Merge 7ec82b4 into ba578ff

examples/plotting/README.rst

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+Plotting Data using Matplotlib
+==============================
+Below is a gallery of examples on how to make nice publication quality plots and
+figures using Matplotlib.

examples/plotting/making_a_gif.py

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+"""
+============
+Making a GIF
+============
+
+In this example we will show how to use matplotlib to create a GIF from a 4D STEM
+dataset.  This is useful for quickly showing a dataset in a presentation or
+publication.
+"""
+
+import pyxem as pxm
+import matplotlib.pyplot as plt
+from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
+import matplotlib.font_manager as fm
+import numpy as np
+
+fontprops = fm.FontProperties(size=18, family="serif")
+family = "serif"
+
+# Load the data
+tilt = pxm.data.tilt_boundary_data()
+
+
+# Define some functions for plotting
+def plot_index(
+    signal,
+    index,
+    navigator,
+    ax1=None,
+    ax2=None,
+    fig=None,
+    image1=None,
+    image2=None,
+    cmap="hot",
+):
+    """
+    Plot the signal at some index along with a partial navigator.  This is
+    useful when making GIFs showing a raster across some entire dataset.
+    """
+    if ax1 is None:
+        fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 6))
+
+    partial_nav = navigator.data.copy()
+    partial_nav[index[0] + 1 :, :] = np.nan
+    partial_nav[index[0], index[1] :] = np.nan
+    if image1 is None:
+        max_val = np.max(navigator.data)
+        min_val = np.min(navigator.data)
+
+        image1 = ax1.imshow(
+            partial_nav,
+            cmap="gray",
+            extent=signal.axes_manager.navigation_extent,
+            vmax=max_val,
+            vmin=min_val,
+        )
+        ax1.axis("on")
+        ax1.set_title("Virtual Image", size=20, family=family)
+        ax1.set_ylabel("y axis (nm)", size=16, family=family)
+        ax1.set_xlabel("x axis (nm)", size=16, family=family)
+        ax1.set_xticks([])
+        ax1.set_yticks([])
+        scalebar = AnchoredSizeBar(
+            ax1.transData,
+            2,
+            "2 nm",
+            "lower left",
+            pad=0.8,
+            color="w",
+            frameon=False,
+            size_vertical=0.5,
+            fontproperties=fontprops,
+        )
+
+        ax1.add_artist(scalebar)
+    else:  # Update the image
+        image1.set_data(partial_nav)
+
+    if image2 is None:
+        image2 = ax2.imshow(
+            signal.inav[index[1], index[0]].data,
+            cmap=cmap,
+            extent=signal.axes_manager.signal_extent,
+        )
+        ax2.axis("on")
+        ax2.set_title("Diffraction Pattern", size=20, family=family)
+        ax2.set_ylabel("k$_y$ axis ($\AA^{-1}$)", size=16, family=family)
+        ax2.set_xlabel("k$_x$ axis ($\AA^{-1}$)", size=16, family=family)
+        ax2.set_xticks([])
+        ax2.set_yticks([])
+        scalebar2 = AnchoredSizeBar(
+            ax2.transData,
+            1,
+            "1 $\AA^{-1}$",
+            "lower left",
+            pad=0.8,
+            color="white",
+            frameon=False,
+            size_vertical=0.025,
+            fontproperties=fontprops,
+        )
+
+        ax2.add_artist(scalebar2)
+    else:
+        image2.set_data(signal.inav[index[1], index[0]].data)
+    return ax1, ax2, image1, image2, fig
+
+
+# %%
+# Plot the navigator and the diffraction pattern
+
+navigator = tilt.sum(axis=(2, 3))
+plot_index(tilt, index=(4, 4), navigator=navigator)
+
+# %%
+# Make this into a matplotlib animation:
+
+
+def animate_4DSTEM(
+    signal,
+    navigator=None,
+    step=1,
+):
+    if navigator is None:
+        navigator = signal.sum(axis=(2, 3))
+
+    ax1, ax2, image1, image2, fig = plot_index(
+        signal, index=(0, 0), navigator=navigator
+    )
+    indexes = list(np.ndindex(signal.axes_manager.navigation_shape[::-1]))
+    indexes = indexes[::step]
+
+    def animate(i):
+        plot_index(
+            signal,
+            index=(indexes[i][0], indexes[i][1]),
+            ax1=ax1,
+            ax2=ax2,
+            image1=image1,
+            image2=image2,
+            fig=fig,
+            navigator=navigator,
+        )
+
+    ani = FuncAnimation(fig, animate, frames=len(indexes), interval=10, repeat=False)
+
+    ani.save(
+        "4DSTEM.gif",
+    )
+
+
+animate_4DSTEM(tilt)
+
+# %%