scripts: add scale.py

Simple script to enable downsampling a Zarr array.

src/scripts/scale.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+import argparse
+import os
+import zarr
+from skimage.transform import pyramid_gaussian, pyramid_laplacian
+
+parser = argparse.ArgumentParser()
+parser.add_argument("input_array")
+parser.add_argument("output_directory")
+parser.add_argument(
+    "--method", choices=("gaussian", "laplacian"), default="gaussian"
+)
+parser.add_argument("--downscale", type=int, default=2)
+parser.add_argument("--max_layer", type=int, default=4)
+ns = parser.parse_args()
+
+if ns.method == "gaussian":
+    method = pyramid_gaussian
+else:
+    method = pyramid_laplacian
+
+
+# 1. Graph
+base = zarr.open_array(ns.input_array)
+pyramid = [base]
+pyramid.extend(method(base, downscale=2, max_layer=4, multichannel=False))
+
+assert not os.path.exists(ns.output_directory)
+store = zarr.DirectoryStore(ns.output_directory)
+grp = zarr.group(store)
+grp.create_dataset("base", data=base)
+
+
+# 2. Generate datasets
+series = []
+for i, dataset in enumerate(pyramid):
+    if i == 0:
+        path = "base"
+    else:
+        path = "%s" % i
+        grp.create_dataset(path, data=pyramid[i])
+    series.append({"path": path})
+
+# 3. Generate metadata block
+multiscales = []
+multiscale = {
+    "version": "0.1",
+    "name": "default",
+    "datasets": series,
+    "type": ns.method,
+}
+multiscales.append(multiscale)
+grp.attrs["multiscales"] = multiscales