Our thanks to Dectris, Ltd for their sponsorship of this meeting
The purpose of this session is to discuss the issue involved in validating metadata that accompanies Eiger images. Some of the metadata is or can be generated by Dectris. Some of the metadata is or can be generated by the beamline. Some of the metadata is the responsibility of the user and may not even be known until long after the data collection. Here we will focus on the process of validation. After the morning tea break we will discuss the specifics of what metadata is essential for MX images, and what is optional.
nxvalidate -a NXmx -l ~/definitions LysTest01_4706_data_master.h5
against an Eiger9M lysozyme dataset at NSLS-II produced the following report:
message="Missing required global file_name attribute" sev=error dataPath=/ dataFile=LysTest01_4706_data_master.h5 message="Missing required global file_time attribute" sev=error dataPath=/ dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Required field missing" nxdlPath=/NXentry/definition sev=error dataPath=/entry/definition dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Required field missing" nxdlPath=/NXentry/NXinstrument/NXdetector/depends_on sev=error dataPath=/entry/instrument/detector/depends_on dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Required field missing" nxdlPath=/NXentry/NXinstrument/NXdetector/data sev=error dataPath=/entry/instrument/detector/data dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Required group missing" nxdlPath=/NXentry/NXinstrument/NXdetector/NXdetector_module sev=error dataPath=/entry/instrument/detector dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Data type mismatch, expected NX_BOOLEAN, got H5T_STD_I32LE" nxdlPath=/NXentry/NXinstrument/NXdetector/pixel_mask_applied sev=error dataPath=/entry/instrument/detector/pixel_mask_applied dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Data type mismatch, expected NX_BOOLEAN, got H5T_STD_I32LE" nxdlPath=/NXentry/NXinstrument/NXdetector/countrate_correction_applied sev=error dataPath=/entry/instrument/detector/countrate_correction_applied dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Required group missing" nxdlPath=/NXentry/NXsample/NXbeam sev=error dataPath=/entry/sample dataFile=LysTest01_4706_data_master.h5 9 errors and 105 warnings found when validating LysTest01_4706_data_master.h5
9 errors and 105 warnings found when validating LysTest01_4706_data_master.h5 message="Missing required global file_name attribute" ... sev=error dataPath=/ dataFile=LysTest01_4706_data_master.h5 message="Missing required global file_time attribute" ... sev=error dataPath=/ dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Required field missing" ... nxdlPath=/NXentry/definition ... sev=error dataPath=/entry/definition dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Required field missing" ... nxdlPath=/NXentry/NXinstrument/NXdetector/depends_on ... sev=error dataPath=/entry/instrument/detector/depends_on dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Required field missing" ... nxdlPath=/NXentry/NXinstrument/NXdetector/data ... sev=error dataPath=/entry/instrument/detector/data dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Required group missing" ... nxdlPath=/NXentry/NXinstrument/NXdetector/NXdetector_module ... sev=error dataPath=/entry/instrument/detector dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Data type mismatch, expected NX_BOOLEAN, got H5T_STD_I32LE" ... nxdlPath=/NXentry/NXinstrument/NXdetector/pixel_mask_applied ... sev=error dataPath=/entry/instrument/detector/pixel_mask_applied dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Data type mismatch, expected NX_BOOLEAN, got H5T_STD_I32LE" ... nxdlPath=/NXentry/NXinstrument/NXdetector/countrate_correction_applied ... sev=error dataPath=/entry/instrument/detector/countrate_correction_applied dataFile=LysTest01_4706_data_master.h5 definition=NXmx.nxdl.xml message="Required group missing" ... nxdlPath=/NXentry/NXsample/NXbeam ... sev=error dataPath=/entry/sample dataFile=LysTest01_4706_data_master.h5