update of docu

doc/html/_sources/user-manual.txt

@@ -1486,8 +1486,49 @@ The block starts with the *FOURIER* keyword and may contain the following entrie
 .. _msr-fourier-block-phase:
 
 **phase**
-  The initial phase of the input data is given here in degrees. Optionally the phase parameter from the :ref:`FITPARAMETER block <msr-fitparameter-block>` can be given, 
+  If a real Fourier shall be plotted, it is necessary to adopt the phases of the different detectors. The number of potentially provided phases can be either **one**, which means that this phase will be applied to *all* Fourier spectra, 
-  *e.g.* par3, which would take the value of parameter number 3. 
+  or the number of phases have to correspond to the number of runs in the plot block.
+  
+  Currently there are three options:
+  
+  #. The phases for each run/detector are given explicitly, *i.e.* 
+  
+     .. code-block:: bash
+     
+        phase val0 sep val1 sep ... sep valN
+        
+     where ``val0``, ``val1``, etc. are explicitly given phases (*i.e.* doubles), and ``sep`` is one of the following allowed separators: ``space``, ``,``, ``;``, or ``tab``.
+     For example
+     
+     .. code-block:: bash
+     
+        phase   -3.2, 175.9
+        
+  #. The phases for each run/detector are given as phase parameter from the :ref:`FITPARAMETER block <msr-fitparameter-block>`, *e.g.* par3, which would 
+     take the value of parameter number 3. More explicitly
+     
+     .. code-block:: bash
+     
+        phase parX0 sep parX1 sep ... sep parXN
+        
+     where the same rules applies as for explicit phase values. An example could look like this
+     
+     .. code-block:: bash
+     
+        phase par7, par12, par17, par22, par27, par32, par37, par42, par47, par52, par57, par62, par67, par72, par77, par82
+  
+  #. Often the phases in the parameter block follow a clear list structure. This allows to write the Fourier phase parameters in a more compact form
+  
+     .. code-block:: none
+     
+        phase par(X0, offset, #param)
+        
+     with ``X0`` the first phase parameter index, ``offset`` being the offset to the next phase parameter, and ``#param`` being the number of phase parameters to be used.
+     This means that the previous example can be compacted to
+     
+     .. code-block:: none
+     
+        phase par(7, 5, 16)
   
 .. index:: fourier-block-range_for_phase_correction
 .. _msr-fourier-block-range_for_phase_correction:
@@ -1511,8 +1552,7 @@ Altogether, a possible FOURIER block might look like that:
   fourier_power 12
   apodization NONE
   plot real_and_imag
-  phase 22.6   # par3
+  phase par5, par8
-  range_for_phase_correction all
   range 0.0 17.03
   
 .. index:: msr-plot-block

doc/html/acknowledgement.html

@@ -113,7 +113,7 @@ extremely competent way to deal with his projects as well as to deal with the ch
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/any2many.html

@@ -107,7 +107,7 @@ For a detailed description see <a class="reference internal" href="user-manual.h
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/bugtracking.html

@@ -98,7 +98,7 @@ or send an e-mail to A. Suter at PSI.</p>
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/cite.html

@@ -119,7 +119,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/genindex.html

@@ -987,7 +987,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/index.html

@@ -185,7 +185,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/msr2data.html

@@ -439,7 +439,7 @@ fit serves as template for the second and so on. The template field stays empty
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/mupp.html

@@ -257,7 +257,7 @@ SCRIPT COMMANDS:
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/musr-root.html

@@ -928,7 +928,7 @@ the entry has been added. The last token, <tt class="docutils literal"><span cla
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/musredit.html

@@ -555,7 +555,7 @@ the corresponding fit parameter value, except the phases where the step will be
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/search.html

@@ -94,7 +94,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/setup-dks.html

@@ -359,7 +359,7 @@ The only thing you need <tt class="docutils literal"><span class="pre">DKS</span
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/setup-standard.html

@@ -1486,7 +1486,7 @@ $ musrview test-histo-ROOT-NPP.msr
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/tutorial.html

@@ -448,7 +448,7 @@ For a complete description please refer to the manuals of <a class="reference in
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/user-libs.html

@@ -667,7 +667,7 @@ K(m)&=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>

doc/html/user-manual.html

@@ -1552,8 +1552,42 @@ The argument may be one of the following:</p>
 </dl>
 <span id="index-47"></span><dl class="docutils" id="msr-fourier-block-phase">
 <dt><strong>phase</strong></dt>
-<dd>The initial phase of the input data is given here in degrees. Optionally the phase parameter from the <a class="reference internal" href="#msr-fitparameter-block"><em>FITPARAMETER block</em></a> can be given,
+<dd><p class="first">If a real Fourier shall be plotted, it is necessary to adopt the phases of the different detectors. The number of potentially provided phases can be either <strong>one</strong>, which means that this phase will be applied to <em>all</em> Fourier spectra,
-<em>e.g.</em> par3, which would take the value of parameter number 3.</dd>
+or the number of phases have to correspond to the number of runs in the plot block.</p>
+<p>Currently there are three options:</p>
+<ol class="last arabic">
+<li><p class="first">The phases for each run/detector are given explicitly, <em>i.e.</em></p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>phase val0 sep val1 sep ... sep valN
+</pre></div>
+</div>
+<p>where <tt class="docutils literal"><span class="pre">val0</span></tt>, <tt class="docutils literal"><span class="pre">val1</span></tt>, etc. are explicitly given phases (<em>i.e.</em> doubles), and <tt class="docutils literal"><span class="pre">sep</span></tt> is one of the following allowed separators: <tt class="docutils literal"><span class="pre">space</span></tt>, <tt class="docutils literal"><span class="pre">,</span></tt>, <tt class="docutils literal"><span class="pre">;</span></tt>, or <tt class="docutils literal"><span class="pre">tab</span></tt>.
+For example</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>phase   -3.2, <span class="m">175</span>.9
+</pre></div>
+</div>
+</li>
+<li><p class="first">The phases for each run/detector are given as phase parameter from the <a class="reference internal" href="#msr-fitparameter-block"><em>FITPARAMETER block</em></a>, <em>e.g.</em> par3, which would
+take the value of parameter number 3. More explicitly</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>phase parX0 sep parX1 sep ... sep parXN
+</pre></div>
+</div>
+<p>where the same rules applies as for explicit phase values. An example could look like this</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>phase par7, par12, par17, par22, par27, par32, par37, par42, par47, par52, par57, par62, par67, par72, par77, par82
+</pre></div>
+</div>
+</li>
+<li><p class="first">Often the phases in the parameter block follow a clear list structure. This allows to write the Fourier phase parameters in a more compact form</p>
+<div class="highlight-none"><div class="highlight"><pre><span></span>phase par(X0, offset, #param)
+</pre></div>
+</div>
+<p>with <tt class="docutils literal"><span class="pre">X0</span></tt> the first phase parameter index, <tt class="docutils literal"><span class="pre">offset</span></tt> being the offset to the next phase parameter, and <tt class="docutils literal"><span class="pre">#param</span></tt> being the number of phase parameters to be used.
+This means that the previous example can be compacted to</p>
+<div class="highlight-none"><div class="highlight"><pre><span></span>phase par(7, 5, 16)
+</pre></div>
+</div>
+</li>
+</ol>
+</dd>
 </dl>
 <span id="index-48"></span><dl class="docutils" id="msr-fourier-block-range-for-phase-correction">
 <dt><strong>range_for_phase_correction</strong></dt>
@@ -1570,8 +1604,7 @@ units Mc/s
 fourier_power 12
 apodization NONE
 plot real_and_imag
-phase 22.6   # par3
+phase par5, par8
-range_for_phase_correction all
 range 0.0 17.03
 </pre></div>
 </div>
@@ -2162,7 +2195,7 @@ In case this cannot be ensured, the parallelization can be disabled by <em>&#821
     </div>
     <div class="footer">
         &copy; Copyright 2018, Andreas Suter.
-      Last updated on Aug 23, 2018.
+      Last updated on Oct 15, 2018.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>