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LIMS-2126: Add new strategy pipeline and tidy code #1054

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138 changes: 19 additions & 119 deletions api/src/Page/DC.php
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Original file line number Diff line number Diff line change
Expand Up @@ -1286,7 +1286,7 @@ function _dc_strategies($id)
dc.imageprefix as imp, dc.comments as dcc, dc.blsampleid as sid,
sl.spacegroup as sg, sl.unitcell_a as a, sl.unitcell_b as b, sl.unitcell_c as c, sl.unitcell_alpha as al, sl.unitcell_beta as be, sl.unitcell_gamma as ga,
det.numberofpixelsx, det.detectorpixelsizehorizontal,
CONCAT(IF(sssw.comments, sssw.comments, IF(ssw.comments, ssw.comments, s.shortcomments)), ' Wedge', IFNULL(ssw.wedgenumber, '')) as com
CONCAT(IF(sssw.comments is not null, sssw.comments, IF(ssw.comments is not null, ssw.comments, s.shortcomments)), ' Wedge ', IFNULL(ssw.wedgenumber, '')) as com
FROM screeningstrategy st
INNER JOIN screeningoutput so on st.screeningoutputid = so.screeningoutputid
INNER JOIN screening s on so.screeningid = s.screeningid
Expand All @@ -1296,143 +1296,43 @@ function _dc_strategies($id)
INNER JOIN datacollection dc on s.datacollectionid = dc.datacollectionid
LEFT OUTER JOIN detector det ON dc.detectorid = det.detectorid
WHERE s.datacollectionid = :1
ORDER BY s.shortcomments, ssw.wedgenumber", array($id));

ORDER BY s.screeningid, com, ssw.wedgenumber", array($id));

$nf = array(1 => array('TRAN', 'ATRAN'), 2 => array('A', 'B', 'C', 'AL', 'BE', 'GA', 'OSCRAN', 'RES', 'RANKRES'), 4 => array('TIME'));
$output = array();
foreach ($rows as $r) {
if (!array_key_exists($r['PROGRAMVERSION'], $output))
$output[$r['PROGRAMVERSION']] = array('CELL' => array(), 'STRATS' => array());
}

$nf = array('A', 'B', 'C', 'AL', 'BE', 'GA');
foreach ($rows as &$r) {
$t = $r['PROGRAMVERSION'];
if (!array_key_exists($t, $output))
$output[$t] = array('CELL' => array(), 'STRATS' => array());

$r['ATRAN'] = $r['TRAN'] / 100.0 * $r['DCTRN'];
foreach ($nf as $nff => $cols) {
foreach ($cols as $c) {
$r[$c] = number_format($r[$c], $nff);
}
}

$is_align = false;
foreach ($strat_align as $sa) {
if (!$is_align)
$is_align = strpos($r['PROGRAMVERSION'], $sa) !== false;
$is_align = strpos($t, $sa) !== false;
}

if ($is_align) {
if (!$is_align) {
foreach ($r as $k => &$v) {
if (in_array($k, $nf)) {
$v = number_format(floatval($v), 2);
}
}
array_push($output[$r['PROGRAMVERSION']]['STRATS'], $r);
} else {

$t = $r['PROGRAMVERSION'];

foreach ($r as $k => &$v) {
if (in_array($k, $nf)) {
$v = number_format(floatval($v), 2);
if (in_array($k, array('SG', 'A', 'B', 'C', 'AL', 'BE', 'GA'))) {
$output[$t]['CELL'][$k] = $v;
unset($r[$k]);
}

if ($k == 'TRAN')
$v = number_format($v, 1);
if ($k == 'TIME')
$v = number_format($v, 3);
if ($k == 'OSCRAN')
$v = number_format($v, 2);
if ($k == 'RES')
$v = number_format($v, 2);
if ($k == 'RANKRES')
$v = number_format($v, 2);
}

$output[$t]['CELL']['SG'] = $r['SG'];
unset($r['SG']);

$r['COM'] = str_replace('EDNA', '', $r['COM']);
$r['COM'] = str_replace('Mosflm ', '', $r['COM']);

$r['VPATH'] = join('/', array_slice(explode('/', $r['IMD']), 0, 6));
list(,, $r['BL']) = explode('/', $r['IMD']);

# we dont actually use this in the display view maybe Deprecate?
# detector diameter in mm
if ($r['DETECTORPIXELSIZEHORIZONTAL'] && $r['NUMBEROFPIXELSX']) {
$diam = $r['DETECTORPIXELSIZEHORIZONTAL'] * $r['NUMBEROFPIXELSX'] * 1000;
} else {
// drop back to pilatus 6m diameter
$diam = 415;
}

$r['DIST'] = $this->_r_to_dist($diam, $r['LAM'], $r['RES']);
$r['ATRAN'] = round($r['TRAN'] / 100.0 * $r['DCTRN'], 1);
list($r['NTRAN'], $r['NEXP']) = $this->_norm_et($r['ATRAN'], $r['TIME']);
$r['AP'] = $this->_get_ap($r['DCC']);

array_push($output[$t]['STRATS'], $r);
}
}

$this->_output(array(sizeof($rows), $output));
}

# ------------------------------------------------------------------------
# Normalise transmission fo 25hz data collection
function _norm_et($t, $e)
{
if ($t < 100 && $e > 0.04) {
$f = $e / 0.04;
$maxe = 0.04;
$maxt = ($e / 0.04) * $t;

if ($maxt > 100) {
$maxe *= $maxt / 100;
$maxt = 100;
}
return array(number_format($maxt, 1), number_format($maxe, 3));
} else {
return array($t, $e);
array_push($output[$t]['STRATS'], $r);
}
}

# ------------------------------------------------------------------------
# Convert resolution to detector distance
function _r_to_dist($diam, $lambda, $r)
{
$result = 0;
try {
$b = $lambda / (2 * $r);
$d = 2 * asin($b);
$f = 2 * tan($d);
$result = number_format($diam / $f, 2);
} catch (\Exception $e) {
error_log('Error converting resolution to distance, lambda=' . $lambda . ' r=' . $r . ' Exception: ' . $e->getMessage());
}
return $result;
}

# ------------------------------------------------------------------------
# Work out which aperture is selected
function _get_ap($com)
{
$aps = array(
'Aperture: Large' => 'LARGE_APERTURE',
'Aperture: Medium' => 'MEDIUM_APERTURE',
'Aperture: Small' => 'SMALL_APERTURE',
'Aperture: 10' => 'In_10',
'Aperture: 20' => 'In_20',
'Aperture: 30' => 'In_30',
'Aperture: 50' => 'In_50',
'Aperture: 70' => 'In_70'
);

$app = '';
foreach ($aps as $k => $v) {
if (strpos($com, $k) !== False)
$app = $v;
}

return $app;
$this->_output(array(sizeof($rows), $output));
}


# ------------------------------------------------------------------------
# Image quality indicators from distl
function _image_qi($id)
Expand Down
42 changes: 35 additions & 7 deletions client/src/js/templates/dc/dc_strategy.html
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Original file line number Diff line number Diff line change
@@ -1,5 +1,29 @@

<h2><%-TYPE%></h2>

<%
var showUnitCell = CELL && (CELL.SG || CELL.A || CELL.B || CELL.C || CELL.AL || CELL.BE || CELL.GA)
var showChi = _.some(STRATS, function(r) {
return r.CHI && parseFloat(r.CHI) !== 0
})
var showPhi = _.some(STRATS, function(r) {
return r.PHI && parseFloat(r.PHI) !== 0
})
var showKappa = _.some(STRATS, function(r) {
return r.KAPPA && parseFloat(r.KAPPA) !== 0
})
var showRankingRes = _.some(STRATS, function(r) {
return r.RANKRES && parseFloat(r.RANKRES) !== 0
})

var displayAxis = "Axis"
if (STRATS && STRATS.length > 0 && STRATS[0].ROTATIONAXIS) {
var raw = STRATS[0].ROTATIONAXIS
displayAxis = raw.charAt(0).toUpperCase() + raw.slice(1)
}
%>

<% if (showUnitCell) { %>
<p class="r">
<a class="view button" title="Lookup Unit Cell" href="/cell/a/<%-CELL.A%>/b/<%-CELL.B%>/c/<%-CELL.C%>/al/<%-CELL.AL%>/be/<%-CELL.BE%>/ga/<%-CELL.GA%>"><i class="fa fa-search"></i> Lookup Cell</a>
</p>
Expand Down Expand Up @@ -28,18 +52,20 @@ <h2><%-TYPE%></h2>
</tr>
</tbody>
</table>

<% } %>

<table class="reflow strat">
<thead>
<tr class="stratrow">
<th>Strategy</th>
<th>Description</th>
<th>Axis</th>
<th>Axis Start</th>
<th>Axis Osc</th>
<th><%- displayAxis %> Start (°)</th>
<th><%- displayAxis %> Osc (°)</th>
<% if (showChi) { %> <th>Chi (°)</th> <% } %>
<% if (showPhi) { %> <th>Phi (°)</th> <% } %>
<% if (showKappa) { %> <th>Kappa (°)</th> <% } %>
<th>Res (&#197;)</th>
<th>Ranking Res (&#197;)</th>
<% if (showRankingRes) { %> <th>Ranking Res (&#197;)</th> <% } %>
<th>Rel Trn (%)</th>
<th>Abs Trn (%)</th>
<th>Exposure (s)</th>
Expand All @@ -51,11 +77,13 @@ <h2><%-TYPE%></h2>
<tr class="stratrow" draggable="true" sid="<%-i%>">
<td><%-r.COM%></td>
<td><%-r.COMMENTS%></td>
<td><%-r.ROTATIONAXIS%></td>
<td><%-r.ST%></td>
<td><%-r.OSCRAN%></td>
<% if (showChi) { %> <td><%-r.CHI%></td> <% } %>
<% if (showPhi) { %> <td><%-r.PHI%></td> <% } %>
<% if (showKappa) { %> <td><%-r.KAPPA%></td> <% } %>
<td><%-r.RES%></td>
<td><%-r.RANKRES%></td>
<% if (showRankingRes) { %> <td><%-r.RANKRES%></td> <% } %>
<td><%-r.TRAN%></td>
<td><%-r.ATRAN%></td>
<td><%-r.TIME%></td>
Expand Down
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