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Refactor: Make (x/y)lims and (x/y)lim consistent in plot functions (#69)
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@adrien-berchet
adrien-berchet authored Nov 15, 2022
1 parent 1ef96bb commit 6bc9bdd
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Showing 8 changed files with 218 additions and 231 deletions.
95 changes: 48 additions & 47 deletions examples/Advanced/advanced_plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,8 +43,8 @@ def tree_all(
title="",
diameter=True,
treecol="b",
xlims=None,
ylims=None,
xlim=None,
ylim=None,
**kwargs,
):
"""Subplot with ph, barcode and tree."""
Expand Down Expand Up @@ -83,7 +83,7 @@ def _seg_2d(seg):
# bounds = max(max(ph))
fig1, ax2 = diagram(ph, new_fig=False, subplot=222, color=treecol)
fig1, ax3 = barcode(ph, new_fig=False, subplot=223, color=treecol)
fig1, ax4 = persistence_image(ph, new_fig=False, subplot=224, xlims=xlims, ylims=ylims)
fig1, ax4 = persistence_image(ph, new_fig=False, subplot=224, xlim=xlim, ylim=ylim)
_cm.plt.tight_layout(True)

if kwargs["output_path"] is not None:
Expand All @@ -99,8 +99,8 @@ def neu_all(
title="",
diameter=True,
treecol="b",
xlims=None,
ylims=None,
xlim=None,
ylim=None,
neurite_type="basal_dendrite",
**kwargs,
):
Expand All @@ -126,7 +126,7 @@ def neu_all(
# bounds = max(max(ph))
fig1, ax2 = diagram(ph, new_fig=False, subplot=222, color=treecol)
fig1, ax3 = barcode(ph, new_fig=False, subplot=223, color=treecol)
fig1, ax4 = persistence_image(ph, new_fig=False, subplot=224, xlims=xlims, ylims=ylims)
fig1, ax4 = persistence_image(ph, new_fig=False, subplot=224, xlim=xlim, ylim=ylim)
_cm.plt.tight_layout(True)

if kwargs["output_path"] is not None:
Expand Down Expand Up @@ -508,7 +508,7 @@ def gaussian_kernel_resample(ph, num_samples=None, scale_persistent_comp=10):
return _np.transpose(kernel.resample(size=num_samples))


def gaussian_kernel_rot(ph, new_fig=True, subplot=111, xlims=None, ylims=None, angle=0, **kwargs):
def gaussian_kernel_rot(ph, new_fig=True, subplot=111, xlim=None, ylim=None, angle=0, **kwargs):
"""Plot the gaussian kernel of the ph diagram that is given."""

def rotation(x, y, angle=0.0):
Expand All @@ -521,12 +521,12 @@ def rotation(x, y, angle=0.0):
ymin = min(_np.transpose(ph_r)[1])
ymax = max(_np.transpose(ph_r)[1])

if xlims is None:
xlims = [xmin, xmax]
if ylims is None:
ylims = [ymin, ymax]
if xlim is None:
xlim = [xmin, xmax]
if ylim is None:
ylim = [ymin, ymax]

X, Y = _np.mgrid[xlims[0] : xlims[1] : 100j, ylims[0] : ylims[1] : 100j]
X, Y = _np.mgrid[xlim[0] : xlim[1] : 100j, ylim[0] : ylim[1] : 100j]

values = _np.transpose(ph_r)
kernel = stats.gaussian_kde(values)
Expand All @@ -541,19 +541,19 @@ def rotation(x, y, angle=0.0):
return Z, _view.common.plot_style(fig=fig, ax=ax, **kwargs)


def gaussian_kernel_weighted(ph, new_fig=True, subplot=111, xlims=None, ylims=None, **kwargs):
def gaussian_kernel_weighted(ph, new_fig=True, subplot=111, xlim=None, ylim=None, **kwargs):
"""Plot the gaussian kernel of the ph diagram that is given."""
xmin = min(_np.transpose(ph)[0])
xmax = max(_np.transpose(ph)[0])
ymin = min(_np.transpose(ph)[1])
ymax = max(_np.transpose(ph)[1])

if xlims is None:
xlims = [xmin, xmax]
if ylims is None:
ylims = [ymin, ymax]
if xlim is None:
xlim = [xmin, xmax]
if ylim is None:
ylim = [ymin, ymax]

X, Y = _np.mgrid[xlims[0] : xlims[1] : 100j, ylims[0] : ylims[1] : 100j]
X, Y = _np.mgrid[xlim[0] : xlim[1] : 100j, ylim[0] : ylim[1] : 100j]

values = _np.transpose(ph)
kernel = stats.gaussian_kde(values)
Expand All @@ -569,20 +569,20 @@ def gaussian_kernel_weighted(ph, new_fig=True, subplot=111, xlims=None, ylims=No


def gaussian_kernel_superposition(
ph, new_fig=True, subplot=111, xlims=None, ylims=None, color="r", **kwargs
ph, new_fig=True, subplot=111, xlim=None, ylim=None, color="r", **kwargs
):
"""Plot the gaussian kernel of the ph diagram that is given."""
xmin = min(_np.transpose(ph)[0])
xmax = max(_np.transpose(ph)[0])
ymin = min(_np.transpose(ph)[1])
ymax = max(_np.transpose(ph)[1])

if xlims is None:
xlims = [xmin, xmax]
if ylims is None:
ylims = [ymin, ymax]
if xlim is None:
xlim = [xmin, xmax]
if ylim is None:
ylim = [ymin, ymax]

X, Y = _np.mgrid[xlims[0] : xlims[1] : 100j, ylims[0] : ylims[1] : 100j]
X, Y = _np.mgrid[xlim[0] : xlim[1] : 100j, ylim[0] : ylim[1] : 100j]

values = _np.transpose(ph)
kernel = stats.gaussian_kde(values)
Expand All @@ -593,13 +593,12 @@ def gaussian_kernel_superposition(
fig, ax = _view.common.get_figure(new_fig=new_fig, subplot=subplot)

ax.pcolor(Zn, vmin=0.0, vmax=1.0, cmap=_view.common.plt.cm.inferno)
# ax.contour(Z, extent=xlims+ylims)

for p in ph:

ax.scatter(p[0], p[1], c=color)

return _view.common.plot_style(fig=fig, ax=ax, xlim=xlims, ylim=ylims, **kwargs)
return _view.common.plot_style(fig=fig, ax=ax, xlim=xlim, ylim=ylim, **kwargs)


def tree_br(
Expand Down Expand Up @@ -652,8 +651,8 @@ def tree_gaussian_kernel(
title="",
diameter=True,
treecol="b",
xlims=None,
ylims=None,
xlim=None,
ylim=None,
**kwargs,
):
"""Subplot with ph, barcode and tree within spheres."""
Expand Down Expand Up @@ -686,7 +685,7 @@ def _seg_2d(seg):
else:
raise Exception("Plane value not recognised")

fig1, ax2 = gaussian_kernel_weighted(ph, new_fig=False, subplot=122, xlims=xlims, ylims=ylims)
fig1, ax2 = gaussian_kernel_weighted(ph, new_fig=False, subplot=122, xlim=xlim, ylim=ylim)

_view.common.plt.tight_layout(True)

Expand All @@ -703,8 +702,6 @@ def tree_ph(
title="",
diameter=True,
treecol="b",
xlims=None,
ylims=None,
**kwargs,
):
"""Subplot with ph, barcode and tree within spheres."""
Expand Down Expand Up @@ -754,10 +751,10 @@ def tree_evol(
title="",
diameter=True,
treecol="b",
xlims=None,
ylims=None,
xlim=None,
ylim=None,
barcode_xlim=None,
barcode_ylim=None,
kernel_xlim=None,
kernel_ylim=None,
**kwargs,
):
"""Subplot with ph, barcode and tree within spheres."""
Expand Down Expand Up @@ -790,9 +787,13 @@ def _seg_2d(seg):
else:
raise Exception("Plane value not recognised")

fig1, ax3 = barcode(ph, new_fig=False, subplot=222, color=treecol, xlim=xlim, ylim=ylim)
fig1, ax3 = barcode(
ph, new_fig=False, subplot=222, color=treecol, xlim=barcode_xlim, ylim=barcode_ylim
)

fig1, ax4 = gaussian_kernel_weighted(ph, new_fig=False, subplot=224, xlims=xlims, ylims=ylims)
fig1, ax4 = gaussian_kernel_weighted(
ph, new_fig=False, subplot=224, xlim=kernel_xlim, ylim=kernel_ylim
)

_view.common.plt.tight_layout(True)

Expand All @@ -803,20 +804,20 @@ def _seg_2d(seg):


def image_diff_time(
Z1, Z2, time_steps=100, new_fig=True, subplot=111, xlims=None, ylims=None, **kwargs
Z1, Z2, time_steps=100, new_fig=True, subplot=111, xlim=None, ylim=None, **kwargs
):
"""Take as input a set of images and plots their difference."""
xmin = min(Z1[1][1].get_xlim() + Z2[1][1].get_xlim())
xmax = max(Z1[1][1].get_xlim() + Z2[1][1].get_xlim())
ymin = min(Z1[1][1].get_ylim() + Z2[1][1].get_ylim())
ymax = max(Z1[1][1].get_ylim() + Z2[1][1].get_ylim())

if xlims is None:
xlims = [xmin, xmax]
if ylims is None:
ylims = [ymin, ymax]
if xlim is None:
xlim = [xmin, xmax]
if ylim is None:
ylim = [ymin, ymax]

X, Y = _np.mgrid[xlims[0] : xlims[1] : 100j, ylims[0] : ylims[1] : 100j]
X, Y = _np.mgrid[xlim[0] : xlim[1] : 100j, ylim[0] : ylim[1] : 100j]

img1 = Z1[0] / Z1[0].max()
img2 = Z2[0] / Z2[0].max()
Expand All @@ -827,8 +828,8 @@ def image_diff_time(

_view.common.plt.colorbar()

kwargs["xlim"] = xlims
kwargs["ylim"] = ylims
kwargs["xlim"] = xlim
kwargs["ylim"] = ylim

return _view.common.plot_style(fig=fig, ax=ax, **kwargs)

Expand Down Expand Up @@ -1096,7 +1097,7 @@ def plot_persistent_homology_video(
return ph


def multiple_trees_plot(trees, phs, xlim=None, ylim=None, title_1="Asymmetry"):
def multiple_trees_plot(trees, phs, title_1="Asymmetry"):
"""Plot multiple trees."""
plt.figure()
N = len(trees)
Expand All @@ -1116,7 +1117,7 @@ def multiple_trees_plot(trees, phs, xlim=None, ylim=None, title_1="Asymmetry"):

view.plot.barcode(phs[i], new_fig=False, subplot=(3, N, i + 1 + N), title="", xlim=lims)
view.plot.persistence_image(
phs[i], new_fig=False, subplot=(3, N, i + 1 + 2 * N), title="", xlims=lims, ylims=lims
phs[i], new_fig=False, subplot=(3, N, i + 1 + 2 * N), title="", xlim=lims, ylim=lims
)


Expand Down
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