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Feat/cbar for ortho plot #473

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merged 2 commits into from
Jun 12, 2023
Merged

Feat/cbar for ortho plot #473

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32dbc5b
feat: :sparkles: added colorbar for ortho_plot
Jun 12, 2023
ab43252
refactor: :recycle: took out image naming
Jun 12, 2023
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36 changes: 31 additions & 5 deletions ants/viz/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1511,6 +1511,10 @@ def plot_ortho(
# overlay arguments
overlay_cmap="jet",
overlay_alpha=0.9,
cbar=False,
cbar_length=0.8,
cbar_dx=0.0,
cbar_vertical=True,
# background arguments
black_bg=True,
bg_thresh_quant=0.01,
Expand Down Expand Up @@ -1544,9 +1548,6 @@ def plot_ortho(
Use mask_image and/or threshold_image to preprocess images to be be
overlaid and display the overlays in a given range. See the wiki examples.

TODO:
- add colorbar option

ANTsR function: N/A

Arguments
Expand Down Expand Up @@ -1582,6 +1583,19 @@ def plot_ortho(
level of transparency for any overlays. Smaller value means
the overlay is more transparent. See matplotlib.

cbar: boolean
if true, a colorbar will be added to the plot

cbar_length: float
length of the colorbar relative to the image

cbar_dx: float
horizontal shift of the colorbar relative to the image

cbar_vertical: boolean
if true, the colorbar will be vertical, if false, it will be
horizontal underneath the image

axis : integer
which axis to plot along if image is 3D

Expand Down Expand Up @@ -1887,6 +1901,7 @@ def reorient_slice(x, axis):
if overlay is not None:
xz_overlay = reorient_slice(overlay[:, xyz[1], :], 1)
ax.imshow(xz_overlay, alpha=overlay_alpha, cmap=overlay_cmap, vmin=vminol, vmax=vmaxol )

if xyz_lines:
# add lines
l = mlines.Line2D(
Expand Down Expand Up @@ -1953,10 +1968,11 @@ def reorient_slice(x, axis):
ax = plt.subplot(gs[1, 1])
else:
ax = plt.subplot(gs[0, 2])
ax.imshow(xy_slice, cmap=cmap, vmin=vmin, vmax=vmax)
im = ax.imshow(xy_slice, cmap=cmap, vmin=vmin, vmax=vmax)
if overlay is not None:
xy_overlay = reorient_slice(overlay[:, :, xyz[2]], 2)
ax.imshow(xy_overlay, alpha=overlay_alpha, cmap=overlay_cmap, vmin=vminol, vmax=vmaxol )
im = ax.imshow(xy_overlay, alpha=overlay_alpha, cmap=overlay_cmap, vmin=vminol, vmax=vmaxol)

if xyz_lines:
# add lines
l = mlines.Line2D(
Expand Down Expand Up @@ -2041,6 +2057,16 @@ def reorient_slice(x, axis):
ax.imshow(np.zeros(image.shape[:-1]), cmap="Greys_r")
ax.axis("off")

if cbar:
cbar_start = (1 - cbar_length) / 2
if cbar_vertical:
cax = fig.add_axes([0.9 + cbar_dx, cbar_start, 0.03, cbar_length])
cbar_orient = "vertical"
else:
cax = fig.add_axes([cbar_start, 0.08 + cbar_dx, cbar_length, 0.03])
cbar_orient = "horizontal"
fig.colorbar(im, cax=cax, orientation=cbar_orient)

## multi-channel images ##
elif image.components > 1:
raise ValueError("Multi-channel images not currently supported!")
Expand Down