deploy: 51b45c7

_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.

introduction.html

@@ -75,11 +75,10 @@ <h2>Experimental Geometry<a class="headerlink" href="#experimental-geometry" tit
 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. <em>NXRefine</em>
-reduces the data independently for each rotation scan before merging
-them to create a single 3D data volume.</p>
+three) to fill in the missing data, with small detector translations
+between each scan and/or changes to the orientation of the rotation
+axis. <em>NXRefine</em> reduces the data independently for each rotation scan
+before merging them to create a single 3D data volume.</p>
 <div class="figure align-center" id="id1">
 <a class="reference internal image-reference" href="_images/experimental-geometry.png"><img alt="_images/experimental-geometry.png" src="_images/experimental-geometry.png" style="width: 80%;" /></a>
 <p class="caption"><span class="caption-text"><em>Example of the experimental geometry used in NXRefine, with the
@@ -209,23 +208,24 @@ <h2>Sample Orientation<a class="headerlink" href="#sample-orientation" title="Pe
 from the goniometer center to the detector, at the point where the
 incident beam would intersect, is <span class="math notranslate nohighlight">\(l_{sd}\)</span>. The incident beam
 wavelength is <span class="math notranslate nohighlight">\(\lambda\)</span>.</p>
-<p>In the refinement procedure implemented by <em>NXRefine</em>, the orientation
-matrix, <span class="math notranslate nohighlight">\(\mathcal{U}\)</span>, is generated by selecting two Bragg peaks,
-whose (<em>h</em>, <em>k</em>, <em>l</em>) values are determined using initial estimates of
-the instrument angles and the sample <em>d</em>-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
-<span class="math notranslate nohighlight">\(\mathcal{B}\)</span> matrix to be derived. Once the two peaks have been
+<p>In the refinement procedure implemented by <em>NXRefine</em>, it is assumed
+that the space group and approximate lattice parameters are known in
+advance, allowing an original estimate of the <span class="math notranslate nohighlight">\(\mathcal{B}\)</span> matrix
+to be derived. The orientation matrix, <span class="math notranslate nohighlight">\(\mathcal{U}\)</span>, is then
+generated by selecting two Bragg peaks, whose (<em>h</em>, <em>k</em>, <em>l</em>) values are
+determined using initial estimates of the instrument angles and the
+sample <em>d</em>-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
 <span class="math notranslate nohighlight">\(\mathcal{U}\)</span>, from which all the other peaks are assigned (<em>h</em>,
 <em>k</em>, <em>l</em>) 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 <span class="math notranslate nohighlight">\(\mathcal{U}\)</span> 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.</p>
+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.</p>
 <p>The refinement process, along with the tools that <em>NXRefine</em> provide to
 facilitate peak assignments, are described in a later section.</p>
 </div>