.path.Path.LINETO,
matplotlib.path.Path.LINETO,
matplotlib.path.Path.CLOSEPOLY,
]
pathCS1 = matplotlib.path.Path(verts, codes)
return pathCS1, verts
t = np.arange(0.0,1.5,0.25)
s = np.sin(2*np.pi*t)
mfigure = matplotlib.figure.Figure(figsize=(5,4), dpi=100)
ax = mfigure.add_subplot(111)
pthCS1, vrtCS1 = getCustomSymbol1(0,0, 1,1)
# here either marker=pthCS1 or marker=np.array(vrtCS1)
# have the same effect:
ax.plot(t,s, marker=pthCS1, markerfacecolor='orange', markersize=10.0)
#ax.plot(t,s, marker=np.array(vrtCS1), markerfacecolor='orange', markersize=10.0)
fig = plt.figure() # create something (fig num 1) for fig_manager
figman = matplotlib._pylab_helpers.Gcf.get_fig_manager(1)
figman.canvas.figure = mfigure # needed
mfigure.set_canvas(figman.canvas) # needed
plt.show()
This runs fine for me in newer matplotlib, but fails in the older:
$ python3.2 test.py
matplotlib version 1.2.0
$ python2.7 test.py # marker=pthCS1
matplotlib version 0.99.3
Traceback (most recent call last):
File "test.py", line 36, in <module>
ax.plot(t,s, marker=pthCS1, markerfacecolor='orange', markersize=10.0)
...
File "/usr/lib/pymodules/python2.7/matplotlib/lines.py", line 804, in set_marker
self._markerFunc = self._markers[marker]
KeyError: Path([[-0.5 -0.5]
[-0.5 0.5]
[ 0.5 0.5]
[ 0.5 -0.5]
[-0.5 -0.5]], [ 1 2 2 2 79])
$ python2.7 test.py # marker=np.array(vrtCS1)
matplotlib version 0.99.3
Traceback (most recent call last):
File "test.py", line 38, in <module>
ax.plot(t,s, marker=np.array(vrtCS1), markerfacecolor='orange', markersize=10.0)
...
File "/usr/lib/pymodules/python2.7/matplotlib/lines.py", line 798, in set_marker
if marker not in self._markers:
TypeError: unhashable type: 'numpy.ndarray'
However, when it works in Python 3.2, the markers again keep their size across zoom of the graph, as I'd expect:
... though note this issue: Custom marker created from vertex list scales wrong · Issue #1980 · matplotlib/matplotlib · GitHub, in respect to this type of custom markers.
Through Paths in PatchCollection
I've picked up parts of this code from some internet postings, but cannot find the links now. In any case, we can avoid drawing the markers and PatchCollection can be used, to draw what should be the markers. Here is the code, which runs in older matplotlib:
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.figure
import matplotlib.path, matplotlib.patches, matplotlib.collections
import numpy as np
def getCustomSymbol1(inx, iny, sc, yasp):
verts = [
(inx-0.5*sc, iny-0.5*sc*yasp), # (0., 0.), # left, bottom
(inx-0.5*sc, iny+0.5*sc*yasp), # (0., 1.), # left, top
(inx+0.5*sc, iny+0.5*sc*yasp), # (1., 1.), # right, top
(inx+0.5*sc, iny-0.5*sc*yasp), # (1., 0.), # right, bottom
(inx-0.5*sc, iny-0.5*sc*yasp), # (0., 0.), # ignored
]
codes = [matplotlib.path.Path.MOVETO,
matplotlib.path.Path.LINETO,
matplotlib.path.Path.LINETO,
matplotlib.path.Path.LINETO,
matplotlib.path.Path.CLOSEPOLY,
]
pathCS1 = matplotlib.path.Path(verts, codes)
return pathCS1
def getXyIter(inarr):
# this supports older numpy, where nditer is not available
if np.__version__ >= "1.6.0":
return np.nditer(inarr.tolist())
else:
dimensions = inarr.shape
xlen = dimensions[1]
xinds = np.arange(0, xlen, 1)
return np.transpose(np.take(inarr, xinds, axis=1))
t = np.arange(0.0,1.5,0.25)
s = np.sin(2*np.pi*t)
mfigure = matplotlib.figure.Figure(figsize=(5,4), dpi=100)
ax = mfigure.add_subplot(111)
ax.plot(t,s)
customMarkers=[]
for x, y in getXyIter(np.array([t,s])): #np.nditer([t,s]):
#printse("%f:%f\n" % (x,y))
pathCS1 = getCustomSymbol1(x,y,0.05,1.5*500.0/400.0)
patchCS1 = matplotlib.patches.PathPatch(pathCS1, facecolor='orange', lw=1) # no
customMarkers.append(patchCS1)
pcolm = matplotlib.collections.PatchCollection(customMarkers)
pcolm.set_alpha(0.9)
ax.add_collection(pcolm)
fig = plt.figure() # create something (fig num 1) for fig_manager
figman = matplotlib._pylab_helpers.Gcf.get_fig_manager(1)
figman.canvas.figure = mfigure # needed
mfigure.set_canvas(figman.canvas) # needed
plt.show()
Now, here I tried to take figure initial aspect ratio into consideration and indeed, at first render, the "markers" look right in respect to size - but...:
... when we try to do arbitrary zoom, it is obvious that the paths have been specified in data coordinates, and so their sizes change depending on the zoom rect. (Another nuissance is that facecolor='orange' is not obeyed; but that can be fixed with pcolm.set_facecolor('orange'))
So, is there a way that I can use PatchCollection as markers for older matplotlib, in the sense that the rendered paths would be defined in screen coordinates, so they would not change their size upon arbitrary zooming?

Answer 1

Many thanks to #tcaswell for the comment on blended transform - in trying to figure out why that doesn't work for me, I finally found the solution. First, the code - using, essentially, the default marker engine of matplotlib (depending on whether using older matplotlib (0.99) or newer one):
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.figure
import numpy as np
# create vertices and Path of custom symbol
def getCustomSymbol1():
verts = [
(0.0, 0.0), # left, bottom
(0.0, 0.7), # left, top
(1.0, 1.0), # right, top
(0.8, 0.0), # right, bottom
(0.0, 0.0), # ignored
]
codes = [matplotlib.path.Path.MOVETO,
matplotlib.path.Path.LINETO,
matplotlib.path.Path.LINETO,
matplotlib.path.Path.LINETO,
matplotlib.path.Path.CLOSEPOLY,
]
pathCS1 = matplotlib.path.Path(verts, codes)
return pathCS1, verts
if matplotlib.__version__ < "1.0.0":
# define a marker drawing function, that uses
# the above custom symbol Path
def _draw_mypath(self, renderer, gc, path, path_trans):
gc.set_snap(renderer.points_to_pixels(self._markersize) >= 2.0)
side = renderer.points_to_pixels(self._markersize)
transform = matplotlib.transforms.Affine2D().translate(-0.5, -0.5).scale(side)
rgbFace = self._get_rgb_face()
mypath, myverts = getCustomSymbol1()
renderer.draw_markers(gc, mypath, transform,
path, path_trans, rgbFace)
# add this function to the class prototype of Line2D
matplotlib.lines.Line2D._draw_mypath = _draw_mypath
# add marker shortcut/name/command/format spec '#' to Line2D class,
# and relate it to our custom marker drawing function
matplotlib.lines.Line2D._markers['#'] = '_draw_mypath'
matplotlib.lines.Line2D.markers = matplotlib.lines.Line2D._markers
else:
import matplotlib.markers
def _set_mypath(self):
self._transform = matplotlib.transforms.Affine2D().translate(-0.5, -0.5)
self._snap_threshold = 2.0
mypath, myverts = getCustomSymbol1()
self._path = mypath
self._joinstyle = 'miter'
matplotlib.markers.MarkerStyle._set_mypath = _set_mypath
matplotlib.markers.MarkerStyle.markers['#'] = 'mypath'
matplotlib.lines.Line2D.markers = matplotlib.markers.MarkerStyle.markers
# proceed as usual - use the new marker '#'
t = np.arange(0.0,1.5,0.25)
s = np.sin(2*np.pi*t)
mfigure = matplotlib.figure.Figure(figsize=(5,4), dpi=100)
ax = mfigure.add_subplot(111)
ax.plot(t,s, marker='#', color='b', markerfacecolor='orange', markersize=20.0)
fig = plt.figure() # create something (fig num 1) for fig_manager
figman = matplotlib._pylab_helpers.Gcf.get_fig_manager(1)
figman.canvas.figure = mfigure # needed
mfigure.set_canvas(figman.canvas) # needed
plt.show()
It shows a slightly "creative" marker (if I may say so myself :) ) - and this is how it behaves under zoom:
... that is, exactly as I want it - markers keep their position in data coordinates; however preserve their size under zooming.
Discussion
One of the most confusing things for me here, was the following: Essentially, you can specify a rectangle through an x,y coordinate as "location", and size (height/width). So if I specify a rectangle at x,y=(2,3); with halfsize 2 (so, square); then I can calculate its path as vertices through:
[(x-hs,y-hs), (x-hs,y+hs), (x+hs,y+hs), (x+hs,y-hs)]
This is, essentially, what getCustomSymbol1 was trying to return all along. In addition, for instance matplotlib.patches.Rectangle is instantiated through location and size, as in Rectangle((x,y), width, height).
Now, the problem is - what I actually wanted, is that markers, as shapes, stay on their position - in data coordinates, so moving and zooming the graph keeps their position as data; however, they should have kept their size under zooming.
This means that I want (x,y) specified in one coordinate system (data), and size (or width, height, or halfsize) specified in another coordinate system, in this case, the screen coordinate system: since I want the shapes to keep their size under zoom, I actually want to keep their size in screen pixels the same!
That is why no transformation as such would help in my case - any transformation would work on all the vertices of a path, as interpreted in a single coordinate system! Whereas, what I want, would be to get something like:
hsd = screen2dataTransform(10px)
[(x-hsd,y-hsd), (x-hsd,y+hsd), (x+hsd,y+hsd), (x+hsd,y-hsd)]
... and this recalculation of the vertices of the marker path would have to be repeated each time the zoom level, or the figure pan, or the window size changes.
As such, vertices/paths (and patches) and transformation alone cannot be used for this purpose. However, thankfully, we can use matplotlibs own engine; we simply have to know that any call to ax.plot(...marker=...) actually delegates the drawing of markers to matplotlib.lines.Line2D; and Line2D maintains an internal dict, which relates the marker one-character format specifier/command (like 'o', '*' etc) to a specific drawing function; and the drawing function, finally, does the size transformation in code like (in the solution code above, the drawing is for the most part taken from the 's' (square) marker implementation):
side = renderer.points_to_pixels(self._markersize)
transform = matplotlib.transforms.Affine2D().translate(-0.5, -0.5).scale(side)
Note that this is the case for older matplotlib (0.99.3 in my case); for newer matplotlib (1.2.0 in my case), there is a separate class MarkerStyle which maintains the relationship between the marker format specifier, and the function - and the function is not _draw_ anymore, it is just _set_ - but other than that, it is the same principle.
NB: I'm actually not sure when MarkerStyle was introduced, I could only find matplotlib.markers — Matplotlib 1.3.x documentation and it doesn't say; so that if matplotlib.__version__ < "1.0.0": in the code above could be wrong; but worksforme (fornow).
Because the markers size is, so to speak, managed separately (from its position) - that means that you don't have to do any special calculation in your custom marker Path specification; all you need to do is make sure its vertices fit in the range (0.0,0.0) to (1.0, 1.0) - the marker drawing engine will do the rest.
Well, I hope I understood this right - but if there are other approaches that work like this, I'd sure like to know about those :)
Hope this helps someone,
Cheers!