diff --git a/PyXRF/_sources/release-notes.rst.txt b/PyXRF/_sources/release-notes.rst.txt
index 029973566..c212553b0 100644
--- a/PyXRF/_sources/release-notes.rst.txt
+++ b/PyXRF/_sources/release-notes.rst.txt
@@ -2,6 +2,21 @@
 Release Notes
 =============
 
+
+v1.0.28 (2024-06-20)
+====================
+
+Fixed
+-----
+
+- Compatibility with Matplotlib 3.9.0: deprecated ``BrokenBarHCollection`` was replaced with ``PolyCollection``.
+
+Added
+-----
+
+- Optimized data loaded from Tiled server for SRX beamline.
+
+
 v1.0.27 (2024-04-18)
 ====================
 
diff --git a/PyXRF/index.html b/PyXRF/index.html
index d115ade8d..e0544912e 100644
--- a/PyXRF/index.html
+++ b/PyXRF/index.html
@@ -84,6 +84,7 @@ <h1>Table of Contents<a class="headerlink" href="#table-of-contents" title="Perm
 </li>
 <li class="toctree-l1"><a class="reference internal" href="credits.html">Credits</a></li>
 <li class="toctree-l1"><a class="reference internal" href="release-notes.html">Release Notes</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="release-notes.html#v1-0-28-2024-06-20">v1.0.28 (2024-06-20)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="release-notes.html#v1-0-27-2024-04-18">v1.0.27 (2024-04-18)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="release-notes.html#v1-0-26-2024-04-07">v1.0.26 (2024-04-07)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="release-notes.html#v1-0-25-2024-01-18">v1.0.25 (2024-01-18)</a></li>
diff --git a/PyXRF/release-notes.html b/PyXRF/release-notes.html
index 71a3d8611..c9e38d04a 100644
--- a/PyXRF/release-notes.html
+++ b/PyXRF/release-notes.html
@@ -32,33 +32,48 @@
             
   <section id="release-notes">
 <h1>Release Notes<a class="headerlink" href="#release-notes" title="Permalink to this heading">¶</a></h1>
-<section id="v1-0-27-2024-04-18">
-<h2>v1.0.27 (2024-04-18)<a class="headerlink" href="#v1-0-27-2024-04-18" title="Permalink to this heading">¶</a></h2>
+<section id="v1-0-28-2024-06-20">
+<h2>v1.0.28 (2024-06-20)<a class="headerlink" href="#v1-0-28-2024-06-20" title="Permalink to this heading">¶</a></h2>
 <section id="fixed">
 <h3>Fixed<a class="headerlink" href="#fixed" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
-<li><p>Fixed ‘Save spectra for pixels in selected region’ (‘Maps’ tab).</p></li>
-<li><p>Selection of axes scale (Pixels vs. Positions) is not reset after each fitting of the map.</p></li>
+<li><p>Compatibility with Matplotlib 3.9.0: deprecated <code class="docutils literal notranslate"><span class="pre">BrokenBarHCollection</span></code> was replaced with <code class="docutils literal notranslate"><span class="pre">PolyCollection</span></code>.</p></li>
 </ul>
 </section>
 <section id="added">
 <h3>Added<a class="headerlink" href="#added" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
+<li><p>Optimized data loaded from Tiled server for SRX beamline.</p></li>
+</ul>
+</section>
+</section>
+<section id="v1-0-27-2024-04-18">
+<h2>v1.0.27 (2024-04-18)<a class="headerlink" href="#v1-0-27-2024-04-18" title="Permalink to this heading">¶</a></h2>
+<section id="id1">
+<h3>Fixed<a class="headerlink" href="#id1" title="Permalink to this heading">¶</a></h3>
+<ul class="simple">
+<li><p>Fixed ‘Save spectra for pixels in selected region’ (‘Maps’ tab).</p></li>
+<li><p>Selection of axes scale (Pixels vs. Positions) is not reset after each fitting of the map.</p></li>
+</ul>
+</section>
+<section id="id2">
+<h3>Added<a class="headerlink" href="#id2" title="Permalink to this heading">¶</a></h3>
+<ul class="simple">
 <li><p>APS AXO quantitative calibration standard.</p></li>
 </ul>
 </section>
 </section>
 <section id="v1-0-26-2024-04-07">
 <h2>v1.0.26 (2024-04-07)<a class="headerlink" href="#v1-0-26-2024-04-07" title="Permalink to this heading">¶</a></h2>
-<section id="id1">
-<h3>Fixed<a class="headerlink" href="#id1" title="Permalink to this heading">¶</a></h3>
+<section id="id3">
+<h3>Fixed<a class="headerlink" href="#id3" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Compatibility with recent Numba: removed unsupported <code class="docutils literal notranslate"><span class="pre">np.asarray</span></code> function
 in the code compiled by Numba.</p></li>
 </ul>
 </section>
-<section id="id2">
-<h3>Added<a class="headerlink" href="#id2" title="Permalink to this heading">¶</a></h3>
+<section id="id4">
+<h3>Added<a class="headerlink" href="#id4" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>New <code class="docutils literal notranslate"><span class="pre">make_hdf</span></code> parameter: <code class="docutils literal notranslate"><span class="pre">catalog</span></code>.</p></li>
 <li><p>New <code class="docutils literal notranslate"><span class="pre">pyxrf</span></code> CLI parameter: <code class="docutils literal notranslate"><span class="pre">--catalog-name</span></code> or <code class="docutils literal notranslate"><span class="pre">-c</span></code>.</p></li>
@@ -68,8 +83,8 @@ <h3>Added<a class="headerlink" href="#id2" title="Permalink to this heading">¶<
 </section>
 <section id="v1-0-25-2024-01-18">
 <h2>v1.0.25 (2024-01-18)<a class="headerlink" href="#v1-0-25-2024-01-18" title="Permalink to this heading">¶</a></h2>
-<section id="id3">
-<h3>Fixed<a class="headerlink" href="#id3" title="Permalink to this heading">¶</a></h3>
+<section id="id5">
+<h3>Fixed<a class="headerlink" href="#id5" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Formatting of TXT file saved by ‘Save Spectrum/Fit’: the first column now
 contains the energy values in kEv (previously, the first column contained
@@ -77,8 +92,8 @@ <h3>Fixed<a class="headerlink" href="#id3" title="Permalink to this heading">¶<
 <li><p>Fixed issue with Dask v2023.9.3 and recent Numpy/Numba.</p></li>
 </ul>
 </section>
-<section id="id4">
-<h3>Added<a class="headerlink" href="#id4" title="Permalink to this heading">¶</a></h3>
+<section id="id6">
+<h3>Added<a class="headerlink" href="#id6" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Quantitative calibration standards AXO C1 and C10 were added.</p></li>
 </ul>
@@ -92,14 +107,14 @@ <h3>Changed<a class="headerlink" href="#changed" title="Permalink to this headin
 </section>
 <section id="v1-0-24-2023-05-12">
 <h2>v1.0.24 (2023-05-12)<a class="headerlink" href="#v1-0-24-2023-05-12" title="Permalink to this heading">¶</a></h2>
-<section id="id5">
-<h3>Fixed<a class="headerlink" href="#id5" title="Permalink to this heading">¶</a></h3>
+<section id="id7">
+<h3>Fixed<a class="headerlink" href="#id7" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Compatibility with Dask/Distributed v2023.04.x.</p></li>
 </ul>
 </section>
-<section id="id6">
-<h3>Added<a class="headerlink" href="#id6" title="Permalink to this heading">¶</a></h3>
+<section id="id8">
+<h3>Added<a class="headerlink" href="#id8" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Support for loading data generated by updated Bluesky plans (Community Xspress3 IOC).</p></li>
 </ul>
@@ -107,8 +122,8 @@ <h3>Added<a class="headerlink" href="#id6" title="Permalink to this heading">¶<
 </section>
 <section id="v1-0-23-2022-03-19">
 <h2>v1.0.23 (2022-03-19)<a class="headerlink" href="#v1-0-23-2022-03-19" title="Permalink to this heading">¶</a></h2>
-<section id="id7">
-<h3>Fixed<a class="headerlink" href="#id7" title="Permalink to this heading">¶</a></h3>
+<section id="id9">
+<h3>Fixed<a class="headerlink" href="#id9" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>PyXRF is now compatible with PyQT 5.15.</p></li>
 </ul>
@@ -116,8 +131,8 @@ <h3>Fixed<a class="headerlink" href="#id7" title="Permalink to this heading">¶<
 </section>
 <section id="v1-0-22-2022-02-28">
 <h2>v1.0.22 (2022-02-28)<a class="headerlink" href="#v1-0-22-2022-02-28" title="Permalink to this heading">¶</a></h2>
-<section id="id8">
-<h3>Added<a class="headerlink" href="#id8" title="Permalink to this heading">¶</a></h3>
+<section id="id10">
+<h3>Added<a class="headerlink" href="#id10" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Extended functionality of quantitative analysis feature: additional combo box allows
 to select reference emission line from the list of emission lines with existing calibration.
@@ -127,8 +142,8 @@ <h3>Added<a class="headerlink" href="#id8" title="Permalink to this heading">¶<
 calibration (old functionality)</p></li>
 </ul>
 </section>
-<section id="id9">
-<h3>Fixed<a class="headerlink" href="#id9" title="Permalink to this heading">¶</a></h3>
+<section id="id11">
+<h3>Fixed<a class="headerlink" href="#id11" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Fixed the code for loading step scan data at SRX. PyXRF can now load the step scan
 data recorded using 2023-1.0 environment.</p></li>
@@ -138,8 +153,8 @@ <h3>Fixed<a class="headerlink" href="#id9" title="Permalink to this heading">¶<
 </section>
 <section id="v1-0-21-2022-12-11">
 <h2>v1.0.21 (2022-12-11)<a class="headerlink" href="#v1-0-21-2022-12-11" title="Permalink to this heading">¶</a></h2>
-<section id="id10">
-<h3>Added<a class="headerlink" href="#id10" title="Permalink to this heading">¶</a></h3>
+<section id="id12">
+<h3>Added<a class="headerlink" href="#id12" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p><code class="docutils literal notranslate"><span class="pre">make_hdf</span></code> now supports <code class="docutils literal notranslate"><span class="pre">Fly1D</span></code>, <code class="docutils literal notranslate"><span class="pre">dmesh</span></code> and <code class="docutils literal notranslate"><span class="pre">dscan</span></code> (HXN).</p></li>
 <li><p>New parameter <code class="docutils literal notranslate"><span class="pre">fail_for_plan_types</span></code> is added <code class="docutils literal notranslate"><span class="pre">make_hdf</span></code>. The parameter accepts
@@ -151,8 +166,8 @@ <h3>Added<a class="headerlink" href="#id10" title="Permalink to this heading">¶
 </section>
 <section id="v1-0-20-2022-08-19">
 <h2>v1.0.20 (2022-08-19)<a class="headerlink" href="#v1-0-20-2022-08-19" title="Permalink to this heading">¶</a></h2>
-<section id="id11">
-<h3>Changed<a class="headerlink" href="#id11" title="Permalink to this heading">¶</a></h3>
+<section id="id13">
+<h3>Changed<a class="headerlink" href="#id13" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Current working directory can now be changed at any time. The respective button is not deactivated after the first HDF5 file is opened.
 The working directory is used to create new HDF5 files (<code class="docutils literal notranslate"><span class="pre">Load</span> <span class="pre">Run..</span></code>) and as a default directory for ‘Open’ and ‘Save’ dialog boxes.</p></li>
@@ -160,8 +175,8 @@ <h3>Changed<a class="headerlink" href="#id11" title="Permalink to this heading">
 <code class="docutils literal notranslate"><span class="pre">nano_stage_x</span></code>, <code class="docutils literal notranslate"><span class="pre">nano_stage_y</span></code>, <code class="docutils literal notranslate"><span class="pre">nano_stage_z</span></code>, <code class="docutils literal notranslate"><span class="pre">nano_stage_topx</span></code>, <code class="docutils literal notranslate"><span class="pre">nano_stage_topz</span></code>.</p></li>
 </ul>
 </section>
-<section id="id12">
-<h3>Fixed<a class="headerlink" href="#id12" title="Permalink to this heading">¶</a></h3>
+<section id="id14">
+<h3>Fixed<a class="headerlink" href="#id14" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Compatibility with Numba v0.56.x.</p></li>
 </ul>
@@ -169,15 +184,15 @@ <h3>Fixed<a class="headerlink" href="#id12" title="Permalink to this heading">¶
 </section>
 <section id="v1-0-19-2022-08-19">
 <h2>v1.0.19 (2022-08-19)<a class="headerlink" href="#v1-0-19-2022-08-19" title="Permalink to this heading">¶</a></h2>
-<section id="id13">
-<h3>Added<a class="headerlink" href="#id13" title="Permalink to this heading">¶</a></h3>
+<section id="id15">
+<h3>Added<a class="headerlink" href="#id15" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>New button <code class="docutils literal notranslate"><span class="pre">Add</span> <span class="pre">All</span> <span class="pre">Elements</span></code> is added to Image Wizard. The button adds all element emission lines to the selection.</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">Auto</span></code> checkbox is added to the windows ‘Fitting Parameters for Individual Emission Lines’ and ‘Shared Detailed Fitting Parameters’.</p></li>
 </ul>
 </section>
-<section id="id14">
-<h3>Changed<a class="headerlink" href="#id14" title="Permalink to this heading">¶</a></h3>
+<section id="id16">
+<h3>Changed<a class="headerlink" href="#id16" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>The value of the parameter <code class="docutils literal notranslate"><span class="pre">Userpeak.._delta_center</span></code> is now displayed as absolute energy (true peak position in keV)
 instead of relative energy (difference between the absolute energy and the ‘base’ energy 5 keV) in the window
@@ -187,8 +202,8 @@ <h3>Changed<a class="headerlink" href="#id14" title="Permalink to this heading">
 </section>
 <section id="v1-0-18-2022-08-08">
 <h2>v1.0.18 (2022-08-08)<a class="headerlink" href="#v1-0-18-2022-08-08" title="Permalink to this heading">¶</a></h2>
-<section id="id15">
-<h3>Changed<a class="headerlink" href="#id15" title="Permalink to this heading">¶</a></h3>
+<section id="id17">
+<h3>Changed<a class="headerlink" href="#id17" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>The algorithm for loading SRX raw data from databroker now fixes corrupt rows by replacing the data
 with data from the preceding or next valid row.</p></li>
@@ -199,14 +214,14 @@ <h3>Changed<a class="headerlink" href="#id15" title="Permalink to this heading">
 </section>
 <section id="v1-0-17-2022-06-16">
 <h2>v1.0.17 (2022-06-16)<a class="headerlink" href="#v1-0-17-2022-06-16" title="Permalink to this heading">¶</a></h2>
-<section id="id16">
-<h3>Added<a class="headerlink" href="#id16" title="Permalink to this heading">¶</a></h3>
+<section id="id18">
+<h3>Added<a class="headerlink" href="#id18" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Support for Python 3.10</p></li>
 </ul>
 </section>
-<section id="id17">
-<h3>Fixed<a class="headerlink" href="#id17" title="Permalink to this heading">¶</a></h3>
+<section id="id19">
+<h3>Fixed<a class="headerlink" href="#id19" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Updated the code for loading raw data at SRX beamline to be compatible with Databroker V1
 (intake version).</p></li>
@@ -218,14 +233,14 @@ <h3>Fixed<a class="headerlink" href="#id17" title="Permalink to this heading">¶
 </section>
 <section id="v1-0-16-2022-05-26">
 <h2>v1.0.16 (2022-05-26)<a class="headerlink" href="#v1-0-16-2022-05-26" title="Permalink to this heading">¶</a></h2>
-<section id="id18">
-<h3>Added<a class="headerlink" href="#id18" title="Permalink to this heading">¶</a></h3>
+<section id="id20">
+<h3>Added<a class="headerlink" href="#id20" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Support for the detector <code class="docutils literal notranslate"><span class="pre">xs4</span></code> (SRX beamline).</p></li>
 </ul>
 </section>
-<section id="id19">
-<h3>Changed<a class="headerlink" href="#id19" title="Permalink to this heading">¶</a></h3>
+<section id="id21">
+<h3>Changed<a class="headerlink" href="#id21" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Databroker v1 is used for loading data at SRX beamline.</p></li>
 </ul>
@@ -233,14 +248,14 @@ <h3>Changed<a class="headerlink" href="#id19" title="Permalink to this heading">
 </section>
 <section id="v1-0-15-2022-04-06">
 <h2>v1.0.15 (2022-04-06)<a class="headerlink" href="#v1-0-15-2022-04-06" title="Permalink to this heading">¶</a></h2>
-<section id="id20">
-<h3>Added<a class="headerlink" href="#id20" title="Permalink to this heading">¶</a></h3>
+<section id="id22">
+<h3>Added<a class="headerlink" href="#id22" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>SRX data, new format: support for step scans using top stages.</p></li>
 </ul>
 </section>
-<section id="id21">
-<h3>Fixed<a class="headerlink" href="#id21" title="Permalink to this heading">¶</a></h3>
+<section id="id23">
+<h3>Fixed<a class="headerlink" href="#id23" title="Permalink to this heading">¶</a></h3>
 <ul class="simple">
 <li><p>Fixed a bug in <code class="docutils literal notranslate"><span class="pre">fit_pixel_data_and_save()</span></code> that prevented saving maps as ‘TXT’ files.</p></li>
 <li><p>SRX data, new format: proper handling of scan data using both <code class="docutils literal notranslate"><span class="pre">xs</span></code> and <code class="docutils literal notranslate"><span class="pre">xs2</span></code> detectors.</p></li>
@@ -313,6 +328,7 @@ <h3>Navigation</h3>
 <li class="toctree-l1"><a class="reference internal" href="questions.html">Frequently asked questions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="credits.html">Credits</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Release Notes</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#v1-0-28-2024-06-20">v1.0.28 (2024-06-20)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#v1-0-27-2024-04-18">v1.0.27 (2024-04-18)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#v1-0-26-2024-04-07">v1.0.26 (2024-04-07)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#v1-0-25-2024-01-18">v1.0.25 (2024-01-18)</a></li>
diff --git a/PyXRF/searchindex.js b/PyXRF/searchindex.js
index 8d19c482c..19b1e2121 100644
--- a/PyXRF/searchindex.js
+++ b/PyXRF/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["credits", "data_input", "data_output", "index", "installation", "questions", "release-notes", "summed_spectrum_fit", "work_at_beamlines"], "filenames": ["credits.rst", "data_input.rst", "data_output.rst", "index.rst", "installation.rst", "questions.rst", "release-notes.rst", "summed_spectrum_fit.rst", "work_at_beamlines.rst"], "titles": ["Credits", "Load data into pyxrf", "Output data from pyxrf", "About PyXRF", "Installation", "Frequently asked questions", "Release Notes", "Spectrum fitting", "Data analysis at NSLS II beamlines"], "terms": {"we": [0, 1, 7, 8], "kindli": 0, "request": 0, "you": [0, 1, 2, 4, 7, 8], "cite": 0, "follow": [0, 3, 6, 7, 8], "articl": 0, "us": [0, 1, 3, 4, 6, 7], "pyxrf": [0, 6, 7], "li": 0, "hanfei": 0, "yan": 0, "wei": 0, "xu": 0, "dantong": 0, "yu": 0, "anni": 0, "heroux": 0, "wah": 0, "keat": 0, "lee": 0, "stuart": 0, "i": [0, 1, 2, 3, 4, 6, 7, 8], "campbel": 0, "yong": 0, "": [0, 7], "chu": 0, "python": [0, 3, 4, 6], "base": [0, 3, 4, 6, 7], "x": [0, 1, 3, 6], "rai": [0, 3], "fluoresc": [0, 3], "analysi": [0, 3, 6], "packag": [0, 3, 4], "proceed": 0, "volum": 0, "10389": 0, "nanoimag": 0, "instrument": 0, "method": 0, "iii": 0, "103890u": 0, "2017": 0, "doi": 0, "10": [0, 6, 7], "1117": 0, "12": [0, 3], "2272585": 0, "http": [0, 1, 5, 8], "dx": 0, "org": 0, "defin": [1, 7, 8], "work": [1, 6, 8], "directori": [1, 4, 6, 8], "select": [1, 3, 4, 6, 7], "button": [1, 2, 6, 7], "shown": [1, 7], "figur": [1, 7], "1": [1, 6, 7], "after": [1, 2, 6, 7, 8], "can": [1, 3, 4, 6, 7, 8], "click": [1, 2, 7], "thi": [1, 3, 7, 8], "an": [1, 3, 4, 6], "exampl": [1, 4, 5, 6, 8], "from": [1, 3, 4, 6, 7], "hxn": [1, 6, 8], "beam": [1, 4], "line": [1, 3, 6], "nsl": [1, 3, 5], "ii": [1, 3, 5], "current": [1, 6], "mainli": 1, "support": [1, 4, 6], "onc": [1, 6, 7], "see": [1, 4, 7, 8], "name": [1, 6, 7, 8], "set": [1, 7], "scan2d_19568_sum": 1, "which": [1, 4, 7, 8], "just": 1, "next": [1, 4, 6, 7, 8], "blue": 1, "label": 1, "channel": [1, 4, 6], "fit": [1, 2, 3, 6], "2": [1, 6, 7], "The": [1, 3, 4, 5, 6, 7, 8], "_sum": 1, "mean": [1, 6], "pixel": [1, 2, 3, 6], "sum": [1, 3, 5, 6, 8], "three": [1, 6], "detector": [1, 6, 7], "sai": 1, "vortex": 1, "In": [1, 8], "order": [1, 8], "plot": [1, 3, 6], "spectrum": [1, 3, 6, 8], "exp": 1, "right": [1, 7], "part": [1, 3, 7], "gui": [1, 3, 4, 6, 8], "As": 1, "default": [1, 4, 6, 8], "onli": [1, 3, 6, 8], "If": [1, 4, 6, 7, 8], "also": [1, 2, 4, 7, 8], "want": [1, 7, 8], "each": [1, 3, 6, 7], "checkbox": [1, 6], "again": [1, 6], "time": [1, 3, 6, 7], "either": [1, 7], "all": [1, 3, 4, 6, 7, 8], "one": [1, 6, 7, 8], "3": [1, 4, 6, 7], "most": 1, "ar": [1, 4, 6, 7, 8], "well": 1, "align": 1, "need": [1, 3, 7, 8], "more": [1, 3, 4, 6, 7], "differ": [1, 6, 7], "pleas": [1, 5, 7, 8], "download": [1, 4], "standard": [1, 6], "link": [1, 5], "drive": 1, "googl": 1, "com": [1, 5, 8], "d": 1, "0b45mm22ef9tnqzfksw0xa01mbk": 1, "view": [1, 7], "contain": [1, 3, 4, 5, 6], "posit": [1, 6], "y": 1, "motor": [1, 6], "scaler": [1, 6], "normal": [1, 6, 7], "creat": [1, 3, 4, 6, 8], "similar": [1, 8], "For": [1, 4, 7, 8], "test": 1, "purpos": 1, "paramet": [1, 3, 6, 8], "0b45mm22ef9tnyw11oxozrxvic1": 1, "provid": 1, "user": [1, 3, 6, 8], "do": [1, 3, 8], "howev": 1, "should": [1, 8], "never": 1, "manual": [1, 3], "easili": [1, 3, 7, 8], "dure": 1, "step": [1, 4, 6, 7, 8], "automat": [1, 2, 3, 8], "peak": [1, 3, 6], "find": [1, 3, 6], "input": [1, 3, 6], "spec": 1, "transfer": [1, 8], "hdf": [1, 8], "take": [1, 7, 8], "github": [1, 5, 8], "blob": [1, 5, 8], "master": [1, 5, 8], "specfile_to_hdf": 1, "ipynb": [1, 5, 8], "done": [2, 7, 8], "save": [2, 6, 7, 8], "hdf5": [2, 3, 6], "file": [2, 3, 6, 8], "mai": [2, 4, 7, 8], "tiff": 2, "txt": [2, 6], "format": [2, 3, 6, 8], "bottom": [2, 7], "panel": [2, 7], "sophist": 3, "visual": [3, 6], "data": [3, 6, 7], "high": 3, "level": 3, "engin": 3, "comprehens": 3, "command": 3, "design": [3, 4], "rigor": 3, "physic": 3, "calcul": 3, "power": 3, "interfac": [3, 6], "theoret": 3, "map": [3, 5, 6, 7], "develop": 3, "stefan": 3, "vogt": 3, "ap": [3, 6], "offer": 3, "some": 3, "uniqu": 3, "featur": [3, 6], "element": [3, 6], "spend": 3, "extra": 3, "forward": [3, 7], "observ": [3, 6], "real": [3, 7], "while": [3, 6], "adjust": [3, 7], "help": 3, "perform": [3, 5], "sensit": 3, "appropri": 3, "initi": 3, "guess": 3, "construct": 3, "your": [3, 4, 7, 8], "own": [3, 7], "algorithm": [3, 6], "advanc": 3, "mode": [3, 6], "wa": [3, 4, 8], "strategi": [3, 6], "full": 3, "control": [3, 6], "batch": [3, 6], "quick": 3, "multipl": [3, 6, 8], "dataset": [3, 8], "xane": 3, "databas": [3, 6], "A": [3, 8], "specif": 3, "o": [3, 4], "obtain": 3, "directli": [3, 6], "bnl": 3, "experiment": [3, 8], "instal": 3, "start": [3, 6, 7, 8], "updat": [3, 6, 7], "deactiv": [3, 6], "conda": 3, "environ": [3, 6, 8], "beamlin": [3, 6], "load": [3, 4, 6], "configur": [3, 7], "how": [3, 4, 7], "add": [3, 6], "json": [3, 8], "emiss": [3, 6], "remov": [3, 4, 6, 8], "individu": [3, 6], "output": [3, 6, 7], "structur": 3, "other": [3, 6], "frequent": 3, "ask": 3, "question": 3, "doe": 3, "first": [3, 6, 7, 8], "given": [3, 6, 7], "e": [3, 4, 7, 8], "ka1": 3, "activ": [3, 4, 8], "ka2": 3, "kb1": 3, "report": 3, "bug": [3, 6], "credit": 3, "releas": 3, "note": [3, 8], "v1": 3, "0": 3, "27": 3, "2024": 3, "04": 3, "18": 3, "26": 3, "07": 3, "25": 3, "01": 3, "24": 3, "2023": 3, "05": 3, "23": 3, "2022": 3, "03": 3, "19": 3, "22": 3, "02": 3, "28": 3, "21": 3, "11": [3, 4], "20": 3, "08": 3, "17": 3, "06": 3, "16": 3, "15": 3, "v0": 3, "9": [3, 4], "4": 3, "7": 3, "index": [3, 6], "modul": 3, "search": [3, 8], "page": 3, "linux": [4, 6], "mac": 4, "window": [4, 6, 7], "system": 4, "easiest": 4, "wai": 4, "forg": 4, "anaconda": 4, "instruct": [4, 7], "ident": 4, "experi": [4, 7], "problem": 4, "particular": 4, "get": 4, "stuck": 4, "try": 4, "resolv": 4, "mamba": 4, "drop": 4, "replac": [4, 6], "includ": [4, 6, 7], "miniforg": 4, "distribut": [4, 6], "It": [4, 6, 8], "exist": [4, 6, 8], "miniconda": 4, "n": 4, "overrid": 4, "c": [4, 6], "python_abi": 4, "cp": 4, "detail": [4, 6], "simpli": [4, 7, 8], "when": [4, 6, 8], "etc": [4, 7, 8], "env": 4, "pip": 4, "miniconda3": 4, "latest": [4, 6], "version": [4, 6], "suffici": 4, "run": [4, 6, 8], "minimum": 4, "number": [4, 7, 8], "much": 4, "larger": 4, "applic": 4, "conveni": 4, "manag": 4, "alreadi": [4, 7, 8], "comput": [4, 6], "proce": 4, "open": [4, 6], "termin": 4, "prompt": 4, "menu": 4, "platform": 4, "close": 4, "restart": 4, "new": [4, 5, 6, 8], "desir": 4, "g": 4, "v3": 4, "pypi": 4, "xraylib": 4, "scikit": 4, "recommend": 4, "necessari": 4, "third": 4, "parti": 4, "pyqt5": 4, "sourc": [4, 8], "edit": 4, "cd": 4, "root": 4, "repositori": 4, "our": 4, "type": [4, 6, 8], "upgrad": [4, 6], "2d": [5, 6, 7], "result": [5, 7, 8], "elemnt": 5, "refer": [5, 6, 7, 8], "comparison": 5, "between": [5, 6], "roi": 5, "isol": 5, "compare_roi_sum_and_fit": 5, "both": [5, 6], "ka": 5, "kb": 5, "consist": 5, "issu": [5, 6], "spectra": 6, "region": 6, "tab": 6, "ax": 6, "scale": 6, "v": 6, "reset": 6, "axo": 6, "quantit": 6, "calibr": [6, 7], "compat": 6, "recent": 6, "numba": 6, "unsupport": 6, "np": 6, "asarrai": 6, "function": [6, 8], "code": [6, 8], "compil": 6, "make_hdf": [6, 8], "catalog": 6, "cli": 6, "extend": 6, "corrupt": 6, "databrok": [6, 8], "te": 6, "column": [6, 7], "now": 6, "energi": [6, 7], "valu": [6, 7], "kev": [6, 7], "previous": 6, "dask": 6, "v2023": 6, "numpi": 6, "c1": 6, "c10": 6, "were": 6, "gener": 6, "blueski": 6, "plan": 6, "commun": 6, "xspress3": 6, "ioc": 6, "pyqt": 6, "5": 6, "addit": 6, "combo": 6, "box": 6, "allow": 6, "list": [6, 7], "coeffici": 6, "appli": [6, 7], "old": [6, 8], "scan": 6, "srx": 6, "record": 6, "matplotlib": 6, "fly1d": 6, "dmesh": 6, "dscan": 6, "fail_for_plan_typ": 6, "accept": 6, "ignor": [6, 8], "rais": 6, "except": 6, "singl": 6, "row": 6, "middl": 6, "ani": [6, 7], "respect": 6, "dialog": 6, "cours": 6, "stage": 6, "nano_stage_x": 6, "nano_stage_i": 6, "nano_stage_z": 6, "nano_stage_topx": 6, "nano_stage_topz": 6, "56": 6, "imag": 6, "wizard": 6, "auto": 6, "share": 6, "userpeak": 6, "_delta_cent": 6, "displai": 6, "absolut": 6, "true": 6, "instead": 6, "rel": [6, 7], "raw": 6, "preced": 6, "valid": 6, "total": 6, "hidden": 6, "finish": 6, "intak": 6, "pyxrf_batch": 6, "v2022": 6, "xs4": 6, "top": 6, "fit_pixel_data_and_sav": [6, 8], "prevent": 6, "proper": 6, "handl": 6, "xs2": 6, "readm": 6, "doc": 6, "config": 6, "pkg": 6, "6": 6, "api": [6, 8], "like": 6, "broker": 6, "init": 6, "xfm": 6, "previou": [6, 7], "synchron": 6, "prepar": 6, "tomographi": 6, "reconstruct": 6, "movi": 6, "equat": 6, "norm_data": 6, "data1": 6, "data2": 6, "quadrat": 6, "form": 6, "background": 6, "mask": 6, "without": 6, "readi": 7, "move": [7, 8], "upper": 7, "left": 7, "corner": 7, "io": [7, 8], "don": 7, "t": [7, 8], "have": 7, "scratch": 7, "small": 7, "call": 7, "pop": 7, "up": 7, "a0": 7, "a1": 7, "incid": 7, "Then": [7, 8], "same": 7, "mani": 7, "found": 7, "intens": 7, "opinion": 7, "later": [7, 8], "import": [7, 8], "otherwis": 7, "let": 7, "focu": 7, "zoom": 7, "turn": 7, "miss": 7, "down": 7, "arrow": 7, "keyboard": 7, "brows": 7, "immedi": 7, "vari": 7, "inform": [7, 8], "z": 7, "max": 7, "cross": 7, "section": 7, "barn": 7, "atom": 7, "here": 7, "clearli": 7, "fe": 7, "confirm": 7, "delet": 7, "del": 7, "chang": 7, "happi": 7, "lower": 7, "process": [7, 8], "longer": 7, "instanc": [7, 8], "than": 7, "30": 7, "second": [7, 8], "ha": 7, "veri": 7, "usual": [7, 8], "fast": 7, "becaus": 7, "multiprocess": 7, "under": 8, "2017q1": 8, "folder": 8, "At": 8, "go": 8, "ipython": 8, "1000": 8, "fname": 8, "scan_1000": 8, "h5": 8, "argument": 8, "runid": 8, "filenam": 8, "sever": 8, "minut": 8, "200by200": 8, "warn": 8, "keyword": 8, "1100": 8, "id": 8, "end": 8, "transform": 8, "within": 8, "rang": 8, "prefix": 8, "abc_": 8, "scan2d_": 8, "wd": 8, "param_file_nam": 8, "param_fil": 8, "write": 8, "loop": 8, "jupyt": 8, "notebook": 8, "batch_mode_fit": 8, "model": 8, "load_data_from_db": 8, "py": 8, "machin": 8, "connect": 8, "accordingli": 8, "read": 8, "db_config": 8, "hxn_db_config": 8, "where": 8, "handler": 8, "regist": 8, "ad": 8, "map_data2d_hxn": 8, "fetch_data_from_db": 8, "those": 8, "suitcas": 8}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"credit": 0, "load": [1, 7, 8], "data": [1, 2, 8], "pyxrf": [1, 2, 3, 4, 5, 8], "hdf5": 1, "file": [1, 7], "structur": 1, "other": 1, "format": 1, "output": [2, 5], "from": [2, 8], "about": 3, "tabl": 3, "content": 3, "indic": 3, "instal": 4, "start": 4, "updat": 4, "deactiv": 4, "conda": 4, "environ": 4, "frequent": 5, "ask": 5, "question": 5, "doe": 5, "pixel": [5, 7, 8], "fit": [5, 7, 8], "onli": 5, "first": 5, "peak": [5, 7], "given": 5, "element": [5, 7], "i": 5, "e": 5, "ka1": 5, "line": [5, 7, 8], "all": 5, "activ": 5, "ka2": 5, "kb1": 5, "how": [5, 8], "can": 5, "report": 5, "bug": 5, "releas": 6, "note": 6, "v1": 6, "0": 6, "27": 6, "2024": 6, "04": 6, "18": 6, "fix": 6, "ad": 6, "26": 6, "07": 6, "25": 6, "01": 6, "chang": 6, "24": 6, "2023": 6, "05": 6, "12": 6, "23": 6, "2022": 6, "03": 6, "19": 6, "22": 6, "02": 6, "28": 6, "21": 6, "11": 6, "20": 6, "08": 6, "17": 6, "06": 6, "16": 6, "15": 6, "v0": 6, "9": 6, "4": 6, "7": 6, "spectrum": 7, "automat": 7, "find": 7, "creat": 7, "paramet": 7, "json": 7, "plot": 7, "emiss": 7, "add": [7, 8], "remov": 7, "sum": 7, "individu": 7, "analysi": 8, "nsl": 8, "ii": 8, "beamlin": 8, "fluoresc": 8, "databas": 8, "command": 8, "configur": 8, "more": 8, "us": 8}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 58}, "alltitles": {"Credits": [[0, "credits"]], "Load data into pyxrf": [[1, "load-data-into-pyxrf"]], "Load hdf5 file into pyxrf": [[1, "load-hdf5-file-into-pyxrf"]], "Structure of hdf5 file": [[1, "structure-of-hdf5-file"]], "Other format": [[1, "other-format"]], "Output data from pyxrf": [[2, "output-data-from-pyxrf"]], "About PyXRF": [[3, "about-pyxrf"]], "Table of Contents": [[3, "table-of-contents"]], "Contents:": [[3, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "Starting PyXRF": [[4, "starting-pyxrf"]], "Updating PyXRF": [[4, "updating-pyxrf"]], "Deactivating Conda environment": [[4, "deactivating-conda-environment"]], "Frequently asked questions": [[5, "frequently-asked-questions"]], "Does PyXRF pixel fitting output only the first peak of a given element (i.e., only Ka1 line) or all activated elemental lines (ka1, ka2, kb1\u2026)?": [[5, "does-pyxrf-pixel-fitting-output-only-the-first-peak-of-a-given-element-i-e-only-ka1-line-or-all-activated-elemental-lines-ka1-ka2-kb1"]], "How can I report a bug?": [[5, "how-can-i-report-a-bug"]], "Release Notes": [[6, "release-notes"]], "v1.0.27 (2024-04-18)": [[6, "v1-0-27-2024-04-18"]], "Fixed": [[6, "fixed"], [6, "id1"], [6, "id3"], [6, "id5"], [6, "id7"], [6, "id9"], [6, "id12"], [6, "id17"], [6, "id21"]], "Added": [[6, "added"], [6, "id2"], [6, "id4"], [6, "id6"], [6, "id8"], [6, "id10"], [6, "id13"], [6, "id16"], [6, "id18"], [6, "id20"]], "v1.0.26 (2024-04-07)": [[6, "v1-0-26-2024-04-07"]], "v1.0.25 (2024-01-18)": [[6, "v1-0-25-2024-01-18"]], "Changed": [[6, "changed"], [6, "id11"], [6, "id14"], [6, "id15"], [6, "id19"]], "v1.0.24 (2023-05-12)": [[6, "v1-0-24-2023-05-12"]], "v1.0.23 (2022-03-19)": [[6, "v1-0-23-2022-03-19"]], "v1.0.22 (2022-02-28)": [[6, "v1-0-22-2022-02-28"]], "v1.0.21 (2022-12-11)": [[6, "v1-0-21-2022-12-11"]], "v1.0.20 (2022-08-19)": [[6, "v1-0-20-2022-08-19"]], "v1.0.19 (2022-08-19)": [[6, "v1-0-19-2022-08-19"]], "v1.0.18 (2022-08-08)": [[6, "v1-0-18-2022-08-08"]], "v1.0.17 (2022-06-16)": [[6, "v1-0-17-2022-06-16"]], "v1.0.16 (2022-05-26)": [[6, "v1-0-16-2022-05-26"]], "v1.0.15 (2022-04-06)": [[6, "v1-0-15-2022-04-06"]], "v0.0.9.4": [[6, "v0-0-9-4"]], "v0.0.9": [[6, "v0-0-9"]], "v0.0.7": [[6, "v0-0-7"]], "v0.0.4": [[6, "v0-0-4"]], "Spectrum fitting": [[7, "spectrum-fitting"]], "Automatic peak finding (create parameter json file)": [[7, "automatic-peak-finding-create-parameter-json-file"]], "Load parameter file": [[7, "load-parameter-file"]], "Plot emission lines": [[7, "plot-emission-lines"]], "Add/Remove elements": [[7, "add-remove-elements"]], "Summed spectrum fitting": [[7, "summed-spectrum-fitting"]], "Individual Pixel fitting": [[7, "individual-pixel-fitting"]], "Data analysis at NSLS II beamlines": [[8, "data-analysis-at-nsls-ii-beamlines"]], "Load fluorescence data from database": [[8, "load-fluorescence-data-from-database"]], "Pixel fitting from command line": [[8, "pixel-fitting-from-command-line"]], "PyXRF configuration at beamlines": [[8, "pyxrf-configuration-at-beamlines"]], "How to add more beamlines to use PyXRF": [[8, "how-to-add-more-beamlines-to-use-pyxrf"]]}, "indexentries": {}})
\ No newline at end of file
+Search.setIndex({"docnames": ["credits", "data_input", "data_output", "index", "installation", "questions", "release-notes", "summed_spectrum_fit", "work_at_beamlines"], "filenames": ["credits.rst", "data_input.rst", "data_output.rst", "index.rst", "installation.rst", "questions.rst", "release-notes.rst", "summed_spectrum_fit.rst", "work_at_beamlines.rst"], "titles": ["Credits", "Load data into pyxrf", "Output data from pyxrf", "About PyXRF", "Installation", "Frequently asked questions", "Release Notes", "Spectrum fitting", "Data analysis at NSLS II beamlines"], "terms": {"we": [0, 1, 7, 8], "kindli": 0, "request": 0, "you": [0, 1, 2, 4, 7, 8], "cite": 0, "follow": [0, 3, 6, 7, 8], "articl": 0, "us": [0, 1, 3, 4, 6, 7], "pyxrf": [0, 6, 7], "li": 0, "hanfei": 0, "yan": 0, "wei": 0, "xu": 0, "dantong": 0, "yu": 0, "anni": 0, "heroux": 0, "wah": 0, "keat": 0, "lee": 0, "stuart": 0, "i": [0, 1, 2, 3, 4, 6, 7, 8], "campbel": 0, "yong": 0, "": [0, 7], "chu": 0, "python": [0, 3, 4, 6], "base": [0, 3, 4, 6, 7], "x": [0, 1, 3, 6], "rai": [0, 3], "fluoresc": [0, 3], "analysi": [0, 3, 6], "packag": [0, 3, 4], "proceed": 0, "volum": 0, "10389": 0, "nanoimag": 0, "instrument": 0, "method": 0, "iii": 0, "103890u": 0, "2017": 0, "doi": 0, "10": [0, 6, 7], "1117": 0, "12": [0, 3], "2272585": 0, "http": [0, 1, 5, 8], "dx": 0, "org": 0, "defin": [1, 7, 8], "work": [1, 6, 8], "directori": [1, 4, 6, 8], "select": [1, 3, 4, 6, 7], "button": [1, 2, 6, 7], "shown": [1, 7], "figur": [1, 7], "1": [1, 6, 7], "after": [1, 2, 6, 7, 8], "can": [1, 3, 4, 6, 7, 8], "click": [1, 2, 7], "thi": [1, 3, 7, 8], "an": [1, 3, 4, 6], "exampl": [1, 4, 5, 6, 8], "from": [1, 3, 4, 6, 7], "hxn": [1, 6, 8], "beam": [1, 4], "line": [1, 3, 6], "nsl": [1, 3, 5], "ii": [1, 3, 5], "current": [1, 6], "mainli": 1, "support": [1, 4, 6], "onc": [1, 6, 7], "see": [1, 4, 7, 8], "name": [1, 6, 7, 8], "set": [1, 7], "scan2d_19568_sum": 1, "which": [1, 4, 7, 8], "just": 1, "next": [1, 4, 6, 7, 8], "blue": 1, "label": 1, "channel": [1, 4, 6], "fit": [1, 2, 3, 6], "2": [1, 6, 7], "The": [1, 3, 4, 5, 6, 7, 8], "_sum": 1, "mean": [1, 6], "pixel": [1, 2, 3, 6], "sum": [1, 3, 5, 6, 8], "three": [1, 6], "detector": [1, 6, 7], "sai": 1, "vortex": 1, "In": [1, 8], "order": [1, 8], "plot": [1, 3, 6], "spectrum": [1, 3, 6, 8], "exp": 1, "right": [1, 7], "part": [1, 3, 7], "gui": [1, 3, 4, 6, 8], "As": 1, "default": [1, 4, 6, 8], "onli": [1, 3, 6, 8], "If": [1, 4, 6, 7, 8], "also": [1, 2, 4, 7, 8], "want": [1, 7, 8], "each": [1, 3, 6, 7], "checkbox": [1, 6], "again": [1, 6], "time": [1, 3, 6, 7], "either": [1, 7], "all": [1, 3, 4, 6, 7, 8], "one": [1, 6, 7, 8], "3": [1, 4, 6, 7], "most": 1, "ar": [1, 4, 6, 7, 8], "well": 1, "align": 1, "need": [1, 3, 7, 8], "more": [1, 3, 4, 6, 7], "differ": [1, 6, 7], "pleas": [1, 5, 7, 8], "download": [1, 4], "standard": [1, 6], "link": [1, 5], "drive": 1, "googl": 1, "com": [1, 5, 8], "d": 1, "0b45mm22ef9tnqzfksw0xa01mbk": 1, "view": [1, 7], "contain": [1, 3, 4, 5, 6], "posit": [1, 6], "y": 1, "motor": [1, 6], "scaler": [1, 6], "normal": [1, 6, 7], "creat": [1, 3, 4, 6, 8], "similar": [1, 8], "For": [1, 4, 7, 8], "test": 1, "purpos": 1, "paramet": [1, 3, 6, 8], "0b45mm22ef9tnyw11oxozrxvic1": 1, "provid": 1, "user": [1, 3, 6, 8], "do": [1, 3, 8], "howev": 1, "should": [1, 8], "never": 1, "manual": [1, 3], "easili": [1, 3, 7, 8], "dure": 1, "step": [1, 4, 6, 7, 8], "automat": [1, 2, 3, 8], "peak": [1, 3, 6], "find": [1, 3, 6], "input": [1, 3, 6], "spec": 1, "transfer": [1, 8], "hdf": [1, 8], "take": [1, 7, 8], "github": [1, 5, 8], "blob": [1, 5, 8], "master": [1, 5, 8], "specfile_to_hdf": 1, "ipynb": [1, 5, 8], "done": [2, 7, 8], "save": [2, 6, 7, 8], "hdf5": [2, 3, 6], "file": [2, 3, 6, 8], "mai": [2, 4, 7, 8], "tiff": 2, "txt": [2, 6], "format": [2, 3, 6, 8], "bottom": [2, 7], "panel": [2, 7], "sophist": 3, "visual": [3, 6], "data": [3, 6, 7], "high": 3, "level": 3, "engin": 3, "comprehens": 3, "command": 3, "design": [3, 4], "rigor": 3, "physic": 3, "calcul": 3, "power": 3, "interfac": [3, 6], "theoret": 3, "map": [3, 5, 6, 7], "develop": 3, "stefan": 3, "vogt": 3, "ap": [3, 6], "offer": 3, "some": 3, "uniqu": 3, "featur": [3, 6], "element": [3, 6], "spend": 3, "extra": 3, "forward": [3, 7], "observ": [3, 6], "real": [3, 7], "while": [3, 6], "adjust": [3, 7], "help": 3, "perform": [3, 5], "sensit": 3, "appropri": 3, "initi": 3, "guess": 3, "construct": 3, "your": [3, 4, 7, 8], "own": [3, 7], "algorithm": [3, 6], "advanc": 3, "mode": [3, 6], "wa": [3, 4, 6, 8], "strategi": [3, 6], "full": 3, "control": [3, 6], "batch": [3, 6], "quick": 3, "multipl": [3, 6, 8], "dataset": [3, 8], "xane": 3, "databas": [3, 6], "A": [3, 8], "specif": 3, "o": [3, 4], "obtain": 3, "directli": [3, 6], "bnl": 3, "experiment": [3, 8], "instal": 3, "start": [3, 6, 7, 8], "updat": [3, 6, 7], "deactiv": [3, 6], "conda": 3, "environ": [3, 6, 8], "beamlin": [3, 6], "load": [3, 4, 6], "configur": [3, 7], "how": [3, 4, 7], "add": [3, 6], "json": [3, 8], "emiss": [3, 6], "remov": [3, 4, 6, 8], "individu": [3, 6], "output": [3, 6, 7], "structur": 3, "other": [3, 6], "frequent": 3, "ask": 3, "question": 3, "doe": 3, "first": [3, 6, 7, 8], "given": [3, 6, 7], "e": [3, 4, 7, 8], "ka1": 3, "activ": [3, 4, 8], "ka2": 3, "kb1": 3, "report": 3, "bug": [3, 6], "credit": 3, "releas": 3, "note": [3, 8], "v1": 3, "0": 3, "28": 3, "2024": 3, "06": 3, "20": 3, "27": 3, "04": 3, "18": 3, "26": 3, "07": 3, "25": 3, "01": 3, "24": 3, "2023": 3, "05": 3, "23": 3, "2022": 3, "03": 3, "19": 3, "22": 3, "02": 3, "21": 3, "11": [3, 4], "08": 3, "17": 3, "16": 3, "15": 3, "v0": 3, "9": [3, 4], "4": 3, "7": 3, "index": [3, 6], "modul": 3, "search": [3, 8], "page": 3, "linux": [4, 6], "mac": 4, "window": [4, 6, 7], "system": 4, "easiest": 4, "wai": 4, "forg": 4, "anaconda": 4, "instruct": [4, 7], "ident": 4, "experi": [4, 7], "problem": 4, "particular": 4, "get": 4, "stuck": 4, "try": 4, "resolv": 4, "mamba": 4, "drop": 4, "replac": [4, 6], "includ": [4, 6, 7], "miniforg": 4, "distribut": [4, 6], "It": [4, 6, 8], "exist": [4, 6, 8], "miniconda": 4, "n": 4, "overrid": 4, "c": [4, 6], "python_abi": 4, "cp": 4, "detail": [4, 6], "simpli": [4, 7, 8], "when": [4, 6, 8], "etc": [4, 7, 8], "env": 4, "pip": 4, "miniconda3": 4, "latest": [4, 6], "version": [4, 6], "suffici": 4, "run": [4, 6, 8], "minimum": 4, "number": [4, 7, 8], "much": 4, "larger": 4, "applic": 4, "conveni": 4, "manag": 4, "alreadi": [4, 7, 8], "comput": [4, 6], "proce": 4, "open": [4, 6], "termin": 4, "prompt": 4, "menu": 4, "platform": 4, "close": 4, "restart": 4, "new": [4, 5, 6, 8], "desir": 4, "g": 4, "v3": 4, "pypi": 4, "xraylib": 4, "scikit": 4, "recommend": 4, "necessari": 4, "third": 4, "parti": 4, "pyqt5": 4, "sourc": [4, 8], "edit": 4, "cd": 4, "root": 4, "repositori": 4, "our": 4, "type": [4, 6, 8], "upgrad": [4, 6], "2d": [5, 6, 7], "result": [5, 7, 8], "elemnt": 5, "refer": [5, 6, 7, 8], "comparison": 5, "between": [5, 6], "roi": 5, "isol": 5, "compare_roi_sum_and_fit": 5, "both": [5, 6], "ka": 5, "kb": 5, "consist": 5, "issu": [5, 6], "compat": 6, "matplotlib": 6, "deprec": 6, "brokenbarhcollect": 6, "polycollect": 6, "optim": 6, "tile": 6, "server": 6, "srx": 6, "spectra": 6, "region": 6, "tab": 6, "ax": 6, "scale": 6, "v": 6, "reset": 6, "axo": 6, "quantit": 6, "calibr": [6, 7], "recent": 6, "numba": 6, "unsupport": 6, "np": 6, "asarrai": 6, "function": [6, 8], "code": [6, 8], "compil": 6, "make_hdf": [6, 8], "catalog": 6, "cli": 6, "extend": 6, "corrupt": 6, "databrok": [6, 8], "te": 6, "column": [6, 7], "now": 6, "energi": [6, 7], "valu": [6, 7], "kev": [6, 7], "previous": 6, "dask": 6, "v2023": 6, "numpi": 6, "c1": 6, "c10": 6, "were": 6, "gener": 6, "blueski": 6, "plan": 6, "commun": 6, "xspress3": 6, "ioc": 6, "pyqt": 6, "5": 6, "addit": 6, "combo": 6, "box": 6, "allow": 6, "list": [6, 7], "coeffici": 6, "appli": [6, 7], "old": [6, 8], "scan": 6, "record": 6, "fly1d": 6, "dmesh": 6, "dscan": 6, "fail_for_plan_typ": 6, "accept": 6, "ignor": [6, 8], "rais": 6, "except": 6, "singl": 6, "row": 6, "middl": 6, "ani": [6, 7], "respect": 6, "dialog": 6, "cours": 6, "stage": 6, "nano_stage_x": 6, "nano_stage_i": 6, "nano_stage_z": 6, "nano_stage_topx": 6, "nano_stage_topz": 6, "56": 6, "imag": 6, "wizard": 6, "auto": 6, "share": 6, "userpeak": 6, "_delta_cent": 6, "displai": 6, "absolut": 6, "true": 6, "instead": 6, "rel": [6, 7], "raw": 6, "preced": 6, "valid": 6, "total": 6, "hidden": 6, "finish": 6, "intak": 6, "pyxrf_batch": 6, "v2022": 6, "xs4": 6, "top": 6, "fit_pixel_data_and_sav": [6, 8], "prevent": 6, "proper": 6, "handl": 6, "xs2": 6, "readm": 6, "doc": 6, "config": 6, "pkg": 6, "6": 6, "api": [6, 8], "like": 6, "broker": 6, "init": 6, "xfm": 6, "previou": [6, 7], "synchron": 6, "prepar": 6, "tomographi": 6, "reconstruct": 6, "movi": 6, "equat": 6, "norm_data": 6, "data1": 6, "data2": 6, "quadrat": 6, "form": 6, "background": 6, "mask": 6, "without": 6, "readi": 7, "move": [7, 8], "upper": 7, "left": 7, "corner": 7, "io": [7, 8], "don": 7, "t": [7, 8], "have": 7, "scratch": 7, "small": 7, "call": 7, "pop": 7, "up": 7, "a0": 7, "a1": 7, "incid": 7, "Then": [7, 8], "same": 7, "mani": 7, "found": 7, "intens": 7, "opinion": 7, "later": [7, 8], "import": [7, 8], "otherwis": 7, "let": 7, "focu": 7, "zoom": 7, "turn": 7, "miss": 7, "down": 7, "arrow": 7, "keyboard": 7, "brows": 7, "immedi": 7, "vari": 7, "inform": [7, 8], "z": 7, "max": 7, "cross": 7, "section": 7, "barn": 7, "atom": 7, "here": 7, "clearli": 7, "fe": 7, "confirm": 7, "delet": 7, "del": 7, "chang": 7, "happi": 7, "lower": 7, "process": [7, 8], "longer": 7, "instanc": [7, 8], "than": 7, "30": 7, "second": [7, 8], "ha": 7, "veri": 7, "usual": [7, 8], "fast": 7, "becaus": 7, "multiprocess": 7, "under": 8, "2017q1": 8, "folder": 8, "At": 8, "go": 8, "ipython": 8, "1000": 8, "fname": 8, "scan_1000": 8, "h5": 8, "argument": 8, "runid": 8, "filenam": 8, "sever": 8, "minut": 8, "200by200": 8, "warn": 8, "keyword": 8, "1100": 8, "id": 8, "end": 8, "transform": 8, "within": 8, "rang": 8, "prefix": 8, "abc_": 8, "scan2d_": 8, "wd": 8, "param_file_nam": 8, "param_fil": 8, "write": 8, "loop": 8, "jupyt": 8, "notebook": 8, "batch_mode_fit": 8, "model": 8, "load_data_from_db": 8, "py": 8, "machin": 8, "connect": 8, "accordingli": 8, "read": 8, "db_config": 8, "hxn_db_config": 8, "where": 8, "handler": 8, "regist": 8, "ad": 8, "map_data2d_hxn": 8, "fetch_data_from_db": 8, "those": 8, "suitcas": 8}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"credit": 0, "load": [1, 7, 8], "data": [1, 2, 8], "pyxrf": [1, 2, 3, 4, 5, 8], "hdf5": 1, "file": [1, 7], "structur": 1, "other": 1, "format": 1, "output": [2, 5], "from": [2, 8], "about": 3, "tabl": 3, "content": 3, "indic": 3, "instal": 4, "start": 4, "updat": 4, "deactiv": 4, "conda": 4, "environ": 4, "frequent": 5, "ask": 5, "question": 5, "doe": 5, "pixel": [5, 7, 8], "fit": [5, 7, 8], "onli": 5, "first": 5, "peak": [5, 7], "given": 5, "element": [5, 7], "i": 5, "e": 5, "ka1": 5, "line": [5, 7, 8], "all": 5, "activ": 5, "ka2": 5, "kb1": 5, "how": [5, 8], "can": 5, "report": 5, "bug": 5, "releas": 6, "note": 6, "v1": 6, "0": 6, "28": 6, "2024": 6, "06": 6, "20": 6, "fix": 6, "ad": 6, "27": 6, "04": 6, "18": 6, "26": 6, "07": 6, "25": 6, "01": 6, "chang": 6, "24": 6, "2023": 6, "05": 6, "12": 6, "23": 6, "2022": 6, "03": 6, "19": 6, "22": 6, "02": 6, "21": 6, "11": 6, "08": 6, "17": 6, "16": 6, "15": 6, "v0": 6, "9": 6, "4": 6, "7": 6, "spectrum": 7, "automat": 7, "find": 7, "creat": 7, "paramet": 7, "json": 7, "plot": 7, "emiss": 7, "add": [7, 8], "remov": 7, "sum": 7, "individu": 7, "analysi": 8, "nsl": 8, "ii": 8, "beamlin": 8, "fluoresc": 8, "databas": 8, "command": 8, "configur": 8, "more": 8, "us": 8}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 58}, "alltitles": {"Credits": [[0, "credits"]], "Load data into pyxrf": [[1, "load-data-into-pyxrf"]], "Load hdf5 file into pyxrf": [[1, "load-hdf5-file-into-pyxrf"]], "Structure of hdf5 file": [[1, "structure-of-hdf5-file"]], "Other format": [[1, "other-format"]], "Output data from pyxrf": [[2, "output-data-from-pyxrf"]], "About PyXRF": [[3, "about-pyxrf"]], "Table of Contents": [[3, "table-of-contents"]], "Contents:": [[3, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "Starting PyXRF": [[4, "starting-pyxrf"]], "Updating PyXRF": [[4, "updating-pyxrf"]], "Deactivating Conda environment": [[4, "deactivating-conda-environment"]], "Frequently asked questions": [[5, "frequently-asked-questions"]], "Does PyXRF pixel fitting output only the first peak of a given element (i.e., only Ka1 line) or all activated elemental lines (ka1, ka2, kb1\u2026)?": [[5, "does-pyxrf-pixel-fitting-output-only-the-first-peak-of-a-given-element-i-e-only-ka1-line-or-all-activated-elemental-lines-ka1-ka2-kb1"]], "How can I report a bug?": [[5, "how-can-i-report-a-bug"]], "Release Notes": [[6, "release-notes"]], "v1.0.28 (2024-06-20)": [[6, "v1-0-28-2024-06-20"]], "Fixed": [[6, "fixed"], [6, "id1"], [6, "id3"], [6, "id5"], [6, "id7"], [6, "id9"], [6, "id11"], [6, "id14"], [6, "id19"], [6, "id23"]], "Added": [[6, "added"], [6, "id2"], [6, "id4"], [6, "id6"], [6, "id8"], [6, "id10"], [6, "id12"], [6, "id15"], [6, "id18"], [6, "id20"], [6, "id22"]], "v1.0.27 (2024-04-18)": [[6, "v1-0-27-2024-04-18"]], "v1.0.26 (2024-04-07)": [[6, "v1-0-26-2024-04-07"]], "v1.0.25 (2024-01-18)": [[6, "v1-0-25-2024-01-18"]], "Changed": [[6, "changed"], [6, "id13"], [6, "id16"], [6, "id17"], [6, "id21"]], "v1.0.24 (2023-05-12)": [[6, "v1-0-24-2023-05-12"]], "v1.0.23 (2022-03-19)": [[6, "v1-0-23-2022-03-19"]], "v1.0.22 (2022-02-28)": [[6, "v1-0-22-2022-02-28"]], "v1.0.21 (2022-12-11)": [[6, "v1-0-21-2022-12-11"]], "v1.0.20 (2022-08-19)": [[6, "v1-0-20-2022-08-19"]], "v1.0.19 (2022-08-19)": [[6, "v1-0-19-2022-08-19"]], "v1.0.18 (2022-08-08)": [[6, "v1-0-18-2022-08-08"]], "v1.0.17 (2022-06-16)": [[6, "v1-0-17-2022-06-16"]], "v1.0.16 (2022-05-26)": [[6, "v1-0-16-2022-05-26"]], "v1.0.15 (2022-04-06)": [[6, "v1-0-15-2022-04-06"]], "v0.0.9.4": [[6, "v0-0-9-4"]], "v0.0.9": [[6, "v0-0-9"]], "v0.0.7": [[6, "v0-0-7"]], "v0.0.4": [[6, "v0-0-4"]], "Spectrum fitting": [[7, "spectrum-fitting"]], "Automatic peak finding (create parameter json file)": [[7, "automatic-peak-finding-create-parameter-json-file"]], "Load parameter file": [[7, "load-parameter-file"]], "Plot emission lines": [[7, "plot-emission-lines"]], "Add/Remove elements": [[7, "add-remove-elements"]], "Summed spectrum fitting": [[7, "summed-spectrum-fitting"]], "Individual Pixel fitting": [[7, "individual-pixel-fitting"]], "Data analysis at NSLS II beamlines": [[8, "data-analysis-at-nsls-ii-beamlines"]], "Load fluorescence data from database": [[8, "load-fluorescence-data-from-database"]], "Pixel fitting from command line": [[8, "pixel-fitting-from-command-line"]], "PyXRF configuration at beamlines": [[8, "pyxrf-configuration-at-beamlines"]], "How to add more beamlines to use PyXRF": [[8, "how-to-add-more-beamlines-to-use-pyxrf"]]}, "indexentries": {}})
\ No newline at end of file