[bench] add nifti file benchmark

Author: fangq

benchmark/benchcodecs.py

@@ -0,0 +1,73 @@
+"""
+    Speed benchmark for saving/loading numpy arrays using various compression codecs
+"""
+import jdata as jd
+import numpy as np
+import time
+import os
+
+print("jdata version:" + jd.__version__)
+
+codecs = [
+    "npy",
+    "npz",
+    "bjd",
+    "zlib",
+    "lzma",
+    "lz4",
+    "blosc2blosclz",
+    "blosc2lz4",
+    "blosc2lz4hc",
+    "blosc2zlib",
+    "blosc2zstd",
+]
+nthread = 8
+
+
+def benchmark(codec, x):
+    t0 = time.time()
+    ext = suffix
+    if codec == "npy":
+        ext = "." + codec
+        np.save("matrix_" + codec + ext, x)
+    elif codec == "npz":
+        ext = "." + codec
+        np.savez_compressed("matrix_" + codec + ext, x)
+    elif codec == "bjd":
+        ext = "." + codec
+        jd.save(x, "matrix_" + codec + ext, {"encode": False})
+    else:
+        jd.save(x, "matrix_" + codec + ext, {"compression": codec, "nthread": nthread})
+    dt = time.time() - t0  # saving time
+    res = {"codec": codec, "save": dt}
+    if codec == "npy":
+        y = np.load("matrix_" + codec + ext)
+    elif codec == "npz":
+        y = np.load("matrix_" + codec + ext)["arr_0"]
+    else:
+        y = jd.load("matrix_" + codec + ext, {"nthread": nthread})  # loading
+    res["sum"] = y.sum()
+    res["load"] = time.time() - t0 - dt  # loading time
+    res["size"] = os.path.getsize("matrix_" + codec + ext)
+    print(res)
+    return res
+
+
+## a highly compressible matrix
+x = np.eye(10000)
+
+## a less compressible random matrix
+# np.random.seed(0)
+# x = np.random.rand(2000,2000)
+
+print("\n- Testing binary JSON (BJData) files (.jdb) ...")
+
+suffix = ".jdb"
+res = list(map(benchmark, codecs, [x] * len(codecs)))
+# print(np.array(res))
+
+print("\n- Testing text-based JSON files (.jdt) ...")
+
+suffix = ".jdt"
+res = list(map(benchmark, codecs, [x] * len(codecs)))
+# print(np.array(res))

benchmark/benchnifti.py

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+import time
+import os
+import glob
+import urllib.request
+import zipfile
+import tempfile
+import shutil
+
+import nibabel as nib
+import numpy as np
+import jdata as jd
+
+tempdir = tempfile.mkdtemp()
+
+url = "https://github.com/neurolabusc/niivue-images/archive/refs/heads/main.zip"
+fname = os.path.join(tempdir, "niivue-images.zip")
+urllib.request.urlretrieve(url, fname)
+
+with zipfile.ZipFile(fname, "r") as zip_ref:
+    zip_ref.extractall(tempdir)
+
+niifiles = glob.glob(os.path.join(tempdir, "niivue-images-main/", "*.nii.gz"))
+
+for ff in niifiles:
+    # benchmark loading time from nib.load()
+    t0 = time.time()
+    img = nib.load(ff)
+    data = np.asarray(img.dataobj)
+    try:
+        s1 = np.sum(data).item()
+    except:
+        s1 = -1
+    dt1 = time.time() - t0
+
+    # benchmark loading time from jd.loadnifti()
+    t1 = time.time()
+    nii = jd.loadnifti(ff)
+    s2 = np.sum(nii["NIFTIData"]).item()
+    dt2 = time.time() - t1
+    jd.show(
+        {
+            "file": ff,
+            "nib": [list(data.shape), data.dtype.str, s1],
+            "jd": [list(nii["NIFTIData"].shape), nii["NIFTIData"].dtype.str, s2],
+            "nibtime": dt1,
+            "jdtime": dt2,
+            "speedup": dt1 / dt2,
+        }
+    )
+
+try:
+    shutil.rmtree(tempdir)
+except OSError as e:
+    print(f"unable to delete the temporary folder: {e}")