improve HDF5, netcdf benchmark accuracy

Author: scivision

h5py_write_speed.py

@@ -16,7 +16,7 @@
 xb = random(SIZE) > 0.5  # mean ~ 0.5
 xbl = xb.tolist()
 
-with tempfile.NamedTemporaryFile() as fn:
+with tempfile.NamedTemporaryFile(suffix=".h5") as fn:
     with h5py.File(fn, "w") as h:
         tic = time()
         h["bool"] = xb
@@ -29,4 +29,5 @@
         # %% here's what nidaqmx gives us
         tic = time()
         h["listbool"] = xbl
-        print(f"{time()-tic:3e} sec. to write boolean from bool list")
+# outside context manager to help ensure HDF5 file is finalized
+print(f"{time()-tic:3e} sec. to write boolean from bool list")

netcdf_write_speed.py

@@ -19,7 +19,6 @@
 from numpy import packbits
 import xarray
 from time import time
-import os
 
 
 SIZE = (3, 200000)  # arbitrary size to test
@@ -30,23 +29,20 @@
 Xb = xarray.DataArray(xb, name="bool")
 
 
-with tempfile.NamedTemporaryFile(suffix=".nc", delete=False) as f:
+with tempfile.NamedTemporaryFile(suffix=".nc") as f:
     tic = time()
     Xb.to_netcdf(f.name, "w")
-os.unlink(f.name)
 print(f"{time()-tic:.3f} sec. to write boolean from Numpy bool")
 
-with tempfile.NamedTemporaryFile(suffix=".nc", delete=False) as f:
+with tempfile.NamedTemporaryFile(suffix=".nc") as f:
     tic = time()
     xi = packbits(xbl, axis=0)  # each column becomes uint8 BIG-ENDIAN
     Xi = xarray.DataArray(xi, name="uint8")
     Xi.to_netcdf(f.name, "w", engine="netcdf4")
-os.unlink(f.name)
 print(f"{time()-tic:.3f} sec. to write uint8")
 # %% here's what nidaqmx gives us
-with tempfile.NamedTemporaryFile(suffix=".nc", delete=False) as f:
+with tempfile.NamedTemporaryFile(suffix=".nc") as f:
     tic = time()
     Xbl = xarray.DataArray(xbl, name="listbool")
     Xbl.to_netcdf(f.name, "w")
-os.unlink(f.name)
 print(f"{time()-tic:.3f} sec. to write boolean from bool list")