fastplotlib · kushalkolar · Apr 12, 2025 · Apr 12, 2025 · Apr 12, 2025 · Apr 12, 2025
@@ -57,6 +57,7 @@
     "subsection_order": ExplicitOrder(
         [
             "../../examples/image",
+            "../../examples/image_volume",
             "../../examples/heatmap",
             "../../examples/image_widget",
             "../../examples/gridplot",

@@ -0,0 +1,2 @@
+Image Volume Examples
+=====================
@@ -0,0 +1,83 @@
+"""
+Volume movie
+============
+
+"""
+
+# test_example = false
+# sphinx_gallery_pygfx_docs = 'screenshot'
+
+import numpy as np
+from scipy.ndimage import gaussian_filter
+import fastplotlib as fpl
+from tqdm import tqdm
+
+
+def generate_data(p=1, noise=.5, T=256, framerate=30, firerate=2., ):
+    gamma = np.array([.9])
+    dims = (128, 128, 30)  # size of image
+    sig = (4, 4, 2)  # neurons size
+    bkgrd = 10
+    N = 150  # number of neurons
+    np.random.seed(0)
+    centers = np.asarray([[np.random.randint(s, x - s)
+                           for x, s in zip(dims, sig)] for i in range(N)])
+    Y = np.zeros((T,) + dims, dtype=np.float32)
+    trueSpikes = np.random.rand(N, T) < firerate / float(framerate)
+    trueSpikes[:, 0] = 0
+    truth = trueSpikes.astype(np.float32)
+    for i in tqdm(range(2, T)):
+        if p == 2:
+            truth[:, i] += gamma[0] * truth[:, i - 1] + gamma[1] * truth[:, i - 2]
+        else:
+            truth[:, i] += gamma[0] * truth[:, i - 1]
+    for i in tqdm(range(N)):
+        Y[:, centers[i, 0], centers[i, 1], centers[i, 2]] = truth[i]
+    tmp = np.zeros(dims)
+    tmp[tuple(np.array(dims)//2)] = 1.
+    print("gaussing filtering")
+    z = np.linalg.norm(gaussian_filter(tmp, sig).ravel())
+
+    print("finishing")
+    Y = bkgrd + noise * np.random.randn(*Y.shape) + 10 * gaussian_filter(Y, (0,) + sig) / z
+
+    return Y
+
+
+voldata = generate_data()
+
+fig = fpl.Figure(cameras="3d", controller_types="orbit", size=(700, 560))
+
+vmin, vmax = fpl.utils.quick_min_max(voldata)
+
+volume = fig[0, 0].add_image_volume(voldata[0], vmin=vmin, vmax=vmax, interpolation="linear", cmap="gnuplot2")
+
+hlut = fpl.HistogramLUTTool(voldata, volume)
+
+fig[0, 0].docks["right"].size = 100
+fig[0, 0].docks["right"].controller.enabled = False
+fig[0, 0].docks["right"].add_graphic(hlut)
+fig[0, 0].docks["right"].auto_scale(maintain_aspect=False)
+
+fig.show()
+
+
+i = 0
+def update():
+    global i
+
+    volume.data = voldata[i]
+
+    i += 1
+    if i == voldata.shape[0]:
+        i = 0
+
+
+fig.add_animations(update)
+
+
+# NOTE: fpl.loop.run() should not be used for interactive sessions
+# See the "JupyterLab and IPython" section in the user guide
+if __name__ == "__main__":
+    print(__doc__)
+    fpl.loop.run()
@@ -0,0 +1,29 @@
+"""
+Volume Mip mode
+===============
+
+View a volume, uses the fly controller by default so you can fly around the scene using WASD keys and the mouse:
+https://docs.pygfx.org/stable/_autosummary/controllers/pygfx.controllers.FlyController.html#pygfx.controllers.FlyController
+"""
+
+# test_example = false
+# sphinx_gallery_pygfx_docs = 'screenshot'
+
+import numpy as np
+import fastplotlib as fpl
+import imageio.v3 as iio
+
+voldata = iio.imread("imageio:stent.npz").astype(np.float32)
+
+fig = fpl.Figure(cameras="3d", controller_types="orbit", size=(700, 560))
+
+fig[0, 0].add_image_volume(voldata, mode="iso")
+
+fig.show()
+
+
+# NOTE: fpl.loop.run() should not be used for interactive sessions
+# See the "JupyterLab and IPython" section in the user guide
+if __name__ == "__main__":
+    print(__doc__)
+    fpl.loop.run()
@@ -0,0 +1,56 @@
+"""
+Volume non-orthogonal slicing
+=============================
+
+Perform non-orthogonal slicing of image volumes.
+
+For an example with UI sliders see the "Volume modes" example.
+"""
+
+# test_example = true
+# sphinx_gallery_pygfx_docs = 'screenshot'
+
+import numpy as np
+import fastplotlib as fpl
+import imageio.v3 as iio
+
+
+voldata = iio.imread("imageio:stent.npz").astype(np.float32)
+
+fig = fpl.Figure(
+    cameras="3d",
+    controller_types="orbit",
+    size=(700, 560)
+)
+
+vol = fig[0, 0].add_image_volume(voldata, mode="slice")
+
+# a plane is defined by ax + by + cz + d = 0
+# the plane property sets (a, b, c, d)
+vol.plane = (0, 0.5, 0.5, -70)
+
+# just a pre-saved camera state to view the plot area
+state = {
+    "position": np.array([-160.0,  105.0,  205.0]),
+    "rotation": np.array([-0.1, -0.6, -0.07,  0.8]),
+    "scale": np.array([1., 1., 1.]),
+    "reference_up": np.array([0., 1., 0.]),
+    "fov": 50.0,
+    "width": 128.0,
+    "height": 128.0,
+    "depth": 315,
+    "zoom": 0.75,
+    "maintain_aspect": True,
+    "depth_range": None
+}
+
+fig.show()
+
+fig[0, 0].camera.set_state(state)
+
+
+# NOTE: fpl.loop.run() should not be used for interactive sessions
+# See the "JupyterLab and IPython" section in the user guide
+if __name__ == "__main__":
+    print(__doc__)
+    fpl.loop.run()
@@ -0,0 +1,75 @@
+"""
+Volume share buffers
+====================
+
+Share the data buffer between two graphics. This example creates one Graphic using MIP rendering, and another graphic
+to display a slice of the volume. We can share the data buffer on the GPU between these graphics.
+"""
+
+# test_example = true
+# sphinx_gallery_pygfx_docs = 'screenshot'
+
+from imgui_bundle import imgui
+import fastplotlib as fpl
+from fastplotlib.ui import EdgeWindow
+import imageio.v3 as iio
+from skimage.filters import gaussian
+
+
+data = iio.imread("imageio:stent.npz")
+
+
+figure = fpl.Figure(
+    cameras="3d",
+    controller_types="orbit",
+    size=(700, 560),
+)
+
+# MIP rendering is the default `mode`
+vol_mip = figure[0, 0].add_image_volume(gaussian(data, sigma=2.0))
+
+# make another graphic to show a slice of the volume
+vol_slice = figure[0, 0].add_image_volume(
+    vol_mip.data,  # pass the data property from the previous volume so they share the same buffer on the GPU
+    mode="slice",
+    plane=(0, -0.5, -0.5, 50),
+    offset=(150, 0, 0)  # place the graphic at x=150
+)
+
+
+class GUI(EdgeWindow):
+    def __init__(self, figure, title="change data buffer", location="right", size=200):
+        super().__init__(figure, title=title, location=location, size=size)
+        self._sigma = 2
+
+    def update(self):
+        changed, self._sigma = imgui.slider_int("sigma", v=self._sigma, v_min=0, v_max=5)
+
+        if changed:
+            vol_mip.data = gaussian(data, sigma=self._sigma)
+            vol_mip.reset_vmin_vmax()
+            vol_slice.reset_vmin_vmax()
+
+        imgui.text("Select plane defined by:\nax + by + cz + d = 0")
+        _, a = imgui.slider_float("a", v=vol_slice.plane[0], v_min=-1, v_max=1.0)
+        _, b = imgui.slider_float("b", v=vol_slice.plane[1], v_min=-1, v_max=1.0)
+        _, c = imgui.slider_float("c", v=vol_slice.plane[2], v_min=-1, v_max=1.0)
+
+        largest_dim = max(vol_slice.data.value.shape)
+        _, d = imgui.slider_float(
+            "d", v=vol_slice.plane[3], v_min=0, v_max=largest_dim * 2
+        )
+
+        vol_slice.plane = (a, b, c, d)
+
+gui = GUI(figure)
+figure.add_gui(gui)
+
+figure.show()
+
+
+# NOTE: fpl.loop.run() should not be used for interactive sessions
+# See the "JupyterLab and IPython" section in the user guide
+if __name__ == "__main__":
+    print(__doc__)
+    fpl.loop.run()
@@ -0,0 +1,64 @@
+"""
+Volume non-orthogonal slicing animation
+=======================================
+
+Perform non-orthogonal slicing of image volumes.
+
+For an example with UI sliders see the "Volume modes" example.
+"""
+
+# test_example = false
+# sphinx_gallery_pygfx_docs = 'animate 8s'
+
+import numpy as np
+import fastplotlib as fpl
+import imageio.v3 as iio
+
+
+voldata = iio.imread("imageio:stent.npz").astype(np.float32)
+
+fig = fpl.Figure(
+    cameras="3d",
+    controller_types="orbit",
+    size=(700, 560)
+)
+
+vol = fig[0, 0].add_image_volume(voldata, mode="slice")
+
+# a plane is defined by ax + by + cz + d = 0
+# the plane property sets (a, b, c, d)
+vol.plane = (0, 0.5, 0.5, -20)
+
+# just a pre-saved camera state to view the plot area
+state = {
+    "position": np.array([-110.0,  160.0,  240.0]),
+    "rotation": np.array([-0.25, -0.5, -0.15,  0.85]),
+    "scale": np.array([1., 1., 1.]),
+    "reference_up": np.array([0., 1., 0.]),
+    "fov": 50.0,
+    "width": 128.0,
+    "height": 128.0,
+    "depth": 315,
+    "zoom": 0.75,
+    "maintain_aspect": True,
+    "depth_range": None
+}
+
+def update():
+    # increase d by 1
+    vol.plane = (0, 0.5, 0.5, vol.plane[-1] - 1)
+    if vol.plane[-1] < -200:
+        vol.plane = (0, 0.5, 0.5, -20)
+
+fig[0, 0].add_animations(update)
+
+fig.show()
+
+fig[0, 0].camera.set_state(state)
+
+
+# NOTE: fpl.loop.run() should not be used for interactive sessions
+# See the "JupyterLab and IPython" section in the user guide
+if __name__ == "__main__":
+    print(__doc__)
+    fpl.loop.run()