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trends.html
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<!DOCTYPE html>
<html lang="en">
<head>
<title>Trends in X-ray data processing</title>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" type="text/css" href="css/dc.css"/>
<style>
html { margin: 0 auto; max-width: 1500px; overflow-y: scroll; }
body { font: 14px sans-serif; line-height: 20px; margin: 0; }
.clearfix:before, .clearfix:after {
display: table; line-height: 0; content: ""; }
.clearfix:after { clear: both; }
h2 { text-align: center; margin-bottom: 10px; color: #444; }
h1#loading { text-align: center; color: #aaa; font-size: 40px; }
strong { color: #333; }
a.reset { text-decoration: none; padding: 0 3px;
color: white; background: teal; }
a.reset:hover { text-decoration: underline; }
#subh { text-align:center; font-size:14px; color:#444; margin-top: 0; }
#options { text-align:center; color:#444; margin-top: 0;}
#footnote { font-size: 12px; text-align: center; color:#444; padding: 8px 0; }
#chart-facility select { min-width: 180px; min-height: 440px; }
#chart-facility { margin-right: 80px; margin-bottom: 10px; }
.dc-chart g.chart-body { clip-path: none; }
text.x-axis-label { font-size: 12px; }
</style>
</head>
<body>
<h2>Trends in the PDB entries</h2>
<p id="subh">
A different presentation of the same data as on
<a href="xray.html">the main page</a>.
<br/>X axis:
<input type="radio" id="reldate" name="date" value="release"> release
<input type="radio" id="depdate" name="date" value="deposit"> deposition date
Y axis:
<input type="radio" id="abs" name="absolute" value="y"> counts
<input type="radio" id="rel" name="absolute" value="n"> percentage
<h1 id="loading">LOADING DATA...</h1>
<div id="chart-facility" style="visibility: hidden;">
<strong>Facility</strong>
<a class="reset" href="#">reset</a>
<div class="clearfix"></div>
</div>
<div id="all-data" style="visibility: hidden;">
<div id="chart-detec">
<strong>Detector Technology</strong>
<div class="clearfix"></div>
</div>
<div id="chart-solution">
<strong>Solution Technique</strong>
<div class="clearfix"></div>
</div>
<div id="chart-reduc">
<strong>Reduction Software</strong>
<div class="clearfix"></div>
</div>
<div id="chart-scaling">
<strong>Scaling Software</strong>
<div class="clearfix"></div>
</div>
<div id="chart-refinement">
<strong>Refinement Software</strong> (before Servalcat)
<div class="clearfix"></div>
</div>
</div>
<div id="footnote" style="clear:both;">
<a href="https://github.com/project-gemmi/pdb-stats">
Source code and info...</a>
</div>
<script src="https://d3js.org/d3.v4.min.js"></script>
<!--script src="js/d3.v4.js"></script-->
<script src="js/crossfilter.js"></script>
<script src="js/dc.min.js"></script>
<script>
"use strict";
var facility_chart = dc.selectMenu('#chart-facility');
var detec_chart = dc.seriesChart('#chart-detec');
var reduc_chart = dc.seriesChart('#chart-reduc');
var scaling_chart = dc.seriesChart('#chart-scaling');
var solution_chart = dc.seriesChart('#chart-solution');
var refinement_chart = dc.seriesChart('#chart-refinement');
var params = window.location.hash.substr(1).split('&');
var PER_QUARTER = (params.indexOf('quarter') !== -1);
var DEPOS = (params.indexOf('depos') !== -1);
var YEARS = [2004, PER_QUARTER ? 2024.125 : 2024.00];
if (PER_QUARTER) YEARS[1] += 0.125;
if (DEPOS) { // deposition date
document.getElementById('depdate').checked = true;
} else {
document.getElementById('reldate').checked = true;
}
var AS_PERCENT = (params.indexOf('percent') !== -1);
if (AS_PERCENT) {
document.getElementById('rel').checked = true;
} else {
document.getElementById('abs').checked = true;
}
d3.json('data.json', function(json) {
document.getElementById("loading").innerText = "SORTING DATA...";
window.setTimeout(function() { setup(json); }, 0);
});
function setup(json) {
var SOURCES = {
'H': 'home source',
'F': 'XFEL (any)',
'?': 'synchrotron',
'-': 'unspecified',
'a': 'APS (US, IL)',
'e': 'ESRF (FR)',
'd': 'Diamond LS (UK)',
's': 'Swiss LS (CH)',
'A': 'ALS (US, Cal)',
'S': 'Stanford SRL (US)',
'n': 'NSLS (US, NY)',
'h': 'Shanghai SRF (CN)',
'p': 'Photon Factory (JP)',
'8': 'SPring-8 (JP)',
'b': 'BESSY (DE)',
'u': 'Australian S (AU)',
'f': 'SOLEIL (FR)',
'k': 'PAL/PLS (KR)',
'c': 'CLSI (CA)',
't': 'NSRRC (TW)',
'C': 'CHESS (US, NY)',
'm': 'MAX (SE)',
'D': 'DESY (DE)',
'L': 'LNLS (BR)',
'Z': 'ALBA (ES)',
'E': 'Elettra (IT)',
'B': 'Beijing SRF (CN)',
'U': 'SRS (UK)',
'I': 'Indus (IN)',
'y': 'SLAC (US, Cal)',
'K': 'KSRS (RU, Moscow)',
'z': 'CAMD (US, LA)',
'i': 'AichiSR (JP)',
'g': 'SAGA-LS (JP)',
'T': 'Siam Photon P. (TH)',
};
var DETECT = ['?', 'CCD', 'PAD', 'IP'];
var DETECT_FULL = ['Not specified', 'CCD', 'Pixel Array Detector',
'Image Plate'];
var REDUC_SOFT = { 'X':'XDS', 'H':'HKL', 'M':'Mosflm', 'd':'d*TREK',
'D':'DIALS', 'O': 'Other', '-':'unknown' };
var SCALE_SOFT = { 'A':'Aimless', 'S':'SCALA', 'H':'HKL', 'X':'XSCALE',
'd':'d*TREK', 'O': 'Other', '-':'unknown' };
var REF_SOFT = { 'R':'Refmac', 'P':'Phenix', 'B':'BUSTER', 'C': 'CNS',
'-':'other/mix' };
var STRUCT_SOL = ['known structure', 'MR', 'SAD', 'MAD', 'MIR/SIR',
'SIRAS', 'MIRAS', 'unspecified / other'];
function reuse_d0_for_date() {
var date_field = DEPOS ? 8 : 9; // d[8] is dep. date, d[9] is release date
if (PER_QUARTER) {
json.forEach(function (d) {
d[0] = ((d[date_field] >> 5) / 3) | 0;
});
} else {
json.forEach(function (d) {
d[0] = ((d[date_field] >> 5) / 12) | 0;
});
}
}
reuse_d0_for_date();
// Examples of dc.lineChart and seriesChart use a list of to items
// as dimension. For large number of rows, sorting lists inside
// dimension() is very slow, ~100x times slower than sorting numbers.
// It was too slow, so we switched to using bit manipulations instead.
var data = crossfilter();
data.add(json);
var facil_dim = data.dimension(function(d) { return d[1]; });
var detec_dim = data.dimension(function(d) { return (d[2] << 16) | d[0]; });
var solution_dim = data.dimension(function(d) { return (d[6] << 16) | d[0]; });
var reduc_dim = data.dimension(function(d) { return (d[3].charCodeAt(0) << 16) | d[0]; });
var scaling_dim = data.dimension(function(d) { return (d[3].charCodeAt(1) << 16) | d[0]; });
var ref_dim = data.dimension(function(d) { return (d[3].charCodeAt(2) << 16) | d[0]; });
d3.select('#loading').remove();
d3.select('#chart-facility').style('visibility', null);
d3.select('#all-data').style('visibility', null);
function setup_reset(chart) {
var root_el = chart.root().node();
var reset_el = root_el.getElementsByClassName('reset')[0];
reset_el.style.visibility = 'hidden';
reset_el.onclick = function() {
chart.filterAll();
dc.redrawAll();
return false;
};
}
function setup_plot(chart, dim) {
var gr = dim.group();
chart
.width(480)
.height(480)
.chart(function(c) { return dc.lineChart(c).renderDataPoints(true); })
.dimension(dim)
.group(gr)
.x(d3.scaleLinear().domain(YEARS))
.brushOn(false)
.clipPadding(10)
.elasticY(true)
.mouseZoomable(false)
.legend(dc.legend().x(60).y(30))
.keyAccessor(PER_QUARTER ? function(p) { return (p.key & 0xffff) / 4 + 1989.125; }
: function(p) { return (p.key & 0xffff) + 1989; })
.valueAccessor(function(p) {
if (AS_PERCENT) {
var key = chart.keyAccessor();
var all = chart.group().all();
var total = 0;
for (var i = 0; i < all.length; i++) {
if (key(all[i]) === key(p)) total += all[i].value;
}
return total !== 0 ? 100 * p.value / total : 0;
} else {
return p.value;
}
});
chart.xAxis().tickFormat(d3.format('d'));
chart.yAxis().tickFormat(d3.format('d'));
chart.margins().left += 10;
return chart;
}
facility_chart
.dimension(facil_dim)
.group(facil_dim.group())
.title(function(p) { return SOURCES[p.key] + ': ' + p.value; })
.order(function(a, b){ return b.value - a.value; })
.controlsUseVisibility(true)
.multiple(true).numberVisible(20);
setup_reset(facility_chart);
setup_plot(detec_chart, detec_dim)
.seriesAccessor(function(p) { return DETECT_FULL[p.key >> 16]; });
setup_plot(solution_chart, solution_dim)
.seriesAccessor(function(p) { return STRUCT_SOL[p.key >> 16]; });
setup_plot(reduc_chart, reduc_dim)
.seriesAccessor(function(p) { return REDUC_SOFT[String.fromCharCode(p.key >> 16)]; });
setup_plot(scaling_chart, scaling_dim)
.seriesAccessor(function(p) { return SCALE_SOFT[String.fromCharCode(p.key >> 16)]; });
setup_plot(refinement_chart, ref_dim)
.seriesAccessor(function(p) { return REF_SOFT[String.fromCharCode(p.key >> 16)]; });
var plots = [detec_chart, solution_chart, reduc_chart, scaling_chart, refinement_chart];
function set_x_axis_labels() {
var label = (DEPOS ? ' Deposition ' : 'Release ') + (PER_QUARTER ? 'Quarter' : 'Year');
for (var i = 0; i < plots.length; ++i) {
plots[i].xAxisLabel(label);
}
}
set_x_axis_labels();
var on_resize = function() {
dc.renderAll();
};
on_resize();
d3.select(window).on('resize', on_resize);
d3.selectAll('input').on('change', function() {
if (this.name === 'date') {
DEPOS = (this.value === 'deposit');
reuse_d0_for_date();
// removing and readding all data might be inefficient,
// but it's fast enough and I don't know a simpler way.
data.remove(function() { return true; });
data.add(json);
set_x_axis_labels();
dc.renderAll();
} else if (this.name === 'absolute') {
AS_PERCENT = (this.value === 'n');
dc.renderAll();
}
});
}
</script>
</body>
</html>