def test_raster_extraction(self):
print ('\n Testing RIS extraction: \n')
self.parser= XMLparser("test_maps/raster-images.hdf.xml","e","RIS",None,True)
self.create_dump_dir(self.parser.xml_file + "_dump")
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
self.tear_down(self.parser.xml_file + "_dump")
def test_one_dimensional_sds_extraction(self):
print ('\n Testing one-dimensional SDS extraction: \n')
self.parser= XMLparser("test_maps/one-dimensional-sds.xml","e","SDS",None,True)
self.create_dump_dir(self.parser.xml_file + "_dump")
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
self.tear_down(self.parser.xml_file + "_dump")
def test_vdata_extraction(self):
print ('\n Testing VData extraction: \n')
self.parser= XMLparser("test_maps/vdata-tables.hdf.xml","e","VData",None,True)
self.create_dump_dir(self.parser.xml_file + "_dump")
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
self.tear_down(self.parser.xml_file + "_dump")
def dump_files(self,op,object,output_format,verbose):
'''
dumps HDF files objects from the map files found
'''
for filename in self.hdfFoundFiles:
file_path=filename[1].replace("/","")
if not os.path.exists(self.dir + file_path + "_dump"):# Be careful with relative paths in Linux
try:
os.makedirs(self.dir + file_path + "_dump")
print "Directory created :" + file_path + "_dump"
except:
print "Failed to create a sub directory to store the output files: " + "maps/" + file_path + "_dump"
exit(-1)
else:
print "The output directory already exist: " + file_path + "_dump"
parser= XMLparser( self.dir + file_path,op,object,output_format,verbose)
if parser.tree!= None:
code=parser.parseAndDumpMapContent()
if code==0:
self.tear_down(self.dir + file_path + "_dump")
def test_airs_sds_extraction(self):
print ('\n Testing AIRS SDS extraction: \n')
self.parser= XMLparser("test_maps/AIRS.NASA.PROD.hdf.xml","e","ALL",None,True)
self.create_dump_dir(self.parser.xml_file + "_dump")
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
def test_listing(self):
print ('\n Testing map listing: \n')
self.parser= XMLparser("test_maps/multidimensional_chunked_sds.hdf.xml","l","ALL",None,True)
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
def test_unexisting_xml(self):
print ('\n This should be a warning message: \n')
self.parser= XMLparser("test_maps/thisfiledoesnotexist.xml","e","ALL",None,True)
self.assertEquals(self.parser.tree,None)
self.tear_down()
def test_invalid_xml(self):
self.parser= XMLparser("test_maps/incorrect-invalid-xml.hdf.xml","e","ALL",None,True)
self.assertEquals(self.parser.tree,None)
self.tear_down()
class TestMapReader(unittest.TestCase):
def setUp(self):
'''
'''
def create_dump_dir(self,dir):
if not os.path.exists(dir):
os.makedirs(dir)
def tear_down(self,dir=''):
print "Tear down ... "
if os.path.exists(dir):
shutil.rmtree(dir)
self.parser=None
def test_invalid_xml(self):
self.parser= XMLparser("test_maps/incorrect-invalid-xml.hdf.xml","e","ALL",None,True)
self.assertEquals(self.parser.tree,None)
self.tear_down()
def test_unexisting_xml(self):
print ('\n This should be a warning message: \n')
self.parser= XMLparser("test_maps/thisfiledoesnotexist.xml","e","ALL",None,True)
self.assertEquals(self.parser.tree,None)
self.tear_down()
def test_listing(self):
print ('\n Testing map listing: \n')
self.parser= XMLparser("test_maps/multidimensional_chunked_sds.hdf.xml","l","ALL",None,True)
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
def test_multi_dimensional_sds_extraction(self):
print ('\n Testing multi-dimensional SDS extraction: \n')
self.parser= XMLparser("test_maps/multidimensional_chunked_sds.hdf.xml","e","SDS",None,True)
self.create_dump_dir(self.parser.xml_file + "_dump")
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
self.tear_down(self.parser.xml_file + "_dump")
def test_two_dimensional_sds_extraction(self):
print ('\n Testing 2-dimensional SDS extraction: \n')
self.parser= XMLparser("test_maps/two-dimensional-chunked-sds.hdf.xml","e","SDS",None,True)
self.create_dump_dir(self.parser.xml_file + "_dump")
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
self.tear_down(self.parser.xml_file + "_dump")
def test_one_dimensional_sds_extraction(self):
print ('\n Testing one-dimensional SDS extraction: \n')
self.parser= XMLparser("test_maps/one-dimensional-sds.xml","e","SDS",None,True)
self.create_dump_dir(self.parser.xml_file + "_dump")
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
self.tear_down(self.parser.xml_file + "_dump")
def test_vdata_extraction(self):
print ('\n Testing VData extraction: \n')
self.parser= XMLparser("test_maps/vdata-tables.hdf.xml","e","VData",None,True)
self.create_dump_dir(self.parser.xml_file + "_dump")
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
self.tear_down(self.parser.xml_file + "_dump")
def test_raster_extraction(self):
print ('\n Testing RIS extraction: \n')
self.parser= XMLparser("test_maps/raster-images.hdf.xml","e","RIS",None,True)
self.create_dump_dir(self.parser.xml_file + "_dump")
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
self.tear_down(self.parser.xml_file + "_dump")
def test_airs_sds_extraction(self):
print ('\n Testing AIRS SDS extraction: \n')
self.parser= XMLparser("test_maps/AIRS.NASA.PROD.hdf.xml","e","ALL",None,True)
self.create_dump_dir(self.parser.xml_file + "_dump")
code=self.parser.parseAndDumpMapContent()
self.assertEqual(code,0)
def RunFromXML(self, filename):
parsed = XMLparser(filename)
#The output of XMLparse contains at least two arrays of dictionarys, one for dgsreduction keywords and one for other keywords
# datadictsdgs
# datadictsother
for d in range(len(parsed.datadictsdgs)):
#initialize the text variables.
self.loadtext = ''
self.vantext = ''
self.reductiontext = ''
#Deal with the vanadium sensitivity correction
vandict = self.loadvan(parsed)
#determine the scantype
#single OR sweep
if parsed.datadictsother[d][
'ScanType'] == 'single' or parsed.datadictsother[d][
'ScanType'] == 'sweep':
FileName = parsed.datadictsother[d]['Instrument'] + "_" + str(
parsed.datadictsother[d]['Runs'][0])
#Load each file and fix the time-series to start at 'zero'
data = Load(Filename=FileName)
self.loadtext += 'Data files loaded ' + FileName + '\n'
path = data.getRun()['Filename'].value
#do the correction for log times
CorrectLogTimes('data')
self.loadtext += 'Data files corrected for log times\n'
monitors = Load_2_Monitors(path)
monitors = monitors.rename()
if parsed.datadictsother[d]['FilterBadPulses']:
data = FilterBadPulses(InputWorkspace=data)
self.loadtext += "Bad pulses filtered from data files\n"
#filter by additional log values.
if parsed.datadictsother[d]['FilterNames'] != None:
for cntr, part in enumerate(
parsed.datadictsother[d]['FilterNames']):
data = FilterByLogValue(
InputWorkspace='data',
LogName=part,
MinimumValue=parsed.datadictsother[d]['FilterMin']
[cntr],
MaximumValue=parsed.datadictsother[d]['FilterMax']
[cntr],
TimeTolerance=0,
LogBoundary='Left')
self.loadtext += "Data filtered by " + part + " between " + str(
MinimumValue) + " and " + str(MaximumValue) + ".\n"
#print "Data filtered by "+part+" between "+str(parsed.datadictsother[d]['FilterMin'][cntr])+" and "+str(parsed.datadictsother[d]['FilterMax'][cntr])+".\n"
#now deal with all the other runs, if there are more than one.
if len(parsed.datadictsother[d]['Runs']) > 1:
for i in range(1, len(parsed.datadictsother[d]['Runs'])):
FileName = parsed.datadictsother[d][
'Instrument'] + "_" + str(
parsed.datadictsother[d]['Runs'][i])
#Load each file and fix the time-series to start at 'zero'
datatemp = Load(Filename=FileName)
path = datatemp.getRun()['Filename'].value
self.loadtext += 'Data files loaded ' + FileName + '\n'
#Fix all of the time series log values to start at the same time as the proton_charge
#do the correction for log times
CorrectLogTimes('datatemp')
self.loadtext += 'Data files corrected for log times\n'
monitorstemp = Load_2_Monitors(path)
monitors += monitorstemp
if parsed.datadictsother[d]['FilterBadPulses']:
datatemp = FilterBadPulses(InputWorkspace=datatemp)
self.loadtext += "Bad pulses filtered from data files\n"
#filter by additional log values.
if parsed.datadictsother[d]['FilterNames'] != None:
for cntr, part in enumerate(
parsed.datadictsother[d]['FilterNames']):
datatemp = FilterByLogValue(
InputWorkspace='datatemp',
LogName=part,
MinimumValue=parsed.datadictsother[d]
['FilterMin'][cntr],
MaximumValue=parsed.datadictsother[d]
['FilterMax'][cntr],
TimeTolerance=0,
LogBoundary='Left')
self.loadtext += "Data filtered by " + part + " between " + str(
MinimumValue) + " and " + str(
MaximumValue) + ".\n"
data += datatemp
self.loadtext += 'Data added to the previous workspace\n'
#This is where the reduction is done.
if parsed.datadictsother[d]['ScanType'] == 'single':
self.ProcessWorkspace(data, monitors,
parsed.datadictsdgs[d],
parsed.datadictsother[d], vandict)
else:
#split up the sweep by the sweep variable.
logvalue = parsed.datadictsother[d]['LogValue']
logvaluemin = parsed.datadictsother[d]['LogValueMin']
logvaluemax = parsed.datadictsother[d]['LogValueMax']
logvaluestep = parsed.datadictsother[d]['LogValueStep']
#Check if the logvalue has been set
if logvalue == None or data.run().hasProperty(
logvalue) == False:
raise ValueError(
"No LogValue given OR the given log value was not found in the file."
)
#need to split the data by an independt variable , some log value.
#Create the array of logvalue BOUNDARIES
if logvaluemin == None:
logvaluemin = array(
data.run().getProperty(logvalue).value).min()
if logvaluemax == None:
logvaluemax = array(
dat.run().getProperty(logvalue).value).max()
if logvaluestep == None:
logvaluestep = logvaluemax - logvaluemin
bounds = arange(float(logvaluemin),
float(logvaluemax) + float(logvaluestep),
float(logvaluestep))
#Get the time correlation correct if you set the time correlation keyword.
#To first approximation, set the time to zero for the first.
for i in range(len(bounds) - 1):
dataslice = FilterByLogValue(
InputWorkspace=data,
LogName=logvalue,
MinimumValue=float(bounds[i]),
MaximumValue=float(bounds[i + 1]))
if dataslice.getNumberEvents() > 0:
values = array(
dataslice.run().getProperty(logvalue).value)
self.reductiontext = "Processing data for " + logvalue + " between " + str(
bounds[i]) + " and " + str(
bounds[i + 1]) + ", mean=" + str(
values.mean()) + " std=" + str(
values.std()) + "\n"
self.ProcessWorkspace(dataslice, monitors,
parsed.datadictsdgs[d],
parsed.datadictsother[d],
vandict)
if parsed.datadictsother[d]['ScanType'] == 'step':
for currentrun in parsed.datadictsother[d]['Runs']:
FileName = parsed.datadictsother[d][
'Instrument'] + "_" + str(currentrun)
#Load each file and fix the time-series to start at 'zero'
data = Load(Filename=FileName)
self.loadtext = 'Data files loaded ' + FileName + '\n'
path = data.getRun()['Filename'].value
#do the correction for log times
CorrectLogTimes('data')
monitors = Load_2_Monitors(path)
self.loadtext += 'Data files corrected for log times\n'
if parsed.datadictsother[d]['FilterBadPulses']:
data = FilterBadPulses(InputWorkspace=data)
self.loadtext += "Bad pulses filtered from data files\n"
#filter by additional log values.
if parsed.datadictsother[d]['FilterNames'] != None:
for cntr, part in enumerate(
parsed.datadictsother[d]['FilterNames']):
data = FilterByLogValue(
InputWorkspace='data',
LogName=part,
MinimumValue=parsed.datadictsother[d]
['FilterMin'][cntr],
MaximumValue=parsed.datadictsother[d]
['FilterMax'][cntr],
TimeTolerance=0,
LogBoundary='Left')
self.loadtext += "Data filtered by " + part + " between " + str(
MinimumValue) + " and " + str(
MaximumValue) + ".\n"
self.reductiontext = ''
self.ProcessWorkspace(data, monitors,
parsed.datadictsdgs[d],
parsed.datadictsother[d], vandict)
import pandas
import numpy
import psycopg2
import Utils
from XMLparser import XMLparser
#For testing purposes
if __name__ == "__main__":
print("Framing Payment Data...", Utils.DATA_HOSPITAL_PAYMENT)
p1 = XMLparser(Utils.DATA_HOSPITAL_PAYMENT, Utils.PaymentTags)
f1 = p1.parse()
print("Done.")
while(True):
flag = input("Print out portion of data?(y/n)")
if(flag == "y"):
print(f1)
break
if(flag == "n"):
break
print("Framing Comp&Death Data...", Utils.DATA_COMPLICATIONS)
p2 = XMLparser(Utils.DATA_COMPLICATIONS, Utils.CompTags)
f2 = p2.parse()
print("Done.")
while(True):
flag = input("Print out portion of data?(y/n)")
if(flag == "y"):
print(f1)
break
if(flag == "n"):
