improved python code

nexusformat · Jun 15, 2022 · 0aba057 · 0aba057
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diff --git a/manual/source/examples/h5py/external_example_write/external_example_write.py b/manual/source/examples/h5py/external_example_write/external_example_write.py
@@ -5,7 +5,7 @@
 This example is based on ``writer_2_1``.
 """
 
-import os
+from pathlib import Path
 import h5py
 import numpy
 
@@ -16,58 +16,53 @@
 # ---------------------------
 
 # get some data
-filename = os.path.join(os.path.dirname(__file__), "..", "simple_example.dat")
+filename = str(Path(__file__).parent.parent / "simple_example.dat")
 buffer = numpy.loadtxt(filename).T
 tthData = buffer[0]  # float[]
 countsData = numpy.asarray(buffer[1], "int32")  # int[]
 
 # put the angle data in an external (non-NeXus) HDF5 data file
-f = h5py.File(FILE_HDF5_ANGLES, "w")
-ds = f.create_dataset("angles", data=tthData)
-ds.attrs["units"] = "degrees"
-f.close()  # be CERTAIN to close the file
-
+with h5py.File(FILE_HDF5_ANGLES, "w") as f:
+    ds = f.create_dataset("angles", data=tthData)
+    ds.attrs["units"] = "degrees"
 
 # put the detector counts in an external HDF5 data file
 # with *incomplete* NeXus structure (no NXdata group)
-f = h5py.File(FILE_HDF5_COUNTS, "w")
-nxentry = f.create_group("entry")
-nxentry.attrs["NX_class"] = "NXentry"
-nxinstrument = nxentry.create_group("instrument")
-nxinstrument.attrs["NX_class"] = "NXinstrument"
-nxdetector = nxinstrument.create_group("detector")
-nxdetector.attrs["NX_class"] = "NXdetector"
-ds = nxdetector.create_dataset("counts", data=countsData)
-ds.attrs["units"] = "counts"
-# link the "two_theta" data stored in separate file
-local_addr = nxdetector.name + "/two_theta"
-f[local_addr] = h5py.ExternalLink(FILE_HDF5_ANGLES, "/angles")
-f.close()
+with h5py.File(FILE_HDF5_COUNTS, "w") as f:
+    nxentry = f.create_group("entry")
+    nxentry.attrs["NX_class"] = "NXentry"
+    nxinstrument = nxentry.create_group("instrument")
+    nxinstrument.attrs["NX_class"] = "NXinstrument"
+    nxdetector = nxinstrument.create_group("detector")
+    nxdetector.attrs["NX_class"] = "NXdetector"
+    ds = nxdetector.create_dataset("counts", data=countsData)
+    ds.attrs["units"] = "counts"
+    # link the "two_theta" data stored in separate file
+    local_addr = nxdetector.name + "/two_theta"
+    f[local_addr] = h5py.ExternalLink(FILE_HDF5_ANGLES, "/angles")
 
 # create a master NeXus HDF5 file
-f = h5py.File(FILE_HDF5_MASTER, "w")
-f.attrs["default"] = "entry"
-nxentry = f.create_group("entry")
-nxentry.attrs["NX_class"] = "NXentry"
-nxentry.attrs["default"] = "data"
-nxdata = nxentry.create_group("data")
-nxdata.attrs["NX_class"] = "NXdata"
-
-# link in the signal data
-local_addr = "/entry/data/counts"
-external_addr = "/entry/instrument/detector/counts"
-f[local_addr] = h5py.ExternalLink(FILE_HDF5_COUNTS, external_addr)
-nxdata.attrs["signal"] = "counts"
+with h5py.File(FILE_HDF5_MASTER, "w") as f:
+    f.attrs["default"] = "entry"
+    nxentry = f.create_group("entry")
+    nxentry.attrs["NX_class"] = "NXentry"
+    nxentry.attrs["default"] = "data"
+    nxdata = nxentry.create_group("data")
+    nxdata.attrs["NX_class"] = "NXdata"
 
-# link in the axes data
-local_addr = "/entry/data/two_theta"
-f[local_addr] = h5py.ExternalLink(FILE_HDF5_ANGLES, "/angles")
-nxdata.attrs["axes"] = "two_theta"
-nxdata.attrs["two_theta_indices"] = [
-    0,
-]
+    # link in the signal data
+    local_addr = "/entry/data/counts"
+    external_addr = "/entry/instrument/detector/counts"
+    f[local_addr] = h5py.ExternalLink(FILE_HDF5_COUNTS, external_addr)
+    nxdata.attrs["signal"] = "counts"
 
-local_addr = "/entry/instrument"
-f[local_addr] = h5py.ExternalLink(FILE_HDF5_COUNTS, "/entry/instrument")
+    # link in the axes data
+    local_addr = "/entry/data/two_theta"
+    f[local_addr] = h5py.ExternalLink(FILE_HDF5_ANGLES, "/angles")
+    nxdata.attrs["axes"] = "two_theta"
+    nxdata.attrs["two_theta_indices"] = [
+        0,
+    ]
 
-f.close()
+    local_addr = "/entry/instrument"
+    f[local_addr] = h5py.ExternalLink(FILE_HDF5_COUNTS, "/entry/instrument")
diff --git a/manual/source/examples/h5py/plotting/reader_attributes_trail.py b/manual/source/examples/h5py/plotting/reader_attributes_trail.py
@@ -1,11 +1,10 @@
-import os
+from pathlib import Path
 import h5py
 
-filename = os.path.join(
-    os.path.dirname(__file__),
-    "..",
-    "simple_example_basic",
-    "simple_example_basic.nexus.hdf5",
+filename = str(
+    Path(__file__).parent.parent
+    / "simple_example_basic"
+    / "simple_example_basic.nexus.hdf5"
 )
 with h5py.File(filename, "r") as nx:
     # find the default NXentry group

diff --git a/manual/source/examples/h5py/simple_example_basic/simple_example_basic_read.py b/manual/source/examples/h5py/simple_example_basic/simple_example_basic_read.py
@@ -4,12 +4,11 @@
 import h5py  # HDF5 support
 
 fileName = "simple_example_basic.nexus.hdf5"
-f = h5py.File(fileName, "r")
-for item in f.attrs.keys():
-    print(item + ":", f.attrs[item])
-mr = f["/entry/mr_scan/mr"]
-i00 = f["/entry/mr_scan/I00"]
-print("%s\t%s\t%s" % ("#", "mr", "I00"))
-for i in range(len(mr)):
-    print("%d\t%g\t%d" % (i, mr[i], i00[i]))
-f.close()
+with h5py.File(fileName, "r") as f:
+    for item in f.attrs.keys():
+        print(item + ":", f.attrs[item])
+    mr = f["/entry/mr_scan/mr"]
+    i00 = f["/entry/mr_scan/I00"]
+    print("%s\t%s\t%s" % ("#", "mr", "I00"))
+    for i in range(len(mr)):
+        print("%d\t%g\t%d" % (i, mr[i], i00[i]))
diff --git a/manual/source/examples/h5py/simple_example_basic/simple_example_basic_write.py b/manual/source/examples/h5py/simple_example_basic/simple_example_basic_write.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """Writes a NeXus HDF5 file using h5py and numpy"""
 
-import os
+from pathlib import Path
 import datetime
 import h5py  # HDF5 support
 import numpy
@@ -11,51 +11,47 @@
 timestamp = datetime.datetime.now().astimezone().isoformat()
 
 # load data from two column format
-infilename = filename = os.path.join(
-    os.path.dirname(__file__), "..", "simple_example.dat"
-)
-data = numpy.loadtxt(infilename).T
+data_filename = str(Path(__file__).parent.parent / "simple_example.dat")
+data = numpy.loadtxt(data_filename).T
 mr_arr = data[0]
 i00_arr = numpy.asarray(data[1], "int32")
 
 # create the HDF5 NeXus file
-f = h5py.File(fileName, "w")
-# point to the default data to be plotted
-f.attrs["default"] = "entry"
-# give the HDF5 root some more attributes
-f.attrs["file_name"] = fileName
-f.attrs["file_time"] = timestamp
-f.attrs["instrument"] = "APS USAXS at 32ID-B"
-f.attrs["creator"] = "simple_example_basic_write.py"
-f.attrs["NeXus_version"] = "4.3.0"
-f.attrs["HDF5_Version"] = h5py.version.hdf5_version
-f.attrs["h5py_version"] = h5py.version.version
-
-# create the NXentry group
-nxentry = f.create_group("entry")
-nxentry.attrs["NX_class"] = "NXentry"
-nxentry.attrs["default"] = "mr_scan"
-nxentry.create_dataset("title", data="1-D scan of I00 v. mr")
-
-# create the NXentry group
-nxdata = nxentry.create_group("mr_scan")
-nxdata.attrs["NX_class"] = "NXdata"
-nxdata.attrs["signal"] = "I00"  # Y axis of default plot
-nxdata.attrs["axes"] = "mr"  # X axis of default plot
-nxdata.attrs["mr_indices"] = [
-    0,
-]  # use "mr" as the first dimension of I00
-
-# X axis data
-ds = nxdata.create_dataset("mr", data=mr_arr)
-ds.attrs["units"] = "degrees"
-ds.attrs["long_name"] = "USAXS mr (degrees)"  # suggested X axis plot label
-
-# Y axis data
-ds = nxdata.create_dataset("I00", data=i00_arr)
-ds.attrs["units"] = "counts"
-ds.attrs["long_name"] = "USAXS I00 (counts)"  # suggested Y axis plot label
-
-f.close()  # be CERTAIN to close the file
+with h5py.File(fileName, "w") as f:
+    # point to the default data to be plotted
+    f.attrs["default"] = "entry"
+    # give the HDF5 root some more attributes
+    f.attrs["file_name"] = fileName
+    f.attrs["file_time"] = timestamp
+    f.attrs["instrument"] = "APS USAXS at 32ID-B"
+    f.attrs["creator"] = "simple_example_basic_write.py"
+    f.attrs["NeXus_version"] = "4.3.0"
+    f.attrs["HDF5_Version"] = h5py.version.hdf5_version
+    f.attrs["h5py_version"] = h5py.version.version
+
+    # create the NXentry group
+    nxentry = f.create_group("entry")
+    nxentry.attrs["NX_class"] = "NXentry"
+    nxentry.attrs["default"] = "mr_scan"
+    nxentry.create_dataset("title", data="1-D scan of I00 v. mr")
+
+    # create the NXentry group
+    nxdata = nxentry.create_group("mr_scan")
+    nxdata.attrs["NX_class"] = "NXdata"
+    nxdata.attrs["signal"] = "I00"  # Y axis of default plot
+    nxdata.attrs["axes"] = "mr"  # X axis of default plot
+    nxdata.attrs["mr_indices"] = [
+        0,
+    ]  # use "mr" as the first dimension of I00
+
+    # X axis data
+    ds = nxdata.create_dataset("mr", data=mr_arr)
+    ds.attrs["units"] = "degrees"
+    ds.attrs["long_name"] = "USAXS mr (degrees)"  # suggested X axis plot label
+
+    # Y axis data
+    ds = nxdata.create_dataset("I00", data=i00_arr)
+    ds.attrs["units"] = "counts"
+    ds.attrs["long_name"] = "USAXS I00 (counts)"  # suggested Y axis plot label
 
 print("wrote file:", fileName)
diff --git a/manual/source/examples/h5py/simple_example_test/simple_example_test_read.py b/manual/source/examples/h5py/simple_example_test/simple_example_test_read.py
@@ -38,12 +38,14 @@ def process(fileName):
         f = h5py.File(fileName, "r")
     except Exception:
         return False
-    print(f.filename)
-    print("keys: ", f.keys())
-    print_attr(f, "f")
-    for k in f.keys():
-        print_child(f[k], "%s://%s" % (fileName, k))
-    f.close()
+    try:
+        print(f.filename)
+        print("keys: ", f.keys())
+        print_attr(f, "f")
+        for k in f.keys():
+            print_child(f[k], "%s://%s" % (fileName, k))
+    finally:
+        f.close()
     return True
 
 

diff --git a/manual/source/examples/h5py/simple_example_test/simple_example_test_write.py b/manual/source/examples/h5py/simple_example_test/simple_example_test_write.py
@@ -53,40 +53,40 @@
         data["I00"].append(float(y))
 
     # create the HDF5 NeXus file
-    f = h5py.File(fileName, "w")
-    f.attrs["file_name"] = fileName
-    f.attrs["creator"] = "Pete R. Jemian <[email protected]> using h5py"
-    f.attrs["HDF5_Version"] = h5py.version.hdf5_version
-    f.attrs["NeXus_version"] = "4.2.1"
-    f.attrs["h5py_version"] = h5py.version.version
-    f.attrs["file_time"] = timestamp
-    f.attrs["file_update_time"] = timestamp
-    f.attrs["default"] = "entry"  # identify default NXentry group
+    with h5py.File(fileName, "w") as f:
+        f.attrs["file_name"] = fileName
+        f.attrs["creator"] = "Pete R. Jemian <[email protected]> using h5py"
+        f.attrs["HDF5_Version"] = h5py.version.hdf5_version
+        f.attrs["NeXus_version"] = "4.2.1"
+        f.attrs["h5py_version"] = h5py.version.version
+        f.attrs["file_time"] = timestamp
+        f.attrs["file_update_time"] = timestamp
+        f.attrs["default"] = "entry"  # identify default NXentry group
 
-    nxentry = f.create_group("entry")
-    nxentry.attrs["NX_class"] = "NXentry"  # identify NeXus base class
-    nxentry.attrs["default"] = "mr_scan"  # identify default NXdata group
+        nxentry = f.create_group("entry")
+        nxentry.attrs["NX_class"] = "NXentry"  # identify NeXus base class
+        nxentry.attrs["default"] = "mr_scan"  # identify default NXdata group
 
-    # store the scan data
-    nxdata = nxentry.create_group("mr_scan")
-    nxdata.attrs["NX_class"] = "NXdata"  # identify NeXus base class
-    nxdata.attrs["signal"] = "I00"  # identify default data to plot
-    nxdata.attrs["axes"] = "mr"  # identify default dimension scale to plot
+        # store the scan data
+        nxdata = nxentry.create_group("mr_scan")
+        nxdata.attrs["NX_class"] = "NXdata"  # identify NeXus base class
+        nxdata.attrs["signal"] = "I00"  # identify default data to plot
+        nxdata.attrs["axes"] = "mr"  # identify default dimension scale to plot
 
-    mr = nxdata.create_dataset("mr", data=data["mr"])
-    mr.attrs["units"] = "degrees"
+        mr = nxdata.create_dataset("mr", data=data["mr"])
+        mr.attrs["units"] = "degrees"
 
-    i00 = nxdata.create_dataset("I00", data=data["I00"])
-    i00.attrs["units"] = "counts"
+        i00 = nxdata.create_dataset("I00", data=data["I00"])
+        i00.attrs["units"] = "counts"
 
-    # fill in some optional metadata
-    nxentry.create_dataset("title", data="APS USAXS instrument MR (alignment) scan")
-    nxentry.create_dataset("start_time", data="2010-04-25T10:20:56-0500")
-    nxentry.create_dataset("end_time", data="2010-04-25T10:21:16-0500")
-    nxentry.create_dataset("experiment_identifier", data="spec file 04_25.dat, scan #8")
-    nxentry.create_dataset(
-        "experiment_description", data="alignment scan of the USAXS collimating optics"
-    )
-
-    # be CERTAIN to close the file
-    f.close()
+        # fill in some optional metadata
+        nxentry.create_dataset("title", data="APS USAXS instrument MR (alignment) scan")
+        nxentry.create_dataset("start_time", data="2010-04-25T10:20:56-0500")
+        nxentry.create_dataset("end_time", data="2010-04-25T10:21:16-0500")
+        nxentry.create_dataset(
+            "experiment_identifier", data="spec file 04_25.dat, scan #8"
+        )
+        nxentry.create_dataset(
+            "experiment_description",
+            data="alignment scan of the USAXS collimating optics",
+        )
diff --git a/manual/source/examples/h5py/simple_example_write1/simple_example_write1.py b/manual/source/examples/h5py/simple_example_write1/simple_example_write1.py
@@ -7,33 +7,31 @@
 in the Introduction chapter
 """
 
-import os
+from pathlib import Path
 import h5py
 import numpy
 
-filename = os.path.join(os.path.dirname(__file__), "..", "simple_example.dat")
+filename = str(Path(__file__).parent.parent / "simple_example.dat")
 buffer = numpy.loadtxt(filename).T
 tthData = buffer[0]  # float[]
 countsData = numpy.asarray(buffer[1], "int32")  # int[]
 
-f = h5py.File("simple_example_write1.hdf5", "w")  # create the HDF5 NeXus file
-# since this is a simple example, no attributes are used at this point
+with h5py.File("simple_example_write1.hdf5", "w") as f:  # create the HDF5 NeXus file
+    # since this is a simple example, no attributes are used at this point
 
-nxentry = f.create_group("Scan")
-nxentry.attrs["NX_class"] = "NXentry"
+    nxentry = f.create_group("Scan")
+    nxentry.attrs["NX_class"] = "NXentry"
 
-nxdata = nxentry.create_group("data")
-nxdata.attrs["NX_class"] = "NXdata"
-nxdata.attrs["signal"] = "counts"
-nxdata.attrs["axes"] = "two_theta"
-nxdata.attrs["two_theta_indices"] = [
-    0,
-]
+    nxdata = nxentry.create_group("data")
+    nxdata.attrs["NX_class"] = "NXdata"
+    nxdata.attrs["signal"] = "counts"
+    nxdata.attrs["axes"] = "two_theta"
+    nxdata.attrs["two_theta_indices"] = [
+        0,
+    ]
 
-tth = nxdata.create_dataset("two_theta", data=tthData)
-tth.attrs["units"] = "degrees"
+    tth = nxdata.create_dataset("two_theta", data=tthData)
+    tth.attrs["units"] = "degrees"
 
-counts = nxdata.create_dataset("counts", data=countsData)
-counts.attrs["units"] = "counts"
-
-f.close()  # be CERTAIN to close the file
+    counts = nxdata.create_dataset("counts", data=countsData)
+    counts.attrs["units"] = "counts"