NeXus Data Format

https://www.nexusformat.org/
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NeXus is a common data format for neutron, x-ray, and muon science, developed as an international...
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### Clone and Install NeXpy from GitHub

Source: https://www.nexusformat.org/NeXpy.html

Clone the NeXpy repository from GitHub and install the package locally. Ensure your Python script directory is in your default path.

```bash
> git clone https://github.com/nexpy/nexpy.git
> cd nexpy
> python setup.py install
```

--------------------------------

### NXscan Proposal - Paul (Temperature Scan Example)

Source: https://www.nexusformat.org/Scans.html

An example of Paul's NXscan proposal demonstrating a temperature scan with specified units, number of points, and index.

```XML
<NXscan>
    <temperature label="T" units="K" type=FLOAT[2] num_points=25 index=3>
      10,100
    </temperature>
  </NXscan>
```

--------------------------------

### NXscan Proposal - Paul (Raster Scan Example)

Source: https://www.nexusformat.org/Scans.html

An example of Paul's NXscan proposal illustrating a raster scan with 'x' and 'y' axes, specifying their names, types, number of points, and indices.

```XML
<NXscan>
     <x name="x" type=FLOAT[2] num_points=11 index 4>
         0,10
     </x>
     <y name="y" type=FLOAT[2] num_points=4 index 3>
         5,8
     </y>
   </NXscan>
```

--------------------------------

### NXarea_detector Inheritance Example

Source: https://www.nexusformat.org/Objects_or_Interfaces.html

Illustrates a potential inheritance hierarchy where NXarea_detector inherits from NXdetector and NXbeamline_component.

```text
NXarea_detector:NXdetector:NXbeamline_component
```

--------------------------------

### Launch NeXpy GUI Shell

Source: https://www.nexusformat.org/NeXpy.html

Command to start the NeXpy graphical user interface shell.

```shell
> nexpy
```

--------------------------------

### Display NXdir Online Help

Source: https://www.nexusformat.org/NXdir.html

Prints the available command-line arguments and options for NXdir. Use this to understand all functionalities.

```bash
nxdir --help
```

--------------------------------

### NXmonitor Addition for Scan Start Time

Source: https://www.nexusformat.org/Monochromatic_Neutron_and_X-ray_Reflectometry.html

This proposed addition to NXmonitor allows recording the start time for each scan point, useful for normalization and efficiency corrections.

```XML
<start_time type="NX_FLOAT[n]" units="seconds">
       {Start time for each scan point}
    </start_time>
```

--------------------------------

### Nexus File Structure Example

Source: https://www.nexusformat.org/Telco_20150909.html

Illustrates a Nexus file structure for a 2D image with wavelength, defining data signals, axes, and transformations for detector and sample components.

```nexus
entry
        data
              @signal=data
              @axes=temperature,theta,firstdim,seconddim,wavelength
              @theta_indices=0,1
              @/entry/sample/temperature_indices=0
              ...
              #  this  becomes  a  bit  redunant
              ...
              data[2,31,100,100,256]
        instrument
              detector
                    @signal=data
                    @axes=/entry/instrument/detector/transformations/arm,theta,firstdim,seconddim,wavelength
                    @/entry/sample/temperature_indices=0
                    @theta_indices=0,1
                    @wavelength_indices=2,3,4
                    @firstdim_indices=2
                    @seconddim_indices=3
                    @thirddim_indices=2,3
                    depends_on=/entry/instrument/detector/seconddim
                    data[2,31,100,100,256]
                    wavelength[100,100,256]
                          @units=nm
                    firstdim[100]
                          @depends_on=/entry/instrument/detector/transformations/arm
                          @transformation_type=translation
                          @vetcor=0.5,0.5,0
                    thirddim[100,100]
                          @depends_on=firstdim
                          @transformation_type=translation
                          @vetcor=0,0,1
                    seconddim[100]
                          @depends_on=thirddim
                          @transformation_type=translation
                          @vetcor=0.5,-0.5,0
                    transformations
                          theta[2,31]
                                @depends_on=.
                                @transformation_type=rotation
                                @vetcor=1,0,0
                          arm[1]
                                @depends_on=theta
                                @transformation_type=translation
                                @vetcor=0,0,1
        sample
              depends_on=/entry/sample/transformations/phi
              temperature[2]
                    units=C
              transformations
                    phi[2,31]
                          @depends_on=.
                          @transformation_type=rotation
                          @vetcor=0,1,0
```

--------------------------------

### NeXus Parameter Naming and Description

Source: https://www.nexusformat.org/Telco_20170308.html

Shows examples of NeXus parameter descriptions and discusses naming conventions for groups and attributes. Highlights the need for clarity and consistency.

```text
`sensor_material` is described as “the name of this converter material” for “radiation [..] not directly sensed by the detector”. Can this description be expanded to include directly detected radiation?
```

```text
Same for `sensor_thickness`.
```

```text
`flatfield_applied` is currently called `flatfield_correction_applied`. This is arguably in better agreement with `angular_calibration_applied`. Can we keep it?
```

```text
Are the group names binding or only their NX classes? For example, EIGER calls the `NXcollection` group `detectorSpecific`, not `collection`. Similarly, the `NXdetector_module` group is planned to be called `module` not `detector_module`.
```

```text
What does the required parameter `/entry/instrument/detector/data[np,i,j]` entail?
```

```text
A parameter like `detector_number` that gives the serial number should be made mandatory. Or it could be an attribute to `/entry/instrument/detector/description`?
```

--------------------------------

### Install SDS Link

Source: https://www.nexusformat.org/Jnexustut.html

Installs a previously prepared link to an SDS into the NeXus file's group hierarchy. This call is made after navigating to the desired location for the link.

```Java
nf.makelink(nl);
```

--------------------------------

### NXbrowse Help Command

Source: https://www.nexusformat.org/NXbrowse.f90.html

Prints the available commands for the NXbrowse utility.

```Fortran
print *, "NXbrowse commands : DIR"
                print *, "                    OPEN <group_name>"
                print *, "                    READ <data_name>"
                print *, "                    CLOSE"
                print *, "                    HELP"
                print *, "                    EXIT"
```

--------------------------------

### Example of GitHub Issue Tracking

Source: https://www.nexusformat.org/Telco_20160531.html

This snippet shows examples of how GitHub issues are referenced and discussed within the meeting agenda. It includes issue numbers and brief status updates.

```text
1. 329 - can we remove the issue branch from the repository?
1. 419 - still waiting on a response from Stuart where to install the header files
1. 425 - done
1. 426 - Maybe Tobias can have a look at it
1. 420/421 - currently working on it (this work should be continued by the original author - the code is a total mess)
```

--------------------------------

### NXopen

Source: https://www.nexusformat.org/NAPI_Routines.html

Opens a NeXus file and initializes its structure. Returns a handle to the file structure.

```APIDOC
## NXopen

### Description
Opens the NeXus file, and creates and initializes the NeXus file structure. The returned handle is a pointer to this structure.

### Usage
```
status = NXopen (file_name, access_method, file_id)
```

### Parameters
#### Input Arguments
* **file_name** (char *) - Name of NeXus file to be opened
* **access_method** (int) - File Access: NXACC_READ, NXACC_RDWR, NXACC_CREATE, NXACC_CREATE4, NXACC_CREATE5, NXACC_CREATEXML

#### Output Arguments
* **file_id** (NXhandle *) - Identifier of NeXus file
```

--------------------------------

### NXdetector Axis Attributes Example

Source: https://www.nexusformat.org/Telco_20150617.html

An example of how to attribute detector axes within an NXdetector group, analogous to NXdata. This scheme is proposed for detectors that may not directly use NXdata.

```nexus
    Fluo : NXdetector
      @signal = data
      @axes = (,,,energy)
      @energy_indices = (3)
      data[10,20,180,1024]
          @interpretation = spectrum
      energy[1024]
          @units = keV
```

--------------------------------

### Creating and Populating an NXsample Group

Source: https://www.nexusformat.org/NeXpy.html

Demonstrates how to create an NXsample group and add an NXfield for temperature, both using keyword arguments and attribute assignment.

```python
>>> temperature = NXfield(40.0, units='K')
>>> sample = NXsample(temperature=temperature)
>>> print sample.tree
sample:NXsample
  temperature = 40.0
  units = K
```

```python
>>> sample = NXsample()
>>> sample.temperature=NXfield(40.0, units='K')
sample:NXsample
  temperature = 40.0
  units = K
```

--------------------------------

### Example NXdata Group with Proposed Errors Attribute

Source: https://www.nexusformat.org/Proposal_NeXus_Errors.html

This example demonstrates an NXdata group structure incorporating the proposed 'errors' attribute to link primary and secondary data signals to their respective error SDSs.

```xml
<NXdata name="data">
    <primary_data signal="1" axes="x1:y1" errors="e1">...</primary_data>
    <x>...</x>
    <y>...</y>
    <e1>...</e1>
    <secondary_data signal="2" axes="x:y" errors="e2">...</secondary_data>
    <e2>...</e2>
</NXdata>
```

--------------------------------

### Windows 32 Example Batch File for NeXus API

Source: https://www.nexusformat.org/Japinotes.html

This batch file shows how to set the Java classpath and the NeXus shared library path for executing a Java program on Windows 32-bit systems.

```batch
set JL=-Dneutron.nexus.JNEXUSLIB=..\jnexus\bin\win32\jnexus.dll
java -classpath C:\jdk1.1.5\lib\classes.zip;..\jnexus.jar;. %JL% TestJapi
```

--------------------------------

### Example NXdata Group with Coordinates

Source: https://www.nexusformat.org/Proposal_NeXus_Coordinates.html

This example shows how an NXdata group can be defined with a 'signal' SDS and a 'coordinates' attribute specifying the SDSs that define the pixel locations. The 'number_vertices' attribute is included for cases where coordinates represent pixel vertices.

```nexus
<NXdata name="data">
   <data signal="1" coordinates="polar_angle:azimuthal_angle" number_vertices="8">...</data>
   <polar_angle>...</polar_angle>
   <azimuthal_angle>...</azimuthal_angle>
</NXdata>
```

--------------------------------

### NXgetinfo

Source: https://www.nexusformat.org/NAPI_Routines.html

Gets the rank, dimensions, and data type of the currently open data set.

```APIDOC
## NXgetinfo

### Description
Gets the rank, dimensions, and data type of the currently open data set.

### Usage
```
status = NXgetinfo (file_id, rank, dimensions[], data_type)
```

### Arguments
#### Input Arguments
* **file_id** (NXhandle) - Identifier of NeXus file

#### Output Arguments
* **rank** (int *) - Rank of data
* **dimensions** (int[]) - Dimensions of data
* **data_type** (int *) - Data Type: NX_CHAR, NX_FLOAT32, NX_FLOAT64, NX_INT8, NX_UINT8, NX_INT16, NX_UINT16, NX_INT32, NX_UINT32
```

--------------------------------

### Run NXbrowse from Terminal

Source: https://www.nexusformat.org/NXbrowse.html

Execute NXbrowse from the command line by providing the NeXus file name. If no file name is specified, the program will prompt the user.

```bash
nxbrowse <file_name>
```

--------------------------------

### Create a New NeXus File

Source: https://www.nexusformat.org/Jnexustut.html

Opens a new NeXus file for creation. The constructor takes the file name and an access code.

```Java
NexusFile nf = new NexusFile(name, NexusFile.NXACC_CREATE);
```

--------------------------------

### Unix Example Shell Script for NeXus API

Source: https://www.nexusformat.org/Japinotes.html

This script demonstrates how to set the classpath and specify the NeXus shared library path for running a Java program on a Unix-like system.

```shell
#!/sbin/sh
java -classpath /usr/lib/classes.zip:../jnexus.jar:.
   -Dneutron.nexus.JNEXUSLIB=../bin/du40/libjnexus.so TestJapi
```

--------------------------------

### Load NeXus File in Python Shell

Source: https://www.nexusformat.org/NeXpy.html

Demonstrates how to import the nexus API and load a NeXus file within a standard Python shell.

```python
>>> from nexpy.api import nexus
>>> a=nexus.load('data/chopper.nxs')
```

--------------------------------

### NXdata with data_uncertainty attribute

Source: https://www.nexusformat.org/2014_axes_and_uncertainties.html

Example of an NXdata group where the uncertainty dataset is defined by the 'data_uncertainty' attribute.

```HDF5
NXroot
  NXentry
    NXdata
      @signal="data"
      @data_axes="xy"
      @data_uncertainty="esd"
      data: float[300, 300]
      xy: float[300, 300]
      esd: float[300, 300]
```

--------------------------------

### NXdata with uncertainty attribute on dataset

Source: https://www.nexusformat.org/2014_axes_and_uncertainties.html

Example of an NXdata group where the uncertainty is defined by the 'uncertainty' attribute directly on the dataset.

```HDF5
NXroot
  NXentry
    NXdata
      @signal="data"
      @data_axes="xy"
      data: float[300, 300]
        @uncertainty="esd"
      xy: float[300, 300]
      esd: float[300, 300]
```

--------------------------------

### Create and Transfer Data in Nexus File

Source: https://www.nexusformat.org/Jnexustut.html

Demonstrates creating a dataset and transferring data using putdata and getdata. Data is passed as an Object, requiring arrays even for single values.

```Java
int iData[][] = new iData[3][10];
// write it
nf.putdata(iData);
// read it
nf.getdata(iData);
```

--------------------------------

### NXmonotas Example XML Structure

Source: https://www.nexusformat.org/NXmonotas_example-NIAC2006.html

This XML file demonstrates the structure of a NeXus file for triple-axis spectrometry data. It includes metadata about the experiment, sample, and user.

```xml
<?xml version="1.0" encoding="UTF-8"?>
<!--
URL:     http://www.nexus.anl.gov/classes/xml/NXmononxtas.xml
Editor:  NIAC
NIAC Version: 0.80
Date: 27 Apr 2005
$Id$

Template of a generic NeXus file containing neutron or x-ray triple-axis data.

-->
<NXroot filename="NXmononxtas_example.xml">

 <NXentry name="entry_0">
  <title> La1.2Sr1.8Mn2O7 m=2.4g phonons </title> 
  <definition version="1.0" URL="http://www.nexus.anl.gov/instruments/xml/NXmononxtas.xml">
   NXmononxtas 
  </definition>
  <start_time type="ISO8601">
   2000-05-23T19:37 
  </start_time>
  <end_time type="ISO8601">
   2000-05-23T21:04 
  </end_time>
  <duration type="NX_INT32" units="seconds">
   1620 
  </duration>
  <command_line>
   sc en 2.0 den 0.25 np 21 mn 1013000 
  </command_line>
  <NXuser name="Stephan Rosenkranz">
   <name type="NX_CHAR">
    Stephan Rosenkranz 
   </name>
   <affiliation type="NX_CHAR">
    Argonne National Laboratory 
   </affiliation>
  </NXuser>

  <NXsample name="sample">
   <name type="NX_CHAR">
    Bilayer Manganite 
   </name>
   <unit_cell type="NX_FLOAT32[1,6])">
    3.874 3.874 20.145 90.000 90.000 90.000 
   </unit_cell>
   <plane_vector_0 type="NX_FLOAT32[3]">
    -1.0 0.0 0.0 
   </plane_vector_0>
   <plane_vector_1 type="NX_FLOAT32[3]">
    0.0 0.0 1.0 
   </plane_vector_1>
   <temperature type="NX_FLOAT32[21]" units="K">
    295.2380 295.2360 295.2350 295.2320 295.2310 295.2290 
    295.2270 295.2260 295.2250 295.2230 295.2220 295.2200 
    295.2190 295.2180 295.2180 295.2170 295.2160 295.2160 
    295.2150 295.2150 295.2150 
   </temperature>
   <polar_angle type="NX_FLOAT32[21]" units="degrees">
    41.172 41.172 41.172 41.172 41.172 41.172 41.172 41.172 
    41.172 41.172 41.172 41.172 41.172 41.172 41.172 41.172 
    41.172 41.172 41.172 41.172 41.172 
   </polar_angle>
   <rotation_angle type="NX_FLOAT32[21]" units="degrees">
    218.439 218.976 219.518 220.065 220.617 221.174 221.736 
    222.304 222.878 223.458 224.044 224.637 225.236 225.843 
    226.457 227.080 227.710 228.349 228.998 229.656 230.324 
   </rotation_angle>
   <azimuthal_angle type="NX_FLOAT32" units="degrees">
    180.0 
   </azimuthal_angle>
   <Qh type="NX_FLOAT32[21]">
    2.0000 2.0000 2.0000 2.0000 2.0000 2.0000 2.0000 2.0000 
    2.0000 2.0000 2.0000 2.0000 2.0000 2.0000 2.0000 2.0000 
    2.0000 2.0000 2.0000 2.0000 2.0000 
   </Qh>
   <Qk type="NX_FLOAT32[21]">
    0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 
    0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 
    0.0000 0.0000 0.0000 0.0000 0.0000 
   </Qk>
   <Ql type="NX_FLOAT32[21]">
    0.6000 0.6000 0.6000 0.6000 0.6000 0.6000 0.6000 0.6000 
    0.6000 0.6000 0.6000 0.6000 0.6000 0.6000 0.6000 0.6000 
    0.6000 0.6000 0.6000 0.6000 0.6000 
   </Ql>
   <energy_transfer type="NX_FLOAT32[21]" units="meV">
    2.0000 2.2500 2.5000 2.7500 3.0000 3.2500 3.5000 3.7500 
    4.0000 4.2500 4.5000 4.7500 5.0000 5.2500 5.5000 5.7500 
    6.0000 6.2500 6.5000 6.7500 7.0000 
   </energy_transfer>
  </NXsample>

 
```

--------------------------------

### NXputslab

Source: https://www.nexusformat.org/NAPI_Routines.html

Writes a subset of a multidimensional data array into the currently open dataset, specified by starting indices and the size of each dimension.

```APIDOC
## NXputslab

### Description
Writes a subset of a multidimensional data array, specified by the starting indices and size of each dimension, into the currently open dataset.

### Usage
```
status = NXputslab (file_id, data, start[], size[])
```

### Input Arguments
* **file_id** (NXhandle) - Identifier of NeXus file
* **data** (void *) - Data values
* **start[]** (int) - Indices of starting values in each dimension
* **size[]** (int) - Length of slab in each dimension
```
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