From 866d6240d82e92ae3afb8a63f8e22a1e71cdfc08 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 17 Jan 2025 14:24:10 +0100 Subject: [PATCH] Completing first round of edits on base classes for NXem --- base_classes/NXoptical_system_em.nxdl.xml | 36 +++++++++++++----- .../NXprocessing_reference_frame.nxdl.xml | 16 +++++--- base_classes/NXscanbox_em.nxdl.xml | 35 ------------------ base_classes/NXstage_lab.nxdl.xml | 37 +++++-------------- 4 files changed, 47 insertions(+), 77 deletions(-) diff --git a/base_classes/NXoptical_system_em.nxdl.xml b/base_classes/NXoptical_system_em.nxdl.xml index c75949aec..a49fd020d 100644 --- a/base_classes/NXoptical_system_em.nxdl.xml +++ b/base_classes/NXoptical_system_em.nxdl.xml @@ -99,6 +99,31 @@ The unit of the nominal dose rate is e-/(angstrom^2*s). + + Nominal dose rate. + + + + In the process of passing through an :ref:`NXlens_em` electrons are typically accelerated + on a helical path about the optical axis. This causes an image rotation whose strength + is affected by the magnification. + + Microscopes may be equipped with compensation methods (implemented in hardware + or software) that reduce but not necessarily eliminate this rotation. + + See `L. Reimer <https://doi.org/10.1007/978-3-540-38967-5>`_ for details. + + + + + Distance which lies between the principal plane of the lens and the focal point + along the optical axis. + + This concept is related to term `Focal Length`_ of the EMglossary standard. + + .. _Focal Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000029 + + Details about an imaging setting used during acquisition to correct perspective @@ -127,14 +152,5 @@ .. _Dynamic Refocusing: https://purls.helmholtz-metadaten.de/emg/EMG_00000017 - - - Distance which lies between the principal plane of the lens and the focal point - along the optical axis. - - This concept is related to term `Focal Length`_ of the EMglossary standard. - - .. _Focal Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000029 - - + diff --git a/base_classes/NXprocessing_reference_frame.nxdl.xml b/base_classes/NXprocessing_reference_frame.nxdl.xml index 1fdf7c9b3..1b420d686 100644 --- a/base_classes/NXprocessing_reference_frame.nxdl.xml +++ b/base_classes/NXprocessing_reference_frame.nxdl.xml @@ -23,12 +23,17 @@ --> - Details about eventually relevant named directions that may give - reasons for anisotropies. + Base class to document details about processing reference frames. - The classical example is mechanical processing where one has to - specify which directions (e.g. rolling, transverse, and normal - direction) align how with the direction of the base vectors of the + Directional differences in processing materials can cause anisotropies + of material properties. Mechanical processing is one example where + the rotation of the NXsample_reference_frame with respect to another + processing_reference_frame is relevant. + + Fields with suffix alias should be used to specify + + how the base vectors of the reference frame for the (macroscopic) sampleare aligned different + directions (e.g. rolling, transverse, and normal direction) align how with the direction of the base vectors of the :ref:`NXsample_reference_frame`. It is assumed that the configuration is inspected by looking towards @@ -43,6 +48,7 @@ the base vectors of this coordinate system as :math:`X_p, Y_p, Z_p`. + Alias diff --git a/base_classes/NXscanbox_em.nxdl.xml b/base_classes/NXscanbox_em.nxdl.xml index 36be13cbd..417c6df45 100644 --- a/base_classes/NXscanbox_em.nxdl.xml +++ b/base_classes/NXscanbox_em.nxdl.xml @@ -46,16 +46,6 @@ of reproducibility in the way how the beam is scanned over the surface. - - - TODO discuss with the electron microscopists. - - - - - TODO discuss with the electron microscopists. - - @@ -76,31 +66,6 @@ .. _Flyback Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000028 - - - TODO discuss with the electron microscopists. - - - - - TODO discuss with the electron microscopists. - - - - - TODO discuss with the electron microscopists. - - - - - TODO discuss with the electron microscopists. - - - - - TODO discuss with the electron microscopists. - - diff --git a/base_classes/NXstage_lab.nxdl.xml b/base_classes/NXstage_lab.nxdl.xml index be12b82c8..03134db79 100644 --- a/base_classes/NXstage_lab.nxdl.xml +++ b/base_classes/NXstage_lab.nxdl.xml @@ -100,48 +100,45 @@ * `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, + 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 + electrical_biasing_chip, or 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. + Free-text field to give a term how that stage_lab instance 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. + via an application definition. The interpretation of this tilt should be specialized - and thus detailed via the application definition. + via an application definition. The interpretation of this rotation should be specialized - and thus detailed via the application definition. + via an application definition. The interpretation of this position should be specialized - and thus detailed via the application definition. + via an application definition. @@ -155,19 +152,5 @@ - +