Restructure python examples

manual/source/examples/h5py/create_data.sh

@@ -2,26 +2,44 @@
 
 # (re)build all data files and text descriptions of data files
 
-#python BasicReader.py
-#python TestReader.py
-#python TestWriter.py
+ORIGINAL_WD=$(pwd)
+SCRIPT_ROOT="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 
-python BasicWriter.py
-punx tree prj_test.nexus.hdf5 > prj_test.nexus_structure.txt
-h5dump prj_test.nexus.hdf5 > prj_test.nexus_h5dump.txt
+PUNX_REMOVE_HEADER="+5"
 
-python externalExample.py
-punx tree external_angles.hdf5 > external_angles_structure.txt
+ROOT=$SCRIPT_ROOT/simple_example_basic
+cd $ROOT
+python $ROOT/simple_example_basic_write.py
+punx tree $ROOT/simple_example_basic.nexus.hdf5 | tail -n $PUNX_REMOVE_HEADER > $ROOT/simple_example_basic.nexus_structure.txt
+h5dump $ROOT/simple_example_basic.nexus.hdf5 > $ROOT/simple_example_basic.nexus_h5dump.txt
+python $ROOT/simple_example_basic_read.py
+
+ROOT=$SCRIPT_ROOT/simple_example_test
+cd $ROOT
+python simple_example_test_write.py
+python simple_example_test_read.py
+rm simple_example_test.nexus.hdf5
+
+ROOT=$SCRIPT_ROOT/simple_example_write1
+cd $ROOT
+python simple_example_write1.py
+punx tree simple_example_write1.hdf5 | tail -n $PUNX_REMOVE_HEADER > simple_example_write1_structure.txt
+h5dump simple_example_write1.hdf5 > simple_example_write1_h5dump.txt
+
+ROOT=$SCRIPT_ROOT/simple_example_write2
+cd $ROOT
+python simple_example_write2.py
+punx tree simple_example_write2.hdf5 | tail -n $PUNX_REMOVE_HEADER > simple_example_write2_structure.txt
+h5dump simple_example_write2.hdf5 > simple_example_write2_h5dump.txt
+
+ROOT=$SCRIPT_ROOT/external_example_write
+cd $ROOT
+python external_example_write.py
+punx tree external_angles.hdf5 | tail -n $PUNX_REMOVE_HEADER > external_angles_structure.txt
 h5dump external_angles.hdf5 > external_angles_h5dump.txt
-punx tree external_counts.hdf5 > external_counts_structure.txt
+punx tree external_counts.hdf5 | tail -n $PUNX_REMOVE_HEADER > external_counts_structure.txt
 h5dump external_counts.hdf5 > external_counts_h5dump.txt
-punx tree external_master.hdf5 > external_master_structure.txt
+punx tree external_master.hdf5 | tail -n $PUNX_REMOVE_HEADER > external_master_structure.txt
 h5dump external_master.hdf5 > external_master_h5dump.txt
 
-python writer_1_3.py
-punx tree writer_1_3.hdf5 > writer_1_3_structure.txt
-h5dump writer_1_3.hdf5 > writer_1_3_h5dump.txt
-
-python writer_2_1.py
-punx tree writer_2_1.hdf5 > writer_2_1_structure.txt
-h5dump writer_2_1.hdf5 > writer_2_1_h5dump.txt
+cd $ORIGINAL_WD

manual/source/examples/h5py/external_example_write/external_example_write.py

@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+"""
+Writes a NeXus HDF5 file using h5py with links to data in other HDF5 files.
+
+This example is based on ``writer_2_1``.
+"""
+
+import os
+import h5py
+import numpy
+
+FILE_HDF5_MASTER = "external_master.hdf5"
+FILE_HDF5_ANGLES = "external_angles.hdf5"
+FILE_HDF5_COUNTS = "external_counts.hdf5"
+
+# ---------------------------
+
+# get some data
+filename = os.path.join(os.path.dirname(__file__), "..", "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
+
+
+# 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()
+
+# 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"
+
+# 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,
+]
+
+local_addr = "/entry/instrument"
+f[local_addr] = h5py.ExternalLink(FILE_HDF5_COUNTS, "/entry/instrument")
+
+f.close()