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2. Examples of writing and reading NeXus data files

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2.2.1. Example NeXus C programs using native HDF5 commands

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2.1.1. Example NeXus programs using NAPI

2.1.1.1. NAPI Simple 2-D Write Example (C, F77, F90)

Code examples are provided in this section that write 2-D data to a NeXus HDF5 file in C, F77, and F90 languages using the NAPI.

The following code reads a two-dimensional set counts with dimension scales of t and phi using local routines, and then writes a NeXus file containing a single NXentry group and a single NXdata group. This is the simplest data file that conforms to the NeXus standard. The same code is provided in C, F77, and F90 versions. Compare these code examples with Example NeXus C programs using native HDF5 commands.

NAPI C Example: write simple NeXus file

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#include "napi.h"

int main()
{
    int counts[50][1000], n_t=1000, n_p=50, dims[2], i;
    float t[1000], phi[50];
    NXhandle file_id;
/* 
 * Read in data using local routines to populate phi and counts
 *
 * for example you may create a getdata() function and call
 *
 *      getdata (n_t, t, n_p, phi, counts);
 */
/* Open output file and output global attributes */
    NXopen ("NXfile.nxs", NXACC_CREATE5, &file_id);
      NXputattr (file_id, "user_name", "Joe Bloggs", 10, NX_CHAR);
/* Open top-level NXentry group */
      NXmakegroup (file_id, "Entry1", "NXentry");
      NXopengroup (file_id, "Entry1", "NXentry");
/* Open NXdata group within NXentry group */
        NXmakegroup (file_id, "Data1", "NXdata");
        NXopengroup (file_id, "Data1", "NXdata");
/* Output time channels */
          NXmakedata (file_id, "time_of_flight", NX_FLOAT32, 1, &n_t);
          NXopendata (file_id, "time_of_flight");
            NXputdata (file_id, t);
            NXputattr (file_id, "units", "microseconds", 12, NX_CHAR);
          NXclosedata (file_id);
/* Output detector angles */
          NXmakedata (file_id, "polar_angle", NX_FLOAT32, 1, &n_p);
          NXopendata (file_id, "polar_angle");
            NXputdata (file_id, phi);
            NXputattr (file_id, "units", "degrees", 7, NX_CHAR);
          NXclosedata (file_id);
/* Output data */
          dims[0] = n_t;
          dims[1] = n_p;
          NXmakedata (file_id, "counts", NX_INT32, 2, dims);
          NXopendata (file_id, "counts");
            NXputdata (file_id, counts);
            i = 1;
            NXputattr (file_id, "signal", &i, 1, NX_INT32);
            NXputattr (file_id, "axes",  "polar_angle:time_of_flight", 26, NX_CHAR);
          NXclosedata (file_id);
/* Close NXentry and NXdata groups and close file */
        NXclosegroup (file_id);
      NXclosegroup (file_id);
    NXclose (&file_id);
    return;
}

NAPI F77 Example: write simple NeXus file

Note

The F77 interface is no longer being developed.

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      program WRITEDATA
      
      include 'NAPIF.INC'
      integer*4 status, file_id(NXHANDLESIZE), counts(1000,50), n_p, n_t, dims(2)
      real*4 t(1000), phi(50)

!Read in data using local routines
      call getdata (n_t, t, n_p, phi, counts)
!Open output file
      status = NXopen ('NXFILE.NXS', NXACC_CREATE, file_id)
        status = NXputcharattr 
     +         (file_id, 'user', 'Joe Bloggs', 10, NX_CHAR)
!Open top-level NXentry group
        status = NXmakegroup (file_id, 'Entry1', 'NXentry')
        status = NXopengroup (file_id, 'Entry1', 'NXentry')
!Open NXdata group within NXentry group
          status = NXmakegroup (file_id, 'Data1', 'NXdata')
          status = NXopengroup (file_id, 'Data1', 'NXdata')
!Output time channels
            status = NXmakedata 
     +         (file_id, 'time_of_flight', NX_FLOAT32, 1, n_t)
            status = NXopendata (file_id, 'time_of_flight')
              status = NXputdata (file_id, t)
              status = NXputcharattr 
     +         (file_id, 'units', 'microseconds', 12, NX_CHAR)
            status = NXclosedata (file_id)
!Output detector angles
            status = NXmakedata (file_id, 'polar_angle', NX_FLOAT32, 1, n_p)
            status = NXopendata (file_id, 'polar_angle')
              status = NXputdata (file_id, phi)
              status = NXputcharattr (file_id, 'units', 'degrees', 7, NX_CHAR)
            status = NXclosedata (file_id)
!Output data
            dims(1) = n_t
            dims(2) = n_p
            status = NXmakedata (file_id, 'counts', NX_INT32, 2, dims)
            status = NXopendata (file_id, 'counts')
              status = NXputdata (file_id, counts)
              status = NXputattr (file_id, 'signal', 1, 1, NX_INT32)
              status = NXputattr
     +          (file_id, 'axes', 'polar_angle:time_of_flight', 26, NX_CHAR)
            status = NXclosedata (file_id)
!Close NXdata and NXentry groups and close file
          status = NXclosegroup (file_id)
        status = NXclosegroup (file_id)
      status = NXclose (file_id)

      stop
      end

NAPI F90 Example: write simple NeXus file

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program WRITEDATA
      
   use NXUmodule

   type(NXhandle) :: file_id
   integer, pointer :: counts(:,:)
   real, pointer :: t(:), phi(:)

!Use local routines to allocate pointers and fill in data
   call getlocaldata (t, phi, counts)
!Open output file
   if (NXopen ("NXfile.nxs", NXACC_CREATE, file_id) /= NX_OK) stop
   if (NXUwriteglobals (file_id, user="Joe Bloggs") /= NX_OK) stop
!Set compression parameters
   if (NXUsetcompress (file_id, NX_COMP_LZW, 1000) /= NX_OK) stop
!Open top-level NXentry group
   if (NXUwritegroup (file_id, "Entry1", "NXentry") /= NX_OK) stop
   !Open NXdata group within NXentry group
      if (NXUwritegroup (file_id, "Data1", "NXdata") /= NX_OK) stop
   !Output time channels
         if (NXUwritedata (file_id, "time_of_flight", t, "microseconds") /= NX_OK) stop
   !Output detector angles
         if (NXUwritedata (file_id, "polar_angle", phi, "degrees") /= NX_OK) stop
   !Output data
         if (NXUwritedata (file_id, "counts", counts, "counts") /= NX_OK) stop
            if (NXputattr (file_id, "signal", 1) /= NX_OK) stop
            if (NXputattr (file_id, "axes", "polar_angle:time_of_flight") /= NX_OK) stop
   !Close NXdata group
      if (NXclosegroup (file_id) /= NX_OK) stop
!Close NXentry group
   if (NXclosegroup (file_id) /= NX_OK) stop
!Close NeXus file
   if (NXclose (file_id) /= NX_OK) stop

end program WRITEDATA

2.1.1.2. NAPI Python Simple 3-D Write Example

A single code example is provided in this section that writes 3-D data to a NeXus HDF5 file in the Python language using the NAPI. The data file may be retrieved from the repository of NeXus data file examples:

data:http://svn.nexusformat.org/definitions/exampledata/simple3D.h5

The data to be written to the file is a simple three-dimensional array (2 x 3 x 4) of integers. The single dataset is intended to demonstrate the order in which each value of the array is stored in a NeXus HDF5 data file.

NAPI Python Example: write simple NeXus file

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#!/usr/bin/python

import sys
import nxs
import numpy

nf = nxs.open("simple3D.h5", "w5")

nf.makegroup("entry","NXentry")
nf.opengroup("entry","NXentry")

nf.makegroup("data","NXdata")
nf.opengroup("data","NXdata")

a = numpy.zeros((2,3,4),dtype=numpy.int)
val = 0
for i in range(2):
    for j in range(3):
        for k in range(4):
            a[i,j,k] = val
            val = val + 1

nf.makedata("test",'int32',[2,3,4])
nf.opendata("test")
nf.putdata(a)
nf.putattr("signal",1)
nf.closedata()

nf.closegroup() # NXdata
nf.closegroup() # NXentry

nf.close()

exit

2.1.1.3. View a NeXus HDF5 file using h5dump

For the purposes of an example, it is instructive to view the content of the NeXus HDF5 file produced by the above program. Since HDF5 is a binary file format, we cannot show the contents of the file directly in this manual. Instead, we first we view the content by showing the output from the h5dump tool provided as part of the HDF5 tool kit: h5dump simple3D.h5

NAPI Python Example: h5dump output of NeXus HDF5 file

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HDF5 "simple3D.h5" {
GROUP "/" {
   ATTRIBUTE "NeXus_version" {
      DATATYPE  H5T_STRING {
            STRSIZE 5;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "4.1.0"
      }
   }
   ATTRIBUTE "file_name" {
      DATATYPE  H5T_STRING {
            STRSIZE 11;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "simple3D.h5"
      }
   }
   ATTRIBUTE "HDF5_Version" {
      DATATYPE  H5T_STRING {
            STRSIZE 5;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "1.6.6"
      }
   }
   ATTRIBUTE "file_time" {
      DATATYPE  H5T_STRING {
            STRSIZE 24;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "2011-11-18 17:26:27+0100"
      }
   }
   GROUP "entry" {
      ATTRIBUTE "NX_class" {
         DATATYPE  H5T_STRING {
               STRSIZE 7;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
         DATASPACE  SCALAR
         DATA {
         (0): "NXentry"
         }
      }
      GROUP "data" {
         ATTRIBUTE "NX_class" {
            DATATYPE  H5T_STRING {
                  STRSIZE 6;
                  STRPAD H5T_STR_NULLTERM;
                  CSET H5T_CSET_ASCII;
                  CTYPE H5T_C_S1;
               }
            DATASPACE  SCALAR
            DATA {
            (0): "NXdata"
            }
         }
         DATASET "test" {
            DATATYPE  H5T_STD_I32LE
            DATASPACE  SIMPLE { ( 2, 3, 4 ) / ( 2, 3, 4 ) }
            DATA {
            (0,0,0): 0, 1, 2, 3,
            (0,1,0): 4, 5, 6, 7,
            (0,2,0): 8, 9, 10, 11,
            (1,0,0): 12, 13, 14, 15,
            (1,1,0): 16, 17, 18, 19,
            (1,2,0): 20, 21, 22, 23
            }
            ATTRIBUTE "signal" {
               DATATYPE  H5T_STD_I32LE
               DATASPACE  SCALAR
               DATA {
               (0): 1
               }
            }
         }
      }
   }
}
}

2.1.1.4. View a NeXus HDF5 file using h5toText.py

The output of h5dump contains a lot of structural information about the HDF5 file that can distract us from the actual content we added to the file. Next, we show the output from a custom Python tool (h5toText.py) that we describe in a later section (h5toText support module) of this chapter. This tool was developed to show the actual data content of an HDF5 file that we create.

NAPI Python Example: h5toText output of NeXus HDF5 file

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simple3D.h5:NeXus data file
  @NeXus_version = 4.1.0
  @file_name = simple3D.h5
  @HDF5_Version = 1.6.6
  @file_time = 2011-11-18 17:26:27+0100
  entry:NXentry
    @NX_class = NXentry
    data:NXdata
      @NX_class = NXdata
      test:NX_INT32[2,3,4] = __array
        @signal = 1
        __array = [
            [
              [0, 1, 2, 3]
              [4, 5, 6, 7]
              [8, 9, 10, 11]
            ]
            [
              [12, 13, 14, 15]
              [16, 17, 18, 19]
              [20, 21, 22, 23]
            ]
          ]

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