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small additions/correction to release_6.0.htm [ci skip]
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added papers, some prettier indentation, used https://validator.w3.org/
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KrisThielemans committed Jan 6, 2024
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<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
<html>
<!DOCTYPE HTML>
<html lang="en">
<head>
<title>Summary of changes in STIR release 6.0</title>
</head>
Expand All @@ -14,7 +14,6 @@ <h1>Summary of changes in STIR release 6.0</h1>
<h2>Overall summary</h2>
<p>
This release is a major upgrade adding Time of Flight (TOF) capabilities to STIR.
See also the (enormous) <a href="https://github.com/UCL/STIR/pull/304"</a>PR #304</a>.
</p>


Expand All @@ -23,7 +22,7 @@ <h2>Overall summary</h2>
</p>

<p>Overall code management and assistance was Kris Thielemans (UCL and ASC). Other main contributors
include: Nikos Efthimious (UCL, University of Hull, UPenn, MGH) for the TOF framework and list-mode
include: Nikos Efthimiou (UCL, University of Hull, UPenn, MGH) for the TOF framework and list-mode
reconstruction, Elise Emond (UCL) for adapting TOF framework for projection-data,
Palak Wadhwa (University of Leeds) for adaptations and testing on GE Signa PET/MR data,
Robert Twyman for extending projector symmetries to TOF and formalising ROOT-based testing,
Expand All @@ -45,7 +44,7 @@ <h2>Patch release info</h2>
<h2> Summary for end users (also to be read by developers)</h2>

<h3>Changes breaking backwards compatibility from a user-perspective</h3>
<ul>
<ul>
<li> </li>
</ul>

Expand All @@ -59,12 +58,33 @@ <h3>New functionality</h3>
<h4>General</h4>
<ul>
<li>
TOF of course. This is mostly transparent, i.e. normally no changes are required
<p>
TOF of course! This is mostly transparent, i.e. normally no changes are required
to the reconstruction code etc. When using Interfile or ROOT files, certain new keywords
are required, see <a href="https://github.com/UCL/STIR/blob/master/examples/samples/PET_TOF_Interfile_header_Signa_PETMR.hs">examples/samples/PET_TOF_Interfile_header_Signa_PETMR.hs</a>
and <a href="https://github.com/UCL/STIR/blob/master/examples/samples/root_header.hroot">examples/samples/root_header.hroot</a>. See also the updated STIR_glossary.
<br /><br />
<b>Limitations</b><br />
and <a href="https://github.com/UCL/STIR/blob/master/examples/samples/root_header.hroot">examples/samples/root_header.hroot</a>.
See also the updated STIR_glossary.
<br>
Please cite the following papers:
</p>
<ul>
<li>
Efthimiou, N., Emond, E., Wadhwa, P., Cawthorne, C., Tsoumpas, C., Thielemans, K., 2019.
<cite>Implementation and validation of time-of-flight PET image reconstruction module for listmode and sinogram projection data in the STIR library.</cite>
Phys Med Biol 64, 035004. <a href="https://doi.org/10.1088/1361-6560/aaf9b9">DOI: 10.1088/1361-6560/aaf9b9</a>.
</li>
<li>
Wadhwa, P., Thielemans, K., Efthimiou, N., Wangerin, K., Keat, N., Emond, E., Deller, T., Bertolli, O., Deidda, D., Delso, G., Tohme, M., Jansen, F., Gunn, R.N., Hallett, W., Tsoumpas, C., 2021.
<cite>PET image reconstruction using physical and mathematical modelling for time of flight PET-MR scanners in the STIR library.</cite>
Methods, Methods on simulation in biomedicine 185, 110–119. <a href="https://doi.org/10.1016/j.ymeth.2020.01.005">DOI: 10.1016/j.ymeth.2020.01.005</a>
</li>
</ul>
<p>
See also the (enormous) <a href="https://github.com/UCL/STIR/pull/304">PR #304</a>.
</p>
<p>
<b>Limitations</b><br>
</p>
<ul>
<li>
Currently on the <code>matrix</code> based projectors support TOF.
Expand Down Expand Up @@ -93,7 +113,7 @@ <h4>Python (and MATLAB)</h4>
<li>
added <code>LORAs2Points</code>,<code>LORInCylinderCoordinates</code>,
<code>LORInAxialAndSinogramCoordinates</code> and <code>PointOnCylinder</code>.
<br />
<br>
<b>Warning</b>: renamed <code>FloatLOR</code> to <code>LOR</code>, and same for
derived classes.
</li>
Expand All @@ -112,7 +132,7 @@ <h4>General</h4>
<li>The default for arc-correction has changed to <i>N</i>, i.e. <code>false</code>.</li>
<li>Default value for span is now 11 for Siemens and 2 for GE scanners.</li>
<li>The span=0 case (i.e. span-3 for segment 0, span=1 for oblique ones, erroneously
by STIR used for the GE Advance) is no deprecated. GE uses span=2.<br />
by STIR used for the GE Advance) is no deprecated. GE uses span=2.<br>
(Reading a "span=0" case is still supported)</li>
</ol>
</li>
Expand All @@ -133,7 +153,7 @@ <h3>Changed functionality</h3>
<ul>
<li>
We now always check (in <code>ProjDataInfo*NoArcCorr</code>) if number of tangential positions in the projection data exceeds the maximum number
of non arc-corrected bins set for the scanner. If it is, an error is raised.
of non arc-corrected bins set for the scanner. If it is, an error is raised. You might therefore have to adapt your interfile header.
</li>
<li>
Write <code>STIR6.0</code> as Interfile key version to denote TOF changes.
Expand All @@ -160,7 +180,7 @@ <h3>Documentation changes</h3>
</li>
</ul>

<h3>test changes</h3>
<h3>Test changes</h3>
<h4>recon_test_pack changes</h4>
<ul>
<li>
Expand All @@ -172,72 +192,71 @@ <h4>recon_test_pack changes</h4>
</ul>

<h4>C++ tests</h4>
<ul>
<li>
additional tests for TOF, expansion of some existing tests for TOF
</li>
</ul>

<H2>What's new for developers (aside from what should be obvious
from the above):</H2>

<h3>Major bugs fixed</h3>
<ul>
<li>see above</li>
</ul>

<h3>Backward incompatibities</h3>
<ul>
<li>
<code>ListModeData</code> now has a <code>shared_ptr<const ProjDataInfo> proj_data_info_sptr</code>
<code>protected</code> member, and the <code>scanner_sptr</code> member has been removed.<br />
<b>Warning:</b> If your derived class had its own <code>proj_data_info_sptr</code>, it should be removed.
</li>
<li>
<code>virtual ListModeData::get_scanner_ptr()</code> is replaced by <code>ListModeData::get_scanner()</code>.
</li>
<li>
<code>ProjDataInfo*NoArcCorr::get_bin_for_det_pair</code> is now private.
Use <code>get_bin_for_det_pos_pair</code> instead.
</li>
</ul>

<h3>New functionality</h3>

<h4>TOF related</h4>
<ul>
<li><code>Scanner</code> now allows storing TOF information. This is currently not yet done for all
TOF-capable scanners though. Contributions welcome!
</li>
<li>
All projection-data related classes and their members now have a TOF bin index and related information.
At present, old-style accessors are in an awkward format such as
<pre>
auto sino = proj_data.get_sinogram(ax_pos_num, segment_num, false, timing_pos);
</pre>
These are deprecated since version 5.2 and should be replaced by
<pre>
const SinogramIndices sinogram_idxs{ax_pos_num, segment_num, timing_pos};
auto sino = proj_data.get_sinogram(sinogram_idxs);
</pre>
</li>
<li>
List-mode data for TOF-capable scanners need to pass this through appropriately of course.
</li>
</ul>
<ul>
<li>
additional tests for TOF, expansion of some existing tests for TOF
</li>
</ul>

<H2>What's new for developers (aside from what should be obvious
from the above):</H2>

<h3>Backward incompatibities</h3>
<ul>
<li>
<code>ListModeData</code> now has a <code>shared_ptr&lt;const ProjDataInfo&gt; proj_data_info_sptr</code>
<code>protected</code> member, and the <code>scanner_sptr</code> member has been removed.<br>
<b>Warning:</b> If your derived class had its own <code>proj_data_info_sptr</code>, it should be removed.
</li>
<li>
<code>virtual ListModeData::get_scanner_ptr()</code> is replaced by <code>ListModeData::get_scanner()</code>.
</li>
<li>
<code>ProjDataInfo*NoArcCorr::get_bin_for_det_pair</code> is now private.
Use <code>get_bin_for_det_pos_pair</code> instead.
</li>
</ul>

<h3>New functionality</h3>

<h4>TOF related</h4>
<ul>
<li><code>Scanner</code> now allows storing TOF information. This is currently not yet done for all
TOF-capable scanners though. Contributions welcome!
</li>
<li>
All projection-data related classes and their members now have a TOF bin index and related information.
At present, old-style accessors are in an awkward format such as
<pre>
auto sino = proj_data.get_sinogram(ax_pos_num, segment_num, false, timing_pos_num);
</pre>
These are deprecated since version 5.2 and should be replaced by
<pre>
const SinogramIndices sinogram_idxs{ax_pos_num, segment_num, timing_pos_num};
auto sino = proj_data.get_sinogram(sinogram_idxs);
</pre>
</li>
<li>
List-mode data for TOF-capable scanners need to pass the relevant information through appropriately of course.
</li>
</ul>

<h4>Non-TOF related</h4>
<ul>
<li>
projectors now have a <code>clone()</code> member, currently returning a bare pointer (like other STIR classes)
</li>
<li><code>Bin</code> can now be output to stream as text</li>
<li>added <code>RunTests::check_if_equal</code> for <code>Bin</code></li>
<li>
<code>KeyParser</code> has a new facility to add an alias to a keyword. This can be used to rename a keyword
for instance while remaining backwards compatible. By default, a warning will be written, but this can be disabled.
</li>
</ul>
<h4>Non-TOF related</h4>
<ul>
<li>
Projectors now have a <code>clone()</code> member, currently returning a bare pointer (like other STIR classes).
</li>
<li>
<code>Bin</code> can now be output to stream as text.
</li>
<li>
Added <code>RunTests::check_if_equal</code> for <code>Bin</code>.
</li>
<li>
<code>KeyParser</code> has a new facility to add an alias to a keyword. This can be used to rename a keyword
for instance while remaining backwards compatible. By default, a warning will be written, but this can be disabled.
</li>
</ul>


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