Updated documentation

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 9800261d7694b1938fc07fd9f04eb21f
+config: 01758d6abc92b55ae71bc3b7746b8a05
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_sources/changelog.rst.txt

@@ -14,6 +14,10 @@ Changelog & to-do
 Changelog
 ---------
 
+v1.2.0 November 2019, R.G. van Holstein
+ - Added computation of statistical uncertainty (photon and background noise) on measured star polarization in PDI part
+ - Added contrast curves for the detection of polarized extended sources and polarized point source with PDI
+
 v1.1.0 October 2019, R.G. van Holstein & J. Milli
  - Added angular differential imaging (ADI) including principal component analysis (PCA) of total intensity images for pupil-tracking observations
  - Added mean combination of ADI final images to command-line option :code:`irdap --meancombine`
@@ -43,10 +47,9 @@ v0.1.2 June 2019, R.G. van Holstein:
 To-do high priority
 -------------------
 
-   - Add possibility to not collapse data of pre-processing so that ADI can be done more accurately.
    - Add possibility to crop images when doing ADI to save time
    - Add possibility to use CENTER-frames with a different exposure time than the OBJECT-frames
-   - Create contrast curves of final PDI-and ADI-images 
+   - Create contrast curves of final ADI-images 
    - Add ADI+PCA for polarimetric data reduction of pupil-tracking observations
    - Add accurate (calibrated) model correction for narrowband filters
    - Add option to apply accurate plate scale and distortion correction for data (especially important for pupil-tracking and bright sources; do we need calibrations?)

docs/build/html/_sources/instructions.rst.txt

@@ -78,6 +78,8 @@ For the polarimetric differential imaging (PDI) part, IRDAP computes the double
 - ``reduced_pdi\no_star_pol_subtr``, containing the final images with the polarization of the star still present;
 - ``reduced_pdi\star_pol_subtr``, containing the final images with the polarization of the star subtracted.
 
+Finally, if FLUX-files are included in the raw data, IRDAP creates contrast curves for the detection of polarized extended sources and polarized point sources. 
+
 .. important::
    By default, the polarization of the star is determined with an annulus over the AO residuals. However, for the most accurate results the annulus should only contain signal from the star, and no signal from for example a circumstellar disk, companion or background star. Therefore the user often needs to adjust the input parameter :ref:`annulus_star <Basic PDI options>` in the configuration file.
 

docs/build/html/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.1.0',
+    VERSION: '1.2.0',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

docs/build/html/acknowledgements.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Acknowledgements &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Acknowledgements &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 

docs/build/html/changelog.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Changelog &amp; to-do &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Changelog &amp; to-do &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -61,7 +61,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 
@@ -171,6 +171,12 @@ <h1>Changelog &amp; to-do<a class="headerlink" href="#changelog-to-do" title="Pe
 <div class="section" id="changelog">
 <h2>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h2>
 <dl class="docutils">
+<dt>v1.2.0 November 2019, R.G. van Holstein</dt>
+<dd><ul class="first last simple">
+<li>Added computation of statistical uncertainty (photon and background noise) on measured star polarization in PDI part</li>
+<li>Added contrast curves for the detection of polarized extended sources and polarized point source with PDI</li>
+</ul>
+</dd>
 <dt>v1.1.0 October 2019, R.G. van Holstein &amp; J. Milli</dt>
 <dd><ul class="first last simple">
 <li>Added angular differential imaging (ADI) including principal component analysis (PCA) of total intensity images for pupil-tracking observations</li>
@@ -215,10 +221,9 @@ <h2>Changelog<a class="headerlink" href="#changelog" title="Permalink to this he
 <h2>To-do high priority<a class="headerlink" href="#to-do-high-priority" title="Permalink to this headline">¶</a></h2>
 <blockquote>
 <div><ul class="simple">
-<li>Add possibility to not collapse data of pre-processing so that ADI can be done more accurately.</li>
 <li>Add possibility to crop images when doing ADI to save time</li>
 <li>Add possibility to use CENTER-frames with a different exposure time than the OBJECT-frames</li>
-<li>Create contrast curves of final PDI-and ADI-images</li>
+<li>Create contrast curves of final ADI-images</li>
 <li>Add ADI+PCA for polarimetric data reduction of pupil-tracking observations</li>
 <li>Add accurate (calibrated) model correction for narrowband filters</li>
 <li>Add option to apply accurate plate scale and distortion correction for data (especially important for pupil-tracking and bright sources; do we need calibrations?)</li>

docs/build/html/citing.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Citing IRDAP &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Citing IRDAP &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -61,7 +61,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 

docs/build/html/configfile.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Configuration file &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Configuration file &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -61,7 +61,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 

docs/build/html/contributing.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Contributing &amp; issues &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Contributing &amp; issues &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -61,7 +61,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 

docs/build/html/example.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Example reduction &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Example reduction &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -61,7 +61,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 

docs/build/html/genindex.html

@@ -9,7 +9,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Index &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Index &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 

docs/build/html/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>IRDAP &mdash; IRDAP 1.1.0 documentation</title>
+  <title>IRDAP &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 

docs/build/html/installation.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Installation &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Installation &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -61,7 +61,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 

docs/build/html/instructions.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Usage instructions &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Usage instructions &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -61,7 +61,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 
@@ -245,6 +245,7 @@ <h2>PDI in a nutshell<a class="headerlink" href="#pdi-in-a-nutshell" title="Perm
 <li><code class="docutils literal notranslate"><span class="pre">reduced_pdi\no_star_pol_subtr</span></code>, containing the final images with the polarization of the star still present;</li>
 <li><code class="docutils literal notranslate"><span class="pre">reduced_pdi\star_pol_subtr</span></code>, containing the final images with the polarization of the star subtracted.</li>
 </ul>
+<p>Finally, if FLUX-files are included in the raw data, IRDAP creates contrast curves for the detection of polarized extended sources and polarized point sources.</p>
 <div class="admonition important">
 <p class="first admonition-title">Important</p>
 <p class="last">By default, the polarization of the star is determined with an annulus over the AO residuals. However, for the most accurate results the annulus should only contain signal from the star, and no signal from for example a circumstellar disk, companion or background star. Therefore the user often needs to adjust the input parameter <a class="reference internal" href="configfile.html#basic-pdi-options"><span class="std std-ref">annulus_star</span></a> in the configuration file.</p>

docs/build/html/mailinglist.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Mailing list &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Mailing list &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -61,7 +61,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>
 
 

docs/build/html/search.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Search &mdash; IRDAP 1.1.0 documentation</title>
+  <title>Search &mdash; IRDAP 1.2.0 documentation</title>
 
 
 
@@ -59,7 +59,7 @@
 
 
               <div class="version">
-                1.1.0
+                1.2.0
               </div>