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Merged
gavinmischler merged 2 commits into from
Feb 14, 2025
Merged

Add threshold and vmin/vmax to plot_brain_overlay #211

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8ea3cf3
Add threshold and vmin/vmax to plot_brain_overlay
gavinmischler Feb 14, 2025
985f077
Update __init__.py
gavinmischler Feb 14, 2025
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2 changes: 1 addition & 1 deletion naplib/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,5 +56,5 @@ def set_logging(level: Union[int, str]):
from .data import Data, join_fields, concat
import naplib.naplab

__version__ = "2.3.0"
__version__ = "2.4.0"

81 changes: 46 additions & 35 deletions naplib/visualization/brain_plots.py
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Expand Up @@ -69,18 +69,18 @@ def _view(hemi, mode: str = "lateral", backend: str = "mpl"):
center = dict(x=0, y=0, z=0)
return eye, center
else:
return (20, 160) if hemi == "lh" else (40, 20)
return (10, 170) if hemi == "lh" else (10, 10)

raise ValueError(f"Unknown `mode`: {mode}.")


def _plot_hemi(hemi, cmap="coolwarm", ax=None, view="best", thresh=None, vmin=None, vmax=None):
def _plot_hemi(hemi, cmap="coolwarm", ax=None, view="best", threshold=None, vmin=None, vmax=None):
surfdist_viz(
*hemi.surf,
hemi.overlay,
*_view(hemi.hemi, mode=view),
cmap=cmap,
threshold=thresh,
threshold=threshold,
alpha=hemi.alpha,
bg_map=hemi.sulc,
bg_on_stat=True,
Expand All @@ -93,7 +93,7 @@ def _plot_hemi(hemi, cmap="coolwarm", ax=None, view="best", thresh=None, vmin=No


def plot_brain_overlay(
brain, cmap="coolwarm", ax=None, hemi='both', denorm=False, view="best", cmap_quantile=1.0, **kwargs
brain, cmap="coolwarm", ax=None, hemi='both', view="best", vmin=None, vmax=None, cmap_quantile=1.0, threshold=None, **kwargs
):
"""
Plot brain overlay on the 3D cortical surface using matplotlib.
Expand All @@ -111,16 +111,21 @@ def plot_brain_overlay(
hemi : {'both', 'lh', 'rh'}, default='both'
Hemisphere(s) to plot. If 'both', then 2 subplots are created, one for each hemisphere.
Otherwise only one hemisphere is displayed with its overlay.
denorm : bool, default=False
Whether to center the overlay labels around 0 or not before sending to the colormap.
view : {'lateral','medial','frontal','top','best'}, default='best'
Which view to plot for each hemisphere.
Which view to plot for each hemisphere.
vmin : float, optional
Minimum value for colormap. If not given, will use cmap_quantile or range or overlay values.
vmax : float, optional
Maximum value for colormap. If not given, will use cmap_quantile or range or overlay values.
cmap_quantile : float | tuple of floats (optional), default=1.0
If a single float less than 1, will only use the central ``cmap_quantile`` portion of the range
of values to create the vmin and vmax for the colormap. For example, if set to 0.95,
then only the middle 95% of the values will be used to set the range of the colormap. If a tuple,
then it should specify 2 quantiles, one for the vmin and one for the vmax, such as (0.025, 0.975),
which would be equivalent to passing a single value of 0.95.
threshold : positive float, optional
If given, then only values on the overlay which are less -threshold or greater than threshold will
be shown.
**kwargs : kwargs
Any other kwargs to pass to matplotlib.pyplot.figure (such as figsize)

Expand All @@ -146,45 +151,51 @@ def plot_brain_overlay(
if hemi in ['both', 'b']:
assert len(ax) == 2


if cmap_quantile is not None:
if isinstance(cmap_quantile, float):
assert cmap_quantile <= 1 and cmap_quantile > 0
cmap_diff = (1.0 - cmap_quantile) / 2.
vmin_l = np.quantile(brain.lh.overlay[brain.lh.overlay!=0], cmap_diff)
vmax_l = np.quantile(brain.lh.overlay[brain.lh.overlay!=0], 1.0 - cmap_diff)
vmin_r = np.quantile(brain.rh.overlay[brain.rh.overlay!=0], cmap_diff)
vmax_r = np.quantile(brain.rh.overlay[brain.rh.overlay!=0], 1.0 - cmap_diff)
elif isinstance(cmap_quantile, tuple):
vmin_l = np.quantile(brain.lh.overlay[brain.lh.overlay!=0], cmap_quantile[0])
vmax_l = np.quantile(brain.lh.overlay[brain.lh.overlay!=0], cmap_quantile[1])
vmin_r = np.quantile(brain.rh.overlay[brain.rh.overlay!=0], cmap_quantile[0])
vmax_r = np.quantile(brain.rh.overlay[brain.rh.overlay!=0], cmap_quantile[1])
if vmin is None or vmax is None:
if cmap_quantile is not None:
if isinstance(cmap_quantile, float):
assert cmap_quantile <= 1 and cmap_quantile > 0
cmap_diff = (1.0 - cmap_quantile) / 2.
vmin_l = np.quantile(brain.lh.overlay[brain.lh.overlay!=0], cmap_diff)
vmax_l = np.quantile(brain.lh.overlay[brain.lh.overlay!=0], 1.0 - cmap_diff)
vmin_r = np.quantile(brain.rh.overlay[brain.rh.overlay!=0], cmap_diff)
vmax_r = np.quantile(brain.rh.overlay[brain.rh.overlay!=0], 1.0 - cmap_diff)
elif isinstance(cmap_quantile, tuple):
vmin_l = np.quantile(brain.lh.overlay[brain.lh.overlay!=0], cmap_quantile[0])
vmax_l = np.quantile(brain.lh.overlay[brain.lh.overlay!=0], cmap_quantile[1])
vmin_r = np.quantile(brain.rh.overlay[brain.rh.overlay!=0], cmap_quantile[0])
vmax_r = np.quantile(brain.rh.overlay[brain.rh.overlay!=0], cmap_quantile[1])
else:
raise ValueError('cmap_quantile must be either a float or a tuple')
else:
raise ValueError('cmap_quantile must be either a float or a tuple')
else:
vmin_l = brain.lh.overlay[brain.lh.overlay!=0].min()
vmax_l = brain.lh.overlay[brain.lh.overlay!=0].max()
vmin_r = brain.rh.overlay[brain.rh.overlay!=0].min()
vmax_r = brain.rh.overlay[brain.rh.overlay!=0].max()
vmin_l = brain.lh.overlay[brain.lh.overlay!=0].min()
vmax_l = brain.lh.overlay[brain.lh.overlay!=0].max()
vmin_r = brain.rh.overlay[brain.rh.overlay!=0].min()
vmax_r = brain.rh.overlay[brain.rh.overlay!=0].max()


# determine vmin and vmax
if hemi in ['both', 'b']:
vmin = min([vmin_l, vmin_r])
vmax = max([vmax_l, vmax_r])
if vmin is None:
vmin = min([vmin_l, vmin_r])
if vmax is None:
vmax = max([vmax_l, vmax_r])
elif hemi in ['left','lh']:
vmin = vmin_l
vmax = vmax_l
if vmin is None:
vmin = vmin_l
if vmax is None:
vmax = vmax_l
elif hemi in ['right','rh']:
vmin = vmin_r
vmax = vmax_r
if vmin is None:
vmin = vmin_r
if vmax is None:
vmax = vmax_r


if ax[0] is not None:
_plot_hemi(brain.lh, cmap, ax[0], view=view, vmin=vmin, vmax=vmax)
_plot_hemi(brain.lh, cmap, ax[0], view=view, vmin=vmin, vmax=vmax, threshold=threshold)
if ax[1] is not None:
_plot_hemi(brain.rh, cmap, ax[1], view=view, vmin=vmin, vmax=vmax)
_plot_hemi(brain.rh, cmap, ax[1], view=view, vmin=vmin, vmax=vmax, threshold=threshold)

return fig, ax

Expand Down