.. auto-generated by script ../../../../utils/nxdl2rst.py from the NXDL source NXmx.nxdl.xml .. index:: ! NXmx (application definition) ! mx (application definition) see: mx (application definition); NXmx .. _NXmx: ==== NXmx ==== **Status**: application definition, extends :ref:`NXobject`, version 1.5 **Description**: functional application definition for macromolecular crystallography **Symbols**: These symbols will be used below to coordinate datasets with the same shape. Most MX x-ray detectors will produce two-dimensional images. Some will produce three-dimensional images, using one of the indices to select a detector element. **dataRank**: rank of the ``data`` field **np**: number of scan points **i**: number of detector pixels in the slowest direction **j**: number of detector pixels in the second slowest direction **k**: number of detector pixels in the third slowest direction **Groups cited**: :ref:`NXattenuator`, :ref:`NXbeam`, :ref:`NXcollection`, :ref:`NXdata`, :ref:`NXdetector_group`, :ref:`NXdetector_module`, :ref:`NXdetector`, :ref:`NXentry`, :ref:`NXinstrument`, :ref:`NXsample`, :ref:`NXtransformations` .. index:: NXentry (base class); used in application definition, NXinstrument (base class); used in application definition, NXattenuator (base class); used in application definition, NXdetector_group (base class); used in application definition, NXdetector (base class); used in application definition, NXtransformations (base class); used in application definition, NXcollection (base class); used in application definition, NXdetector_module (base class); used in application definition, NXsample (base class); used in application definition, NXbeam (base class); used in application definition, NXdata (base class); used in application definition **Structure**: **(entry)**: :ref:`NXentry` .. index:: title (field) **title**: (optional) :ref:`NX_CHAR ` .. index:: start time (field) **start_time**: (optional) :ref:`NX_DATE_TIME ` .. index:: end time (field) **end_time**: (optional) :ref:`NX_DATE_TIME ` .. index:: definition (field) **definition**: :ref:`NX_CHAR ` NeXus NXDL schema to which this file conforms Obligatory value: ``NXmx`` **(instrument)**: :ref:`NXinstrument` **(attenuator)**: (optional) :ref:`NXattenuator` .. index:: attenuator transmission (field) **attenuator_transmission**: (optional) :ref:`NX_NUMBER ` {units=\ :ref:`NX_UNITLESS `} **(detector_group)**: (optional) :ref:`NXdetector_group` Optional logical grouping of detector elements. Each detector element is represented as an NXdetector group with its own detector data array. Each detector data array may be further decomposed into array sections by use of NXdetector_module groups. The names are given in the group names field. The groups are defined hierarchically, with names given in the group_names field, unique identifiing indices given in the field group_index, and the level in the hierarchy given in the group_parent field. For example if an x-ray detector, DET, consists of four elements in a rectangular array:: DTL DTR DLL DLR We could have:: group_names: ["DET", "DTL", "DTR", "DLL", "DLR"] group_index: [1, 2, 3, 4, 5] group_parent: [-1, 1, 1, 1, 1] .. index:: group names (field) **group_names[ref(group_index)]**: :ref:`NX_CHAR ` An array of the names of the detector elements or hierarchical groupings of detector elements. Specified in the base classes as comma separated list of names, but new code should use an array of names as quoted strings. .. index:: group index (field) **group_index[i]**: :ref:`NX_INT ` An array of unique indices for detector elements or groupings of detector elements. Each element is a unique ID for the corresponding group named in the field group_names. The IDs are positive integers starting with 1. .. index:: group parent (field) **group_parent[ref(group_index)]**: :ref:`NX_INT ` An array of the hierarchical levels of the parents of detector elements or groupings of detector elements. A top-level element or grouping has parent level -1 **(detector)**: :ref:`NXdetector` Normally the detector group will have the name ``detector``. However, in the case of multiple detector elements, each element needs a uniquely named NXdetector group. .. index:: depends on (field) **depends_on**: :ref:`NX_CHAR ` .. index:: data (field) **data[np, i, j, k]**: :ref:`NX_NUMBER ` For a dimension-2 detector, the rank of the data array will be 3. For a dimension-3 detector, the rank of the data array will be 4. This allows for the introduction of the frame number as the first index. .. index:: description (field) **description**: (optional) :ref:`NX_CHAR ` name/manufacturer/model/etc. information .. index:: time per channel (field) **time_per_channel**: (optional) :ref:`NX_CHAR ` {units=\ :ref:`NX_TIME `} todo: define more clearly .. index:: distance (field) **distance**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`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. .. index:: dead time (field) **dead_time**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_TIME `} Detector dead time .. index:: count time (field) **count_time**: (optional) :ref:`NX_NUMBER ` {units=\ :ref:`NX_TIME `} Elapsed actual counting time .. index:: beam center x (field) **beam_center_x**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`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. .. index:: beam center y (field) **beam_center_y**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`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. .. index:: angular calibration applied (field) **angular_calibration_applied**: (optional) :ref:`NX_BOOLEAN ` True when the angular calibration has been applied in the electronics, false otherwise. .. index:: angular calibration (field) **angular_calibration[i, j, k]**: (optional) :ref:`NX_FLOAT ` Angular calibration data. .. index:: flatfield applied (field) **flatfield_applied**: (optional) :ref:`NX_BOOLEAN ` True when the flat field correction has been applied in the electronics, false otherwise. .. index:: flatfield (field) **flatfield[i, j, k]**: (optional) :ref:`NX_FLOAT ` Flat field correction data. .. index:: flatfield error (field) **flatfield_error[i, j, k]**: (optional) :ref:`NX_FLOAT ` Errors of the flat field correction data. .. index:: pixel mask applied (field) **pixel_mask_applied**: (optional) :ref:`NX_BOOLEAN ` True when the pixel mask correction has been applied in the electronics, false otherwise. .. index:: pixel mask (field) **pixel_mask[i, j, k]**: (optional) :ref:`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. If the full bit depths is not required, providing a mask with fewer bits is permissible. .. index:: countrate correction applied (field) **countrate_correction_applied**: (optional) :ref:`NX_BOOLEAN ` True when a count-rate correction has already been applied in the data recorded here, false otherwise. .. index:: bit depth readout (field) **bit_depth_readout**: (optional) :ref:`NX_INT ` How many bits the electronics record per pixel. .. index:: detector readout time (field) **detector_readout_time**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_TIME `} Time it takes to read the detector (typically milliseconds). This is important to know for time resolved experiments. .. index:: frame time (field) **frame_time**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_TIME `} This is time for each frame. This is exposure_time + readout time. .. index:: gain setting (field) **gain_setting**: (optional) :ref:`NX_CHAR ` The gain setting of the detector. This influences background. .. index:: saturation value (field) **saturation_value**: (optional) :ref:`NX_INT ` The value at which the detector goes into saturation. Data above this value is known to be invalid. .. index:: sensor material (field) **sensor_material**: (optional) :ref:`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. .. index:: sensor thickness (field) **sensor_thickness**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`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. .. index:: threshold energy (field) **threshold_energy**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`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. .. index:: type (field) **type**: (optional) :ref:`NX_CHAR ` Description of type such as scintillator, ccd, pixel, image plate, CMOS, ... **(transformations)**: (optional) :ref:`NXtransformations` Suggested location for axes (transformations) to do with the detector **(collection)**: (optional) :ref:`NXcollection` Suggested container for detailed non-standard detector information like corrections applied automatically or performance settings. **(detector_module)**: :ref:`NXdetector_module` Many detectors consist of multiple smaller modules that are operated in sync and store their data in a common dataset. To allow consistent parsing of the experimental geometry, this application definiton requires all detectors to define a detector module, even if there is only one. This group specifies the hyperslab of data in the data array associated with the detector that contains the data for this module. If the module is associated with a full data array, rather than with a hyperslab within a larger array, then a single module should be defined, spanning the entire array. .. index:: data origin (field) **data_origin**: :ref:`NX_INT ` A dimension-2 or dimension-3 field which gives the indices of the origin of the hyperslab of data for this module in the main area detector image in the parent NXdetector module. The data_origin is 0-based. The frame number dimension (np) is omitted. The order of indices is i, j or i, j, k, i.e. slow to fast. .. index:: data size (field) **data_size**: :ref:`NX_INT ` Two or three values for the size of the module in pixels in each direction. .. index:: data stride (field) **data_stride**: (optional) :ref:`NX_INT ` Two or three values for the stride of the module in pixels in each direction. By default the stride is [1,1] or [1,1,1], and this is the most likely case. This optional field is included for completeness. .. index:: module offset (field) **module_offset**: :ref:`NX_NUMBER ` {units=\ :ref:`NX_LENGTH `} Offset of the module in regards to the origin of the detector in an arbitrary direction. .. index:: transformation type (field attribute) **@transformation_type**: :ref:`NX_CHAR ` Obligatory value: ``translation`` .. index:: vector (field attribute) **@vector**: :ref:`NX_CHAR ` .. index:: offset (field attribute) **@offset**: :ref:`NX_CHAR ` .. index:: depends on (field attribute) **@depends_on**: :ref:`NX_CHAR ` .. index:: fast pixel direction (field) **fast_pixel_direction**: :ref:`NX_NUMBER ` {units=\ :ref:`NX_LENGTH `} Values along the direction of fastest varying pixel direction.The direction itself is given through the vector attribute .. index:: transformation type (field attribute) **@transformation_type**: :ref:`NX_CHAR ` Obligatory value: ``translation`` .. index:: vector (field attribute) **@vector**: :ref:`NX_CHAR ` .. index:: offset (field attribute) **@offset**: :ref:`NX_CHAR ` .. index:: depends on (field attribute) **@depends_on**: :ref:`NX_CHAR ` .. index:: slow pixel direction (field) **slow_pixel_direction**: :ref:`NX_NUMBER ` {units=\ :ref:`NX_LENGTH `} Values along the direction of slow varying pixel direction. The direction itself is given through the vector attribute .. index:: transformation type (field attribute) **@transformation_type**: :ref:`NX_CHAR ` Obligatory value: ``translation`` .. index:: vector (field attribute) **@vector**: :ref:`NX_CHAR ` .. index:: offset (field attribute) **@offset**: :ref:`NX_CHAR ` .. index:: depends on (field attribute) **@depends_on**: :ref:`NX_CHAR ` **(sample)**: :ref:`NXsample` .. index:: name (field) **name**: (optional) :ref:`NX_CHAR ` Descriptive name of sample .. index:: depends on (field) **depends_on**: (optional) :ref:`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. .. index:: temperature (field) **temperature**: (optional) :ref:`NX_CHAR ` {units=\ :ref:`NX_TEMPERATURE `} **(beam)**: :ref:`NXbeam` .. index:: incident wavelength (field) **incident_wavelength**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_WAVELENGTH `} In the case of a monchromatic beam this is the scalar wavelength. In the case of a polychromatic beam this is an array of the wavelengths with the relative weights in incident_wavelength_weight. .. index:: incident wavelength weight (field) **incident_wavelength_weight**: (optional) :ref:`NX_FLOAT ` In the case of a polychromatic beam this is an array of the relative weights of the corresponding wavelengths in incident_wavelength. .. index:: incident wavelength spread (field) **incident_wavelength_spread**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_WAVELENGTH `} The wavelength spread FWHM for the corresponding wavelength(s) in incident_savelength. .. index:: flux (field) **flux**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_FLUX `} flux incident on beam plane area in photons per second per unit area .. index:: total flux (field) **total_flux**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_FREQUENCY `} flux incident on beam plane in photons per second .. index:: incident beam size (field) **incident_beam_size[]**: (optional) :ref:`NX_FLOAT ` {units=\ :ref:`NX_LENGTH `} Two-element array of FWHM (if Gaussian or Airy function) or diameters (if top hat) of beam in the order x, y .. index:: profile (field) **profile**: (optional) :ref:`NX_CHAR ` The beam profile, such as Gaussian, Airy function, or top-hat. .. index:: incident polarisation stokes (field) **incident_polarisation_stokes[np, 4]**: (optional) :ref:`NX_CHAR ` **incident_wavelength_spectrum**: (optional) :ref:`NXdata` **(transformations)**: (optional) :ref:`NXtransformations` Suggested location for sample goniometer or other axes (transformations) **(data)**: :ref:`NXdata` **NXDL Source**: https://github.com/nexusformat/definitions/blob/master/applications/NXmx.nxdl.xml