diff --git a/base_classes/NXchamber.nxdl.xml b/base_classes/NXchamber.nxdl.xml new file mode 100644 index 0000000000..bf552400c0 --- /dev/null +++ b/base_classes/NXchamber.nxdl.xml @@ -0,0 +1,57 @@ + + + +<<<<<<<< HEAD:base_classes/NXchamber.nxdl.xml + + + Base class for a chamber in an instrument that stores real or simulated objects. + + + + Given name for the chamber of this component e.g. analysis chamber + or buffer chamber, load-lock chamber, microscope column, glove box. + + + + + Free-text field for describing details about the chamber. + For example out of which material was the chamber built. + + + +======== + + + Base class for simulation of ion extraction from matter via laser and/or voltage + pulsing. + + + + + +>>>>>>>> upstream/main:base_classes/NXapm_simulation.nxdl.xml + diff --git a/base_classes/NXroi.nxdl.xml b/base_classes/NXroi.nxdl.xml new file mode 100644 index 0000000000..94857e74cb --- /dev/null +++ b/base_classes/NXroi.nxdl.xml @@ -0,0 +1,34 @@ + + + + + + Base class to describe a region-of-interest analyzed. + + + + Details about processing steps. + + + + diff --git a/base_classes/NXsingle_crystal.nxdl.xml b/base_classes/NXsingle_crystal.nxdl.xml new file mode 100644 index 0000000000..44f6e92c30 --- /dev/null +++ b/base_classes/NXsingle_crystal.nxdl.xml @@ -0,0 +1,72 @@ + + + + + + Description of a single crystal material or a single crystalline phase in a material. + + There is the option of using Busing-Levy convention (as orginally designed in NXsample) + or using a more detailed description with NXrotation_set. + + + + This will follow the Busing-Levy convention: + W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464 + + + + + + + + Orientation matrix of single crystal sample using Busing-Levy convention: + W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464 + + + + + + + + + UB matrix of single crystal sample using Busing-Levy convention: + W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464. This is + the multiplication of the orientation_matrix, given above, + with the :math:`B` matrix which can be derived from the lattice constants. + + + + + + + + + Detailed description of single crystal orientation and misorientation. + + + + + Unit cell of the single crystal. + + + diff --git a/base_classes/NXstage_lab.nxdl.xml b/base_classes/NXstage_lab.nxdl.xml new file mode 100644 index 0000000000..84f83789a8 --- /dev/null +++ b/base_classes/NXstage_lab.nxdl.xml @@ -0,0 +1,173 @@ + + + + + + Base class for a stage (lab) used to hold, orient, and prepare a specimen. + + Modern stages are multi-functional devices. Stages provide a controlled + environment around the specimen. Stages enable experimentalists to apply + controlled external stimuli on the specimen. A stage_lab is a multi-purpose + /-functional tool that is constructed from multiple actuators, sensors, + and other components. + + With such stages comes the need for storing various (meta)data + that are generated while working and modifying the sample. + + Modern stages realize a hierarchy of components. Two examples are given to help + clarify how :ref:`NXstage_lab` instances should be used: Take a specimen that is + mounted on a multi-axial tilt rotation holder. This holder is fixed in the + support unit which connects the holder to the rest of the instrument. + Evidently different components are all considerable as to represent instances + of stages. + + In another example, taken from atom probe microscopy, researchers may work + with wire samples which are clipped into a larger fixing unit to enable + careful specimen handling. Alternatively, a microtip is a silicon post + upon which e.g. an atom probe specimen is mounted. + Multiple microtips are grouped into a microtip array to conveniently enable + loading of multiple specimens into the instrument with fewer operations. + That microtip array is fixed on a holder. Fixture units in atom probe are known + as stubs. Stubs in turn are positioned onto pucks. Pucks are then loaded onto + carousels. A carousel is a carrier unit with which eventually entire sets of + specimens can be moved in between parts of the microscope. All of these units + can be considered stage_lab instances. + + The :ref:`NXstage_lab` base class reflects this hierarchy. To cover for an as flexible + design of complex stages as possible, users should nest multiple instances of + :ref:`NXstage_lab` according to their needs to reflect the differences between what + they consider as the holder and what they consider is the stage. + The alias field can be used to specify the community jargon if necessary. + + However, a much clearer approach to reflect the hierarchy of all :ref:`NXstage_lab` + instances is postfix each instance named stage_lab with integers starting + from 1 as the top level unit. + In the microtip example one could thus use stage_lab1 for the microtip, + stage_lab2 for the microtip array, stage_lab3 holder, etc. + The depends_on keyword should be used to additional clarify the hierarchy + especially when users decide to not follow the above-mentioned postfixing + notation or when is not obvious from the postfixes which stage_lab is at + which level of the stage_lab hierarchy. + + Some examples for stage_labs in applications: + + * A nanoparticle on a copper grid. The copper grid is the holder. + The grid itself is fixed to a stage. + * An atom probe specimen fixed in a stub. In this case the stub can be + considered the holder, while the cryostat temperature control unit is + a component of the stage. + * Samples with arrays of specimens, like a microtip on a microtip array + is an example of an at least three-layer hierarchy commonly employed for + efficient sequential processing of atom probe experiments. + * With one entry of an application definition only one microtip should be + described. Therefore, the microtip is the specimen, + the array is the holder and the remaining mounting unit + that is attached to the cryo-controller is the stage. + * For in-situ experiments with e.g. chips with read-out electronics + as actuators, the chips are again placed in a larger unit. A typical + example are in-situ experiments using e.g. the tools of `Protochips <https://www.protochips.com>`_. + * Other examples are (quasi) in-situ experiments where experimentalists + anneal or deform the specimen via e.g. in-situ tensile testing machines + which are mounted on the specimen holder. + + For specific details and inspiration about stages in electron microscopes: + + * `Holders with multiple axes <https://www.nanotechnik.com/e5as.html>`_ + * `Chip-based designs <https://www.protochips.com/products/fusion/fusion-select-components/>`_ + * `Further chip-based designs <https://www.nanoprobetech.com/about>`_ + * `Stages in transmission electron microscopy <https://doi.org/10.1007/978-3-662-14824-2>`_ (page 103, table 4.2) + * `Further stages in transmission electron microscopy <https://doi.org/10.1007/978-1-4757-2519-3>`_ (page 124ff) + * `Specimens in atom probe <https://doi.org/10.1007/978-1-4614-8721-0>`_ (page 47ff) + * `Exemplar micro-manipulators <https://nano.oxinst.com/products/omniprobe/omniprobe-200>`_ + + We are looking forward to suggestions from the scientists. + + + + Principal design of the stage. + + Exemplar terms could be side_entry, top_entry, + single_tilt, quick_change, multiple_specimen, + bulk_specimen, double_tilt, tilt_rotate, + heating_chip, atmosphere_chip, + electrical_biasing_chip, liquid_cell_chip + + + + + Free-text field to give a term how that a stage_lab at this level of the + stage_lab hierarchy is commonly referred to. Examples could be stub, + puck, carousel, microtip, clip, holder, etc. + + + + + The interpretation of this tilt should be specialized + and thus detailed via the application definition. + + + + + The interpretation of this tilt should be specialized + and thus detailed via the application definition. + + + + + The interpretation of this rotation should be specialized + and thus detailed via the application definition. + + + + + The interpretation of this position should be specialized + and thus detailed via the application definition. + + + + + + + + Voltage applied to the stage to decelerate electrons. + + + + + + +