post-release 1.2.4^230114 with improved scripts

CHANGELOG

@@ -24,3 +24,6 @@ v1.2.0dev May 2021  new version:
 1.2.3  kafe2 version >=2.6, python2 support dropped;
        added script plotData.py for simple plotting of data in yaml format,
        fits from input yaml-file with kafe2go and run_phyFit.py
+1.2.4  Oct. 2022 release with a few fixes
+1.2.4.post-230114 Post-release fixes: imporved example scripts, fix to
+	PhyPraKit.meanFilter()

PhyPraKit/PhyPraKit.py

@@ -136,6 +136,7 @@ def A0_readme():
 #   10-Nov-22    GQ  added stand-alone tools in sub-dir tools/
 #   13-Dec-22    GQ  added delim option to readPicoscope(); also replace decimal ','
 #   27-Dec-22    GQ  fixed border problem for indices <w and >l-w) in meanFilter()
+#                    changed to faster algorithm using numpy.cumsum()
 # ----------------------------------------------------------------------------------
 
 import numpy as np, matplotlib.pyplot as plt
@@ -819,13 +820,24 @@ def meanFilter(a, width=5):
   '''
 # -----------------------------------------------
   l=len(a)
-  av = np.zeros(l) 
   w=int(width/2)
+
+  # slow (explicit) algorithm using inernal loop
+  #av0 = np.empty(l) 
+  #for i in range(0, l):
+  #  km = min(i, w)
+  #  kp = min(l-i-1, w)
+  #  av0[i]= sum(a[i-km:i+kp+1])/(km+kp+1)
+
+  # fast (vectorized) approach using cumulative sum
+  cs = np.empty(l+1) # cumulative sum of array with leading zero
+  cs[1:] = np.cumsum(a)
+  cs[0] = 0.
+  av = np.empty(l) 
   for i in range(0, l):
     km = min(i, w)
     kp = min(l-i-1, w)
-    av[i]= sum(a[i-km:i+kp+1])/(km+kp+1)
-
+    av[i] = (cs[i+kp+1] - cs[i-km]) / (km+kp+1)
   return av
 
 def resample(a, t=None, n=11):

PhyPraKit/__init__.py

@@ -16,6 +16,6 @@
 # Import main components
 from .PhyPraKit import *
 
-_version_suffix = ''  # for suffixes such as 'rc' or 'beta' or 'alpha'
+_version_suffix = '^230114'  # for suffixes such as 'rc' or 'beta' or 'alpha'
 __version__ = _version_info._get_version_string()
 __version__ += _version_suffix

docs/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -222,7 +222,7 @@ table.modindextable td {
 /* -- general body styles --------------------------------------------------- */
 
 div.body {
-    min-width: 450px;
+    min-width: 360px;
     max-width: 800px;
 }
 
@@ -237,16 +237,6 @@ a.headerlink {
     visibility: hidden;
 }
 
-a.brackets:before,
-span.brackets > a:before{
-    content: "[";
-}
-
-a.brackets:after,
-span.brackets > a:after {
-    content: "]";
-}
-
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -335,12 +325,16 @@ p.sidebar-title {
     font-weight: bold;
 }
 
+nav.contents,
+aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
 
+nav.contents,
+aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -379,13 +373,17 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -428,10 +426,6 @@ table.docutils td, table.docutils th {
     border-bottom: 1px solid #aaa;
 }
 
-table.footnote td, table.footnote th {
-    border: 0 !important;
-}
-
 th {
     text-align: left;
     padding-right: 5px;
@@ -615,19 +609,26 @@ ul.simple p {
     margin-bottom: 0;
 }
 
-dl.footnote > dt,
-dl.citation > dt {
+aside.footnote > span,
+div.citation > span {
     float: left;
-    margin-right: 0.5em;
 }
-
-dl.footnote > dd,
-dl.citation > dd {
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+  padding-right: 0.5em;
+}
+aside.footnote > p {
+  margin-left: 2em;
+}
+div.citation > p {
+  margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
     margin-bottom: 0em;
 }
-
-dl.footnote > dd:after,
-dl.citation > dd:after {
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
     content: "";
     clear: both;
 }
@@ -644,10 +645,6 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
-dl.field-list > dt:after {
-    content: ":";
-}
-
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;

docs/_static/documentation_options.js

@@ -1,7 +1,7 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.2.4',
-    LANGUAGE: 'None',
+    VERSION: '1.2.4^230114',
+    LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
     FILE_SUFFIX: '.html',

docs/_static/language_data.js

@@ -5,12 +5,12 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
-var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
+var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
 /* Non-minified version is copied as a separate JS file, is available */
@@ -197,101 +197,3 @@ var Stemmer = function() {
   }
 }
 
-
-
-
-var splitChars = (function() {
-    var result = {};
-    var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
-         1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
-         2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
-         2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
-         3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
-         3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
-         4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
-         8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
-         11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
-         43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
-    var i, j, start, end;
-    for (i = 0; i < singles.length; i++) {
-        result[singles[i]] = true;
-    }
-    var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
-         [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
-         [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
-         [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
-         [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
-         [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
-         [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
-         [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
-         [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
-         [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
-         [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
-         [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
-         [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
-         [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
-         [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
-         [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
-         [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
-         [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
-         [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
-         [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
-         [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
-         [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
-         [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
-         [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
-         [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
-         [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
-         [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
-         [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
-         [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
-         [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
-         [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
-         [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
-         [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
-         [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
-         [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
-         [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
-         [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
-         [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
-         [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
-         [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
-         [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
-         [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
-         [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
-         [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
-         [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
-         [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
-         [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
-         [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
-         [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
-    for (i = 0; i < ranges.length; i++) {
-        start = ranges[i][0];
-        end = ranges[i][1];
-        for (j = start; j <= end; j++) {
-            result[j] = true;
-        }
-    }
-    return result;
-})();
-
-function splitQuery(query) {
-    var result = [];
-    var start = -1;
-    for (var i = 0; i < query.length; i++) {
-        if (splitChars[query.charCodeAt(i)]) {
-            if (start !== -1) {
-                result.push(query.slice(start, i));
-                start = -1;
-            }
-        } else if (start === -1) {
-            start = i;
-        }
-    }
-    if (start !== -1) {
-        result.push(query.slice(start));
-    }
-    return result;
-}
-
-

docs/_static/nature.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- nature theme.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -194,6 +194,8 @@ div.seealso {
     border: 1px solid #ff6;
 }
 
+nav.contents,
+aside.topic,
 div.topic {
     background-color: #eee;
 }

docs/_static/pygments.css

@@ -1,5 +1,10 @@
+pre { line-height: 125%; }
+td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 .highlight .hll { background-color: #ffffcc }
-.highlight  { background: #eeffcc; }
+.highlight { background: #eeffcc; }
 .highlight .c { color: #408090; font-style: italic } /* Comment */
 .highlight .err { border: 1px solid #FF0000 } /* Error */
 .highlight .k { color: #007020; font-weight: bold } /* Keyword */

docs/genindex.html

@@ -1,17 +1,16 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; PhyPraKit 1.2.4 documentation</title>
+    <title>Index &#8212; PhyPraKit 1.2.4^230114 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/nature.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-    <script src="_static/jquery.js"></script>
-    <script src="_static/underscore.js"></script>
     <script src="_static/doctools.js"></script>
+    <script src="_static/sphinx_highlight.js"></script>
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" /> 
   </head><body>
@@ -24,7 +23,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">PhyPraKit 1.2.4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">PhyPraKit 1.2.4^230114 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Index</a></li> 
       </ul>
     </div>  
@@ -731,7 +730,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>
@@ -745,13 +744,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">PhyPraKit 1.2.4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">PhyPraKit 1.2.4^230114 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Index</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2016, Günter Quast.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.5.0.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 6.1.1.
     </div>
   </body>
 </html>