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	tclose figures in order to avoid large memory requirements when looped - sphere…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 14c2ecf26eaf02a9d5d96de31afef8a6ff0a1b3a
	parent b52f4b15ae61b113931003f1b0941ee404d779ca
	Author: Anders Damsgaard <[email protected]>
	Date: Thu, 9 Apr 2015 11:15:00 +0200

	close figures in order to avoid large memory requirements when looped

	Diffstat:
	M python/sphere.py \| 24 +++++++++++++++++++-----

	1 file changed, 19 insertions(+), 5 deletions(-)
	---
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -5218,7 +5218,8 @@ class sim:

	def plotContacts(self, graphics_format = 'png', figsize=[6,6], title=None,
	lower_limit = 0.0, upper_limit = 1.0, alpha=1.0, return_data=False,
	- outfolder='.'):
	+ outfolder='.',
	+ f_min = None, f_max = None):
	'''
	Plot current contact orientations on polar plot

	t@@ -5246,6 +5247,11 @@ class sim:
	# specify the lower limit of force chains to do statistics on
	f_n_lim = lower_limit * f_n_max

	+ if f_min:
	+ f_n_lim = f_min
	+ if f_max:
	+ f_n_max = f_max
	+
	# find the indexes of these contacts
	I = numpy.nonzero(data[:,6] >= f_n_lim)

	t@@ -5285,7 +5291,7 @@ class sim:
	else :
	strikelist.append(2.0*numpy.pi - numpy.arccos(dx/dhoriz))

	- plt.figure(figsize=figsize)
	+ fig = plt.figure(figsize=figsize)
	ax = plt.subplot(111, polar=True, axisbg='white')
	cs = ax.scatter(strikelist, diplist, marker='o',
	c=forcemagnitude,
	t@@ -5324,6 +5330,9 @@ class sim:

	subprocess.call('rm contacts-tmp.txt', shell=True)

	+ fig.clf()
	+ plt.close()
	+
	if return_data:
	return data

	t@@ -5977,7 +5986,7 @@ class sim:


	def visualize(self, method='energy', savefig=True, outformat='png',
	- pickle=False, xlim=False, firststep=0):
	+ pickle=False, xlim=False, firststep=0, f_min=None, f_max=None):
	'''
	Visualize output from the simulation, where the temporal progress is
	of interest. The output will be saved in the current folder with a name
	t@@ -6855,8 +6864,13 @@ class sim:
	fn = "../output/{0}.output{1:0=5}.bin".format(self.sid, i)
	sb.sid = self.sid + ".{:0=5}".format(i)
	sb.readbin(fn, verbose=True)
	- sb.plotContacts(lower_limit=0.25, upper_limit=0.75,
	- outfolder = '../img_out/')
	+ if f_min and f_max:
	+ sb.plotContacts(lower_limit=0.25, upper_limit=0.75,
	+ outfolder = '../img_out/',
	+ f_min = f_min, f_max = f_max)
	+ else:
	+ sb.plotContacts(lower_limit=0.25, upper_limit=0.75,
	+ outfolder = '../img_out/')

	subprocess.call('cd ../img_out/ && ' +
	'convert -quality 100 {}.*.png {}-contacts.avi'.format(