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@@ -75,7 +75,7 @@
     </li>
     <li class="toctree-l3"><a class="reference internal" href="#step-by-step-bay-area-cct-example">Step-by-Step Bay Area CCT Example</a>
         <ul>
-    <li class="toctree-l4"><a class="reference internal" href="#read-in-necesssary-data">Read in necesssary data</a>
+    <li class="toctree-l4"><a class="reference internal" href="#read-in-necessary-data">Read in necessary data</a>
     </li>
     <li class="toctree-l4"><a class="reference internal" href="#run-the-calibration">Run the calibration</a>
     </li>
@@ -153,8 +153,8 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
             <div class="section" itemprop="articleBody">
 
-                <h1 id="coda-calibration-tool-cct-1020-documentation">Coda Calibration Tool (CCT) 1.0.20 documentation</h1>
-<p><sub>2022-07-31; Version 1.0; Authors Barno, Justin | Mayeda, Kevin</sub></p>
+                <h1 id="coda-calibration-tool-cct-1021-documentation">Coda Calibration Tool (CCT) 1.0.21 documentation</h1>
+<p><sub>2023-12-20; Version 1.1; Authors Barno, Justin | Mayeda, Kevin</sub></p>
 <h2 id="about-cct">About CCT</h2>
 <p>The Coda Calibration Tool (CCT) is a Java-based application that stems from a collaborative project by scientists from the USNDC (AFTAC/SDS) and DOE (LLNL) as well as significant input from seismologists from the University of Utah, INGV (Milan) and USGS (Golden, CO), Natural Resources Canada. This tool consolidates research-mode scripts circa 1995 (SAC, C-shell, Fortran) into a robust platform-independent tool using the empirical 1-D method outlined by <a href="https://doi.org/10.1029/96JB00112">Mayeda and Walter (1996)</a> and <a href="https://doi.org/10.1785/0120020020">Mayeda et al. (2003)</a>.</p>
 <p>CCT provides a fast and efficient means of calibrating and processing local and regional coda envelopes to estimate stable source spectra, moment magnitude, and apparent stress, that are roughly 3-to-4 times less variable than estimates derived from traditional direct wave estimates. The source parameters represent averaged values and are virtually free of lateral path heterogeneity and source radiation anisotropy. </p>
@@ -170,15 +170,15 @@ <h2 id="tutorial-guide-for-new-users">Tutorial Guide for New Users</h2>
 <h3 id="getting-started">Getting Started</h3>
 <h4 id="downloading-cct">Downloading CCT</h4>
 <p>The latest version of the Coda Calibration Tool (CCT) can be found on the <a href="https://github.com/LLNL/coda-calibration-tool/releases/">release page</a></p>
-<p>The standalone CCT jar file is calibration-standalone-1.0.20-runnable.jar while the REST services only are available in calibration-application-1.0.20-runnable.jar.</p>
+<p>The standalone CCT jar file is calibration-standalone-1.0.21-runnable.jar while the REST services only are available in calibration-application-1.0.21-runnable.jar.</p>
 <h4 id="downloading-sf-bay-area-example-tarfile">Downloading SF Bay Area example tarfile</h4>
 <p>The complete SF Bay Area calibration which includes SAC waveforms, stacked envelopes and JavaScript
-Object Notation (JSON) parameter files can be <a href="https://doi.org/10.5281/zenodo.6902890">downloaded here</a></p>
+Object Notation (JSON) parameter files can be <a href="https://doi.org/10.5281/zenodo.10019686">downloaded here</a></p>
 <h4 id="running-cct">Running CCT</h4>
 <p>You can launch CCT by executing Java from the command line as:</p>
-<p><code>java -Xmx12g -jar calibration-standalone-1.0.20-runnable.jar</code></p>
+<p><code>java -Xmx12g -jar calibration-standalone-1.0.21-runnable.jar</code></p>
 <p>Or, if you have Java 11+ as:</p>
-<p><code>java -XX:MaxRAMPercentage=70.0 -jar calibration-standalone-1.0.20-runnable.jar</code></p>
+<p><code>java -XX:MaxRAMPercentage=70.0 -jar calibration-standalone-1.0.21-runnable.jar</code></p>
 <p>Generally your -Xmx flag should be set to, at most, ~70% of the physical RAM available on the machine.</p>
 <p>You can add the <code>--spring.profiles.active=file</code> flag to the Java call if your dataset is larger than the physical RAM on your machine.
 This will output a large database file that is also useful if you want to save the entire database or connect to it with an external database browser tool. The tradeoff is that you have to wait for the read/write times of the hard drive so this mode can be slower than the default RAM-only mode.</p>
@@ -192,7 +192,7 @@ <h3 id="recommendations-for-selecting-calibration-data">Recommendations For Sele
 <h3 id="creating-envelopes-with-sac-waveform-data">Creating Envelopes with SAC Waveform Data</h3>
 <h4 id="initial-waveform-data">Initial Waveform Data</h4>
 <ol>
-<li>CCT requires SAC files. Horizontal components are preferred, but you can use verticals, just don’t mix them and keep in separate folders. Envelope tool will stack all components for an event recorded at station X. </li>
+<li>CCT requires SAC files. Horizontal components are preferred, but you can use verticals, just don’t mix them and keep in separate folders. The envelope tool will stack all components for an event recorded at station X. </li>
 </ol>
 <p>The tool will use the SAC header variables for the event name (<strong>KEVNM</strong>) and station name (<strong>KSTNM</strong>) in the SAC header to create the names for the envelope files. </p>
 <div class="admonition note">
@@ -248,7 +248,7 @@ <h4 id="envelope-formation">Envelope Formation</h4>
 </li>
 <li>
 <p>Close the Envelope Tool when the progress bar completes.
-The envelopes will be created in the following directory structure: ...Data_new/Envelopes/YEAR/MONTH/EVID/STATION/STA_COMP_EVID_FREQ1_FREQ2_VEL_.ENV In subsequent steps, you can import all stack envelopes created in this envelope tool with "File &gt; Import stack directory…" and choose the "Envelopes" directory.</p>
+The envelopes will be created in the following directory structure: ...Data_new/Envelopes/YEAR/MONTH/EVID/STATION/STA_COMP_EVID_FREQ1_FREQ2_VEL_.ENV In subsequent steps, you can import all stack envelopes created in this envelope tool with "File &gt; Load Stack Directory…" and choose the "Envelopes" directory.</p>
 </li>
 </ol>
 <h3 id="san-francisco-bay-example-dataset">San Francisco Bay Example Dataset</h3>
@@ -293,15 +293,20 @@ <h4 id="untar-example-file-and-description">Untar Example File and Description</
 </li>
 </ul>
 <h3 id="step-by-step-bay-area-cct-example">Step-by-Step Bay Area CCT Example</h3>
-<h4 id="read-in-necesssary-data">Read in necesssary data</h4>
-<p>Read in stacked envelopes using the pulldown tab: File&gt;Import Stack Directory…
+<h4 id="read-in-necessary-data">Read in necessary data</h4>
+<p>Load in stacked envelopes using the pulldown tab: File&gt;Load Stack Directory…
 <img alt="img" src="img/import_stacks.png" /> <figcaption align = "center">Figure. 6, Importing stacked envelopes in a directory.</figcaption> <br/></p>
 <p>Select the <strong>Envelopes_stack_Kevin_picks</strong> directory</p>
 <p>You will see the following Task-Progress pop-up window as the envelopes are being read in (roughly 7 seconds on my machine).</p>
 <p>Upon completion you’ll see this:</p>
 <p><img alt="img" src="img/import_complete.png" /> <figcaption align = "center">Figure. 7, Dialog showing amount of envelopes imported, errors (if any), and if the process has completed.</figcaption> <br/></p>
-<p>Next, read in the Coda Parameter file: File&gt;Import Coda Param...</p>
+<p>Next, load the Coda Parameter file: File&gt;Load Calibration...</p>
 <p>Select the <strong>Calibration_Parameters_Kevin.json</strong> file (This reads instantly)</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>The example SF Bay Area JSON file has been fine-tuned over multiple calibration iterations. When applying to a new region, you will have to re-run CCT multiple times to adjust picks, remove bad data, adjust minimum and maximum window lengths, and possibly SNR pre-sets.</p>
+<p>Each time you must export the calibration JSON file to save your changes and use the latest JSON in the next iteration. Keep re-running CCT and repeat the above steps to refine the calibration until you are satisfied with the results. The final calibration JSON file that you export can then be used for routine processing for the region.</p>
+</div>
 <p>To view the data in map form, click the Map button in the upper right. In the upper right map pop-up, select the tile pull-down in the upper right. Be sure the application.properties file is in the working directory if you want to use custom layers. You can click on a station or event to see the corresponding name and view envelopes. </p>
 <p><img alt="img" src="img/map.png" /> <figcaption align = "center">Figure. 8, The CCT map showing a custom WMS layer featuring the <a href="https://basemap.nationalmap.gov/arcgis/rest/services/USGSTopo/MapServer">USGS topographic</a> map.</figcaption> <br/></p>
 <div class="admonition note">
@@ -340,11 +345,11 @@ <h4 id="sorting-re-picking-events">Sorting &amp; Re-Picking Events</h4>
 <p>Also, in the Data pull down tab, you can choose ‘Make Picks Reviewed’ which will change all auto-picked <strong>f-markers</strong> reviewed, if for example you’ve visually checked all the <strong>f-markers</strong> and would like them to be changed to ‘reviewed’. If you export the envelopes then all ‘<strong>ap</strong>’ marks will disappear. </p>
 <div class="admonition important">
 <p class="admonition-title">Important</p>
-<p>To save all the new picks in the current session, under File choose Export Waveforms and you can choose the same Envelope directory, in this case Envelope_stack_Kevin_picks, or create a new directory. The next time you run the calibration, the tool will use the new <strong>f-marker</strong> picks.</p>
+<p>To save all the new picks in the current session, under File choose Save Waveforms and you can choose the same Envelope directory, in this case Envelope_stack_Kevin_picks, or create a new directory. The next time you run the calibration, the tool will use the new <strong>f-marker</strong> picks.</p>
 </div>
 <h4 id="parameters-tab">Parameters tab</h4>
-<p>Allows users to view the calibration parameters during the current calibration and make adjustments, specifically the window length limits (<strong>Min</strong> and <strong>Max</strong>) as well as <strong>SNR</strong> levels (in log 10). These changes will ONLY be kept if you export the calibration (File-&gt;Export Calibration). You will then have to use the newly created <strong>Calibration_Parameters.json</strong> file for the subsequent calibration refinement.</p>
-<p><img alt="img" src="img/parameters_example.png" /> <figcaption align = "center">Figure. 13, The parameters table that defines the core of a calibraition.</figcaption> <br/></p>
+<p>Allows users to view the calibration parameters during the current calibration and make adjustments, specifically the window length limits (<strong>Min</strong> and <strong>Max</strong>) as well as <strong>SNR</strong> levels (in log 10). These changes will ONLY be kept if you export the calibration (File-&gt;Save Calibration). You will then have to use the newly created <strong>Calibration_Parameters.json</strong> file for the subsequent calibration refinement.</p>
+<p><img alt="img" src="img/parameters_example.png" /> <figcaption align = "center">Figure. 13, The parameters table that defines the core of a calibration.</figcaption> <br/></p>
 <h4 id="shape-tab">Shape tab</h4>
 <p>Allows users to view empirical envelope shape parameters and velocity fits to the observed data as a function of distance (see <a href="https://doi.org/10.1785/0120020020">Mayeda et al. 2003</a> for more details). </p>
 <div class="admonition note">
@@ -424,7 +429,7 @@ <h4 id="site-tab">Site tab</h4>
 <p><img alt="img" src="img/site_terms.png" /> <figcaption align = "center">Figure. 17, Plots showing the relative site correction terms for each station, a network average, and a plot relative to any individual station in the correction set.</figcaption> <br/></p>
 <h4 id="measured-mws-tab">Measured Mws tab</h4>
 <p>This feature allows you to measure <strong>M<sub>w</sub></strong>s using an existing calibration for new events in a region. This feature also enables automated processing of new events as they are formed provided the event is located in the calibrated area and a calibrated station recorded the event by using the REST services CCT provides. </p>
-<p>Oftentimes we impose a more strict set of guidelines for calibration, whereas for routine event processing we might relax the minimum window length or change the SNR levels. Save your <strong>M<sub>w</sub></strong>s with File -&gt; Export Measured Mws…</p>
+<p>Oftentimes we impose a more strict set of guidelines for calibration, whereas for routine event processing we might relax the minimum window length or change the SNR levels. Save your <strong>M<sub>w</sub></strong>s with File -&gt; Save Measured Mws…</p>
 <h2 id="glossary-of-terms">Glossary of terms</h2>
 <ul>
 <li>
@@ -987,5 +992,5 @@ <h2 id="configuration-variables">Configuration variables</h2>
 
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