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LIMS-1515: Add energy value to data collections #853

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merged 2 commits into from
Nov 12, 2024
Merged

LIMS-1515: Add energy value to data collections #853

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69b59c8
LIMS-1515: Add energy value to data collections
Nov 1, 2024
808e2e2
LIMS-1515: Use a class constant
Nov 6, 2024
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33 changes: 25 additions & 8 deletions api/src/Page/DC.php
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,8 @@ class DC extends Page
array('/dat/:id', 'get', '_plot'),
);

const EVTOA = 12398.4198;

# ------------------------------------------------------------------------
# Data Collection AJAX Requests
# This is pretty crazy, it will return unioned data collections, energy
Expand Down Expand Up @@ -422,9 +424,12 @@ function _data_collections($single = null)
dc.transmission,
dc.axisrange,
dc.wavelength,
".self::EVTOA."/dc.wavelength as energy,
dc.comments,
1 as epk,
1 as ein,
1 as wpk,
1 as win,
dc.xtalsnapshotfullpath1 as x1,
dc.xtalsnapshotfullpath2 as x2,
dc.xtalsnapshotfullpath3 as x3,
Expand Down Expand Up @@ -556,9 +561,12 @@ function _data_collections($single = null)
min(dc.transmission) as transmission,
min(dc.axisrange) as axisrange,
min(dc.wavelength) as wavelength,
".self::EVTOA."/min(dc.wavelength) as energy,
min(dc.comments) as comments,
1 as epk,
1 as ein,
1 as wpk,
1 as win,
min(dc.xtalsnapshotfullpath1) as x1,
min(dc.xtalsnapshotfullpath2) as x2,
min(dc.xtalsnapshotfullpath3) as x3,
Expand Down Expand Up @@ -705,17 +713,20 @@ function _data_collections($single = null)
es.energyscanid,
1,
es.element,
es.peakfprime,
es.peakfprime as resolution,
es.exposuretime,
es.axisposition,
es.peakfdoubleprime,
es.peakfdoubleprime as numimg,
es.starttime as st,
es.transmissionfactor,
es.inflectionfprime,
es.inflectionfdoubleprime,
es.inflectionfprime as axisrange,
es.inflectionfdoubleprime as wavelength,
1 as energy,
es.comments,
es.peakenergy,
es.inflectionenergy,
".self::EVTOA."/es.peakenergy as wpk,
".self::EVTOA."/es.inflectionenergy as win,
'A',
'A',
'A',
Expand Down Expand Up @@ -805,10 +816,13 @@ function _data_collections($single = null)
TO_CHAR(xrf.starttime, 'DD-MM-YYYY HH24:MI:SS') as st,
xrf.beamtransmission,
1,
xrf.energy,
".self::EVTOA."/xrf.energy as wavelength,
xrf.energy as energy,
xrf.comments,
1,
1,
1 as wpk,
1 as win,
'A',
'A',
'A',
Expand Down Expand Up @@ -899,9 +913,12 @@ function _data_collections($single = null)
1,
1,
1,
1 as energy,
'A',
1,
1,
1 as wpk,
1 as win,
r.xtalsnapshotbefore,
r.xtalsnapshotafter,
'A',
Expand Down Expand Up @@ -974,7 +991,7 @@ function _data_collections($single = null)

// Data collections
if ($dc['TYPE'] == 'data') {
$nf = array(1 => array('AXISSTART', 'CHISTART', 'PHI', 'OVERLAP'), 2 => array('RESOLUTION', 'TRANSMISSION', 'AXISRANGE', 'TOTALDOSE'), 4 => array('WAVELENGTH', 'EXPOSURETIME'));
$nf = array(0 => array('ENERGY'), 1 => array('AXISSTART', 'CHISTART', 'PHI', 'OVERLAP'), 2 => array('RESOLUTION', 'TRANSMISSION', 'AXISRANGE', 'TOTALDOSE'), 4 => array('WAVELENGTH', 'EXPOSURETIME'));

$dc['DIRFULL'] = $dc['DIR'];
$dc['DIR'] = preg_replace('/.*\/' . $this->arg('prop') . '-' . $dc['VN'] . '\//', '', $dc['DIR']);
Expand Down Expand Up @@ -1010,12 +1027,12 @@ function _data_collections($single = null)

$dc['FILETEMPLATE'] = preg_replace('/.*\/' . $this->arg('prop') . '-' . $dc['VN'] . '\//', '', $dc['FILETEMPLATE']);

$nf = array(2 => array('EXPOSURETIME', 'AXISSTART', 'RESOLUTION', 'TRANSMISSION'));
$nf = array(1 => array('EPK', 'EIN'), 2 => array('AXISRANGE', 'WAVELENGTH', 'EXPOSURETIME', 'AXISSTART', 'RESOLUTION', 'TRANSMISSION', 'NUMIMG'), 5 => array('WPK', 'WIN'));
$this->profile('edge');

// MCA Scans
} else if ($dc['TYPE'] == 'mca') {
$nf = array(2 => array('EXPOSURETIME', 'WAVELENGTH', 'TRANSMISSION'));
$nf = array(0 => array('ENERGY'), 2 => array('EXPOSURETIME', 'TRANSMISSION'), 4 => array('WAVELENGTH'));
$dc['DIRFULL'] = $dc['DIR'];
$dc['DIR'] = preg_replace('/.*\/\d\d\d\d\/\w\w\d+-\d+\//', '', $dc['DIR']);

Expand Down
2 changes: 1 addition & 1 deletion client/src/js/templates/dc/dc.html
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Expand Up @@ -24,7 +24,7 @@ <h1 class="title"></h1>
<% if (SI != 1 ) { %> <li data-testid="dc-first-image">First Image: <%-SI%></li><% } %>
<% if ((KAPPA && KAPPA !=0) || (PHI && PHI != 0) || (CHISTART && CHISTART !=0)) { %><li data-testid="dc-kappa-phi-chi"><% if (KAPPA != null) { %>&kappa;: <%-KAPPA%>&deg;<% } %> <% if (PHI != null) { %>&phi;: <%-PHI%>&deg;<% } %> <% if (CHISTART != null) { %>&chi;: <%-CHISTART%>&deg;<% } %></li><% } %>
<li data-testid="dc-resolution">Resolution: <%-RESOLUTION%>&#197;</li>
<li data-testid="dc-wavelength">Wavelength: <%-WAVELENGTH%>&#197;</li>
<li data-testid="dc-wavelength">Wavelength: <%-WAVELENGTH%>&#197; (<%-ENERGY%>eV)</li>
<li data-testid="dc-exposure-time">Exposure: <%-EXPOSURETIME%>s</li>
<%if (DCC > 1 && TOTALDOSE) { %>
<li data-testid="dc-dose">Total Dose: <%-TOTALDOSE%>MGy</li>
Expand Down
10 changes: 5 additions & 5 deletions client/src/js/templates/dc/edge.html
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Expand Up @@ -9,11 +9,11 @@ <h1>
</h1>

<ul class="clearfix half">
<li>Scan File: <%-FILETEMPLATE%></li>
<li>E(Peak): <%-EPK.toFixed(1) %>eV (<% print ((12398.4193/EPK).toFixed(4)) %>&#197;)</li>
<li>f&rsquo;&rsquo;: <%-NUMIMG%> / f&rsquo;: <%-RESOLUTION%>e</li>
<li>E(Inf): <%-EIN.toFixed(1) %>eV (<% print((12398.4193/EIN).toFixed(4)) %>&#197;)</li>
<li>f&rsquo;&rsquo;: <%-WAVELENGTH%> / f&rsquo;: <%-AXISRANGE%>e</li>
<li class="comment">Scan File: <%-FILETEMPLATE%></li>
<li>E(Peak): <%-EPK%>eV (<%-WPK%>&#197;)</li>
<li>f&rsquo;&rsquo;: <%-NUMIMG%>e<sup>-</sup> / f&rsquo;: <%-RESOLUTION%>e<sup>-</sup></li>
<li>E(Inf): <%-EIN%>eV (<%-WIN%>&#197;)</li>
<li>f&rsquo;&rsquo;: <%-WAVELENGTH%>e<sup>-</sup> / f&rsquo;: <%-AXISRANGE%>e<sup>-</sup></li>
<li>Exposure: <%-EXPOSURETIME%>s</li>
<li>Transmission: <%-TRANSMISSION%>%</li>
<li>Beamsize: <%-BSX%>x<%-BSY%>&mu;m</li>
Expand Down
2 changes: 1 addition & 1 deletion client/src/js/templates/dc/grid.html
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Expand Up @@ -8,7 +8,7 @@ <h1 class="title"></h1>
<li>&<%-ROTATIONAXIS%>; Start: <%-AXISSTART%>&deg;</li>
<% if ((KAPPA && KAPPA !=0) || (PHI && PHI != 0) || (CHISTART && CHISTART !=0)) { %><li><% if (KAPPA != null) { %>&kappa;: <%-KAPPA%>&deg;<% } %> <% if (PHI != null) { %>&phi;: <%-PHI%>&deg;<% } %> <% if (CHISTART != null) { %>&chi;: <%-CHISTART%>&deg;<% } %></li><% } %>
<li>Resolution: <%-RESOLUTION%>&#197;</li>
<li>Wavelength: <%-WAVELENGTH%>&#197;</li>
<li>Wavelength: <%-WAVELENGTH%>&#197; (<%-ENERGY%>eV)</li>
<li>Exposure: <%-EXPOSURETIME%>s</li>
<li>Transmission: <%-TRANSMISSION%>%</li>
<li>Beamsize: <%-BSX%>x<%-BSY%>&mu;m</li>
Expand Down
4 changes: 2 additions & 2 deletions client/src/js/templates/dc/mca.html
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Expand Up @@ -10,11 +10,11 @@ <h1>
</h1>

<ul class="clearfix half">
<li>Energy: <%-WAVELENGTH%>eV</li>
<li>Energy: <%-ENERGY%>eV (<%-WAVELENGTH%>&#197;)</li>
<li>Exposure: <%-EXPOSURETIME%>s</li>
<li>Transmission: <%-TRANSMISSION%>%</li>
<li>Beamsize: <%-BSX%>x<%-BSY%>&mu;m</li>
<li>Axis Position: <%-AXISSTART%>&deg;</li>
<li class="comment" title="Click to edit the comment for this mca spectrum">Comment: <span class="COMMENTS"><%-COMMENTS%></span></li>
</ul>
</div>
</div>
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