def _fill_values(self, a_xml_path):
""" fill the values """
dom_tree = etree.parse(open(a_xml_path,'r'))
root = dom_tree.getroot()
expr = "//*[local-name() = $name]"
# get station code
res = root.xpath(expr, name = "StationCode")
if len(res) > 0:
self._context['station_code'] = res[0].text
else:
self._context['station_code'] = UNDEFINED
# get station location
res = root.xpath(expr, name = "StationLocation")
if len(res) > 0:
self._context['station_location'] = res[0].text
else:
self._context['station_location'] = UNDEFINED
# get station coordinates
res = root.xpath(expr, name = "Coordinates")
if len(res) > 0:
dummy_str = res[0].text
if dummy_str != None:
(lat, lon, height) = dummy_str.split(' ')
self._context['station_lat'] = lat
self._context['station_lon'] = lon
self._context['station_height'] = height
self._context['station_gmaps'] = "http://maps.google.com/maps?q=%s,%s+(%s)&iwloc=A&hl=en&z=3" \
% (lat, lon, self._context['station_code'])
self._context['station_static_gmaps'] = \
"http://maps.google.com/staticmap?center=%s,%s&zoom=5&size=400x400&markers=%s,%s,greens" \
% (lat,lon,lat,lon)
# http://maps.google.com/maps?q=-12.4,+130.7+(This%20is%20my%20station%20here)&iwloc=A&hl=en&z=5
# get Detector Code
res = root.xpath(expr, name = "DetectorCode")
if len(res) > 0:
self._context['detector_code'] = res[0].text
else:
self._context['detector_code'] = UNDEFINED
# get detector description
res = root.xpath(expr, name = "DetectorDescription")
if len(res) > 0:
self._context['detector_description'] = res[0].text
else:
self._context['detector_description'] = UNDEFINED
# get sample type
res = root.xpath(expr, name = "SampleType")
if len(res) > 0:
self._context['sample_type'] = res[0].text
else:
self._context['sample_type'] = UNDEFINED
res = root.xpath(expr, name = "ArrivalDate")
if len(res) > 0:
self._context['arrival_date'] = time_utils.getOracleDateFromISO8601(res[0].text)
else:
self._context['arrival_date'] = UNDEFINED
spectrum_expr = "//*[local-name() = $name and contains(@id,$suffix)]"
# get the sample ID to find the spectrum
res = root.xpath('//*[local-name() = $name]/@SID', name = 'SampleInformation')
if len(res) != 1:
raise Exception('Should only have 1 SID in the XML file and found %d. res=[%s]' %(len(res), res))
curr_spectrum_id = res[0]
# res is Element Spectrum
res = root.xpath(spectrum_expr, suffix = curr_spectrum_id, name = 'SpectrumGroup')
if len(res) > 0:
elem = res[0]
# get attribute id
curr_spectrum_id = elem.get('id')
self._context['sample_id'] = '%s' % (curr_spectrum_id.split('-')[1])
# get calibrationIDs
self._context['calibration_ids'] = elem.get('calibrationIDs').split(' ')
# get geometry
res = elem.xpath(expr, name = "Geometry")
if len(res) == 0:
self._context['sample_geometry'] = UNDEFINED
else:
self._context['sample_geometry'] = res[0].text
# get quantity
res = elem.xpath(expr, name = "ProcessedAirVolume")
if len(res) == 0 or res[0].text == UNDEFINED:
self._context['processed_air_volume'] = UNDEFINED
self._context['processed_air_volume_unit'] = ""
else:
self._context['processed_air_volume'] = utils.round_as_string(res[0].text, 3)
self._context['processed_air_volume_unit'] = res[0].get('unit')
# get sample quantity
res = elem.xpath(expr, name = "SampleQuantity")
if len(res) == 0 or res[0].text == UNDEFINED:
self._context['sample_quantity'] = UNDEFINED
self._context['sample_quantity_unit'] = ""
else:
self._context['sample_quantity'] = utils.round_as_string(res[0].text, 3)
self._context['sample_quantity_unit'] = res[0].get('unit')
# get Xe volume
res = elem.xpath(expr, name = "XeVolume")
if len(res) == 0 or res[0].text == UNDEFINED:
self._context['xe_vol'] = UNDEFINED
self._context['xe_vol_unit'] = ""
else:
self._context['xe_vol'] = utils.round_as_string(res[0].text, 3)
self._context['xe_vol_unit'] = res[0].get('unit')
# get collection comments
res = elem.xpath(expr, name = "Comments")
if len(res) == 0 or res[0].text == None or res[0].text == UNDEFINED:
self._context['collection_comments'] = UNDEFINED
else:
comments = []
ios = cStringIO.StringIO(res[0].text.strip())
for line in ios:
comments.append(line.strip())
self._context['collection_comments'] = comments
# all timing information
c_start = time_utils.getOracleDateFromISO8601(elem.xpath(expr, name = "CollectionStart")[0].text)
c_stop = time_utils.getOracleDateFromISO8601(elem.xpath(expr, name = "CollectionStop")[0].text)
a_start = time_utils.getOracleDateFromISO8601(elem.xpath(expr, name = "AcquisitionStart")[0].text)
a_stop = time_utils.getOracleDateFromISO8601(elem.xpath(expr, name = "AcquisitionStop")[0].text)
a_time = time_utils.transformISO8601PeriodInFormattedTime(elem.xpath(expr, name = "RealAcquisitionTime")[0].text)
sampling_time = time_utils.transformISO8601PeriodInFormattedTime(elem.xpath(expr, name = "SamplingTime")[0].text)
decay_time = time_utils.transformISO8601PeriodInFormattedTime(elem.xpath(expr, name = "DecayTime")[0].text)
# to be added
flow_rate = utils.round_as_string(elem.xpath(expr, name = "FlowRate")[0].text, 3)
self._context['collection_start'] = c_start
self._context['collection_stop'] = c_stop
self._context['acquisition_start'] = a_start
self._context['acquisition_stop'] = a_stop
self._context['acquisition_time'] = a_time
self._context['sampling_time'] = sampling_time
self._context['decay_time'] = decay_time
self._context['avg_flow_rate'] = flow_rate
else:
self._context['sample_id'] = UNDEFINED
self._context['sample_geometry'] = UNDEFINED
# add Activity Concentration for Nuclides
#concNuclideExpr = "//*[local-name() = $name and contains(@spectrumIDs,'NOX49-239646-SPHD-G')]"
conc_nuclide_expr = "//*[local-name() = $name and contains(@spectrumIDs,$spectrum_id)]"
res = root.xpath(conc_nuclide_expr, name = "Analysis", spectrum_id = curr_spectrum_id )
if len(res) > 0:
analysis_elem = res[0]
# get all ided nuclides
res = analysis_elem.find("{%s}IdedNuclides"%(XML2HTMLRenderer.c_namespaces['sml']))
q_nuclides = []
nq_nuclides = []
a_nuclides = []
# iterate over the children of ided nuclides => the nuclides
for nuclide in res:
# check that nid_flag is 1 to go in quantified_nuclides otherwise goes into non_quantified_nuclides
nid_flag = nuclide.find('{%s}NuclideIdentificationIndicator'%(XML2HTMLRenderer.c_namespaces['sml'])).get("numericVal")
if nid_flag == '1':
one_dict = {}
# get Name,
one_dict['name'] = nuclide.find('{%s}Name'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['half_life'] = nuclide.find('{%s}HalfLife'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['conc'] = utils.round_as_string(nuclide.find('{%s}Concentration' \
% (XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
one_dict['conc_abs_err'] = utils.round_as_string(nuclide.find('{%s}AbsoluteConcentrationError' \
% (XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
one_dict['conc_rel_err'] = utils.round_as_string(nuclide.find('{%s}RelativeConcentrationError' \
% (XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
q_nuclides.append(one_dict)
else:
one_dict = {}
# get Name,
one_dict['name'] = nuclide.find('{%s}Name'%(XML2HTMLRenderer.c_namespaces['sml'])).text
mdc = nuclide.find('{%s}MDC' % (XML2HTMLRenderer.c_namespaces['sml'])).text
if mdc != "N/A":
one_dict['mdc'] = utils.round_as_string(mdc, RDIGITS)
else:
one_dict['mdc'] = "N/A"
nq_nuclides.append(one_dict)
# in any cases fill Activity results dict
dummy = {}
dummy['name'] = nuclide.find('{%s}Name'%(XML2HTMLRenderer.c_namespaces['sml'])).text
dummy['activity'] = utils.round_as_string(nuclide.find('{%s}Activity' \
% (XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
dummy['activity'] = utils.round_as_string(nuclide.find('{%s}Activity'\
% (XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
dummy['undecay_corr_activity'] = utils.round_as_string(nuclide.find('{%s}UndecayCorrectedActivity'\
% (XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
dummy['activity_abs_err'] = utils.round_as_string(nuclide.find('{%s}AbsoluteActivityError'\
% (XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
dummy['activity_rel_err'] = utils.round_as_string(nuclide.find('{%s}RelativeActivityError'\
% (XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
dummy['lc'] = utils.round_as_string(nuclide.find('{%s}LCActivity'\
% (XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
dummy['ld'] = utils.round_as_string(nuclide.find('{%s}LDActivity'\
% (XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
a_nuclides.append(dummy)
#sort and add nuclides
nq_nuclides.sort(nuclide_compare)
self._context['non_quantified_nuclides'] = nq_nuclides
q_nuclides.sort(nuclide_compare)
self._context['quantified_nuclides'] = q_nuclides
a_nuclides.sort(nuclide_compare)
self._context['activities_nuclides'] = a_nuclides
# Add ROI results
# get ROIInfo
res = analysis_elem.find("{%s}RoiInfo"%(XML2HTMLRenderer.c_namespaces['sml']))
if res == None:
res = []
# iterate over RoiNetCount
roi_results = []
roi_boundaries = []
for roi in res:
if roi.tag.find('RoiNetCount') != -1:
# if it is RoiNetCount
one_dict = {}
one_dict['roi_number'] = roi.find('{%s}RoiNumber'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['name'] = roi.find('{%s}Name'%(XML2HTMLRenderer.c_namespaces['sml'])).text
n_counts = roi.find('{%s}NetCounts'%(XML2HTMLRenderer.c_namespaces['sml'])).text
if n_counts is not None:
(n_c, n_c_err) = n_counts.split(' ')
one_dict['net_counts'] = utils.round_as_string(n_c, RDIGITS)
one_dict['net_counts_err'] = utils.round_as_string(n_c_err, RDIGITS)
else:
one_dict['net_counts'] = "N/A"
one_dict['net_counts_err'] = "N/A"
one_dict['lc'] = utils.round_as_string(roi.find('{%s}LC' \
%(XML2HTMLRenderer.c_namespaces['sml'])).text, RDIGITS)
val = roi.find('{%s}Efficiency' % (XML2HTMLRenderer.c_namespaces['sml'])).text
if val != UNDEFINED:
val = utils.round_as_string(val, RDIGITS)
one_dict['efficiency'] = val
val = roi.find('{%s}AbsoluteEfficiencyError' % (XML2HTMLRenderer.c_namespaces['sml'])).text
if val != UNDEFINED:
val = utils.round_as_string(val, RDIGITS)
one_dict['efficiency_abs_error'] = val
val = roi.find('{%s}RelativeEfficiencyError' % (XML2HTMLRenderer.c_namespaces['sml'])).text
if val != UNDEFINED:
val = utils.round_as_string(val, RDIGITS)
one_dict['efficiency_rel_error'] = val
roi_results.append(one_dict)
elif roi.tag.find('RoiBoundaries') != -1:
# Boundaries
one_dict = {}
one_dict['roi_number'] = roi.find('{%s}RoiNumber'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['gammalow'] = utils.round_as_string(roi.find('{%s}GammaLow'\
%(XML2HTMLRenderer.c_namespaces['sml'])).text, BGDIGITS)
one_dict['gammahigh'] = utils.round_as_string(roi.find('{%s}GammaHigh'\
%(XML2HTMLRenderer.c_namespaces['sml'])).text, BGDIGITS)
one_dict['betalow'] = utils.round_as_string(roi.find('{%s}BetaLow'\
%(XML2HTMLRenderer.c_namespaces['sml'])).text, BGDIGITS)
one_dict['betahigh'] = utils.round_as_string(roi.find('{%s}BetaHigh'\
%(XML2HTMLRenderer.c_namespaces['sml'])).text, BGDIGITS)
roi_boundaries.append(one_dict)
else:
self._log.error("No ROI info for %s" % (self._context['sample_id']))
self._context['roi_results'] = roi_results
self._context['roi_boundaries'] = roi_boundaries
# Add Flags
# timeliness flags
res = analysis_elem.find("{%s}Flags/{%s}TimelinessAndAvailabilityFlags" \
% (XML2HTMLRenderer.c_namespaces['sml'], XML2HTMLRenderer.c_namespaces['sml']))
if res == None:
res = []
flags = []
for timeflag in res:
one_dict = {}
if timeflag.tag.find('CollectionTime') != -1:
one_dict['name'] = 'Sampling Time'
elif timeflag.tag.find('AcquisitionTime') != -1:
one_dict['name'] = 'AcquisitionTime'
elif timeflag.tag.find('DecayTime') != -1:
one_dict['name'] = 'Decay Time'
elif timeflag.tag.find('ResponseTime') != -1:
one_dict['name'] = 'Response Time'
else:
self._log.error("Unknown Timeliness Flag: %s"%(timeflag.tag))
one_dict['name'] = timeflag.tag
one_dict['result'] = timeflag.find('{%s}Pass'%(XML2HTMLRenderer.c_namespaces['sml'])).text
try:
one_dict['value'] = utils.round_as_string(timeflag.find('{%s}Value' \
% (XML2HTMLRenderer.c_namespaces['sml'])).text, HDIGITS)
except Exception, _: #pylint: disable-msg= W0703
#cannot convert this number value so put the string as it is
one_dict['value'] = timeflag.find('{%s}Value'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['test'] = timeflag.find('{%s}Test'%(XML2HTMLRenderer.c_namespaces['sml'])).text
flags.append(one_dict)
# data quality flags
res = analysis_elem.find("{%s}Flags/{%s}DataQualityFlags"% (XML2HTMLRenderer.c_namespaces['sml'], \
XML2HTMLRenderer.c_namespaces['sml']))
if res == None:
res = []
for dqflag in res:
one_dict = {}
if dqflag.tag.find('XeVolume') != -1:
one_dict['name'] = 'Stable Xenon Volume'
else:
self._log.error("Unknown DataQuality Flag: %s"%(dqflag.tag))
one_dict['name'] = dqflag.tag
one_dict['result'] = dqflag.find('{%s}Pass' % (XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['value'] = utils.round_as_string(dqflag.find('{%s}Value' % (XML2HTMLRenderer.c_namespaces['sml'])).text, 3)
one_dict['test'] = dqflag.find('{%s}Test'%(XML2HTMLRenderer.c_namespaces['sml'])).text
flags.append(one_dict)
self._context['flags'] = flags
res = root.xpath("//*[local-name() = $name]", name = "CalibrationInformation")
if len(res) > 0:
# add calibration
res = res[0]
calibrations = []
for calibration in res:
# if calibration is related to the displayed spectrum
cid = calibration.get('ID')
if cid in self._context['calibration_ids']:
one_dict = {}
one_dict['desc'] = calibration.get('Type','N/A')
equation = calibration.find("{%s}Equation"%(XML2HTMLRenderer.c_namespaces['sml']))
if equation is not None:
one_dict['form'] = equation.get('Form','N/A')
one_dict['model'] = equation.get('Model','N/A')
# get coefficients
coefficients = equation.find("{%s}Coefficients"%(XML2HTMLRenderer.c_namespaces['sml'])).text
if coefficients is None:
one_dict['coeffs'] = []
else:
c_list = []
cpt = 0
for coeff in coefficients.split(' '):
c_list.append({'name':'t%s' % (cpt), 'val':coeff})
cpt += 1
one_dict['coeffs'] = c_list
else:
one_dict['form'] = 'N/A'
one_dict['model'] = 'N/A'
calibrations.append(one_dict)
self._context['calibrations'] = calibrations
# add creation time
self._context['creation_date'] = time_utils.getOracleDateFromDateTime(datetime.now())
def _fill_values(self, a_xml_path):
""" extract the values from the XML file """
dom_tree = etree.parse(open(a_xml_path, 'r'))
root = dom_tree.getroot()
expr = "//*[local-name() = $name]"
# get station code
res = root.xpath(expr, name = "StationCode")
if len(res) > 0:
self._context['station_code'] = res[0].text
else:
self._context['station_code'] = UNDEFINED
# get station location
res = root.xpath(expr, name = "StationLocation")
if len(res) > 0:
self._context['station_location'] = res[0].text
else:
self._context['station_location'] = UNDEFINED
# get station coordinates
res = root.xpath(expr, name = "Coordinates")
if len(res) > 0:
dummy_str = res[0].text
if dummy_str != None:
(lat, lon, height) = dummy_str.split(' ')
self._context['station_lat'] = lat
self._context['station_lon'] = lon
self._context['station_height'] = height
self._context['station_gmaps'] = "http://maps.google.com/maps?q=%s,%s+(%s)&iwloc=A&hl=en&z=3" \
% (lat, lon, self._context['station_code'])
self._context['station_static_gmaps'] = \
"http://maps.google.com/staticmap?center=%s,%s&zoom=5&size=400x400&markers=%s,%s,greens" \
% (lat,lon,lat,lon)
# get Detector Code
res = root.xpath(expr, name = "DetectorCode")
if len(res) > 0:
self._context['detector_code'] = res[0].text
else:
self._context['detector_code'] = UNDEFINED
# get detector description
res = root.xpath(expr, name = "DetectorDescription")
if len(res) > 0:
self._context['detector_description'] = res[0].text
else:
self._context['detector_description'] = UNDEFINED
# get sample type
res = root.xpath(expr, name = "SampleType")
if len(res) > 0:
self._context['sample_type'] = res[0].text
else:
self._context['sample_type'] = UNDEFINED
res = root.xpath(expr, name = "ArrivalDate")
if len(res) > 0:
self._context['arrival_date'] = time_utils.getOracleDateFromISO8601(res[0].text)
else:
self._context['arrival_date'] = UNDEFINED
# for the dates, a prefix is needed
# for the moment always take SPHD-G but it has to be configurable
#dateExpr = "//*[local-name() = \"Spectrum\" and ends-with(@id,\"SPHD-G\")]"
# no ends-with in xpath 1.0 use contains instead substring('','') as it is simpler
# and it does the trick
date_expr = "//*[local-name() = $name and contains(@id,$suffix)]"
curr_spectrum_id = None
# res is Element Spectrum
res = root.xpath(date_expr, suffix = 'SPHD', name = 'SpectrumGroup')
if len(res) > 0:
elem = res[0]
# get attribute id
curr_spectrum_id = elem.get('id')
self._context['sample_id'] = '%s' % ( curr_spectrum_id.split('-')[1])
# get calibrationIDs
self._context['calibration_ids'] = elem.get('calibrationIDs').split(' ')
# get geometry
res = elem.xpath(expr, name = "Geometry")
if len(res) == 0 or res[0].text == UNDEFINED:
self._context['sample_geometry'] = UNDEFINED
else:
self._context['sample_geometry'] = res[0].text
# get quantity
res = elem.xpath(expr, name = "AirVolume")
if len(res) == 0:
self._context['processed_air_volume'] = UNDEFINED
self._context['processed_air_volume_unit'] = ""
else:
self._context['processed_air_volume'] = utils.round_as_string(res[0].text, 3)
self._context['processed_air_volume_unit'] = res[0].get('unit') if res[0].get('unit') != UNDEFINED else UNDEFINED
# get Xe volume
res = elem.xpath(expr, name = "XeVolume")
if len(res) == 0 or res[0].text == UNDEFINED:
self._context['xe_vol'] = UNDEFINED
self._context['xe_vol_unit'] = ""
else:
self._context['xe_vol'] = utils.round_as_string(res[0].text, 3)
if res[0].text != UNDEFINED:
self._context['xe_vol_unit'] = res[0].get('unit')
# get collection comments
res = elem.xpath(expr, name = "Comments")
if len(res) == 0 or res[0].text == UNDEFINED:
self._context['collection_comments'] = UNDEFINED
else:
comments = []
ios = cStringIO.StringIO(res[0].text.strip())
for line in ios:
comments.append(line.strip())
self._context['collection_comments'] = comments
# all timing information
c_start = time_utils.getOracleDateFromISO8601(elem.xpath(expr, name = "CollectionStart")[0].text)
c_stop = time_utils.getOracleDateFromISO8601(elem.xpath(expr, name = "CollectionStop")[0].text)
a_start = time_utils.getOracleDateFromISO8601(elem.xpath(expr, name = "AcquisitionStart")[0].text)
a_stop = time_utils.getOracleDateFromISO8601(elem.xpath(expr, name = "AcquisitionStop")[0].text)
a_time = time_utils.transformISO8601PeriodInFormattedTime(elem.xpath(expr, name = "RealAcquisitionTime")[0].text)
sampling_time = time_utils.transformISO8601PeriodInFormattedTime(elem.xpath(expr, name = "SamplingTime")[0].text)
decay_time = time_utils.transformISO8601PeriodInFormattedTime(elem.xpath(expr, name = "DecayTime")[0].text)
# to be added
flow_rate = utils.round_as_string(elem.xpath(expr, name = "FlowRate")[0].text, 3)
self._context['collection_start'] = c_start
self._context['collection_stop'] = c_stop
self._context['acquisition_start'] = a_start
self._context['acquisition_stop'] = a_stop
self._context['acquisition_time'] = a_time
self._context['sampling_time'] = sampling_time
self._context['decay_time'] = decay_time
self._context['avg_flow_rate'] = flow_rate
else:
self._context['sample_id'] = UNDEFINED
self._context['sample_geometry'] = UNDEFINED
# add Activity Concentration for Nuclides
#concNuclideExpr = "//*[local-name() = $name and contains(@spectrumIDs,'NOX49-239646-SPHD-G')]"
conc_nuclide_expr = "//*[local-name() = $name and contains(@spectrumIDs,$spectrum_id)]"
res = root.xpath(conc_nuclide_expr, name = "Analysis", spectrum_id = curr_spectrum_id )
if len(res) > 0:
analysis_elem = res[0]
# get all ided nuclides
res = analysis_elem.find("{%s}IdedNuclides"%(XML2HTMLRenderer.c_namespaces['sml']))
#init structures
q_nuclides = {'peak' : {}, 'decay' : {} }
nq_nuclides = {'peak' : {}, 'decay' : {} }
a_nuclides = {'peak' : {}, 'decay' : {} }
the_mdi = UNDEFINED
# iterate over the children of ided nuclides => the nuclides
for nuclide in res:
method = nuclide.get('method')
if method == 'Peak Fit Method':
method = 'peak'
elif method == 'Decay Analysis Method':
method = 'decay'
# check that nid_flag is 1 to go in quantified_nuclides otherwise goes into non_quantified_nuclides
nid_flag = nuclide.find('{%s}NuclideIdentificationIndicator' % (XML2HTMLRenderer.c_namespaces['sml'])).get("numericVal")
#nid flag is 1 identified
if nid_flag == '1':
one_dict = {}
# get Name,
one_dict['name'] = nuclide.find('{%s}Name' % (XML2HTMLRenderer.c_namespaces['sml'])).text
temp_val = nuclide.find('{%s}Concentration' % (XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['conc'] = utils.round_as_string(temp_val, RDIGITS) if temp_val != UNDEFINED else UNDEFINED
temp_val = nuclide.find('{%s}AbsoluteConcentrationError' % (XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['conc_abs_err'] = utils.round_as_string(temp_val, 3) if temp_val != UNDEFINED else UNDEFINED
temp_val = nuclide.find('{%s}RelativeConcentrationError' % (XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['conc_rel_err'] = utils.round_as_string(temp_val, 3) if temp_val != UNDEFINED else UNDEFINED
#temp_val = nuclide.find('{%s}MDI' % (XML2HTMLRenderer.c_namespaces['sml'])).text
#one_dict['mdi'] = utils.round_as_string(temp_val, RDIGITS) if temp_val != UNDEFINED else UNDEFINED
q_nuclides[method][one_dict['name']] = one_dict
else:
#if it is 0 or 2 it should go there
one_dict = {}
# get Name,
one_dict['name'] = nuclide.find('{%s}Name' % (XML2HTMLRenderer.c_namespaces['sml'])).text
#get MDC
mdc = nuclide.find('{%s}MDC' % (XML2HTMLRenderer.c_namespaces['sml'])).text
if mdc != "N/A":
one_dict['mdc'] = utils.round_as_string(mdc, RDIGITS) if mdc != UNDEFINED else UNDEFINED
else:
# do not put UNDEFINED but a space char
one_dict['mdc'] = SPACECHAR
#get MDI
mdi = nuclide.find('{%s}MDI' % (XML2HTMLRenderer.c_namespaces['sml'])).text
if the_mdi == UNDEFINED and mdi != "N/A":
the_mdi = mdi
# add concetration anyway
temp_val = nuclide.find('{%s}Concentration' % (XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['conc'] = utils.round_as_string(temp_val, RDIGITS) if temp_val != UNDEFINED else UNDEFINED
temp_val = nuclide.find('{%s}AbsoluteConcentrationError' % (XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['conc_abs_err'] = utils.round_as_string(temp_val, 3) if temp_val != UNDEFINED else UNDEFINED
temp_val = nuclide.find('{%s}RelativeConcentrationError' % (XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['conc_rel_err'] = utils.round_as_string(temp_val, 3) if temp_val != UNDEFINED else UNDEFINED
nq_nuclides[method][one_dict['name']] = one_dict
# in any cases fill Activity results dict
one_dict = {}
method = nuclide.get('method')
if method == 'Peak Fit Method':
method = 'peak'
elif method == 'Decay Analysis Method':
method = 'decay'
one_dict['name'] = nuclide.find('{%s}Name'%(XML2HTMLRenderer.c_namespaces['sml'])).text
temp_val = nuclide.find('{%s}Activity'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['activity'] = utils.round_as_string(temp_val, RDIGITS) if temp_val != UNDEFINED else UNDEFINED
temp_val = nuclide.find('{%s}UndecayCorrectedActivity' % (XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['undecay_corr_activity'] = utils.round_as_string(temp_val, RDIGITS) if temp_val != UNDEFINED else UNDEFINED
temp_val = nuclide.find('{%s}AbsoluteActivityError'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['activity_abs_err'] = utils.round_as_string(temp_val, RDIGITS) if temp_val != UNDEFINED else UNDEFINED
temp_val = nuclide.find('{%s}RelativeActivityError'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['activity_rel_err'] = utils.round_as_string(temp_val, RDIGITS) if temp_val != UNDEFINED else UNDEFINED
temp_val = nuclide.find('{%s}LCActivity'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['lc'] = utils.round_as_string(temp_val, RDIGITS) if temp_val != UNDEFINED else UNDEFINED
temp_val = nuclide.find('{%s}LDActivity'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['ld'] = utils.round_as_string(temp_val, RDIGITS) if temp_val != UNDEFINED else UNDEFINED
temp_val = nuclide.find('{%s}MDI'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['mdi'] = utils.round_as_string(temp_val, RDIGITS) if temp_val != UNDEFINED else UNDEFINED
a_nuclides[method][one_dict['name']] = one_dict
self._context['non_quantified_nuclides'] = nq_nuclides
self._context['quantified_nuclides'] = q_nuclides
self._context['activities_nuclides'] = a_nuclides
self._context['mdi'] = the_mdi
# Add Cov matrixes here
# used to respect order of the columns
self._context['matrix_row_order'] = ['XE-131M', 'XE-133M', 'XE-133', 'XE-135']
#first peak fit method
cov_matrix = "//*[local-name() = 'XeCovarianceMatrixes']/*[local-name() = 'XeCovarianceMatrix' and contains(@method,$method)]"
res = root.xpath(cov_matrix, method = "Peak Fit Method")
matrix_result = {'XE-133M': {0: UNDEFINED, 1: UNDEFINED, 2: UNDEFINED, 3: UNDEFINED}, \
'XE-131M': {0: UNDEFINED, 1: UNDEFINED, 2: UNDEFINED, 3: UNDEFINED}, \
'XE-135': {0: UNDEFINED, 1: UNDEFINED, 2: UNDEFINED, 3: UNDEFINED}, \
'XE-133': {0: UNDEFINED, 1: UNDEFINED, 2: UNDEFINED, 3: UNDEFINED}\
}
matrix_col = {'XE-131M':0, 'XE-133M':1, 'XE-133':2, 'XE-135':3}
if len(res) > 0:
matrix_elem = res[0]
for cell in matrix_elem:
key = cell.get('row')
if matrix_result.has_key(key):
one_dict = matrix_result[key]
else:
one_dict = {}
matrix_result[key] = one_dict
col = cell.get('col').upper()
#get position
one_dict[matrix_col[col]] = utils.round_as_string(cell.text, RDIGITS)
self._context['peak_fit_matrix'] = matrix_result
#second Decay Analysis Method
cov_matrix = "//*[local-name() = 'XeCovarianceMatrixes']/*[local-name() = 'XeCovarianceMatrix' and contains(@method,$method)]"
res = root.xpath(cov_matrix, method = "Decay Analysis Method")
matrix_col = {'XE-131M':0, 'XE-133M':1, 'XE-133':2, 'XE-135':3}
if len(res) > 0:
matrix_elem = res[0]
for cell in matrix_elem:
key = cell.get('row')
if matrix_result.has_key(key):
one_dict = matrix_result[key]
else:
one_dict = {}
matrix_result[key] = one_dict
col = cell.get('col').upper()
#get position
one_dict[matrix_col[col]] = utils.round_as_string(cell.text, RDIGITS)
else:
matrix_result = {}
self._context['decay_analysis_matrix'] = matrix_result
# Add Flags
# timeliness flags
res = analysis_elem.find("{%s}Flags/{%s}TimelinessAndAvailabilityFlags" \
% (XML2HTMLRenderer.c_namespaces['sml'], XML2HTMLRenderer.c_namespaces['sml']))
if res == None:
res = []
flags = []
for timeflag in res:
one_dict = {}
if timeflag.tag.find('CollectionTime') != -1:
one_dict['name'] = 'Sampling Time'
elif timeflag.tag.find('AcquisitionTime') != -1:
one_dict['name'] = 'AcquisitionTime'
elif timeflag.tag.find('DecayTime') != -1:
one_dict['name'] = 'Decay Time'
elif timeflag.tag.find('ResponseTime') != -1:
one_dict['name'] = 'Response Time'
else:
self._log.error("Unknown Timeliness Flag: %s"%(timeflag.tag))
one_dict['name'] = timeflag.tag
one_dict['result'] = timeflag.find('{%s}Pass'%(XML2HTMLRenderer.c_namespaces['sml'])).text
try:
temp_val = timeflag.find('{%s}Value' % (XML2HTMLRenderer.c_namespaces['sml']))
one_dict['value'] = utils.round_as_string(temp_val , HDIGITS) if temp_val != UNDEFINED else UNDEFINED
except Exception, _: #pylint: disable-msg= W0703
#cannot convert this number value so put the string as it is
one_dict['value'] = timeflag.find('{%s}Value'%(XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['test'] = timeflag.find('{%s}Test'%(XML2HTMLRenderer.c_namespaces['sml'])).text
flags.append(one_dict)
# data quality flags
res = analysis_elem.find("{%s}Flags/{%s}DataQualityFlags" \
% (XML2HTMLRenderer.c_namespaces['sml'], XML2HTMLRenderer.c_namespaces['sml']))
if res == None:
res = []
for dqflag in res:
one_dict = {}
if dqflag.tag.find('XeVolume') != -1:
one_dict['name'] = 'Stable Xenon Volume'
else:
self._log.error("Unknown DataQuality Flag: %s"%(dqflag.tag))
one_dict['name'] = dqflag.tag
one_dict['result'] = dqflag.find('{%s}Pass' % (XML2HTMLRenderer.c_namespaces['sml'])).text
temp_val = dqflag.find('{%s}Value' % (XML2HTMLRenderer.c_namespaces['sml'])).text
one_dict['value'] = utils.round_as_string(temp_val, 3) if temp_val != UNDEFINED else UNDEFINED
one_dict['test'] = dqflag.find('{%s}Test' % (XML2HTMLRenderer.c_namespaces['sml'])).text
flags.append(one_dict)
self._context['flags'] = flags
res = root.xpath("//*[local-name() = $name]", name = "CalibrationInformation")
if len(res) > 0:
# add calibration
res = res[0]
calibrations = []
eff_equations = []
for calibration in res:
# if calibration is related to the displayed spectrum
cid = calibration.get('ID')
if cid in self._context['calibration_ids']:
one_dict = {}
one_dict['desc'] = calibration.get('Type','N/A')
one_dict['model'] = calibration.get('Model','N/A')
if one_dict['desc'].lower() != 'efficiency':
equation = calibration.find("{%s}Equation" % (XML2HTMLRenderer.c_namespaces['sml']))
if equation is not None:
one_dict['form'] = equation.get('Form','N/A')
# get coefficients
coefficients = equation.find("{%s}Coefficients" % (XML2HTMLRenderer.c_namespaces['sml'])).text
if coefficients is None:
one_dict['coeffs'] = []
else:
c_list = []
cpt = 0
for coeff in coefficients.split(' '):
c_list.append({'name':'t%s' % (cpt), 'val':coeff})
cpt += 1
one_dict['coeffs'] = c_list
else:
one_dict['form'] = 'N/A'
calibrations.append(one_dict)
#Efficiency case for the moment
else:
equations = calibration.findall("{%s}Equation" % (XML2HTMLRenderer.c_namespaces['sml']))
for one_eq in equations:
one_dict = {}
one_dict['form'] = one_eq.get('Form', 'N/A')
one_dict['model'] = one_eq.get('Model', 'N/A')
# get coefficients
coefficients = one_eq.find("{%s}Coefficients"%(XML2HTMLRenderer.c_namespaces['sml'])).text
if coefficients is None:
one_dict['coeffs'] = []
else:
c_list = []
cpt = 0
for coeff in coefficients.split(' '):
c_list.append({'name':'t%s'%(cpt), 'val':coeff})
cpt += 1
one_dict['coeffs'] = c_list
eff_equations.append(one_dict)
self._context['calibrations'] = calibrations
self._context['eff_calibration'] = eff_equations
# add creation time
self._context['creation_date'] = time_utils.getOracleDateFromDateTime(datetime.now())