Python 3.13

.github/workflows/docbuild.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo
@@ -33,13 +33,16 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install .[all]
-        sudo apt-get install -y xvfb
+        sudo apt-get install -y \
+              libgl1 \
+              libglx-mesa0 \
+              libegl1 \
+              libgl1-mesa-dri \
+              libvulkan1 \
+              mesa-vulkan-drivers \
+              vulkan-tools
     - name: Build docs
-      env:
-        XVFB: 1
-        DISPLAY: :99
       run: |
-        Xvfb :99 -screen 0 1280x1024x24 &
         cd docs
         make html
     - name: Upload docs

.github/workflows/nightly_anisotropic_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo

.github/workflows/nightly_basic_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo

.github/workflows/nightly_custom_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo
@@ -28,10 +28,17 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install .[dev,fury,afqbrowser,nn]
+        sudo apt-get install -y \
+              libgl1 \
+              libglx-mesa0 \
+              libegl1 \
+              libgl1-mesa-dri \
+              libvulkan1 \
+              mesa-vulkan-drivers \
+              vulkan-tools
     - name: Lint
       run: |
         flake8 --ignore N802,N806,W503 --select W504 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`
     - name: Test
       run: |
-        export TEST_WITH_XVFB=true
         cd && mkdir for_test && cd for_test && pytest --pyargs AFQ --cov-report term-missing --cov=AFQ -m "nightly_custom" --durations=0

.github/workflows/nightly_reco80_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo

.github/workflows/nightly_reco_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo

.github/workflows/nightly_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo

.github/workflows/test.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         nibabel-pre: [true, false]
 
     steps:

AFQ/_fixes.py

@@ -1,10 +1,13 @@
 import logging
 import math
+import tempfile
+from math import radians
 
 import numpy as np
 from dipy.data import default_sphere
 from dipy.reconst.gqi import squared_radial_component
 from dipy.tracking.streamline import set_number_of_points
+from PIL import Image
 from scipy.linalg import blas, pinvh
 from scipy.special import gammaln, lpmv
 from tqdm import tqdm
@@ -238,3 +241,44 @@ def gaussian_weights(bundle, n_points=100, return_mahalnobis=False, stat=np.mean
     weights = 1 / weights
     # Normalize before returning, so that the weights in each node sum to 1:
     return weights / np.sum(weights, 0)
+
+
+def make_gif(show_m, out_path, n_frames=36, az_ang=-10):
+    """
+    Make a video from a Fury Show Manager.
+
+    Parameters
+    ----------
+    show_m : Fury Show Manager
+        The Fury Show Manager to use for rendering.
+
+    out_path : str
+        The name of the output file.
+
+    n_frames : int
+        The number of frames to render.
+        Default: 36
+
+    az_ang : float
+        The angle to rotate the camera around the
+        z-axis for each frame, in degrees.
+        Default: -10
+    """
+    video = []
+
+    show_m.render()
+    show_m.window.draw()
+
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        for ii in tqdm(range(n_frames), desc="Generating GIF"):
+            frame_fname = f"{tmp_dir}/{ii}.png"
+            show_m.screens[0].controller.rotate((radians(az_ang), 0), None)
+            show_m.render()
+            show_m.window.draw()
+            show_m.snapshot(frame_fname)
+            video.append(frame_fname)
+
+        video = [Image.open(frame) for frame in video]
+        video[0].save(
+            out_path, save_all=True, append_images=video[1:], duration=300, loop=1
+        )

AFQ/api/group.py

@@ -836,7 +836,6 @@ def group_montage(self, bundle_name, size, view, direc, slice_pos=None):
 
         t1_dict = self.export("t1_masked", collapse=False)
         viz_backend_dict = self.export("viz_backend", collapse=False)
-        b0_backend_dict = self.export("b0", collapse=False)
         dwi_affine_dict = self.export("dwi_affine", collapse=False)
         bundles_dict = self.export("bundles", collapse=False)
         best_scalar_dict = self.export(best_scalar, collapse=False)
@@ -847,7 +846,6 @@ def group_montage(self, bundle_name, size, view, direc, slice_pos=None):
             this_sub = self.valid_sub_list[ii]
             this_ses = self.valid_ses_list[ii]
             viz_backend = viz_backend_dict[this_sub][this_ses]
-            b0 = b0_backend_dict[this_sub][this_ses]
             t1 = nib.load(t1_dict[this_sub][this_ses])
             dwi_affine = dwi_affine_dict[this_sub][this_ses]
             bundles = bundles_dict[this_sub][this_ses]
@@ -913,17 +911,15 @@ def group_montage(self, bundle_name, size, view, direc, slice_pos=None):
 
                 pio.kaleido.scope._shutdown_kaleido()
             else:
-                from dipy.viz import window
-
-                direc = np.fromiter(eye.values(), dtype=int)
-                data_shape = np.asarray(nib.load(b0).get_fdata().shape)
-                figure.set_camera(
-                    position=direc * data_shape,
-                    focal_point=data_shape // 2,
-                    view_up=(0, 0, 1),
+                from fury import window
+
+                from AFQ.viz.fury_backend import scene_rotate_forward
+
+                show_m = window.ShowManager(
+                    scene=figure, window_type="offscreen", size=(600, 600)
                 )
-                figure.zoom(0.5)
-                window.snapshot(figure, fname=this_fname, size=(600, 600))
+                scene_rotate_forward(show_m, figure)
+                show_m.snapshot(this_fname)
 
         def _save_file(curr_img, curr_file_num):
             save_path = op.abspath(

AFQ/api/participant.py

@@ -5,7 +5,6 @@
 from time import time
 
 import nibabel as nib
-import numpy as np
 from PIL import Image, ImageDraw, ImageFont
 from tqdm import tqdm
 
@@ -317,17 +316,15 @@ def participant_montage(self, images_per_row=2):
 
                 pio.kaleido.scope._shutdown_kaleido()
             else:
-                from dipy.viz import window
-
-                direc = np.fromiter(eye.values(), dtype=int)
-                data_shape = np.asarray(nib.load(self.export("b0")).get_fdata().shape)
-                figure.set_camera(
-                    position=direc * data_shape,
-                    focal_point=data_shape // 2,
-                    view_up=(0, 0, 1),
+                from fury import window
+
+                from AFQ.viz.fury_backend import scene_rotate_forward
+
+                show_m = window.ShowManager(
+                    scene=figure, window_type="offscreen", size=(600, 600)
                 )
-                figure.zoom(0.5)
-                window.snapshot(figure, fname=this_fname, size=(600, 600))
+                scene_rotate_forward(show_m, figure)
+                show_m.snapshot(this_fname)
 
         def _save_file(curr_img):
             save_path = op.abspath(

AFQ/tasks/viz.py

@@ -385,34 +385,22 @@ def plot_tract_profiles(base_fname, output_dir, scalars, segmentation_imap):
 
 
 @immlib.calc("viz_backend")
-def init_viz_backend(viz_backend_spec="plotly_no_gif", virtual_frame_buffer=False):
+def init_viz_backend(viz_backend_spec="plotly_no_gif"):
     """
     An instance of the `AFQ.viz.utils.viz_backend` class.
 
     Parameters
     ----------
-    virtual_frame_buffer : bool, optional
-        Whether to use a virtual frame buffer. This is  if
-        generating GIFs in a headless environment.
-        Default: False
     viz_backend_spec : str, optional
         Which visualization backend to use.
         See Visualization Backends page in documentation for details
         https://tractometry.org/pyAFQ/reference/viz_backend.html
         One of {"fury", "plotly", "plotly_no_gif"}.
         Default: "plotly_no_gif"
     """
-    if not isinstance(virtual_frame_buffer, bool):
-        raise TypeError("virtual_frame_buffer must be a bool")
     if "fury" not in viz_backend_spec and "plotly" not in viz_backend_spec:
         raise TypeError("viz_backend_spec must contain either 'fury' or 'plotly'")
 
-    if virtual_frame_buffer:
-        from xvfbwrapper import Xvfb
-
-        vdisplay = Xvfb(width=1280, height=1280)
-        vdisplay.start()
-
     return Viz(backend=viz_backend_spec.lower())
 
 

AFQ/tests/test_api.py

@@ -17,7 +17,6 @@
 import toml
 from dipy.io.streamline import load_tractogram
 from dipy.segment.metric import mdf
-from dipy.testing.decorators import xvfb_it
 from pandas.testing import assert_series_equal
 from pcollections._lazy import LazyError
 
@@ -272,7 +271,6 @@ def test_AFQ_no_derivs():
 
 
 @pytest.mark.nightly_custom
-@xvfb_it
 def test_AFQ_fury():
     tmpdir = tempfile.TemporaryDirectory()
     bids_path = op.join(tmpdir.name, "stanford_hardi")