def find_problems(xds_wd):
problems = []
idxref_lp = os.path.join(xds_wd, "IDXREF.LP")
xparm_xds = os.path.join(xds_wd, "XPARM.XDS")
integrate_lp = os.path.join(xds_wd, "INTEGRATE.LP")
correct_lp = os.path.join(xds_wd, "CORRECT.LP")
xdsstat_lp = os.path.join(xds_wd, "XDSSTAT.LP")
if os.path.isfile(idxref_lp):
idexref_has_problem = False
lp = idxreflp.IdxrefLp(idxref_lp)
intness = lp.cluster_integerness()
for h in intness:
if sum(h) > 0 and h[0] / sum(h) < 0.9:
idexref_has_problem = True
if len(lp.subtree_population) > 0:
pp0 = float(lp.subtree_population[0]) / sum(lp.subtree_population)
if pp0 < 0.9: idexref_has_problem = True
else:
idexref_has_problem = True
if not os.path.isfile(xparm_xds): idexref_has_problem = True
if idexref_has_problem:
problems.append("IDXREF")
if os.path.isfile(integrate_lp):
lp = integratelp.IntegrateLp(integrate_lp)
if any(map(lambda x: float(x) > 1.5, lp.sigmars)):
problems.append("INTEGRATE")
if os.path.isfile(correct_lp):
lp = correctlp.CorrectLp(correct_lp)
if not lp.is_ISa_valid() or lp.get_ISa() < 10:
problems.append("CORRECT")
if os.path.isfile(xdsstat_lp):
lp = xdsstat.XdsstatLp(xdsstat_lp)
return problems
def try_indexing_hard(wdir,
show_progress,
decilog,
known_sgnum=None,
known_cell=None,
tol_length=None,
tol_angle=None):
idxref_lp = os.path.join(wdir, "IDXREF.LP")
xdsinp = os.path.join(wdir, "XDS.INP")
lp_org = idxreflp.IdxrefLp(idxref_lp)
if lp_org.is_cell_maybe_half():
backup_needed = ("XDS.INP", ) + xds_files.generated_by_IDXREF
print >> decilog, " !! Cell may be halved. Trying doubled cell."
bk_prefix = make_backup(backup_needed, wdir=wdir, quiet=True)
cell = lp_org.deduce_correct_cell_based_on_integerness()
cell = " ".join(map(lambda x: "%.2f" % x, cell.parameters()))
modify_xdsinp(xdsinp,
inp_params=[("JOB", "IDXREF"),
("SPACE_GROUP_NUMBER", "1"),
("UNIT_CELL_CONSTANTS", cell)])
run_xds(wdir=wdir, show_progress=show_progress)
if idxreflp.IdxrefLp(idxref_lp).is_cell_maybe_half():
revert_files(backup_needed, bk_prefix, wdir=wdir, quiet=True)
print >> decilog, " .. not solved. Next, try decreasing SEPMIN= and CLUSTER_RADIUS=."
bk_prefix = make_backup(backup_needed, wdir=wdir, quiet=True)
modify_xdsinp(xdsinp,
inp_params=[("JOB", "IDXREF"), ("SEPMIN", "4"),
("CLUSTER_RADIUS", "2")])
run_xds(wdir=wdir, show_progress=show_progress)
if idxreflp.IdxrefLp(idxref_lp).is_cell_maybe_half():
print >> decilog, " .. not solved. Give up."
revert_files(backup_needed, bk_prefix, wdir=wdir, quiet=True)
else:
print >> decilog, " Now OK."
remove_backups(backup_needed, bk_prefix, wdir=wdir)
modify_xdsinp(xdsinp, inp_params=[
("SPACE_GROUP_NUMBER", "0"),
])
# If Cell hint exists, try to use it..
if known_sgnum > 0:
flag_try_cell_hint = False
xparm = os.path.join(wdir, "XPARM.XDS")
if not os.path.isfile(xparm):
flag_try_cell_hint = True
else:
xsxds = XPARM(xparm).crystal_symmetry()
xsref = crystal.symmetry(known_cell, known_sgnum)
cosets = reindex.reindexing_operators(xsref, xsxds, tol_length,
tol_angle)
if cosets.double_cosets is None: flag_try_cell_hint = True
if flag_try_cell_hint:
print >> decilog, " Worth trying to use prior cell for indexing."
modify_xdsinp(xdsinp,
inp_params=[
("JOB", "IDXREF"),
("UNIT_CELL_CONSTANTS",
" ".join(map(lambda x: "%.3f" % x,
known_cell))),
("SPACE_GROUP_NUMBER", "%d" % known_sgnum),
])
run_xds(wdir=wdir, show_progress=False)
modify_xdsinp(xdsinp, inp_params=[
("SPACE_GROUP_NUMBER", "0"),
])
def make_kamo_report(bssjobs, topdir, htmlout):
report_html = """\
<html>
<head>
<style>
.dataset_table {
font-family: "Trebuchet MS", Arial, Helvetica, sans-serif;
width: 100%%;
border-collapse: collapse;
}
.dataset_table td, .dataset_table th {
font-size: 1em;
border: 1px solid #98bf21;
padding: 3px 7px 2px 7px;
}
.dataset_table th {
font-size: 1.1em;
text-align: left;
padding-top: 5px;
padding-bottom: 4px;
background-color: #A7C942;
color: #ffffff;
}
.dataset_table tr.alt td {
color: #000000;
background-color: #EAF2D3;
}
h1, h2 { text-align: center; text-indent: 0px; font-weight: bold; hyphenate: none;
page-break-before: always; page-break-inside: avoid; page-break-after: avoid; }
h3, h4, h5, h6 { text-indent: 0px; font-weight: bold;
hyphenate: none; page-break-inside: avoid; page-break-after: avoid; }
</style>
</head>
<body>
<h1>KAMO (auto data processing) report</h1>
<div align="right">
top dir: %s<br>
created on %s
</div>
""" % (os.path.abspath(topdir), time.strftime("%Y-%m-%d %H:%M:%S"))
reports = {}
for jobkey in sorted(bssjobs.jobs):
wd = bssjobs.get_xds_workdir(jobkey)
relwd = os.path.relpath(wd, os.path.dirname(htmlout))
job = bssjobs.jobs[jobkey]
dsname = os.path.basename(wd).replace("xds_", "")
gxparm_xds = os.path.join(wd, "GXPARM.XDS")
correct_lp = os.path.join(wd, "CORRECT.LP")
spot_xds = os.path.join(wd, "SPOT.XDS")
idxref_lp = os.path.join(wd, "IDXREF.LP")
xds_inp = os.path.join(wd, "XDS.INP")
stats_pkl = os.path.join(wd, "merging_stats.pkl")
sampleid = "%s(%.2d)" % job.sample if job.sample is not None else "?"
wavelen = job.wavelength
deltaphi = job.osc_step
lattp, ISa, resn, cmpl, sg = float("nan"), float("nan"), float(
"nan"), float("nan"), "?"
problems = find_problems(wd)
indiv_html = os.path.join(relwd, "report.html")
problems_str = "OK"
if len(problems) > 0:
problems_str = ",".join(problems)
totalphi = job.osc_end - job.osc_start
if os.path.isfile(idxref_lp):
lpobj = idxreflp.IdxrefLp(idxref_lp)
lattp = lpobj.first_subtree_fraction() * 100.
lp = bssjobs._load_if_chached("correctlp", correct_lp)
if lp is not None:
ISa = lp.get_ISa() if lp.is_ISa_valid() else float("nan")
sg = lp.space_group_str()
cmpl = float(lp.table["all"]["cmpl"]
[-1]) if "all" in lp.table else float("nan")
resn = bssjobs._load_if_chached("resn", correct_lp)
if resn is None: resn = bssjobs._load_if_chached("resn", spot_xds)
if resn is None: resn = float("nan")
tmp = '<tr>\n <td><a href="%s">%s</a></td> <td>%s</td> <td>%.4f</td> <td>%.1f</td> <td>%.3f</td> <td>%.1f</td> <td>%s</td> <td>%.1f</td> <td>%.0f</td> <td>%.2f</td> <td>%s</td>\n</tr>\n' % (
indiv_html, dsname, sampleid, wavelen, totalphi, deltaphi, lattp,
sg, resn, cmpl, ISa, problems_str)
reports.setdefault(os.path.dirname(relwd), []).append(tmp)
for wd in sorted(reports):
report_html += "<h3>%s</h3>\n" % wd
report_html += """\
<table class="dataset_table">
<tr>
<th>Dataset</th> <th>Sample ID</th> <th>λ (Å)</th> <th>Total φ (°)</th> <th>Δφ (°)</th> <th>IdxLatt (%)</th> <th>SG</th> <th>Resn (Å)</th> <th>Cmpl (%)</th> <th>ISa</th> <th>Problems</th>
</tr>
"""
report_html += "".join(reports[wd])
report_html += "</table>\n"
report_html += """
</body>
</html>
"""
open(htmlout, "w").write(report_html)
def make_individual_report(xds_wd, html_wd):
problems = []
xds_inp = os.path.join(xds_wd, "XDS.INP")
idxref_lp = os.path.join(xds_wd, "IDXREF.LP")
xparm_xds = os.path.join(xds_wd, "XPARM.XDS")
spot_xds = os.path.join(xds_wd, "SPOT.XDS")
integrate_lp = os.path.join(xds_wd, "INTEGRATE.LP")
correct_lp = os.path.join(xds_wd, "CORRECT.LP")
xdsstat_lp = os.path.join(xds_wd, "XDSSTAT.LP")
stats_pkl = os.path.join(xds_wd, "merging_stats.pkl")
shika_log = os.path.join(xds_wd, "shika.log")
if not os.path.exists(html_wd):
os.makedirs(html_wd)
html = """\
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<script src="%(amcharts_root)s/amcharts.js" charset="utf-8"></script>
<script src="%(amcharts_root)s/serial.js" charset="utf-8"></script>
<script src="%(amcharts_root)s/xy.js" charset="utf-8"></script>
</head>
<body>
<h1>%(title)s</h1>
created on %(cdate)s
""" % dict(title=os.path.abspath(xds_wd),
cdate=time.strftime("%Y-%m-%d %H:%M:%S"),
amcharts_root=amcharts_root)
if os.path.isfile(shika_log):
lines = open(shika_log).readlines()
if len(lines) > 1:
data = map(lambda x: (x.split()[0], x.split()[2]), lines[1:])
html += "<h1>Low resolution spots</h1>\n"
html += """\
<div id="chartdiv_shika" style="width: 640px; height: 400px;"></div>
<script>
var chart_idxref_ibf = AmCharts.makeChart("chartdiv_shika", {
"type": "serial",
"theme": "none",
"legend": {
"useGraphSettings": true
},
"dataProvider": [%s],
"valueAxes": [{
"stackType": "regular",
"gridAlpha": 0.07,
"position": "left",
"title": "Number of located spots by SHIKA"
}],
"graphs": [{
"balloonText": "n_spots: [[value]]",
"fillAlphas": 0.6,
"lineAlpha": 0.4,
"title": "number of spots",
"valueField": "nspt"
}],
"chartCursor": {
"cursorPosition": "mouse"
},
"categoryField": "frame",
"categoryAxis": {
"minorGridEnabled": true,
"title": "frame"
}
});
</script>
""" % (",".join(map(lambda x: '{"frame": %s, "nspt": %s}' % x, data)), )
html += "<h1>IDXREF (Indexing)</h1>\n"
if os.path.isfile(idxref_lp):
SX = idxreflp.SpotXds(spot_xds)
if os.path.isfile(xparm_xds): SX.set_xparm(xparm_xds)
else: SX.set_xdsinp(xds_inp)
i_ui_on_det = SX.indexed_and_unindexed_on_detector(
with_resolution=True)
html += """\
<h3>Indexed/Unindexed spots</h3>
<h4>by frame</h4>
<div id="chartdiv_idxref_indexed_by_frame" style="width: 640px; height: 400px;"></div>
<script>
var chart_idxref_ibf = AmCharts.makeChart("chartdiv_idxref_indexed_by_frame", {
"type": "serial",
"theme": "none",
"legend": {
"useGraphSettings": true
},
"dataProvider": [%s],
"valueAxes": [{
"stackType": "regular",
"gridAlpha": 0.07,
"position": "left",
"title": "Number of located spots"
}],
"graphs": [{
"balloonText": "indexed: [[value]]",
"fillAlphas": 0.6,
"lineAlpha": 0.4,
"title": "Indexed spots",
"valueField": "ind"
}, {
"balloonText": "unindexed: [[value]]",
"fillAlphas": 0.6,
"lineAlpha": 0.4,
"title": "Unindexed spots",
"valueField": "und"
}],
"chartCursor": {
"cursorPosition": "mouse"
},
"categoryField": "frame",
"categoryAxis": {
"minorGridEnabled": true,
"title": "frame"
}
});
</script>
<h4>on detector surface</h4>
<div id="chartdiv_idxref_indexed_on_det" style="width: 640px; height: 640px;"></div>
<script>
var chart_idxref_iod = AmCharts.makeChart("chartdiv_idxref_indexed_on_det", {
"type": "xy",
"theme": "none",
"legend": {
"useGraphSettings": true
},
"dataProvider": [%s],
"valueAxes": [{
"position":"bottom",
"axisAlpha": 0,
"dashLength": 1,
"title": "Detector X"
}, {
"axisAlpha": 0,
"dashLength": 1,
"position": "left",
"title": "Detector Y"
}],
"graphs": [{
"balloonText": "x:[[x]] y:[[y]]; d=[[description]]",
"bullet": "round",
"bulletSize": 4,
"lineAlpha": 0,
"xField": "ix",
"yField": "iy",
"descriptionField": "d",
"title": "Indexed spots",
"hidden": true,
"lineColor": "#FF6600",
"fillAlphas": 0
}, {
"balloonText": "x:[[x]] y:[[y]]; d=[[description]]",
"bullet": "round",
"bulletSize": 4,
"lineAlpha": 0,
"xField": "ux",
"yField": "uy",
"descriptionField": "d",
"title": "Unindexed spots",
"hidden": true,
"lineColor": "#FCD202",
"fillAlphas": 0
}],
"chartCursor": {
"cursorPosition": "mouse"
},
});
</script>
""" % (
",".join(
map(
lambda x: '{"frame": %d, "ind": %s, "und": %s}' %
(x[0], x[1][0], x[1][1]),
SX.indexed_and_unindexed_by_frame())),
",".join(
map(lambda x: '{"ix":%.1f,"iy":%.1f,"d":%.1f}' % x,
i_ui_on_det["indexed"]) +
map(lambda x: '{"ux":%.1f,"uy":%.1f,"d":%.1f}' % x,
i_ui_on_det["unindexed"])),
)
idexref_has_problem = False
lp = idxreflp.IdxrefLp(idxref_lp)
intness = lp.cluster_integerness()
for h in intness:
if sum(h) > 0 and h[0] / sum(h) < 0.9:
idexref_has_problem = True
html += "<h3>Clusters and subtrees</h3>"
html += """
<h4>Cluster integerness</h4>
<div id="chartdiv_idxref_cluster_int" style="width: 640px; height: 400px;"></div>
<script>
var chart_idxref_cluster_int = AmCharts.makeChart("chartdiv_idxref_cluster_int", {
"type": "serial",
"categoryField": "f",
"categoryAxis": {
"gridPosition": "start",
"position": "left",
"title": "fractional part of indices",
},
"legend": {
"useGraphSettings": true
},
"dataProvider": [%s],
"graphs": [{
"balloonText": "h: [[value]]",
"fillAlphas": 0.8,
"lineAlpha": 0.2,
"title": "h",
"type": "column",
"valueField": "h"
}, {
"balloonText": "k: [[value]]",
"fillAlphas": 0.8,
"lineAlpha": 0.2,
"title": "k",
"type": "column",
"valueField": "k"
}, {
"balloonText": "l: [[value]]",
"fillAlphas": 0.8,
"lineAlpha": 0.2,
"title": "l",
"type": "column",
"valueField": "l"
}
],
"guides": [],
"valueAxes": [
{
"position": "top",
"axisAlpha": 0,
"title": "frequency"
}
],
});
</script>
""" % (",".join(
map(
lambda x: '{"f":.%d,"h":%d,"k":%d,"l":%d}' % x,
map(
lambda x: tuple([
x,
] + map(lambda y: intness[y][x], xrange(3))), xrange(6)))))
html += "<h4>Subtree populations</h4>\n<pre>"
accum_pop = 0
for i, pp in enumerate(
map(lambda x: float(x) / sum(lp.subtree_population),
lp.subtree_population)):
html += "%s subtree: %.2f%%\n" % (util.num_th_str(i + 1),
pp * 100.)
if i == 0 and pp < 0.9: idexref_has_problem = True
accum_pop += pp
if accum_pop > 0.9:
break
html += "</pre>"
if not os.path.isfile(xparm_xds): idexref_has_problem = True
if idexref_has_problem:
problems.append("IDXREF")
html += "<h1>INTEGRATE (Integration)</h1>\n"
if os.path.isfile(integrate_lp):
lp = integratelp.IntegrateLp(integrate_lp)
if any(map(lambda x: float(x) > 1.5, lp.sigmars)):
problems.append("INTEGRATE")
html += """\
<h3>Mosaicity and beam divergence</h3>
<div id="chartdiv_integrate_sigmas" style="width: 640px; height: 400px;"></div>
<h3>rotations off from initial orientation</h3>
<div id="chartdiv_integrate_rotxyz" style="width: 640px; height: 400px;"></div>
<script>
var chart1 = AmCharts.makeChart("chartdiv_integrate_sigmas", {
"type": "serial",
"theme": "none",
"legend": {
"useGraphSettings": true
},
"dataProvider": [%s],
"valueAxes": [{
"id":"v1",
"axisColor": "#FF6600",
"axisThickness": 2,
"gridAlpha": 0,
"axisAlpha": 1,
"position": "left"
}, {
"id":"v2",
"axisColor": "#FCD202",
"axisThickness": 2,
"gridAlpha": 0,
"axisAlpha": 1,
"position": "right"
}],
"graphs": [{
"balloonText": "σ<sub>R</sub>: [[value]]",
"valueAxis": "v1",
"lineColor": "#FF6600",
"bullet": "round",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "mosaicity",
"valueField": "sigmar",
"fillAlphas": 0
}, {
"balloonText": "σ<sub>B</sub>: [[value]]",
"valueAxis": "v2",
"lineColor": "#FCD202",
"bullet": "square",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "beam divergence",
"valueField": "sigmad",
"fillAlphas": 0
}],
"chartCursor": {
"cursorPosition": "mouse"
},
"categoryField": "frame",
"categoryAxis": {
"minorGridEnabled": true,
"title": "frame"
}
});
var chart2 = AmCharts.makeChart("chartdiv_integrate_rotxyz", {
"type": "serial",
"theme": "none",
"legend": {
"useGraphSettings": true
},
"dataProvider": [%s],
"valueAxes": [{
"id":"v1",
"axisColor": "#FF6600",
"axisThickness": 2,
"gridAlpha": 0,
"axisAlpha": 1,
"position": "left"
}],
"graphs": [{
"valueAxis": "v1",
"lineColor": "#FF6600",
"bullet": "round",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "rot x",
"valueField": "rotx",
"fillAlphas": 0
}, {
"valueAxis": "v2",
"lineColor": "#FCD202",
"bullet": "square",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "rot y",
"valueField": "roty",
"fillAlphas": 0
}, {
"valueAxis": "v3",
"lineColor": "#B0DE09",
"bullet": "triangleUp",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "rot z",
"valueField": "rotz",
"fillAlphas": 0
}],
"chartCursor": {
"cursorPosition": "mouse"
},
"categoryField": "frame",
"categoryAxis": {
"minorGridEnabled": true,
"title": "frame"
}
});
</script>
""" % (
",".join(
map(lambda x: '{"frame": %d, "sigmar": %s, "sigmad": %s}' % x,
zip(lp.frames, lp.sigmars, lp.sigmads))),
",".join(
map(
lambda x: ",".join(
map(
lambda y:
'{"frame": %d, "rotx": %s, "roty": %s, "rotz": %s}'
% ((y, ) + tuple(x[1].get("rotation", ["NaN"] * 3))
), x[0])), lp.blockparams.items())),
)
html += "<h1>CORRECT (Scaling)</h1>\n"
if os.path.isfile(correct_lp):
lp = correctlp.CorrectLp(correct_lp)
if not lp.is_ISa_valid() or lp.get_ISa() < 10:
problems.append("CORRECT")
html += """\
<table border=0 cellpadding=5 style="text-align:right;">
<tr><th>Space group</th><td colspan=6 style="text-align:left;">%(sg)s</td></tr>
""" % dict( #sgstr=lp.space_group.info(), sgnum=lp.space_group.type().number(),
sg=lp.space_group.info().symbol_and_number()
if lp.space_group is not None else "n/a")
if lp.unit_cell is not None:
html += """\
<tr><th>Unit cell</th><td>%(a).3f</td><td>%(b).3f</td><td>%(c).3f</td><td>%(alpha).3f</td><td>%(beta).3f</td><td>%(gamma).3f</td></tr>
<tr><th>e. s. d.</th><td>%(a_e).3f</td><td>%(b_e).3f</td><td>%(c_e).3f</td><td>%(alpha_e).3f</td><td>%(beta_e).3f</td><td>%(gamma_e).3f</td></tr>
</table>
""" % dict(
a=lp.unit_cell[0],
b=lp.unit_cell[1],
c=lp.unit_cell[2],
alpha=lp.unit_cell[3],
beta=lp.unit_cell[4],
gamma=lp.unit_cell[5],
a_e=lp.unit_cell_esd[0],
b_e=lp.unit_cell_esd[1],
c_e=lp.unit_cell_esd[2],
alpha_e=lp.unit_cell_esd[3],
beta_e=lp.unit_cell_esd[4],
gamma_e=lp.unit_cell_esd[5],
)
else: # in case parameter refinement failed
html += """\
<tr><th>Unit cell</th><td colspan=6>n/a</td></tr>
<tr><th>e. s. d.</th><td colspan=6>n/a</td></tr>
</table>
"""
html += "<h3>ISa</h3>\n<pre>%s</pre>\n" % lp.snippets.get("ISa", "")
html += "<h3>Statistics of all data</h3>\n"
if os.path.isfile(stats_pkl):
sio = StringIO.StringIO()
pickle.load(open(stats_pkl))["stats"].show(out=sio, header=False)
html += "<pre>%s</pre>\n" % sio.getvalue().replace(
"<", "<").replace(">", ">")
else:
html += "<pre>%s</pre>\n" % lp.snippets.get("table1", "")
if lp.error_table != {}:
tmp = map(
lambda x: '{"d":%.3f,"ios":%.2f,"nrej":%d}' % x,
zip(lp.error_table["dmin"], lp.error_table["ios"],
lp.error_table["nrej"]))
tmp = tmp[:-1] # last is about all data
html += """\
<h3>By resolution</h3>
<div id="chartdiv_correct_error" style="width: 640px; height: 400px;"></div>
<script>
var chart_correct_er = AmCharts.makeChart("chartdiv_correct_error", {
"type": "serial",
"theme": "none",
"legend": {
"useGraphSettings": true
},
"dataProvider": [%s],
"valueAxes": [{
"id":"v1",
"axisColor": "#FF6600",
"axisThickness": 2,
"gridAlpha": 0,
"axisAlpha": 1,
"position": "left"
}, {
"id":"v2",
"axisColor": "#FCD202",
"axisThickness": 2,
"gridAlpha": 0,
"axisAlpha": 1,
"position": "right"
}],
"graphs": [{
"balloonText": "Mn(I/sd): [[value]]",
"valueAxis": "v1",
"lineColor": "#FF6600",
"bullet": "round",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "Mean(I/Sigma)",
"valueField": "ios",
"fillAlphas": 0
}, {
"balloonText": "rejected: [[value]]",
"valueAxis": "v2",
"lineColor": "#FCD202",
"bullet": "square",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "Rejected reflections",
"valueField": "nrej",
"fillAlphas": 0
}],
"chartCursor": {
"cursorPosition": "mouse"
},
"categoryField": "d",
"categoryAxis": {
"minorGridEnabled": true,
"title": "resolution"
}
});
</script>
""" % (",".join(tmp))
if os.path.isfile(xdsstat_lp):
lp = xdsstat.XdsstatLp(xdsstat_lp)
if set(("frame", "iobs", "sigma", "ios", "rmeas",
"nmisfits")).issubset(lp.by_frame.keys()):
html += """\
<h3>By frame</h3>
<div id="chartdiv_xdsstat_ios" style="width: 640px; height: 400px;"></div>
<script>
var chart_xdsstat_ios = AmCharts.makeChart("chartdiv_xdsstat_ios", {
"type": "serial",
"theme": "none",
"legend": {
"useGraphSettings": true
},
"dataProvider": [%s],
"valueAxes": [{
"id":"v1",
"axisThickness": 2,
"gridAlpha": 0,
"axisAlpha": 1,
"position": "left"
}, {
"id":"v2",
"axisThickness": 2,
"gridAlpha": 0,
"axisAlpha": 1,
"position": "right"
}],
"graphs": [{
"balloonText": "Mn(I): [[value]]",
"valueAxis": "v1",
"bullet": "round",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "Mean(I)",
"valueField": "i",
"fillAlphas": 0
}, {
"balloonText": "Mn(sd): [[value]]",
"valueAxis": "v1",
"bullet": "round",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "Mean(Sigma)",
"valueField": "sig",
"fillAlphas": 0
}, {
"balloonText": "Mn(I/sd): [[value]]",
"valueAxis": "v2",
"bullet": "square",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "Mean(I/Sigma)",
"hidden": true,
"valueField": "ios",
"fillAlphas": 0
}],
"chartCursor": {
"cursorPosition": "mouse"
},
"categoryField": "frame",
"categoryAxis": {
"minorGridEnabled": true,
"title": "frame"
}
});
</script>
<div id="chartdiv_xdsstat_r" style="width: 640px; height: 400px;"></div>
<script>
var chart_xdsstat_r = AmCharts.makeChart("chartdiv_xdsstat_r", {
"type": "serial",
"theme": "none",
"legend": {
"useGraphSettings": true
},
"dataProvider": [%s],
"valueAxes": [{
"id":"v1",
"axisColor": "#FF6600",
"axisThickness": 2,
"gridAlpha": 0,
"axisAlpha": 1,
"position": "left"
}, {
"id":"v2",
"axisThickness": 2,
"axisColor": "#FCD202",
"gridAlpha": 0,
"axisAlpha": 1,
"position": "right"
}],
"graphs": [{
"balloonText": "R-meas: [[value]]",
"valueAxis": "v1",
"lineColor": "#FF6600",
"bullet": "round",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "R-meas",
"valueField": "r",
"fillAlphas": 0
}, {
"balloonText": "Misfits: [[value]]",
"valueAxis": "v2",
"lineColor": "#FCD202",
"bullet": "square",
"bulletBorderThickness": 1,
"hideBulletsCount": 30,
"title": "#Misfits",
"valueField": "mis",
"fillAlphas": 0
}],
"chartCursor": {
"cursorPosition": "mouse"
},
"categoryField": "frame",
"categoryAxis": {
"minorGridEnabled": true,
"title": "frame"
}
});
</script>
""" % (",".join(
map(
lambda x: '{"frame":%d,"i":%.2f,"sig":%.2f,"ios":%.2f}' %
x,
zip(lp.by_frame["frame"], lp.by_frame["iobs"],
lp.by_frame["sigma"], lp.by_frame["ios"]))), ",".join(
map(
lambda x: '{"frame":%d,"r":%.4f,"mis":%d}' % x,
zip(lp.by_frame["frame"], lp.by_frame["rmeas"],
lp.by_frame["nmisfits"]))))
html += "</body></html>"
htmlout = os.path.join(html_wd, "report.html")
open(htmlout, "w").write(html)
return htmlout, problems