Add scripts to make movies from diffraction data

scripts/make_interval_movie.py

@@ -0,0 +1,77 @@
+import sys, os
+
+import subprocess as sp
+import glob
+
+from instamatic.formats import read_tiff
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+def printer(data):
+    """Print things to stdout on one line dynamically"""
+    sys.stdout.write("\r\x1b[K"+data.__str__())
+    sys.stdout.flush()
+
+
+def tiff2png(interval=10, drc="movie"):
+    fns1 = glob.glob("tiff\*.tif?")
+    fns2 = glob.glob("tiff_image\*.tif?")
+
+    if not os.path.exists(drc):
+        os.mkdir(drc)
+
+    j = 0
+
+    for i, fn1 in enumerate(fns1):
+        if i % (interval - 1) == 0:
+            try:
+                fn2 = fns2[j]
+            except IndexError:
+                break
+            im2, h2 = read_tiff(fn2)
+
+            im2 = im2[150:320, 150:320]
+
+            j += 1
+
+        im1, h1 = read_tiff(fn1)
+
+        fig, (ax1, ax2) = plt.subplots(1,2)
+
+        ax1.imshow(im1, vmax=np.percentile(im1, 99.0), cmap="gray")
+        ax2.imshow(im2, vmax=np.percentile(im1, 99.5), cmap="gray")
+
+        ax1.axis("off")
+        ax2.axis("off")
+
+        plt.tight_layout()
+
+        plt.savefig(f"{drc}/{i:05d}.png", bbox_inches='tight', pad_inches=0, dpi=200)
+        plt.close()
+
+        print(fn1, fn2)
+
+    return drc
+
+
+def main():
+    drc = tiff2png()
+
+    out = "movie.mp4"
+
+    cmd = f"ffmpeg -r 20 -i {drc}/%05d.png -s:v 516x516 -c:v libx264 -profile:v high -crf 20 -pix_fmt yuv420p -r 24 -y movie.mp4".split()
+
+    print()
+    print(" ".join(cmd))
+    print()
+
+    sp.call(cmd)
+    try:
+        os.startfile(out) # windows
+    except AttributeError:
+        sp.call(['open', out]) # macos
+        # subprocess.call(['xdg-open', out]) # linux
+
+if __name__ == '__main__':
+    main()

scripts/make_serialed_movie.py

@@ -0,0 +1,72 @@
+import os
+import matplotlib.pyplot as plt
+from instamatic.formats import read_image
+from instamatic.tools import get_files
+import tqdm, glob
+import numpy as np
+
+plt.rcParams["figure.figsize"] = 10, 10
+plt.rcParams["image.cmap"] = "gray"
+
+fns = get_files("images\image*.h5")
+
+fontdict = {"fontsize": 30}
+vmax_im = 500
+vmax_diff = 1500
+vmin_diff = 0
+
+save = True
+
+number = 0
+
+if not os.path.isdir("movie"):
+    os.mkdir("movie")
+
+for i, fn in enumerate(tqdm.tqdm(fns)):
+    dps = glob.glob(fn.replace("images", "data").replace(".h5", "_*.h5"))
+
+    im, h_im = read_image(fn)
+
+    crystal_coords = np.array(h_im["exp_crystal_coords"])
+
+    for j, dp in enumerate(dps):
+        try:
+            diff, h_diff = read_image(dp)
+        except:
+            print("fail")
+            continue
+
+        x,y = crystal_coords[j]
+
+        fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(21.5, 10), sharex=True, sharey=True)
+
+        ax1.imshow(im, vmax=np.percentile(im, 99.5))
+        ax1.axis('off')
+        ax1.scatter(crystal_coords[:,1], crystal_coords[:,0], marker=".", color="red", s=100)
+        ax1.scatter(y,x, marker="o", color="red", s=200)
+        ax1.set_title(fn, fontdict)
+        ax2.imshow(diff, vmin=vmin_diff, vmax=vmax_diff)
+
+        ax2.axis('off')
+        ax2.set_title(dp, fontdict)
+
+        plt.tight_layout()
+
+        # out = dp.replace("h5", "png").replace("data\\","movie\\")
+        out = "movie\image_{:04d}.png".format(number)
+        number += 1
+
+        if save:
+            plt.savefig(out)
+        else:
+            plt.show()
+        plt.close()
+
+print("Running ffmpeg...")
+
+import subprocess as sp
+cmd = "ffmpeg -r 5 -i movie/image_%04d.png -s:v 1280x720 -c:v libx264 -profile:v high -crf 20 -pix_fmt yuv420p -r 24 -y movie/compilation.mp4".split()
+sp.call(cmd)
+
+print("Done")
+