Status:
contributed definition, extends NXobject, version 1.2
Description:
functional application definition for macromolecular crystallography
Symbols:
These symbols will be used below to coordinate datasets with the same shape.
np: number of scan points
i: number of detector pixels in the slow direction
j: number of detector pixels in the fast direction
Structure:
(entry): NXentry
title: NX_CHAR
start_time: NX_DATE_TIME
end_time: NX_DATE_TIME
definition: NX_CHAR
NeXus NXDL schema to which this file conforms
Obligatory value: NXmx
(instrument): NXinstrument
(attenuator): NXattenuator
attenuator_transmission: NX_NUMBER {units=NX_UNITLESS}
(detector): NXdetector
depends_on: NX_CHAR
data[np, i, j]: NX_NUMBER
description: NX_CHAR
name/manufacturer/model/etc. informationtime_per_channel: NX_CHAR {units=NX_TIME}
todo: define more clearlydistance: NX_FLOAT {units=NX_LENGTH}
Distance from the sample to the beam center. This value is a guidance only, the proper geometry can be found following the depends_on axis chain.dead_time: NX_FLOAT {units=NX_TIME}
Detector dead timecount_time: NX_NUMBER {units=NX_TIME}
Elapsed actual counting timebeam_center_x: NX_FLOAT {units=NX_LENGTH}
This is the x position where the direct beam would hit the detector. This is a length, not a pixel position, and can be outside of the actual detector.beam_center_y: NX_FLOAT {units=NX_LENGTH}
This is the y position where the direct beam would hit the detector. This is a length, not a pixel position, and can be outside of the actual detector.angular_calibration_applied: NX_BOOLEAN
True when the angular calibration has been applied in the electronics, false otherwise.angular_calibration[i, j]: NX_FLOAT
Angular calibration data.flatfield_applied: NX_BOOLEAN
True when the flat field correction has been applied in the electronics, false otherwise.flatfield[i, j]: NX_FLOAT
Flat field correction data.flatfield_error[i, j]: NX_FLOAT
Errors of the flat field correction data.pixel_mask_applied: NX_BOOLEAN
True when the pixel mask correction has been applied in the electronics, false otherwise.pixel_mask[i, j]: NX_INT
The 32-bit pixel mask for the detector. Contains a bit field for each pixel to signal dead, blind or high or otherwise unwanted or undesirable pixels. They have the following meaning:
- bit 0: gap (pixel with no sensor)
- bit 1: dead
- bit 2: under responding
- bit 3: over responding
- bit 4: noisy
- bit 5: -undefined-
- bit 6: pixel is part of a cluster of problematic pixels (bit set in addition to others)
- bit 7: -undefined-
- bit 8: user defined mask (e.g. around beamstop)
- bits 9-30: -undefined-
- bit 31: virtual pixel (corner pixel with interpolated value)
Normal data analysis software would not take pixels into account when a bit in (mask & 0x0000FFFF) is set. Tag bit in the upper two bytes would indicate special pixel properties that normally would not be a sole reason to reject the intensity value (unless lower bits are set.
countrate_correction__applied: NX_BOOLEAN
True when a count-rate correction has already been applied in the data recorded here, false otherwise.bit_depth_readout: NX_INT
How many bits the electronics record per pixel.detector_readout_time: NX_FLOAT {units=NX_TIME}
Time it takes to read the detector (typically milliseconds). This is important to know for time resolved experiments.frame_time: NX_FLOAT {units=NX_TIME}
This is time for each frame. This is exposure_time + readout time.gain_setting: NX_CHAR
The gain setting of the detector. This influences background.saturation_value: NX_INT
The value at which the detector goes into saturation. Data above this value is known to be invalid.sensor_material: NX_CHAR
At times, radiation is not directly sensed by the detector. Rather, the detector might sense the output from some converter like a scintillator. This is the name of this converter material.sensor_thickness: NX_FLOAT {units=NX_LENGTH}
At times, radiation is not directly sensed by the detector. Rather, the detector might sense the output from some converter like a scintillator. This is the thickness of this converter material.threshold_energy: NX_FLOAT {units=NX_ENERGY}
Single photon counter detectors can be adjusted for a certain energy range in which they work optimally. This is the energy setting for this.type: NX_CHAR
Description of type such as scintillator, ccd, pixel, image plate, CMOS, ...(transformations): NXtransformations
Suggested location for axes (transformations) to do with the detector(collection): NXcollection
Suggested container for detailed non-standard detector information like corrections applied automatically or performance settings.(detector_module): NXdetector_module
This is the description of a detector module. Many detectors consist of multiple smaller modules. Sometimes it is important to know the exact position of such modules. This is the purpose of this group. It is a child group to NXdetector.
data_origin: NX_INT
A two value field which gives the index of the start of the modules data in the main area detector image in the underlying NXdetector module.data_size: NX_INT
Two values for the size of the module in pixels in each direction.module_offset: NX_NUMBER {units=NX_LENGTH}
fast_pixel_direction: NX_NUMBER {units=NX_LENGTH}
slow_pixel_direction: NX_NUMBER {units=NX_LENGTH}
fast_pixel_size: NX_NUMBER {units=NX_LENGTH}
slow_pixel_size: NX_NUMBER {units=NX_LENGTH}
(sample): NXsample
name: NX_CHAR
Descriptive name of sampledepends_on: NX_CHAR
This should be an absolute requirement to have for any scan experiment. The reason it is optional is mainly to accommodate XFEL single shot exposures.temperature: NX_CHAR {units=NX_TEMPERATURE}
(beam): NXbeam
(transformations): NXtransformations
Suggested location for sample goniometer or other axes (transformations)(data): NXdata
