L-shaped scalebar

[swharden]

Plotting data with an L-shaped scalebar is very useful in electrophysiology, but it's not easy to do in matplotlib. Right now there's a tool to do it, but the plotting tools should probably be in a differently-named module. Think about the best way to implement this. This ticket has been opened because this module will soon be removed (replaced by something different later) and I don't want to lose track of this excellent piece of code. Once finalized, this feature should be properly documented.

pyabf.plot.scalebar(abf, hideFrame=True)

pyABF/src/pyabf/plot.py

Lines 104 to 185 in d63172d

	def scalebar(abf=None, hideTicks=True, hideFrame=True, fontSize=8, scaleXsize=None, scaleYsize=None, scaleXunits="", scaleYunits="", lineWidth=2):
	"""
	Add an L-shaped scalebar to the current figure.
	This removes current axis labels, ticks, and the figure frame.
	"""
	# if an ABF objet is given, use its sweep units
	if abf:
	scaleXunits = abf.sweepUnitsX
	scaleYunits = abf.sweepUnitsY
	# calculate the current data area
	x1, x2, y1, y2 = plt.axis() # bounds
	xc, yc = (x1+x2)/2, (y1+y2)/2 # center point
	xs, ys = abs(x2-x1), abs(y2-y1) # span
	# determine how big we want the scalebar to be
	if not scaleXsize:
	scaleXsize = abs(plt.xticks()[0][1]-plt.xticks()[0][0])/2
	if not scaleYsize:
	scaleYsize = abs(plt.yticks()[0][1]-plt.yticks()[0][0])/2
	# create the scale bar labels
	lblX = str(scaleXsize)
	lblY = str(scaleYsize)
	# prevent units unecessarially ending in ".0"
	if lblX.endswith(".0"):
	lblX = lblX[:-2]
	if lblY.endswith(".0"):
	lblY = lblY[:-2]
	if scaleXunits == "sec" and "." in lblX:
	lblX = str(int(float(lblX)*1000))
	scaleXunits = "ms"
	# add units to the labels
	lblX = lblX+" "+scaleXunits
	lblY = lblY+" "+scaleYunits
	lblX = lblX.strip()
	lblY = lblY.strip()
	# determine the dimensions of the scalebar
	scaleBarPadX = 0.10
	scaleBarPadY = 0.05
	scaleBarX = x2-scaleBarPadX*xs
	scaleBarX2 = scaleBarX-scaleXsize
	scaleBarY = y1+scaleBarPadY*ys
	scaleBarY2 = scaleBarY+scaleYsize
	# determine the center of the scalebar (where text will go)
	scaleBarXc = (scaleBarX+scaleBarX2)/2
	scaleBarYc = (scaleBarY+scaleBarY2)/2
	# create a scalebar point array suitable for plotting as a line
	scaleBarXs = [scaleBarX2, scaleBarX, scaleBarX]
	scaleBarYs = [scaleBarY, scaleBarY, scaleBarY2]
	# the text shouldn't touch the scalebar, so calculate how much to pad it
	lblPadMult = .005
	lblPadMult += .002*lineWidth
	lblPadX = xs*lblPadMult
	lblPadY = ys*lblPadMult
	# hide the old tick marks
	if hideTicks:
	plt.gca().get_yaxis().set_visible(False)
	plt.gca().get_xaxis().set_visible(False)
	# hide the square around the image
	if hideFrame:
	plt.gca().spines['top'].set_visible(False)
	plt.gca().spines['right'].set_visible(False)
	plt.gca().spines['bottom'].set_visible(False)
	plt.gca().spines['left'].set_visible(False)
	# now do the plotting
	plt.plot(scaleBarXs, scaleBarYs, 'k-', lw=lineWidth)
	plt.text(scaleBarXc, scaleBarY-lblPadY, lblX,
	ha='center', va='top', fontsize=fontSize)
	plt.text(scaleBarX+lblPadX, scaleBarYc, lblY,
	ha='left', va='center', fontsize=fontSize)

[swharden]

This example works for now.
https://github.com/swharden/pyABF/blob/master/docs/getting-started/advanced.md