ModuleNotFoundError: No module named 'utils'

[SnMtlb]

I get an error while running "from utils.visualization_utils import generate_anatomical_volume_figure" . How can I fix it? before that, I run "from dipy.tracking import utils" and it is ok.

[jhlegarreta]

@SnMtlb we had issues in the past making the utils module be imported correctly. Our current solution adds the path of the code to the PYTHONPATH in order to be able to import the module. See an example here.

Otherwise, if you are running this from an IDE, there should be no need to do this (the default settings of the project usually do this for you).

before that, I run "from dipy.tracking import utils" and it is ok.

Note that this is unrelated: importing dipy from anywhere works fine, as DIPY is a package (which is extensively tested), whereas ours is not.

[SnMtlb]

@jhlegarreta, thank you for your reply.

I still wondering how to solve the error that occurred while running "from utils.visualization_utils import generate_anatomical_volume_figure". DO I need to import packages? or try another kind of code? or add "from utils.visualization_utils" to my running path!

[jhlegarreta]

I still wondering how to solve the error that occurred while running "from utils.visualization_utils import generate_anatomical_volume_figure". DO I need to import packages? or try another kind of code? or add "from utils.visualization_utils" to my running path!

As said in the previous reply, you can

See an example here.

on how to likely solve the issue.

DO I need to import packages?

As said, our code is not shipped into some package that you can import.

or try another kind of code?

There is no other kind of code.

[yan519354443]

let me tell you the easiest way to solve this problem. JUST COPY THE FOLLOWING CODE TO THE PREVIOUS CELL BEFORE YOU CALL generate_anatomical_volume_figure IF YOU DO WHAT I SAY, DO NOT FORGET TO DELETE "from utils.visualization_utils import generate_anatomical_volume_figure"

import matplotlib.pyplot as plt

from fury import window

def generate_axial_superior_slice_view(scene, size=(600, 600), offscreen=True): """Generate an axial superior view of the scene. Arguments

scene : window.Scene
    Scene to be transformed.
size : Tuple (int, int)
    Size of each view.
offscreen : bool
    `True` to prevent the scene window from being displayed.
Returns
-------
    A `window.Scene` instance seen from an axial superior view.
"""

axial_scene = window.snapshot(scene, size=size, offscreen=offscreen)

return axial_scene

def generate_sagittal_right_view(scene, size=(600, 600), offscreen=True): """Generate a sagittal right view of the scene. Arguments

scene : window.Scene
    Scene to be transformed.
size : Tuple (int, int)
    Size of each view.
offscreen : bool
    `True` to prevent the scene window from being displayed.
Returns
-------
    A `window.Scene` instance seen from a sagittal right view.
"""

scene.yaw(90)
scene.roll(-90)
scene.reset_camera()
sagittal_scene = window.snapshot(scene, size=size, offscreen=offscreen)

# Reset scene
scene.roll(90)
scene.yaw(-90)

return sagittal_scene

def generate_coronal_anterior_view(scene, size=(600, 600), offscreen=True): """Generate a coronal anterior view of the scene. Arguments

scene : window.Scene
    Scene to be transformed.
size : Tuple (int, int)
    Size of each view.
offscreen : bool
    `True` to prevent the scene window from being displayed.
Returns
-------
    A `window.Scene` instance seen from a coronal anterior view.
"""

scene.yaw(90)
scene.pitch(-90)
scene.reset_camera()
coronal_scene = window.snapshot(scene, size=size, offscreen=offscreen)

# Reset scene
scene.pitch(90)
scene.yaw(-90)

return coronal_scene

def generate_anatomical_volume_views(*actors, size=(600, 600)): """Generate anatomical (coronal anterior, sagittal right and axial superior) views of the actor(s). Arguments

actors : vtkActor
    Actor(s) to be displayed.
size : Tuple (int, int)
    Size of each view.
Returns
-------
    A tuple of `window.Scene` instances containing the anatomical views of
    the actor(s).
"""

offscreen = True

# Create the scene
scene = window.Scene()

# Add the each data volume to the scene
for actor in actors:
    scene.add(actor)

axial_scene = generate_axial_superior_slice_view(
    scene, size=size, offscreen=offscreen)

sagittal_scene = generate_sagittal_right_view(
    scene, size=size, offscreen=offscreen)

coronal_scene = generate_coronal_anterior_view(
    scene, size=size, offscreen=offscreen)

return coronal_scene, sagittal_scene, axial_scene

def generate_anatomical_slice_views( slices, *actors, size=(600, 600)): """Generate anatomical (coronal anterior, sagittal right and axial superior) views of the actor(s) at the provided slices. Arguments

slices: Tuple (int, int, int)
    Image data to be displayed.
actors : vtkActor
    Actor(s) to be displayed.
size : Tuple (int, int)
    Size of each view.
Returns
-------
    A tuple of `window.Scene` instances containing the anatomical views of
    the actor(s).
"""

offscreen = True

# Create the scene
scene = window.Scene()

# Add the each data volume to the scene
for actor in actors:
    scene.add(actor)

# Set the actor to the axial slice to be shown
for actor in actors:
    actor.display(z=slices[2])

axial_scene = generate_axial_superior_slice_view(
    scene, size=size, offscreen=offscreen)

# Set the actor to the sagittal slice to be shown
for actor in actors:
    actor.display(x=slices[0])

sagittal_scene = generate_sagittal_right_view(
    scene, size=size, offscreen=offscreen)

# Set the actor to the coronal slice to be shown
for actor in actors:
    actor.display(y=slices[1])

coronal_scene = generate_coronal_anterior_view(
    scene, size=size, offscreen=offscreen)

return coronal_scene, sagittal_scene, axial_scene

def generate_figure( scene_titles, *scenes, cmap=None, figsize=(20, 20)): """Generate the figure containing the scenes. Arguments

scene_titles : list
    Scene title.
*scenes : ndarray
    Scene data to be displayed.
cmap : str
    Colormap to be applied to the overlay.
figsize : Tuple (int, int)
    Subfigure size.
Returns
-------
    A `Figure` instance containing the provided scene(s).
"""

origin = "lower"

scene_count = len(scenes)

fig, axes = plt.subplots(1, scene_count, figsize=figsize)

# Plot the scenes
for i, (scene, title) in enumerate(zip(scenes, scene_titles)):
    axes[i].imshow(scene, cmap=cmap, origin=origin)
    axes[i].axis("off")
    axes[i].set_title(title)

return fig

def generate_anatomical_volume_figure( *actors, cmap=None, viewsize=(600, 600), figsize=(20, 20)): """Generate anatomical (coronal anterior, sagittal right and axial superior) views of the actor(s). Arguments

actors : vtkActor
    Actor(s) to be displayed.
cmap : str
    Colormap to be applied to the overlay.
viewsize : Tuple (int, int)
    Composite figure size.
figsize : Tuple (int, int)
    Subfigure size.
Returns
-------
    A `Figure` instance containing the anatomical views of the actor(s).
"""

scene_titles = ["Coronal anterior", "Sagittal right", "Axial superior"]

coronal_scene, sagittal_scene, axial_scene = \
    generate_anatomical_volume_views(*actors, size=viewsize)

fig = generate_figure(
    scene_titles, coronal_scene, sagittal_scene, axial_scene, cmap=cmap,
    figsize=figsize)

return fig

def generate_anatomical_slice_figure( slices, *actors, cmap=None, viewsize=(600, 600), figsize=(20, 20)): """Generate anatomical (coronal anterior, sagittal right and axial superior) views of the actor(s) at the provided slices. Arguments

slices: Tuple (int, int, int)
    Image data to be displayed.
actors : vtkActor
    Actor(s) to be displayed.
cmap : str
    Colormap to be applied to the overlay.
viewsize : Tuple (int, int)
    Composite figure size.
figsize : Tuple (int, int)
    Subfigure size.
Returns
-------
    A `Figure` instance containing the anatomical views of the actor(s).
"""

scene_titles = ["Coronal anterior", "Sagittal right", "Axial superior"]

coronal_scene, sagittal_scene, axial_scene = \
    generate_anatomical_slice_views(slices, *actors, size=viewsize)

fig = generate_figure(
    scene_titles, coronal_scene, sagittal_scene, axial_scene, cmap=cmap,
    figsize=figsize)

return fig

[jhlegarreta]

@yan519354443 I kindly reported your comment as it seems inappropriate for a number of reasons.

@SnMtlb Although the suggested solution of copying and pasting the code would work, we want to avoid code duplication, and that is why we put the visualization methods into a separate module that can be imported. As said previously, the solution would be to add the path to the PYTHONPATH, as we do in our CI workflow.

[jhlegarreta]

I'm closing this as there have been no updates or reports whether the proposed solution has been tried. Can be re-opened if needed. Thanks.