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Fix/viz #55

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merged 5 commits into from
Jan 5, 2024
Merged

Fix/viz #55

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e2383db
small bugs
Jan 5, 2024
058f940
opacity & camera angle
emilykubota Jan 5, 2024
04da1e3
default camera
emilykubota Jan 5, 2024
70fb6cd
cam angle
emilykubota Jan 5, 2024
9739423
revert cam angle
emilykubota Jan 5, 2024
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36 changes: 19 additions & 17 deletions fsub_extractor/utils/fury_viz.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ def visualize_sub_bundles(
interactive=False,
show_anat=False,
axial_offset=0,
saggital_offset=0,
sagittal_offset=0,
camera_angle="sagittal",
hemi="lh",
):
Expand All @@ -45,7 +45,7 @@ def visualize_sub_bundles(
show_anat (Optional): Whether to overlay anatomy on the figure (default = False)
axial_offset (Optional): Where to display axial slice (-1,1) where -1 is bottom of image and 1 is top.
(default = 0, which is the middle of the image)
saggital_offset (Optional): Where to display sagittal slice (-1,1) where -1 is left of image and 1 is right.
sagittal_offset (Optional): Where to display sagittal slice (-1,1) where -1 is left of image and 1 is right.
(default = 0, which is the middle of the image)
camera_angle (Optional): Angle for screenshot ('saggital' (default) or 'axial')
hemi (Optional): For sagittal picture, what hemisphere to view from. Accepts either 'lh' or 'rh'.
Expand All @@ -63,7 +63,7 @@ def visualize_sub_bundles(
fsub_streamlines = fsub_streamlines.streamlines

# Repeat the color matrix for each streamline (fsub)
n_fsub_streamlines = np.shape(fsub_streamlines)[0]
n_fsub_streamlines = len(fsub_streamlines)
fsub_color = np.array([fsub_color])
fsub_color = np.repeat(fsub_color, n_fsub_streamlines, axis=0)

Expand All @@ -88,7 +88,7 @@ def visualize_sub_bundles(
orig_streamlines = orig_streamlines.streamlines

# Repeat the color matrix for each streamline (orig)
n_orig_streamlines = np.shape(orig_streamlines)[0]
n_orig_streamlines = len(orig_streamlines)
orig_color = np.array([orig_color])
orig_color = np.repeat(orig_color, n_orig_streamlines, axis=0)

Expand Down Expand Up @@ -124,16 +124,16 @@ def visualize_sub_bundles(
figure.add(slice_actor)

# make a copy to make a sagittal slice
saggital_actor = slice_actor.copy()
sagittal_actor = slice_actor.copy()

# calculate where to display the image based on the offset
saggital_offset = (
saggital_actor.shape[0] - (saggital_actor.shape[0] // 2)
) * saggital_offset
saggital_actor.display(
saggital_actor.shape[0] // 2 + int(saggital_offset), None, None
sagittal_offset = (
sagittal_actor.shape[0] - (sagittal_actor.shape[0] // 2)
) * sagittal_offset
sagittal_actor.display(
sagittal_actor.shape[0] // 2 + int(sagittal_offset), None, None
)
figure.add(saggital_actor)
figure.add(sagittal_actor)

cam = figure.GetActiveCamera()
cam.SetViewUp(0, 0, 0)
Expand All @@ -152,13 +152,14 @@ def visualize_sub_bundles(
window.record(figure, out_path=(fname), size=(1200, 900))


def define_streamline_actor(tck, reference_anatomy, color):
def define_streamline_actor(tck, reference_anatomy, color,opacity=1):
"""Takes in tck reference anatomy files and outputs a fury streamline actor.
Parameters
==========
tck: streamline to plot (.tck)
reference_anatomy: Reference anatomy (.nii.gz)
color = color to plot streamlines as ([R,B,G])
opacity = how opaque to plot the streamlines (0-1)

Outputs
=======
Expand All @@ -172,13 +173,13 @@ def define_streamline_actor(tck, reference_anatomy, color):
streamlines = streamlines.streamlines

# get number of streamlines in order to make them the same color
n_streamlines = np.shape(streamlines)[0]
n_streamlines = len(streamlines)
color = np.array([color])
color = np.repeat(color, n_streamlines, axis=0)

# make the streamline actor
if n_streamlines > 0:
streamlines_actor = actor.line(streamlines, color, opacity=0.1)
streamlines_actor = actor.line(streamlines, color, opacity=opacity)
else:
streamlines_actor = None
return streamlines_actor
Expand Down Expand Up @@ -250,8 +251,9 @@ def visualize_bundles(
interactive,
slice_actor=None,
roi_actor=None,
camera_angle="sagittal",
hemi="lh",
roll_val=0,
camera_angle="sagittal",
filename=None,
):

Expand All @@ -262,10 +264,10 @@ def visualize_bundles(
==========
streamline_actor: list of fury streamline actors (e.g., [output] of define_streamline_actor)
interactive: whether you want an interactive window to pop up
camera_angle: angle of the camera (options: 'saggital' or 'axial', default: 'saggital')
hemi = hemisphere (default: 'lh')
roi_actor: list of fury roi actors (e.g., [output] of define roi_actor)
slice_actor: list fury slice actors (e.g., [output] of define_slice_actor)
camera_angle: view for camera ("sagittal" or "axial", default = "sagittal")
filename: fullpath to save the image (e.g., .png)

note: for plotting multiple streamlines, rois, or slices the function
Expand All @@ -292,7 +294,7 @@ def visualize_bundles(

cam = figure.GetActiveCamera()
cam.SetViewUp(0, 0, 0)

if camera_angle == "sagittal":
if hemi == "lh":
cam.Yaw(270)
Expand Down