deploy: 1e84aba

_sources/experiment.rst.txt

@@ -16,34 +16,38 @@ the storage of x-ray and neutron scattering data. There is a single
 NeXus file associated with each measurement, which consists of one or
 more rotation scans usually at a single temperature or other parametric
 variable. This file contains all the information required for a complete
-analysis, external links to the raw data, beamline monitors, powder
-diffaction calibrations, and metadata generated by the data reduction workflow.
+analysis, including external links to the raw data, beamline monitors,
+powder diffaction calibrations, and metadata generated by the data
+reduction workflow.
 
 In this section, we will describe the *NXRefine* directory framework,
 explaining where the NeXus files are stored and how they are linked to
 the reduced data transformed into reciprocal space. At the beginning of
 each new experiment, the GUI dialogs launched from the :ref:`Experiment
 Menu` can be used to create the experiment directories, NeXus file
-templates, and new NeXus files corresponding to the proposed scans.
+templates, and new NeXus files based on those templates to contain scan
+data.
 
 Experiment Layout
 =================
 In *NXRefine*, it is assumed that all the files associated with a
 particular experiment are stored in a single directory. At synchrotron
 x-ray facilities, it is common to schedule all the measurements
-associated with a particular proposal together, so they would be
-labelled by the proposal number and/or run cycle. For example, on
-beamline 6-ID-D at the Advanced Photon Source, measurements resulting
-from Proposal No. GUP-75969 may be scheduled in a specific run cycle,
-say 23-1, and stored in, *e.g.*, ``/data/6-id-d/GUP-75969-23-1``. This
-directory should contain sub-directories that conform to a particular
-layout, with calibration files stored in the directory ``calibrations``,
-NeXus files containing measurement templates stored in
-``configurations``, settings and log files stored in ``tasks``, and
-experimental data from each sample stored in separate directories with a
-descriptive name. These sample directories then contain sub-directories
-for each crystal, measured during the experiment, containing the
-measured data.
+associated with a particular proposal together, associated with a
+proposal number and/or run cycle. For example, on beamline 6-ID-D at the
+Advanced Photon Source, measurements resulting from Proposal No.
+GUP-75969 may be scheduled in a specific run cycle, say 23-1, and stored
+in, *e.g.*, ``/data/6-id-d/GUP-75969-23-1``. This directory should
+contain sub-directories that conform to a particular layout, with
+calibration files stored in the directory ``calibrations``, NeXus files
+containing measurement templates stored in ``configurations``, settings
+and log files stored in ``tasks``, and experimental data from each
+sample stored in separate directories with a name that is typically
+derived from the chemical formula or a commonly used abbreviation. It is
+common to test and/or measure multiple crystals with the same chemical
+formula, so each of the sample directories contain sub-directories for
+each measured crystal. These contain the NeXus files for each scan and
+linked sub-directories containing the raw data.
 
 Here is the structure of a possible experiment directory. Most of the
 names in this example are chosen to be generic, *i.e.*, they will be
@@ -83,18 +87,18 @@ different for every experiment. The only exceptions are the files in the
     ├── sample2
     ├── sample3
 
-The aim of this directory structure is for all the data and metadata
+The goal of this directory structure is for all the data and metadata
 required to analyze the results to be stored in an easily accessible
 location, although not all files are required by *NXRefine* to be
 present. For example, the powder calibration files can be imported from
 any location.
 
 If an instrument does not exclusively use *NXRefine* for its data
-reduction, it is possible that there already exists a directory
-containing the files that comprise an experiment as described above. To
-avoid any interference with other instrument files, it is possible to
-create the above directory structure within a sub-directory, usually
-called ``nxrefine``, of the instrument's ``experiment`` directory.::
+reduction, it is possible that an experiment directory already exists.
+If so, in order to avoid any interference with other instrument files,
+it is possible to create the above directory structure within a
+sub-directory, called ``nxrefine``, contained within the existing
+``experiment`` directory.::
 
     experiment
     └── nxrefine
@@ -109,9 +113,8 @@ called ``nxrefine``, of the instrument's ``experiment`` directory.::
         .
 
 .. note:: The name of this sub-directory is defined in the server
-          settings, which are described below. Although it can have any
-          name, it is strongly recommended that it be called
-          ``nxrefine`` to simplify parsing of the directory tree.
+          settings, which are described below. It is strongly recommended that it be called by the default name, *i.e.*,
+          ``nxrefine`` to facilitate parsing of the directory tree.
 
 Experiment Sub-Directories
 ==========================
@@ -134,15 +137,25 @@ Experiment Sub-Directories
     NeXus files (described below). The files don't have to be stored in
     this sub-directory, but if they are in another location, it is
     recommended to copy them here for completeness. If the calibrations
-    have been performed by another package, the PONI parameters can be
+    have been performed by another package, the parameters can be
     imported directly from a PONI file.
 
 **configurations**
     The ``configurations`` sub-directory contains NeXus files that act
-    as templates when creating the files used to store the scan results.
-    These files contain scan parameters, such as the goniometer angles,
-    for one or more sample rotations, and are initialized by a *NeXpy*
-    GUI dialog.
+    as templates to be used when creating the files used to store the
+    scan results. There should be a separate template file for each new
+    experimental configuration, *.e.g.*, with a different wavelength or
+    detector distance. If multiple sample rotations are to be performed
+    with different detector translations and/or goniometer angles, the
+    corresponding template files will have entries for each scan
+    containing pre-defined values of the scan variables. These files are
+    initialized by a *NeXpy* GUI dialog.
+
+.. note:: On QM2 at CHESS, it is usually only necessary
+          to create template files with a single entry, since the
+          number of rotation scans is not always pre-determined. When
+          the scans are imported, additional entries are automatically
+          added with the goniometer angles updated with the values in the corresponding scan SPEC file. 
 
 **scripts**
     The ``scripts`` sub-directory is not used directly by *NXRefine*,

_sources/installation.rst.txt

@@ -137,5 +137,5 @@ User Support
 ------------
 If you are interested in using this package, please contact Ray Osborn 
 ([email protected]). Please report any bugs as a 
-`Github issue <https://github.com/nxrefine/nxrefine/issues>`_, with
+`Github issue <https://github.com/nexpy/nxrefine/issues>`_, with
 relevant tracebacks.

experiment.html

@@ -57,31 +57,35 @@ <h1>Experiment Configuration<a class="headerlink" href="#experiment-configuratio
 NeXus file associated with each measurement, which consists of one or
 more rotation scans usually at a single temperature or other parametric
 variable. This file contains all the information required for a complete
-analysis, external links to the raw data, beamline monitors, powder
-diffaction calibrations, and metadata generated by the data reduction workflow.</p>
+analysis, including external links to the raw data, beamline monitors,
+powder diffaction calibrations, and metadata generated by the data
+reduction workflow.</p>
 <p>In this section, we will describe the <em>NXRefine</em> directory framework,
 explaining where the NeXus files are stored and how they are linked to
 the reduced data transformed into reciprocal space. At the beginning of
 each new experiment, the GUI dialogs launched from the <a class="reference internal" href="experiment-menu.html#experiment-menu"><span class="std std-ref">Experiment Menu</span></a> can be used to create the experiment directories, NeXus file
-templates, and new NeXus files corresponding to the proposed scans.</p>
+templates, and new NeXus files based on those templates to contain scan
+data.</p>
 <div class="section" id="experiment-layout">
 <h2>Experiment Layout<a class="headerlink" href="#experiment-layout" title="Permalink to this headline">¶</a></h2>
 <p>In <em>NXRefine</em>, it is assumed that all the files associated with a
 particular experiment are stored in a single directory. At synchrotron
 x-ray facilities, it is common to schedule all the measurements
-associated with a particular proposal together, so they would be
-labelled by the proposal number and/or run cycle. For example, on
-beamline 6-ID-D at the Advanced Photon Source, measurements resulting
-from Proposal No. GUP-75969 may be scheduled in a specific run cycle,
-say 23-1, and stored in, <em>e.g.</em>, <code class="docutils literal notranslate"><span class="pre">/data/6-id-d/GUP-75969-23-1</span></code>. This
-directory should contain sub-directories that conform to a particular
-layout, with calibration files stored in the directory <code class="docutils literal notranslate"><span class="pre">calibrations</span></code>,
-NeXus files containing measurement templates stored in
-<code class="docutils literal notranslate"><span class="pre">configurations</span></code>, settings and log files stored in <code class="docutils literal notranslate"><span class="pre">tasks</span></code>, and
-experimental data from each sample stored in separate directories with a
-descriptive name. These sample directories then contain sub-directories
-for each crystal, measured during the experiment, containing the
-measured data.</p>
+associated with a particular proposal together, associated with a
+proposal number and/or run cycle. For example, on beamline 6-ID-D at the
+Advanced Photon Source, measurements resulting from Proposal No.
+GUP-75969 may be scheduled in a specific run cycle, say 23-1, and stored
+in, <em>e.g.</em>, <code class="docutils literal notranslate"><span class="pre">/data/6-id-d/GUP-75969-23-1</span></code>. This directory should
+contain sub-directories that conform to a particular layout, with
+calibration files stored in the directory <code class="docutils literal notranslate"><span class="pre">calibrations</span></code>, NeXus files
+containing measurement templates stored in <code class="docutils literal notranslate"><span class="pre">configurations</span></code>, settings
+and log files stored in <code class="docutils literal notranslate"><span class="pre">tasks</span></code>, and experimental data from each
+sample stored in separate directories with a name that is typically
+derived from the chemical formula or a commonly used abbreviation. It is
+common to test and/or measure multiple crystals with the same chemical
+formula, so each of the sample directories contain sub-directories for
+each measured crystal. These contain the NeXus files for each scan and
+linked sub-directories containing the raw data.</p>
 <p>Here is the structure of a possible experiment directory. Most of the
 names in this example are chosen to be generic, <em>i.e.</em>, they will be
 different for every experiment. The only exceptions are the files in the
@@ -120,17 +124,17 @@ <h2>Experiment Layout<a class="headerlink" href="#experiment-layout" title="Perm
 ├── sample3
 </pre></div>
 </div>
-<p>The aim of this directory structure is for all the data and metadata
+<p>The goal of this directory structure is for all the data and metadata
 required to analyze the results to be stored in an easily accessible
 location, although not all files are required by <em>NXRefine</em> to be
 present. For example, the powder calibration files can be imported from
 any location.</p>
 <p>If an instrument does not exclusively use <em>NXRefine</em> for its data
-reduction, it is possible that there already exists a directory
-containing the files that comprise an experiment as described above. To
-avoid any interference with other instrument files, it is possible to
-create the above directory structure within a sub-directory, usually
-called <code class="docutils literal notranslate"><span class="pre">nxrefine</span></code>, of the instrument’s <code class="docutils literal notranslate"><span class="pre">experiment</span></code> directory.:</p>
+reduction, it is possible that an experiment directory already exists.
+If so, in order to avoid any interference with other instrument files,
+it is possible to create the above directory structure within a
+sub-directory, called <code class="docutils literal notranslate"><span class="pre">nxrefine</span></code>, contained within the existing
+<code class="docutils literal notranslate"><span class="pre">experiment</span></code> directory.:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>experiment
 └── nxrefine
     ├── tasks
@@ -147,14 +151,13 @@ <h2>Experiment Layout<a class="headerlink" href="#experiment-layout" title="Perm
 <div class="admonition note">
 <p class="admonition-title">Note</p>
 <p>The name of this sub-directory is defined in the server
-settings, which are described below. Although it can have any
-name, it is strongly recommended that it be called
-<code class="docutils literal notranslate"><span class="pre">nxrefine</span></code> to simplify parsing of the directory tree.</p>
+settings, which are described below. It is strongly recommended that it be called by the default name, <em>i.e.</em>,
+<code class="docutils literal notranslate"><span class="pre">nxrefine</span></code> to facilitate parsing of the directory tree.</p>
 </div>
 </div>
 <div class="section" id="experiment-sub-directories">
 <h2>Experiment Sub-Directories<a class="headerlink" href="#experiment-sub-directories" title="Permalink to this headline">¶</a></h2>
-<dl>
+<dl class="simple">
 <dt><strong>tasks</strong></dt><dd><p>The <code class="docutils literal notranslate"><span class="pre">tasks</span></code> sub-directory contains a number of files used by
 <em>NXRefine</em> to store default settings, workflow logs, and a MySQL
 database for recording the status of each workflow component. The
@@ -171,15 +174,29 @@ <h2>Experiment Sub-Directories<a class="headerlink" href="#experiment-sub-direct
 NeXus files (described below). The files don’t have to be stored in
 this sub-directory, but if they are in another location, it is
 recommended to copy them here for completeness. If the calibrations
-have been performed by another package, the PONI parameters can be
+have been performed by another package, the parameters can be
 imported directly from a PONI file.</p>
 </dd>
 <dt><strong>configurations</strong></dt><dd><p>The <code class="docutils literal notranslate"><span class="pre">configurations</span></code> sub-directory contains NeXus files that act
-as templates when creating the files used to store the scan results.
-These files contain scan parameters, such as the goniometer angles,
-for one or more sample rotations, and are initialized by a <em>NeXpy</em>
-GUI dialog.</p>
+as templates to be used when creating the files used to store the
+scan results. There should be a separate template file for each new
+experimental configuration, <em>.e.g.</em>, with a different wavelength or
+detector distance. If multiple sample rotations are to be performed
+with different detector translations and/or goniometer angles, the
+corresponding template files will have entries for each scan
+containing pre-defined values of the scan variables. These files are
+initialized by a <em>NeXpy</em> GUI dialog.</p>
 </dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>On QM2 at CHESS, it is usually only necessary
+to create template files with a single entry, since the
+number of rotation scans is not always pre-determined. When
+the scans are imported, additional entries are automatically
+added with the goniometer angles updated with the values in the corresponding scan SPEC file.</p>
+</div>
+<dl>
 <dt><strong>scripts</strong></dt><dd><p>The <code class="docutils literal notranslate"><span class="pre">scripts</span></code> sub-directory is not used directly by <em>NXRefine</em>,
 but is created by the <code class="docutils literal notranslate"><span class="pre">New</span> <span class="pre">Experiment</span></code> dialog described below. It
 is designed to store macros for use during an experiment.</p>

installation.html

@@ -200,7 +200,7 @@ <h2>Initial Setup<a class="headerlink" href="#initial-setup" title="Permalink to
 <h3>User Support<a class="headerlink" href="#user-support" title="Permalink to this headline">¶</a></h3>
 <p>If you are interested in using this package, please contact Ray Osborn
 (<a class="reference external" href="mailto:ROsborn&#37;&#52;&#48;anl&#46;gov">ROsborn<span>&#64;</span>anl<span>&#46;</span>gov</a>). Please report any bugs as a
-<a class="reference external" href="https://github.com/nxrefine/nxrefine/issues">Github issue</a>, with
+<a class="reference external" href="https://github.com/nexpy/nxrefine/issues">Github issue</a>, with
 relevant tracebacks.</p>
 </div>
 </div>