def plot_persistence_barcode(
persistence=[],
persistence_file="",
alpha=0.6,
max_intervals=1000,
max_barcodes=1000,
inf_delta=0.1,
legend=False,
):
"""This function plots the persistence bar code from persistence values list
or from a :doc:`persistence file <fileformats>`.
:param persistence: Persistence intervals values list grouped by dimension.
:type persistence: list of tuples(dimension, tuple(birth, death)).
:param persistence_file: A :doc:`persistence file <fileformats>` style name
(reset persistence if both are set).
:type persistence_file: string
:param alpha: barcode transparency value (0.0 transparent through 1.0
opaque - default is 0.6).
:type alpha: float.
:param max_intervals: maximal number of intervals to display.
Selected intervals are those with the longest life time. Set it
to 0 to see all. Default value is 1000.
:type max_intervals: int.
:param inf_delta: Infinity is placed at :code:`((max_death - min_birth) x
inf_delta)` above :code:`max_death` value. A reasonable value is
between 0.05 and 0.5 - default is 0.1.
:type inf_delta: float.
:param legend: Display the dimension color legend (default is False).
:type legend: boolean.
:returns: A matplotlib object containing horizontal bar plot of persistence
(launch `show()` method on it to display it).
"""
try:
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
if persistence_file is not "":
if path.isfile(persistence_file):
# Reset persistence
persistence = []
diag = read_persistence_intervals_grouped_by_dimension(
persistence_file=persistence_file
)
for key in diag.keys():
for persistence_interval in diag[key]:
persistence.append((key, persistence_interval))
else:
print("file " + persistence_file + " not found.")
return None
if max_barcodes is not 1000:
print("Deprecated parameter. It has been replaced by max_intervals")
max_intervals = max_barcodes
if max_intervals > 0 and max_intervals < len(persistence):
# Sort by life time, then takes only the max_intervals elements
persistence = sorted(
persistence,
key=lambda life_time: life_time[1][1] - life_time[1][0],
reverse=True,
)[:max_intervals]
persistence = sorted(persistence, key=lambda birth: birth[1][0])
(min_birth, max_death) = __min_birth_max_death(persistence)
ind = 0
delta = (max_death - min_birth) * inf_delta
# Replace infinity values with max_death + delta for bar code to be more
# readable
infinity = max_death + delta
axis_start = min_birth - delta
# Draw horizontal bars in loop
for interval in reversed(persistence):
if float(interval[1][1]) != float("inf"):
# Finite death case
plt.barh(
ind,
(interval[1][1] - interval[1][0]),
height=0.8,
left=interval[1][0],
alpha=alpha,
color=palette[interval[0]],
linewidth=0,
)
else:
# Infinite death case for diagram to be nicer
plt.barh(
ind,
(infinity - interval[1][0]),
height=0.8,
left=interval[1][0],
alpha=alpha,
color=palette[interval[0]],
linewidth=0,
)
ind = ind + 1
if legend:
dimensions = list(set(item[0] for item in persistence))
plt.legend(
handles=[
mpatches.Patch(color=palette[dim], label=str(dim))
for dim in dimensions
],
loc="lower right",
)
plt.title("Persistence barcode")
# Ends plot on infinity value and starts a little bit before min_birth
plt.axis([axis_start, infinity, 0, ind])
return plt
except ImportError:
print("This function is not available, you may be missing matplotlib.")
def plot_persistence_barcode(
persistence=[],
persistence_file="",
alpha=0.6,
max_intervals=1000,
max_barcodes=1000,
inf_delta=0.1,
legend=False,
colormap=None,
axes=None,
fontsize=16,
):
"""This function plots the persistence bar code from persistence values list
, a np.array of shape (N x 2) (representing a diagram
in a single homology dimension),
or from a :doc:`persistence file <fileformats>`.
:param persistence: Persistence intervals values list. Can be grouped by dimension or not.
:type persistence: an array of (dimension, array of (birth, death)) or an array of (birth, death).
:param persistence_file: A :doc:`persistence file <fileformats>` style name
(reset persistence if both are set).
:type persistence_file: string
:param alpha: barcode transparency value (0.0 transparent through 1.0
opaque - default is 0.6).
:type alpha: float.
:param max_intervals: maximal number of intervals to display.
Selected intervals are those with the longest life time. Set it
to 0 to see all. Default value is 1000.
:type max_intervals: int.
:param inf_delta: Infinity is placed at :code:`((max_death - min_birth) x
inf_delta)` above :code:`max_death` value. A reasonable value is
between 0.05 and 0.5 - default is 0.1.
:type inf_delta: float.
:param legend: Display the dimension color legend (default is False).
:type legend: boolean.
:param colormap: A matplotlib-like qualitative colormaps. Default is None
which means :code:`matplotlib.cm.Set1.colors`.
:type colormap: tuple of colors (3-tuple of float between 0. and 1.).
:param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
a new set of axes.
:type axes: `matplotlib.axes.Axes`
:param fontsize: Fontsize to use in axis.
:type fontsize: int
:returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
"""
try:
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from matplotlib import rc
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
persistence = _array_handler(persistence)
if persistence_file != "":
if path.isfile(persistence_file):
# Reset persistence
persistence = []
diag = read_persistence_intervals_grouped_by_dimension(
persistence_file=persistence_file)
for key in diag.keys():
for persistence_interval in diag[key]:
persistence.append((key, persistence_interval))
else:
print("file " + persistence_file + " not found.")
return None
if max_barcodes != 1000:
print(
"Deprecated parameter. It has been replaced by max_intervals")
max_intervals = max_barcodes
if max_intervals > 0 and max_intervals < len(persistence):
# Sort by life time, then takes only the max_intervals elements
persistence = sorted(
persistence,
key=lambda life_time: life_time[1][1] - life_time[1][0],
reverse=True,
)[:max_intervals]
if colormap == None:
colormap = plt.cm.Set1.colors
if axes == None:
fig, axes = plt.subplots(1, 1)
persistence = sorted(persistence, key=lambda birth: birth[1][0])
(min_birth, max_death) = __min_birth_max_death(persistence)
ind = 0
delta = (max_death - min_birth) * inf_delta
# Replace infinity values with max_death + delta for bar code to be more
# readable
infinity = max_death + delta
axis_start = min_birth - delta
# Draw horizontal bars in loop
for interval in reversed(persistence):
if float(interval[1][1]) != float("inf"):
# Finite death case
axes.barh(
ind,
(interval[1][1] - interval[1][0]),
height=0.8,
left=interval[1][0],
alpha=alpha,
color=colormap[interval[0]],
linewidth=0,
)
else:
# Infinite death case for diagram to be nicer
axes.barh(
ind,
(infinity - interval[1][0]),
height=0.8,
left=interval[1][0],
alpha=alpha,
color=colormap[interval[0]],
linewidth=0,
)
ind = ind + 1
if legend:
dimensions = list(set(item[0] for item in persistence))
axes.legend(
handles=[
mpatches.Patch(color=colormap[dim], label=str(dim))
for dim in dimensions
],
loc="lower right",
)
axes.set_title("Persistence barcode", fontsize=fontsize)
# Ends plot on infinity value and starts a little bit before min_birth
axes.axis([axis_start, infinity, 0, ind])
return axes
except ImportError:
print("This function is not available, you may be missing matplotlib.")
def plot_persistence_diagram(
persistence=[],
persistence_file="",
alpha=0.6,
band=0.0,
max_intervals=1000,
max_plots=1000,
inf_delta=0.1,
legend=False,
):
"""This function plots the persistence diagram from persistence values
list or from a :doc:`persistence file <fileformats>`.
:param persistence: Persistence intervals values list grouped by dimension.
:type persistence: list of tuples(dimension, tuple(birth, death)).
:param persistence_file: A :doc:`persistence file <fileformats>` style name
(reset persistence if both are set).
:type persistence_file: string
:param alpha: plot transparency value (0.0 transparent through 1.0
opaque - default is 0.6).
:type alpha: float.
:param band: band (not displayed if :math:`\leq` 0. - default is 0.)
:type band: float.
:param max_intervals: maximal number of intervals to display.
Selected intervals are those with the longest life time. Set it
to 0 to see all. Default value is 1000.
:type max_intervals: int.
:param inf_delta: Infinity is placed at :code:`((max_death - min_birth) x
inf_delta)` above :code:`max_death` value. A reasonable value is
between 0.05 and 0.5 - default is 0.1.
:type inf_delta: float.
:param legend: Display the dimension color legend (default is False).
:type legend: boolean.
:returns: A matplotlib object containing diagram plot of persistence
(launch `show()` method on it to display it).
"""
try:
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
if persistence_file is not "":
if path.isfile(persistence_file):
# Reset persistence
persistence = []
diag = read_persistence_intervals_grouped_by_dimension(
persistence_file=persistence_file
)
for key in diag.keys():
for persistence_interval in diag[key]:
persistence.append((key, persistence_interval))
else:
print("file " + persistence_file + " not found.")
return None
if max_plots is not 1000:
print("Deprecated parameter. It has been replaced by max_intervals")
max_intervals = max_plots
if max_intervals > 0 and max_intervals < len(persistence):
# Sort by life time, then takes only the max_intervals elements
persistence = sorted(
persistence,
key=lambda life_time: life_time[1][1] - life_time[1][0],
reverse=True,
)[:max_intervals]
(min_birth, max_death) = __min_birth_max_death(persistence, band)
delta = (max_death - min_birth) * inf_delta
# Replace infinity values with max_death + delta for diagram to be more
# readable
infinity = max_death + delta
axis_start = min_birth - delta
# line display of equation : birth = death
x = np.linspace(axis_start, infinity, 1000)
# infinity line and text
plt.plot(x, x, color="k", linewidth=1.0)
plt.plot(x, [infinity] * len(x), linewidth=1.0, color="k", alpha=alpha)
plt.text(axis_start, infinity, r"$\infty$", color="k", alpha=alpha)
# bootstrap band
if band > 0.0:
plt.fill_between(x, x, x + band, alpha=alpha, facecolor="red")
# Draw points in loop
for interval in reversed(persistence):
if float(interval[1][1]) != float("inf"):
# Finite death case
plt.scatter(
interval[1][0],
interval[1][1],
alpha=alpha,
color=palette[interval[0]],
)
else:
# Infinite death case for diagram to be nicer
plt.scatter(
interval[1][0], infinity, alpha=alpha, color=palette[interval[0]]
)
if legend:
dimensions = list(set(item[0] for item in persistence))
plt.legend(
handles=[
mpatches.Patch(color=palette[dim], label=str(dim))
for dim in dimensions
]
)
plt.title("Persistence diagram")
plt.xlabel("Birth")
plt.ylabel("Death")
# Ends plot on infinity value and starts a little bit before min_birth
plt.axis([axis_start, infinity, axis_start, infinity + delta])
return plt
except ImportError:
print("This function is not available, you may be missing matplotlib.")
def plot_persistence_diagram(persistence=[],
persistence_file="",
alpha=0.6,
band=0.0,
max_intervals=1000,
max_plots=1000,
inf_delta=0.1,
legend=False,
colormap=None,
axes=None,
fontsize=16,
greyblock=True):
"""This function plots the persistence diagram from persistence values
list, a np.array of shape (N x 2) representing a diagram in a single
homology dimension, or from a :doc:`persistence file <fileformats>`.
:param persistence: Persistence intervals values list. Can be grouped by dimension or not.
:type persistence: an array of (dimension, array of (birth, death)) or an array of (birth, death).
:param persistence_file: A :doc:`persistence file <fileformats>` style name
(reset persistence if both are set).
:type persistence_file: string
:param alpha: plot transparency value (0.0 transparent through 1.0
opaque - default is 0.6).
:type alpha: float.
:param band: band (not displayed if :math:`\leq` 0. - default is 0.)
:type band: float.
:param max_intervals: maximal number of intervals to display.
Selected intervals are those with the longest life time. Set it
to 0 to see all. Default value is 1000.
:type max_intervals: int.
:param inf_delta: Infinity is placed at :code:`((max_death - min_birth) x
inf_delta)` above :code:`max_death` value. A reasonable value is
between 0.05 and 0.5 - default is 0.1.
:type inf_delta: float.
:param legend: Display the dimension color legend (default is False).
:type legend: boolean.
:param colormap: A matplotlib-like qualitative colormaps. Default is None
which means :code:`matplotlib.cm.Set1.colors`.
:type colormap: tuple of colors (3-tuple of float between 0. and 1.).
:param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
a new set of axes.
:type axes: `matplotlib.axes.Axes`
:param fontsize: Fontsize to use in axis.
:type fontsize: int
:param greyblock: if we want to plot a grey patch on the lower half plane for nicer rendering. Default True.
:type greyblock: boolean
:returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
"""
try:
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from matplotlib import rc
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
persistence = _array_handler(persistence)
if persistence_file != "":
if path.isfile(persistence_file):
# Reset persistence
persistence = []
diag = read_persistence_intervals_grouped_by_dimension(
persistence_file=persistence_file)
for key in diag.keys():
for persistence_interval in diag[key]:
persistence.append((key, persistence_interval))
else:
print("file " + persistence_file + " not found.")
return None
if max_plots != 1000:
print(
"Deprecated parameter. It has been replaced by max_intervals")
max_intervals = max_plots
if max_intervals > 0 and max_intervals < len(persistence):
# Sort by life time, then takes only the max_intervals elements
persistence = sorted(
persistence,
key=lambda life_time: life_time[1][1] - life_time[1][0],
reverse=True,
)[:max_intervals]
if colormap == None:
colormap = plt.cm.Set1.colors
if axes == None:
fig, axes = plt.subplots(1, 1)
(min_birth, max_death) = __min_birth_max_death(persistence, band)
delta = (max_death - min_birth) * inf_delta
# Replace infinity values with max_death + delta for diagram to be more
# readable
infinity = max_death + delta
axis_end = max_death + delta / 2
axis_start = min_birth - delta
# bootstrap band
if band > 0.0:
x = np.linspace(axis_start, infinity, 1000)
axes.fill_between(x, x, x + band, alpha=alpha, facecolor="red")
# lower diag patch
if greyblock:
axes.add_patch(
mpatches.Polygon(
[[axis_start, axis_start], [axis_end, axis_start],
[axis_end, axis_end]],
fill=True,
color='lightgrey'))
# Draw points in loop
pts_at_infty = False # Records presence of pts at infty
for interval in reversed(persistence):
if float(interval[1][1]) != float("inf"):
# Finite death case
axes.scatter(
interval[1][0],
interval[1][1],
alpha=alpha,
color=colormap[interval[0]],
)
else:
pts_at_infty = True
# Infinite death case for diagram to be nicer
axes.scatter(interval[1][0],
infinity,
alpha=alpha,
color=colormap[interval[0]])
if pts_at_infty:
# infinity line and text
axes.plot([axis_start, axis_end], [axis_start, axis_end],
linewidth=1.0,
color="k")
axes.plot([axis_start, axis_end], [infinity, infinity],
linewidth=1.0,
color="k",
alpha=alpha)
# Infinity label
yt = axes.get_yticks()
yt = yt[np.where(
yt < axis_end
)] # to avoid ploting ticklabel higher than infinity
yt = np.append(yt, infinity)
ytl = ["%.3f" % e for e in yt] # to avoid float precision error
ytl[-1] = r'$+\infty$'
axes.set_yticks(yt)
axes.set_yticklabels(ytl)
if legend:
dimensions = list(set(item[0] for item in persistence))
axes.legend(handles=[
mpatches.Patch(color=colormap[dim], label=str(dim))
for dim in dimensions
])
axes.set_xlabel("Birth", fontsize=fontsize)
axes.set_ylabel("Death", fontsize=fontsize)
axes.set_title("Persistence diagram", fontsize=fontsize)
# Ends plot on infinity value and starts a little bit before min_birth
axes.axis([axis_start, axis_end, axis_start, infinity + delta / 2])
return axes
except ImportError:
print("This function is not available, you may be missing matplotlib.")
