more docs updates for pre-release v2.0.1

docs/html/Subaerial.html

@@ -819,7 +819,7 @@ <h3>Quick search</h3>
 <div><p>Once the Jacobian is evaluated, uncertainty is progagated by multiplying the
 square of the Jacobian with the squares of the standard deviations defined in the
 stddev parameter.  The covariances are assumed to be zero.  TODO:  explain how this is 
-technically different than the shown propagation equation because the covariances are 
+implemented differently than shown by the propagation equation because the covariances are 
 assumed to be 0.</p>
 </div></blockquote>
 </li>

docs/html/_modules/CBlueApp.html

@@ -129,25 +129,22 @@ <h1>Source code for CBlueApp</h1><div class="highlight"><pre>
         <span class="n">filemenu</span><span class="o">.</span><span class="n">add_command</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;Exit&#39;</span><span class="p">,</span> <span class="n">command</span><span class="o">=</span><span class="n">quit</span><span class="p">)</span>
         <span class="n">menubar</span><span class="o">.</span><span class="n">add_cascade</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;File&#39;</span><span class="p">,</span> <span class="n">menu</span><span class="o">=</span><span class="n">filemenu</span><span class="p">)</span>
 
-        <span class="n">exchangeChoice</span> <span class="o">=</span> <span class="n">tk</span><span class="o">.</span><span class="n">Menu</span><span class="p">(</span><span class="n">menubar</span><span class="p">,</span> <span class="n">tearoff</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-        <span class="n">exchangeChoice</span><span class="o">.</span><span class="n">add_command</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;Lidar System&#39;</span><span class="p">,</span>
-                                   <span class="n">command</span><span class="o">=</span><span class="k">lambda</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">popupmsg</span><span class="p">(</span><span class="s1">&#39;not supported yet...&#39;</span><span class="p">))</span>
-        <span class="n">exchangeChoice</span><span class="o">.</span><span class="n">add_command</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;Properties&#39;</span><span class="p">,</span>
-                                   <span class="n">command</span><span class="o">=</span><span class="k">lambda</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">popupmsg</span><span class="p">(</span><span class="s1">&#39;not supported yet...&#39;</span><span class="p">))</span>
-        <span class="c1"># menubar.add_cascade(label=&#39;Edit&#39;, menu=exchangeChoice)</span>
-
-        <span class="n">exchangeChoice</span> <span class="o">=</span> <span class="n">tk</span><span class="o">.</span><span class="n">Menu</span><span class="p">(</span><span class="n">menubar</span><span class="p">,</span> <span class="n">tearoff</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-        <span class="n">exchangeChoice</span><span class="o">.</span><span class="n">add_command</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;Map Window&#39;</span><span class="p">,</span>
-                                   <span class="n">command</span><span class="o">=</span><span class="k">lambda</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">build_map_panel</span><span class="p">)</span>
-        <span class="n">exchangeChoice</span><span class="o">.</span><span class="n">add_command</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;Graph Window&#39;</span><span class="p">,</span>
-                                   <span class="n">command</span><span class="o">=</span><span class="k">lambda</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">popupmsg</span><span class="p">(</span><span class="s1">&#39;not supported yet...&#39;</span><span class="p">))</span>
-        <span class="n">exchangeChoice</span><span class="o">.</span><span class="n">add_command</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;Table Window&#39;</span><span class="p">,</span>
-                                   <span class="n">command</span><span class="o">=</span><span class="k">lambda</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">popupmsg</span><span class="p">(</span><span class="s1">&#39;not supported yet...&#39;</span><span class="p">))</span>
-        <span class="c1"># menubar.add_cascade(label=&#39;Display&#39;, menu=exchangeChoice)</span>
-
-        <span class="n">exchangeChoice</span> <span class="o">=</span> <span class="n">tk</span><span class="o">.</span><span class="n">Menu</span><span class="p">(</span><span class="n">menubar</span><span class="p">,</span> <span class="n">tearoff</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-        <span class="n">exchangeChoice</span><span class="o">.</span><span class="n">add_command</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;About&#39;</span><span class="p">,</span> <span class="n">command</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">show_about</span><span class="p">)</span>
-        <span class="n">menubar</span><span class="o">.</span><span class="n">add_cascade</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;Help&#39;</span><span class="p">,</span> <span class="n">menu</span><span class="o">=</span><span class="n">exchangeChoice</span><span class="p">)</span>
+        <span class="n">sensor_model_msg</span> <span class="o">=</span> <span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">        Currently, this is only a dummy menu option.  The senor model</span>
+<span class="s1">        configuration for the Reigl VQ-880-G is hard-coded into cBLUE.</span>
+<span class="s1">        Development plans include refactoring the code to read sensor </span>
+<span class="s1">        model information from a separate file and extending support </span>
+<span class="s1">        to other lidar systems, including Leica Chiroptera 4X.</span>
+<span class="s1">        &#39;&#39;&#39;</span>
+
+        <span class="n">sensor_model_choice</span> <span class="o">=</span> <span class="n">tk</span><span class="o">.</span><span class="n">Menu</span><span class="p">(</span><span class="n">menubar</span><span class="p">,</span> <span class="n">tearoff</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+        <span class="n">sensor_model_choice</span><span class="o">.</span><span class="n">add_command</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="sa">u</span><span class="s1">&#39;Reigl VQ-880-G&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="sa">u</span><span class="s1">&#39;</span><span class="se">\u2713</span><span class="s1">&#39;</span><span class="p">),</span>
+                                   <span class="n">command</span><span class="o">=</span><span class="k">lambda</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">popupmsg</span><span class="p">(</span><span class="n">sensor_model_msg</span><span class="p">))</span>
+        <span class="n">menubar</span><span class="o">.</span><span class="n">add_cascade</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;Sensor Model&#39;</span><span class="p">,</span> <span class="n">menu</span><span class="o">=</span><span class="n">sensor_model_choice</span><span class="p">)</span>
+
+        <span class="n">about_menu</span> <span class="o">=</span> <span class="n">tk</span><span class="o">.</span><span class="n">Menu</span><span class="p">(</span><span class="n">menubar</span><span class="p">,</span> <span class="n">tearoff</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+        <span class="n">about_menu</span><span class="o">.</span><span class="n">add_command</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;About&#39;</span><span class="p">,</span> <span class="n">command</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">show_about</span><span class="p">)</span>
+        <span class="n">menubar</span><span class="o">.</span><span class="n">add_cascade</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;Help&#39;</span><span class="p">,</span> <span class="n">menu</span><span class="o">=</span><span class="n">about_menu</span><span class="p">)</span>
 
         <span class="n">tk</span><span class="o">.</span><span class="n">Tk</span><span class="o">.</span><span class="n">config</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">menu</span><span class="o">=</span><span class="n">menubar</span><span class="p">)</span>
 

docs/html/_modules/Subaerial.html

@@ -129,15 +129,6 @@ <h1>Source code for Subaerial</h1><div class="highlight"><pre>
 
         <span class="n">R</span> <span class="o">=</span> <span class="n">R3</span> <span class="o">*</span> <span class="n">R2</span> <span class="o">*</span> <span class="n">R1</span>
 
-        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;R1&#39;</span><span class="p">)</span>
-        <span class="nb">print</span><span class="p">(</span><span class="n">latex</span><span class="p">(</span><span class="n">R1</span><span class="p">))</span>
-        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;R2&#39;</span><span class="p">)</span>
-        <span class="nb">print</span><span class="p">(</span><span class="n">latex</span><span class="p">(</span><span class="n">R2</span><span class="p">))</span>
-        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;R3&#39;</span><span class="p">)</span>
-        <span class="nb">print</span><span class="p">(</span><span class="n">latex</span><span class="p">(</span><span class="n">R3</span><span class="p">))</span>
-        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;R&#39;</span><span class="p">)</span>
-        <span class="nb">print</span><span class="p">(</span><span class="n">latex</span><span class="p">(</span><span class="n">R</span><span class="p">))</span>
-
         <span class="c1"># &quot;functionize&quot; the necessary R components for a and b estimation</span>
         <span class="c1"># (http://docs.sympy.org/latest/modules/utilities/lambdify.html)</span>
         <span class="n">r00</span> <span class="o">=</span> <span class="n">lambdify</span><span class="p">((</span><span class="n">h</span><span class="p">,</span> <span class="n">p</span><span class="p">),</span> <span class="n">R</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">eval_type</span><span class="p">)</span>
@@ -185,13 +176,6 @@ <h1>Source code for Subaerial</h1><div class="highlight"><pre>
 
         <span class="n">M</span> <span class="o">=</span> <span class="n">M2</span> <span class="o">*</span> <span class="n">M1</span>
 
-        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;M1&#39;</span><span class="p">)</span>
-        <span class="nb">print</span><span class="p">(</span><span class="n">latex</span><span class="p">(</span><span class="n">M1</span><span class="p">))</span>
-        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;M2&#39;</span><span class="p">)</span>
-        <span class="nb">print</span><span class="p">(</span><span class="n">latex</span><span class="p">(</span><span class="n">M2</span><span class="p">))</span>
-        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;M&#39;</span><span class="p">)</span>
-        <span class="nb">print</span><span class="p">(</span><span class="n">latex</span><span class="p">(</span><span class="n">M</span><span class="p">))</span>
-
         <span class="k">return</span> <span class="n">M</span></div>
 
 <div class="viewcode-block" id="SensorModel.define_obseration_equation"><a class="viewcode-back" href="../Subaerial.html#Subaerial.SensorModel.define_obseration_equation">[docs]</a>    <span class="k">def</span> <span class="nf">define_obseration_equation</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -932,7 +916,7 @@ <h1>Source code for Subaerial</h1><div class="highlight"><pre>
 <span class="sd">            Once the Jacobian is evaluated, uncertainty is progagated by multiplying the</span>
 <span class="sd">            square of the Jacobian with the squares of the standard deviations defined in the</span>
 <span class="sd">            stddev parameter.  The covariances are assumed to be zero.  TODO:  explain how this is </span>
-<span class="sd">            technically different than the shown propagation equation because the covariances are </span>
+<span class="sd">            implemented differently than shown by the propagation equation because the covariances are </span>
 <span class="sd">            assumed to be 0.</span>
 
 <span class="sd">        :return: (ndarray, ndarray, list[str])</span>

docs/html/_modules/Tpu.html

@@ -404,7 +404,7 @@ <h1>Source code for Tpu</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">metadata</span><span class="p">[</span><span class="s1">&#39;flight line stats&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">flight_line_stats</span><span class="p">)</span>  <span class="c1"># flight line metadata</span>
             <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tpuOutput</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">{}</span><span class="s1">.json&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">las</span><span class="o">.</span><span class="n">las_base_name</span><span class="p">)),</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">outfile</span><span class="p">:</span>
                 <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">metadata</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">ensure_ascii</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-        <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">e</span><span class="p">:</span>
+        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
             <span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="Tpu.run_tpu_multiprocess"><a class="viewcode-back" href="../Tpu.html#Tpu.Tpu.run_tpu_multiprocess">[docs]</a>    <span class="k">def</span> <span class="nf">run_tpu_multiprocess</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sbet_las_generator</span><span class="p">):</span>

docs/html/_sources/install.rst.txt

@@ -3,7 +3,7 @@ Installation
 
 The latest release of cBLUE can be found at https://github.com/forkozi/cBLUE/releases.
 
-cBLUE is designed to run on 64-bit Python 2.7.  Rigorous performance testing was not conducted during tool development, but memory errors were encountered when not using a 64-bit installation of Python to process the Marcos Island test dataset.  Support for Python 3 is deferred to future versions.  
+cBLUE is designed to run on 64-bit Python 2.7.  Support for Python 3 is deferred to future versions.  
 
 The cBLUE source code is available in a private GitHub repository (https://github.com/forkozi/cBLUE).
 
@@ -20,10 +20,12 @@ The following table lists the major files comprising cBLUE:
 	:widths: 14, 30, 10
 
 	CBlueApp.py, initiates the GUI
-	Sbet.py, loads the ASCII trajector files (or sbets), ./
+	Sbet.py, loads the ASCII trajectory files (or "sbets"), ./
 	Las.py, loads the las files, ./
 	Merge.py, merges the trajectory and las data based on timestamps, ./
-	Tpu.py, calculates the TPU (combined subaerial and subaqueous), ./
+	SensorModel.py, defines and allows access to lidar sensor model, ./
+	Jacobian.py, forms and evaluates the Jacobian of a sensor model's laser geolocation equation, ./
+	Tpu.py, coordinates the TPU workflow, ./
 	Subaerial.py, calculates the subaerial TPU, ./
 	Subaqueous.py, calculates the subaqueous TPU, ./
 	Datum.py, loads the zone-specific VDatum zone MCU, ./
@@ -38,9 +40,9 @@ The recommended way to ensure that all of the necessary dependencies are loaded
 
 	conda env create --file <evn file name>
 
-where <env file name> is the path to cBLUE_install.txt, which is included in the cBLUE GitHub repository.  If you don't have access to the private cBLUE repository, please send a request to nick.forfinski@gmail.com, with your GitHub username.
+where <env file name> is the path to cBLUE_install.txt, which is included in the cBLUE GitHub repository.
 
-The major dependencies are summarized in the table below:
+Major dependencies are summarized in the table below:
 
 =======		=============================================================================
 package		comment
@@ -56,10 +58,10 @@ Tkinter		used to create GUI
 
 Starting the GUI
 ----------------
-The GUI can be initiated from the command line with the following command (specify the full path of Gui.py if the current directory is not the location of Gui.py):
+The GUI can be initiated from the command line with the following command (specify the full path of CBlueApp.py if the current directory is not the location of CBlueApp.py):
 
 NOTE: If there are multiple Python installations on the computer running the GUI, ensure the desired installation is specified in the path environment variables or explicitly specify the full path of the relevant python executable in the command. For example:
 
-	(command line)> C:\\Python27\\64-bit\\python.exe Gui.py
+	(command line)> C:\\Python27\\64-bit\\python.exe CBlueApp.py
 
-The GUI can also be initiated by running the Gui.py file from a Python IDE, such as IDLE, PyCharm, or Visual Studio.
+The GUI can also be initiated by running the CBlueApp.py file from a Python IDE, such as IDLE, PyCharm, or Microsoft Visual Studio.