"""utils.py: Utilities for the :mod:`HMatrix` module
"""
import math
from HierMat.block_cluster_tree import BlockClusterTree
from HierMat.cluster_tree import ClusterTree
import matplotlib.pyplot as plt
[docs]def export(obj, form='xml', out_file='out'):
"""Export obj in specified format.
:param obj: object to export
:type obj: BlockClusterTree or ClusterTree or HMat or RMat
:param form: format specifier
:type form: str
:param out_file: path to output file
:type out_file: str
:raises NotImplementedError: if form is not supported
.. note::
implemented so far:
- xml
- dot
- bin
"""
if form == 'xml':
head = '<?xml version="1.0" encoding="utf-8"?>\n'
output = obj.to_xml()
output = head + output
with open(out_file, "w") as out:
out.write(output)
elif form == 'dot':
head = 'graph {\nnodesep=0.1;\nranksep=1.5;\n'
output = obj.to_dot()
tail = '}'
output = head + output + tail
with open(out_file, "w") as out:
out.write(output)
elif form == 'bin':
import pickle
file_handle = open(out_file, "wb")
pickle.dump(obj, file_handle, protocol=-1)
file_handle.close()
else:
raise NotImplementedError()
[docs]def plot(obj, filename=None, **kwargs):
"""plot an object
:param obj: object to plot
:type obj: BlockClusterTree
:param filename: filename to save the plot to (if omitted, the plot will be displayed)
:type filename: str
:param kwargs: optional arguments to specific plot commands
see the respective documentations
"""
if isinstance(obj, BlockClusterTree):
return block_cluster_tree_plot(obj, filename, **kwargs)
else:
raise NotImplementedError('object can not be plotted')
[docs]def block_cluster_tree_plot(obj, filename=None, ticks=False, face_color='#133f52',
admissible_color='#76f7a8', inadmissible_color='#ff234b'):
"""Plot the block cluster tree
:param obj: block cluster tree to plot
:type obj: BlockClusterTree
:param filename: filename to save the plot. if omitted, the plot will be displayed
:type filename: str
:param ticks: show ticks in the plot
:type ticks: bool
:param face_color: background color (see matplotlib for color specs)
:param admissible_color: color for admissible patch
:type admissible_color: str
:param inadmissible_color: color for inadmissible patch
:type inadmissible_color: str
.. note::
depends on :mod:`matplotlib.pyplot`
"""
plt.rc('axes', linewidth=0.5, labelsize=4)
plt.rc('xtick', labelsize=4)
plt.rc('ytick', labelsize=4)
fig = plt.figure(figsize=(3, 3), dpi=400)
fig.patch.set_facecolor(face_color)
# get max of the ticks
x_min, x_max = obj.left_clustertree.get_patch_coordinates()
y_min, y_max = obj.right_clustertree.get_patch_coordinates()
axes = plt.axes()
axes.set_xlim(x_min, x_max + 1)
axes.set_ylim(y_min, y_max + 1)
if ticks:
x_divisors = list(divisor_generator(x_max + 1))
y_divisors = list(divisor_generator(y_max + 1))
if len(x_divisors) > 4:
x_ticks = x_divisors[-4]
else:
x_ticks = x_divisors[-1]
if len(y_divisors) > 4:
y_ticks = y_divisors[-4]
else:
y_ticks = y_divisors[-1]
axes.set_xticks(range(x_min, x_max + 2, x_ticks))
axes.set_yticks(range(y_min, y_max + 2, y_ticks))
else:
axes.set_xticks([])
axes.set_yticks([])
axes.tick_params(length=2, width=0.5)
axes.xaxis.tick_top()
axes.invert_yaxis()
obj.plot_recursion(axes, admissible_color=admissible_color, inadmissible_color=inadmissible_color)
fig.add_axes(axes)
if not filename:
return fig
else:
if not ticks:
# remove whitespace around the plot
plt.subplots_adjust(left=0, right=1, top=1, bottom=0)
else:
plt.subplots_adjust(left=0.1, right=0.9, top=0.9, bottom=0.1)
plt.savefig(filename, format='png', facecolor=fig.get_facecolor(), edgecolor=None)
[docs]def load(filename):
"""Load a :class:`ClusterTree` or :class:`BlockClusterTree` from file
:param filename: file to import
:type filename: String
:return: object
:rtype: BlockClusterTree or ClusterTree
.. note:: Depends on :mod:`pickle`
"""
import pickle
with open(filename, 'rb') as infile:
obj = pickle.load(infile)
return obj
[docs]def divisor_generator(n):
"""Return divisors of n
:param n: integer to find divisors of
:type n: int
:return: divisors
:rtype: list[int]
.. warning::
This is a generator! To get a list with all divisors call::
list(divisor_generator(n))
.. note::
found at
`StackOverflow
<http://stackoverflow.com/questions/171765/what-is-the-best-way-to-get-all-the-divisors-of-a-number>`_
on 2017.03.08
"""
large_divisors = []
for i in xrange(1, int(math.sqrt(n) + 1)):
if n % i == 0:
yield i
if i * i != n:
large_divisors.append(n / i)
for divisor in reversed(large_divisors):
yield divisor
