2.3.3.3.92. NXcxi_ptycho¶
Status:
application definition, extends NXobject
Description:
Application definition for a ptychography experiment, compatible with CXI from v ...
Application definition for a ptychography experiment, compatible with CXI from version 1.6.
This is compatible with CXI from version 1.6 if this application definition is put at the top “entry” level. Above this a “cxi_version” field should be defined. The CXI format is name based, rather than class based, and so it is important to pay attention to the naming convention to be CXI compatible. There are duplications due to the format merger. These should be achieved by linking, with hdf5 Virtual Dataset being used to restructure any data that needs to be remapped. To be fully CXI compatible, all units (including energy) must be in SI units.
An example here is that CXI expects the data to always to have shape (npts_x*npts_y, frame_size_x, frame_size_y). For nexus this is only true for arbitrary scan paths with raster format scans taking shape (npts_x, npts_y, frame_size_x, frame_size_y).
Symbols:
These symbols will be used below to coordinate the shapes of the datasets.
npts_x: The number of points in the x direction
npts_y: Number of points in the y direction.
frame_size_x: Number of detector pixels in x
frame_size_y: Number of detector pixels in y
- Groups cited:
NXbeam, NXcollection, NXdata, NXdetector, NXentry, NXinstrument, NXmonitor, NXsample, NXsource, NXtransformations
Structure:
entry_1: (required) NXentry
start_time: (optional) NX_DATE_TIME ⤆
end_time: (optional) NX_DATE_TIME ⤆
definition: (required) NX_CHAR ⤆
Official NeXus NXDL schema to which this file conforms ...
Official NeXus NXDL schema to which this file conforms
Obligatory value:
NXcxi_ptycho
instrument_1: (required) NXinstrument ⤆
source_1: (required) NXsource ⤆
detector_1: (required) NXdetector ⤆
@axes: (required) NX_CHAR
should have value “[, data]”
@signal: (required) NX_CHAR
should have value “data”
translation: (required) NX_FLOAT {units=NX_LENGTH}
data: (required) NX_INT (Rank: 3 for arbitrary scan, 4 for raster, Dimensions: [npts_x, npts_y, frame_size_x, frame_size_y])
x_pixel_size: (required) NX_FLOAT {units=NX_LENGTH} ⤆
@units: (required) NX_CHAR
y_pixel_size: (required) NX_FLOAT {units=NX_LENGTH} ⤆
@units: (required) NX_CHAR
distance: (required) NX_FLOAT {units=NX_LENGTH} ⤆
The distance between the detector and the sample
@units: (required) NX_CHAR
beam_center_x: (optional) NX_FLOAT {units=NX_LENGTH} ⤆
@units: (required) NX_CHAR
beam_center_y: (optional) NX_FLOAT {units=NX_LENGTH} ⤆
@units: (required) NX_CHAR
transformations: (required) NXtransformations ⤆
data_1: link (suggested target:
/NXentry/NXinstrument/NXdetector/data
)This data must always have shape (npts_x*npts_y, frame_size_x, frame_siz ...
This data must always have shape (npts_x*npts_y, frame_size_x, frame_size_y) regardless of the scan pattern. Use hdf5 virtual dataset to achieve this.
MONITOR: (optional) NXmonitor
data: (required) NX_FLOAT (Rank: 1 for arbitrary scan, 2 for raster, Dimensions: [npts_x, npts_y])
DATA: (required) NXdata
This should be “[x,.]” for arbitrary scanning patterns, and “[x,.,.]” for raster
This should be “data”
x_indices: (required) NX_CHAR
y_indices: (required) NX_CHAR
data: link (suggested target:
/NXentry/NXinstrument/NXdetector/data
)x: link (suggested target:
/NXentry/NXsample/NXtransformations/x
)y: link (suggested target:
/NXentry/NXsample/NXtransformations/y
)data_1: (required) NXcollection
To ensure CXI compatibility the data in this group must always have shape that ...
To ensure CXI compatibility the data in this group must always have shape that is (npts_x*npts_y, frame_size_x, frame_size_y). For nexus-style raster scans it is proposed that hdf5 virtual dataset is used.
data: link (suggested target:
/NXentry/NXinstrument/NXdetector/data
)translation: link (suggested target:
/NXentry/NXinstrument/NXdetector/translation
)sample_1: (required) NXsample
transformations: (required) NXtransformations ⤆
This must contain two fields with the x and y motors that are linked via the ...
This must contain two fields with the x and y motors that are linked via the dependency tree according to the real-life motor layout dependency. For raster scans x and y will have shape (npts_x, npts_y) For arbitrary scans x and y will be (npts_x*npts_y,) An attribute with the units for each motor is required.
@vector: (required) NX_NUMBER
geometry_1: (required) NXcollection
translation: link (suggested target:
/NXentry/NXinstrument/NXdetector/translation
)
Hypertext Anchors¶
List of hypertext anchors for all groups, fields, attributes, and links defined in this class.
/NXcxi_ptycho/entry_1/instrument_1/beam_1/energy@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/beam_1/extent@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/beam_1/incident_beam_divergence-field
/NXcxi_ptycho/entry_1/instrument_1/beam_1/incident_beam_divergence@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/beam_1/incident_beam_energy-field
/NXcxi_ptycho/entry_1/instrument_1/beam_1/incident_beam_energy@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/beam_1/incident_energy_spread-field
/NXcxi_ptycho/entry_1/instrument_1/beam_1/incident_energy_spread@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/detector_1/beam_center_x-field
/NXcxi_ptycho/entry_1/instrument_1/detector_1/beam_center_x@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/detector_1/beam_center_y-field
/NXcxi_ptycho/entry_1/instrument_1/detector_1/beam_center_y@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/detector_1/distance-field
/NXcxi_ptycho/entry_1/instrument_1/detector_1/distance@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/detector_1/transformations-group
/NXcxi_ptycho/entry_1/instrument_1/detector_1/transformations/vector-field
/NXcxi_ptycho/entry_1/instrument_1/detector_1/translation-field
/NXcxi_ptycho/entry_1/instrument_1/detector_1/translation@axes-attribute
/NXcxi_ptycho/entry_1/instrument_1/detector_1/translation@interpretation-attribute
/NXcxi_ptycho/entry_1/instrument_1/detector_1/translation@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/detector_1/x_pixel_size-field
/NXcxi_ptycho/entry_1/instrument_1/detector_1/x_pixel_size@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/detector_1/y_pixel_size-field
/NXcxi_ptycho/entry_1/instrument_1/detector_1/y_pixel_size@units-attribute
/NXcxi_ptycho/entry_1/instrument_1/detector_1@axes-attribute
/NXcxi_ptycho/entry_1/instrument_1/detector_1@signal-attribute