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56  <div class="section" id="module-testDeriv">
57<span id="gsas-ii-scripts"></span><h1><em>GSAS-II Scripts</em><a class="headerlink" href="#module-testDeriv" title="Permalink to this headline">¶</a></h1>
58<div class="section" id="testderiv-check-derivative-computation">
59<h2><em>testDeriv: Check derivative computation</em><a class="headerlink" href="#testderiv-check-derivative-computation" title="Permalink to this headline">¶</a></h2>
60<p>Use this to check derivatives used in structure least squares
61refinement against numerical values computed in this script.</p>
62<p>To use set <tt class="docutils literal"><span class="pre">DEBUG=True</span></tt> in GSASIIstrMain.py (line 22, as of version
631110); run the least squares - one cycle is sufficient.  Do the &#8220;Save
64Results&#8221;; this will write the file testDeriv.dat in the local
65directory.</p>
66<p>Then run this program to see plots of derivatives for all
67parameters refined in the last least squares.  Shown will be numerical
68derivatives generated over all observations (including penalty terms)
69and the corresponding analytical ones produced in the least
70squares. They should match.</p>
71<dl class="function">
72<dt id="testDeriv.main">
73<tt class="descclassname">testDeriv.</tt><tt class="descname">main</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/testDeriv.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#testDeriv.main" title="Permalink to this definition">¶</a></dt>
74<dd><p>Starts main application to compute and plot derivatives</p>
75</dd></dl>
76
77</div>
78<span class="target" id="module-GSASIItestplot"></span><div class="section" id="gsasiitestplot-plotting-for-testderiv">
79<h2><em>GSASIItestplot: Plotting for testDeriv</em><a class="headerlink" href="#gsasiitestplot-plotting-for-testderiv" title="Permalink to this headline">¶</a></h2>
80<p>Plotting module used for script testDeriv.</p>
81<dl class="class">
82<dt id="GSASIItestplot.Plot">
83<em class="property">class </em><tt class="descclassname">GSASIItestplot.</tt><tt class="descname">Plot</tt><big>(</big><em>parent</em>, <em>id=-1</em>, <em>dpi=None</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="_modules/GSASIItestplot.html#Plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIItestplot.Plot" title="Permalink to this definition">¶</a></dt>
84<dd><p>Creates a plotting window</p>
85</dd></dl>
86
87<dl class="class">
88<dt id="GSASIItestplot.PlotNotebook">
89<em class="property">class </em><tt class="descclassname">GSASIItestplot.</tt><tt class="descname">PlotNotebook</tt><big>(</big><em>id=-1</em><big>)</big><a class="reference internal" href="_modules/GSASIItestplot.html#PlotNotebook"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIItestplot.PlotNotebook" title="Permalink to this definition">¶</a></dt>
90<dd><p>creates a Wx application and a plotting notebook</p>
91</dd></dl>
92
93</div>
94<span class="target" id="module-scanCCD"></span><div class="section" id="scanccd-reduce-data-from-scanning-ccd">
95<h2><em>scanCCD: reduce data from scanning CCD</em><a class="headerlink" href="#scanccd-reduce-data-from-scanning-ccd" title="Permalink to this headline">¶</a></h2>
96<p>Quickly prototyped routine for reduction of data from detector described in
97B.H. Toby, T.J. Madden, M.R. Suchomel, J.D. Baldwin, and R.B. Von Dreele,
98&#8220;A Scanning CCD Detector for Powder Diffraction Measurements&#8221;.
99Journal of Applied Crystallography. 46(4): p. 1058-63 (2013).</p>
100<dl class="function">
101<dt id="scanCCD.main">
102<tt class="descclassname">scanCCD.</tt><tt class="descname">main</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/scanCCD.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#scanCCD.main" title="Permalink to this definition">¶</a></dt>
103<dd><p>starts main application to merge data from scanning CCD</p>
104</dd></dl>
105
106</div>
107<span class="target" id="module-makeMacApp"></span><div class="section" id="makemacapp-create-mac-applet">
108<h2><em>makeMacApp: Create Mac Applet</em><a class="headerlink" href="#makemacapp-create-mac-applet" title="Permalink to this headline">¶</a></h2>
109<p>This script creates an AppleScript app to launch GSAS-II. The app is
110created in the directory where the GSAS-II script is located.
111A softlink to Python is created, but is named GSAS-II, so that
112GSAS-II shows up as the name of the app rather than Python in the
113menu bar, etc. Note that this requires finding an app version of Python
114(expected name .../Resources/Python.app/Contents/MacOS/Python in
115directory tree of the calling python interpreter).</p>
116<p>Run this script with one optional argument, the path to the GSASII.py
117The script path may be specified relative to the current path or given
118an absolute path, but will be accessed via an absolute path.
119If no arguments are supplied, the GSASII.py script is assumed to be in the
120same directory as this file.</p>
121<dl class="data">
122<dt id="makeMacApp.AppleScript">
123<tt class="descclassname">makeMacApp.</tt><tt class="descname">AppleScript</tt><em class="property"> = '(*   GSAS-II AppleScript by B. Toby (brian.toby&#64;anl.gov)\n     It can launch GSAS-II by double clicking or by dropping a data file\n     or folder over the app.\n     It runs GSAS-II in a terminal window.\n*)\n\n(* test if a file is present and exit with an error message if it is not  *)\non TestFilePresent(appwithpath)\n\ttell application &quot;System Events&quot;\n\t\tif (file appwithpath exists) then\n\t\telse\n\t\t\tdisplay dialog &quot;Error: file &quot; &amp; appwithpath &amp; &quot; not found. If you have moved this file recreate the AppleScript with bootstrap.py.&quot; with icon caution buttons {{&quot;Quit&quot;}}\n\t\t\treturn\n\t\tend if\n\tend tell\nend TestFilePresent\n\n(* \n------------------------------------------------------------------------\nthis section responds to a double-click. No file is supplied to GSAS-II\n------------------------------------------------------------------------ \n*)\non run\n\tset python to &quot;{:s}&quot;\n\tset appwithpath to &quot;{:s}&quot;\n\tset env to &quot;{:s}&quot;\n\tTestFilePresent(appwithpath)\n\tTestFilePresent(python)\n\ttell application &quot;Terminal&quot;\n\t\tactivate\n\t\tdo script env &amp; python &amp; &quot; &quot; &amp; appwithpath &amp; &quot;; exit&quot;\n\tend tell\nend run\n\n(*\n-----------------------------------------------------------------------------------------------\nthis section handles starting with files dragged into the AppleScript\n o it goes through the list of file(s) dragged in\n o then it converts the colon-delimited macintosh file location to a POSIX filename\n o for every non-directory file dragged into the icon, it starts GSAS-II, passing the file name\n------------------------------------------------------------------------------------------------\n*)\n\non open names\n\tset python to &quot;{:s}&quot;\n\tset appwithpath to &quot;{:s}&quot;\n\tset env to &quot;{:s}&quot;\n \n\tTestFilePresent(appwithpath)\n\trepeat with filename in names\n\t\tset filestr to (filename as string)\n\t\tif filestr ends with &quot;:&quot; then\n                        (* should not happen, skip directories *)\n\t\telse\n\t\t\t(* if this is an input file, open it *)\n\t\t\tset filename to the quoted form of the POSIX path of filename\n\t\t\ttell application &quot;Terminal&quot;\n\t\t\t\tactivate\n\t\t\t\tdo script env &amp; python &amp; &quot; &quot; &amp; appwithpath &amp; &quot; &quot; &amp; filename &amp; &quot;; exit&quot;\n\t\t\tend tell\n\t\tend if\n\tend repeat\nend open\n'</em><a class="headerlink" href="#makeMacApp.AppleScript" title="Permalink to this definition">¶</a></dt>
124<dd><p>Contains an AppleScript to start GSAS-II launching python and the
125GSAS-II python script</p>
126</dd></dl>
127
128<dl class="function">
129<dt id="makeMacApp.RunPython">
130<tt class="descclassname">makeMacApp.</tt><tt class="descname">RunPython</tt><big>(</big><em>image</em>, <em>cmd</em><big>)</big><a class="reference internal" href="_modules/makeMacApp.html#RunPython"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#makeMacApp.RunPython" title="Permalink to this definition">¶</a></dt>
131<dd><p>Run a command in a python image</p>
132</dd></dl>
133
134</div>
135<span class="target" id="module-unit_tests"></span><div class="section" id="unit-tests-self-test-module">
136<h2><em>unit_tests: Self-test Module</em><a class="headerlink" href="#unit-tests-self-test-module" title="Permalink to this headline">¶</a></h2>
137<p>A script that can be run to test a series of self-tests in GSAS-II. At present,
138only modules <tt class="docutils literal"><span class="pre">GSASIIspc</span></tt> and <tt class="docutils literal"><span class="pre">GSASIIlattice</span></tt> have self-tests.</p>
139<dl class="function">
140<dt id="unit_tests.test_GSASIIlattice">
141<tt class="descclassname">unit_tests.</tt><tt class="descname">test_GSASIIlattice</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/unit_tests.html#test_GSASIIlattice"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#unit_tests.test_GSASIIlattice" title="Permalink to this definition">¶</a></dt>
142<dd><p>Test registered self-tests in <tt class="docutils literal"><span class="pre">GSASIIlattice</span></tt>.
143Takes no input and returns nothing. Throws an Exception if a test fails.</p>
144</dd></dl>
145
146<dl class="function">
147<dt id="unit_tests.test_GSASIIspc">
148<tt class="descclassname">unit_tests.</tt><tt class="descname">test_GSASIIspc</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/unit_tests.html#test_GSASIIspc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#unit_tests.test_GSASIIspc" title="Permalink to this definition">¶</a></dt>
149<dd><p>Test registered self-tests in <tt class="docutils literal"><span class="pre">GSASIIspc</span></tt>.
150Takes no input and returns nothing. Throws an Exception if a test fails.</p>
151</dd></dl>
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165  <h3><a href="index.html">Table Of Contents</a></h3>
166  <ul>
167<li><a class="reference internal" href="#"><em>GSAS-II Scripts</em></a><ul>
168<li><a class="reference internal" href="#testderiv-check-derivative-computation"><em>testDeriv: Check derivative computation</em></a></li>
169<li><a class="reference internal" href="#gsasiitestplot-plotting-for-testderiv"><em>GSASIItestplot: Plotting for testDeriv</em></a></li>
170<li><a class="reference internal" href="#scanccd-reduce-data-from-scanning-ccd"><em>scanCCD: reduce data from scanning CCD</em></a></li>
171<li><a class="reference internal" href="#makemacapp-create-mac-applet"><em>makeMacApp: Create Mac Applet</em></a></li>
172<li><a class="reference internal" href="#unit-tests-self-test-module"><em>unit_tests: Self-test Module</em></a></li>
173</ul>
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176
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