diff --git a/_sources/introduction.rst.txt b/_sources/introduction.rst.txt index 33a8416..93f026b 100644 --- a/_sources/introduction.rst.txt +++ b/_sources/introduction.rst.txt @@ -35,11 +35,10 @@ is approximately perpendicular to the beam. Images are collected on an area detector placed in transmission geometry behind the sample. Many area detectors consist of a set of chips with small gaps between them, so sample rotation scans are often repeated multiple times (typically -three) with small detector translations between each one to fill in -these gaps. However, it is also possible to accomplish this just by -adjusting the orientation of the rotation axis itself. *NXRefine* -reduces the data independently for each rotation scan before merging -them to create a single 3D data volume. +three) to fill in the missing data, with small detector translations +between each scan and/or changes to the orientation of the rotation +axis. *NXRefine* reduces the data independently for each rotation scan +before merging them to create a single 3D data volume. .. figure:: /images/experimental-geometry.png :align: center @@ -187,23 +186,24 @@ from the goniometer center to the detector, at the point where the incident beam would intersect, is :math:`l_{sd}`. The incident beam wavelength is :math:`\lambda`. -In the refinement procedure implemented by *NXRefine*, the orientation -matrix, :math:`\mathcal{U}`, is generated by selecting two Bragg peaks, -whose (*h*, *k*, *l*) values are determined using initial estimates of -the instrument angles and the sample *d*-spacings. θ, ω, χ, and Φ are -initially set to their nominal motor angles, while the position and tilt -angles of the detector are estimated using a powder calibrant. It is -assumed that the space group and approximate lattice parameters are -known in advance, allowing an original estimate of the -:math:`\mathcal{B}` matrix to be derived. Once the two peaks have been +In the refinement procedure implemented by *NXRefine*, it is assumed +that the space group and approximate lattice parameters are known in +advance, allowing an original estimate of the :math:`\mathcal{B}` matrix +to be derived. The orientation matrix, :math:`\mathcal{U}`, is then +generated by selecting two Bragg peaks, whose (*h*, *k*, *l*) values are +determined using initial estimates of the instrument angles and the +sample *d*-spacings. θ, ω, χ, and Φ are initially set to their nominal +motor angles, while the position and tilt angles of the detector are +estimated using a powder calibrant. Once the two peaks have been selected, they are used to produce an initial estimate of :math:`\mathcal{U}`, from which all the other peaks are assigned (*h*, *k*, *l*) indices. If these assignments are reasonable, then a large number of peaks are used to refine both the instrumental and sample parameters in order to minimize discrepancies between the calculated and measured peak positions, allowing :math:`\mathcal{U}` to be optimized. -If few peaks are assigned with reasonable accuracy by the selection of -the initial two peaks, it is necessary to select two different peaks. +If only a few peaks are assigned with reasonable accuracy by the +selection of the initial two peaks, it may be necessary to select two +different peaks. The refinement process, along with the tools that *NXRefine* provide to facilitate peak assignments, are described in a later section. diff --git a/introduction.html b/introduction.html index eee375d..0ca3669 100644 --- a/introduction.html +++ b/introduction.html @@ -75,11 +75,10 @@

Experimental GeometryNXRefine -reduces the data independently for each rotation scan before merging -them to create a single 3D data volume.

+three) to fill in the missing data, with small detector translations +between each scan and/or changes to the orientation of the rotation +axis. NXRefine reduces the data independently for each rotation scan +before merging them to create a single 3D data volume.

_images/experimental-geometry.png

Example of the experimental geometry used in NXRefine, with the @@ -209,23 +208,24 @@

Sample Orientation\(l_{sd}\). The incident beam wavelength is \(\lambda\).

-

In the refinement procedure implemented by NXRefine, the orientation -matrix, \(\mathcal{U}\), is generated by selecting two Bragg peaks, -whose (h, k, l) values are determined using initial estimates of -the instrument angles and the sample d-spacings. θ, ω, χ, and Φ are -initially set to their nominal motor angles, while the position and tilt -angles of the detector are estimated using a powder calibrant. It is -assumed that the space group and approximate lattice parameters are -known in advance, allowing an original estimate of the -\(\mathcal{B}\) matrix to be derived. Once the two peaks have been +

In the refinement procedure implemented by NXRefine, it is assumed +that the space group and approximate lattice parameters are known in +advance, allowing an original estimate of the \(\mathcal{B}\) matrix +to be derived. The orientation matrix, \(\mathcal{U}\), is then +generated by selecting two Bragg peaks, whose (h, k, l) values are +determined using initial estimates of the instrument angles and the +sample d-spacings. θ, ω, χ, and Φ are initially set to their nominal +motor angles, while the position and tilt angles of the detector are +estimated using a powder calibrant. Once the two peaks have been selected, they are used to produce an initial estimate of \(\mathcal{U}\), from which all the other peaks are assigned (h, k, l) indices. If these assignments are reasonable, then a large number of peaks are used to refine both the instrumental and sample parameters in order to minimize discrepancies between the calculated and measured peak positions, allowing \(\mathcal{U}\) to be optimized. -If few peaks are assigned with reasonable accuracy by the selection of -the initial two peaks, it is necessary to select two different peaks.

+If only a few peaks are assigned with reasonable accuracy by the +selection of the initial two peaks, it may be necessary to select two +different peaks.

The refinement process, along with the tools that NXRefine provide to facilitate peak assignments, are described in a later section.

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