NMX Data output should be in the nexus-nxmx format
Context and background knowledge
In order to comply with modern data handling and archiving standards for macromolecular crystallography (MX) data, the data output should be in the nexus nxmx format (https://manual.nexusformat.org/classes/applications/NXmx.html). This format is already used at most synchrotron X-ray MX beamlines around the world, and NMX should comply with these standards as much as is possible. The nxmx format is generic to source and is inclusive of neutron MX data. This format is part of the MX "Gold standard" for data, adopted in 2020 after a long deliberation process. https://journals.iucr.org/m/issues/2020/05/00/ti5018/index.html
Note that not all fields are required, and is experiment-specific. Others that are labeled "recommended" are absolutely necessary for NMX data processing. Determining which are required for NMX data is ongoing.
Methodology
For the most part, this will require accessing data from e.g. EPICS PVs and parsing them and putting them in the correct format. Some calculations might be required for determination of orientation- this is in progress.
Outputs
Data arranged in the correct format (see above).
Which interfaces are required?
Integrated into reduction workflow, Python module / function
Test cases
We have simulation data from McStas that we can use for testing.
Executive summary
NMX Data output should be in the nexus-nxmx format
Context and background knowledge
In order to comply with modern data handling and archiving standards for macromolecular crystallography (MX) data, the data output should be in the nexus nxmx format (https://manual.nexusformat.org/classes/applications/NXmx.html). This format is already used at most synchrotron X-ray MX beamlines around the world, and NMX should comply with these standards as much as is possible. The nxmx format is generic to source and is inclusive of neutron MX data. This format is part of the MX "Gold standard" for data, adopted in 2020 after a long deliberation process. https://journals.iucr.org/m/issues/2020/05/00/ti5018/index.html
Inputs
All data properties are detailed here: https://manual.nexusformat.org/classes/applications/NXmx.html
Note that not all fields are required, and is experiment-specific. Others that are labeled "recommended" are absolutely necessary for NMX data processing. Determining which are required for NMX data is ongoing.
Methodology
For the most part, this will require accessing data from e.g. EPICS PVs and parsing them and putting them in the correct format. Some calculations might be required for determination of orientation- this is in progress.
Outputs
Data arranged in the correct format (see above).
Which interfaces are required?
Integrated into reduction workflow, Python module / function
Test cases
We have simulation data from McStas that we can use for testing.
Comments
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