api.rst

API

Defining the various parts of a nexus file

.. autoclass:: nexgen.utils.Point3D

Axes

.. automodule:: nexgen.nxs_utils.axes
    :members:
    :show-inheritance:

Scans

.. automodule:: nexgen.nxs_utils.scan_utils
    :members: identify_osc_axis, identify_grid_scan_axes, calculate_scan_points

.. autoclass:: nexgen.nxs_utils.scan_utils.GridScanOptions
    :members:

.. autoexception:: nexgen.nxs_utils.scan_utils.ScanAxisNotFoundError

.. autoexception:: nexgen.nxs_utils.scan_utils.ScanAxisError

Goniometer

.. automodule:: nexgen.nxs_utils.goniometer
    :members:

Detector

.. automodule:: nexgen.nxs_utils.detector
    :members:
    :inherited-members:
    :show-inheritance:

Source

.. automodule:: nexgen.nxs_utils.source
    :members:
    :show-inheritance:

Sample

.. automodule:: nexgen.nxs_utils.sample
    :members:
    :show-inheritance:

Writing tools

NXmx writers

For a standard NXmx data collection

.. autoclass:: nexgen.nxs_write.nxmx_writer.NXmxFileWriter
    :members:
    :show-inheritance:

For an event-mode data collection using a Tristan detector

.. autoclass:: nexgen.nxs_write.nxmx_writer.EventNXmxFileWriter
    :members:
    :show-inheritance:

For an Electron Diffraction collection using NXmx-like format nexus files. When dealing with an Electron Diffraction dataset, there may also be a need to convert the vectors to mcstas from another coordinate system convention, as well as save the relevant information about the new coordinate system into a NXcoordinate_system_set base class. This writer takes care of these issues.

.. autoclass:: nexgen.nxs_write.nxmx_writer.EDNXmxFileWriter
    :members:
    :show-inheritance:
    :inherited-members:

NXclass writers

All the NXclass writers available can be found in:

.. automodule:: nexgen.nxs_write.NXclassWriters
    :members:

Old tools

Note

Tools such as ScanReader and write_nexus_from_scope have been deprecated as of version 0.8.0. The functionality of call_writers has also been changed.

.. autofunction:: nexgen.command_line.cli_utils.call_writers

Writing blank datasets

Generating blank images

Using an Eiger or Tristan detector mask ...

.. autofunction:: nexgen.tools.data_writer.build_an_eiger

.. autofunction:: nexgen.tools.data_writer.build_a_tristan

.. autofunction:: nexgen.tools.data_writer.generate_image_files

Generating pseudo-events

.. autofunction:: nexgen.tools.data_writer.pseudo_event_list

.. autofunction:: nexgen.tools.data_writer.generate_event_files

VDS writer

.. automodule:: nexgen.tools.vds_tools
    :members:

Copying tools

.. automodule:: nexgen.nxs_copy.copy_nexus
    :members:

.. automodule:: nexgen.nxs_copy.copy_tristan_nexus
    :members:

Utilities

.. automodule:: nexgen.utils
    :members:

Writing tools

.. automodule:: nexgen.nxs_write.write_utils
    :members:

Copying tools

.. automodule:: nexgen.nxs_copy.copy_utils
    :members:

HDF5 metafile reader

Metafile definition:

.. automodule:: nexgen.tools.metafile
    :members:
    :show-inheritance:

When operating a Dectris detector, the goniometer and detector axes values are usually stored in the config/ dataset.

.. autofunction:: nexgen.tools.meta_reader.update_axes_from_meta

If there's a need to write a VDS dataset from data collected on a Dectris detector, it might be useful to first find out the data type using the information stored in the meta file.

.. autofunction:: nexgen.tools.meta_reader.define_vds_data_type

Reader for Singla detector master file

.. autoclass:: nexgen.tools.ED_tools.SinglaMaster
    :members:

.. autofunction:: nexgen.tools.ED_tools.extract_from_SINGLA_master

Tools to calculate the beam center of an Electron Diffraction experiment:

.. autofunction:: nexgen.tools.ED_tools.centroid_max

.. autofunction:: nexgen.tools.ED_tools.find_beam_centre

Logging configuration

.. automodule:: nexgen.log
    :members: