def main():
print '\nAscii Table test\n'
a=ascii_table('c12pg.dat','ascii')
initTest(a)
dataTest(a)
'''
keys=a.dcols.keys()
for i in range(len(keys)):
print keys[i]
#print a.dcols[keys[i]]
a.plot('upper','T9',plotType='ATable', shape='-')
a.plot('upper','ado/CA88',plotType='ATable', shape='-')
a.plot('CA88','ado/fit',plotType='ATable', shape='-')
'''
a=ascii_table('c12.dat','ascii',sep=';')
initTest(a)
dataTest(a)
'''
def run(self):
self.cycles.extend(self.h5s[0].cycle)
self.ages.extend(self.h5s[0].age)
self.hattrs = self.h5s[0].hattr
self.cattrs = self.h5s[0].cattr
self.Tables = self.h5s[0].Table
self.dcols = self.h5s[0].dcol
self.cycle_header = self.h5s[
0].cycle_header #This string handles the name of the cycle
try:
self.A = self.h5s[0].A[0]
except IndexError:
print "Sorry, there is no A vector. This can cause problems for reading abundances. Continue..."
try:
self.Z = self.h5s[0].Z[0]
except IndexError:
print "Sorry, there is no Z vector. This can cause problems for reading abundances. Continue... "
try:
self.isomeric_states = self.h5s[0].isomeric_state[0]
except IndexError:
print "Sorry, there is no isomeric state vector. Continue..."
new = self.h5s[
0].new # This boolean handles the changes to the cycle nomenclature format
if self.filename.endswith(os.sep):
b = str(self.filename) + str(self.preprocName)
else:
b = str(self.filename) + os.sep + str(self.preprocName)
if self.preprocExists:
preprocTable = ascii_table(self.preprocName, self.filename)
if int(preprocTable.hattrs[0]) < len(self.h5files):
self.preprocExists = False
print 'A File was added, rewriteing preprocessor file'
if self.preprocExists:
for i in xrange(len(self.h5files)):
if os.path.basename(
self.h5files[i]
) + '-cyc' not in preprocTable.dcols and self.preprocExists:
print 'A File was renamed, rewriteing preprocessor file'
print preprocTable.dcols[i], os.path.basename(
self.h5files[i]) + '-cyc'
self.preprocExists = False
if not self.preprocExists and os.path.exists(b):
os.system('rm ' + b)
# create list of isotopes stored in this h5 file
try:
for x in xrange(len(self.Tables[0])):
if self.isomeric_states[x] == 1:
self.isotopes.append(self.isos[int(self.Tables[1][x])] +
'-' + str(int(self.Tables[0][x])))
else:
self.isotopes.append(self.isos[int(self.Tables[1][x])]+'-' +str(int(self.Tables[0][x]))+\
self.isomerDelimiter+str(self.isomeric_states[x]-1))
except IndexError:
print 'This file does not contain any tables. Isotopic data must be contained elsewhere.'
t1 = time.time()
# create list of elements stored in this h5 file
asaved = ''
for atmp in self.Z:
if atmp != asaved:
self.elements.append(self.isos[int(atmp)])
asaved = atmp
thread_list = []
print(self.h5s[0].filename)
for x in xrange(len(self.h5files) - 1):
thread_list.append(
self.h5s.append(h5File(self.h5files[x + 1], False, new)))
print(self.h5s[x + 1].filename)
if not self.preprocExists:
self.h5s[x + 1].start()
self.h5s[x + 1].join()
self.h5sStarted[x + 1] = True
#self.h5s[x+1].run()
#print('Active '+ str(threading.active_count()))
# Wait until the threads are done.
#for thread in self.h5s:
# print(thread)
# thread.join()
if not self.preprocExists:
for x in xrange(len(self.h5files) - 1):
self.cycles.extend(self.h5s[x + 1].cycle)
self.ages.extend(self.h5s[x + 1].age)
header=[str(len(self.h5files)),'This is a preprocessor file for the directory: '+str(self.filename),\
'At the time of the creation of this file there were '+str(len(self.h5files))+\
' h5 files.']
try:
self.cycles = sorted(self.cycles, cmp=self.numeric_compare)
except TypeError:
print "There was a problem sorting the cycles. You may have problems later. Please consider reloading(h5T) and trying again"
try:
self.ages = sorted(self.ages, cmp=self.numeric_compare)
except TypeError:
None
print 'Writeing preprocessor files'
data = []
dcols = []
length = 0
for i in xrange(len(self.h5s)):
print self.h5s[i].filename.rpartition('/')[2]
dcols.append(os.path.basename(self.h5s[i].filename) + '-cyc')
dcols.append(os.path.basename(self.h5s[i].filename) + '-age')
data.append(self.h5s[i].cycle)
data.append(self.h5s[i].age)
if len(self.h5s[i].cycle) > length:
length = len(self.h5s[i].cycle)
if len(self.h5s[i].age) > length:
length = len(self.h5s[i].age)
for i in xrange(len(data)):
for j in xrange(length - len(data[i])):
data[i].append(3.14159265)
write(self.preprocName, header, dcols, data, sldir=self.filename)
else:
print 'Reading preprocessor files'
preprocTable = ascii_table(self.preprocName, self.filename)
for i in xrange(len(self.h5s) - 1):
dat = preprocTable.get(
os.path.basename(self.h5s[i + 1].filename) + '-cyc')
dat1 = []
for j in xrange(len(dat)):
if dat[j] != 3.14159265:
dat1.append(dat[j])
dat = dat1
for j in xrange(len(dat)):
dat[j] = str(int(dat[j]))
for k in xrange(10 - len(dat[j])):
dat[j] = '0' + dat[j]
for j in xrange(len(dat)):
self.cycles.append(dat[j])
self.h5s[i + 1].cycle = dat
dat = preprocTable.get(
os.path.basename(self.h5s[i + 1].filename) + '-age')
dat1 = []
for j in xrange(len(dat)):
if dat[j] != 3.14159265:
dat1.append(dat[j])
dat = dat1
self.h5s[i + 1].age = dat
for j in xrange(len(dat)):
self.ages.append(dat[j])
try:
self.cycles = sorted(self.cycles, cmp=self.numeric_compare)
except TypeError:
print "There was a problem sorting the cycles. You may have problems later. Please consider reloading(h5T) and trying again"
try:
self.ages = sorted(self.ages, cmp=self.numeric_compare)
except TypeError:
None
print 'File search complete.'
t2 = time.time()
print "Total duration is " + str(t2 - t1) + " seconds."
return
def all_done(self):
if debug:
print "all done"
if not self.preprocExists:
for x in xrange(len(self.h5s)):
print len(self.h5s[x].cycle)
print len(self.h5s[x].age)
for x in xrange(len(self.h5s)-1):
self.cycles.extend(self.h5s[x+1].cycle)
self.ages.extend(self.h5s[x+1].age)
print len(self.ages)
print len(self.cycles)
header=[str(len(self.h5s)),'This is a preprocessor file for the directory: '+str(self.filepath),\
'At the time of the creation of this file there were '+str(len(self.h5files))+\
' h5 files.']
self.cycles = sorted(self.cycles, cmp=self.numeric_compare)
#self.cycles = sorted(self.cycles, cmp=self.numeric_compare)
"""
for cycle in self.cycles:
print cycle
try:
#self.ages = self.get(self.cycles,'age',1)
except IndexError:
print 'enountered error fetching age'
"""
#self.ages = sorted(self.ages, cmp=self.numeric_compare)
self.textEdit.append('File search complete. You may begin plotting')
print 'Writeing preprocessor files'
data=[]
dcols=[]
length=0
for i in xrange(len(self.h5s)):
dcols.append(self.h5s[i].filename+'-cyc')
dcols.append(self.h5s[i].filename+'-age')
data.append(self.h5s[i].cycle)
data.append(self.h5s[i].age)
if len(self.h5s[i].cycle)>length:
length=len(self.h5s[i].cycle)
if len(self.h5s[i].age)>length:
length=len(self.h5s[i].age)
for i in xrange(len(data)):
for j in xrange(length-len(data[i])):
data[i].append(3.14159265) #identifier number
write(self.preprocName,header,dcols,data,sldir=self.filepath)
else:
print 'Reading preprocessor files'
preprocTable=ascii_table(self.preprocName,self.filepath)
for i in xrange(len(self.h5s)-1):
print self.h5s[i+1].filename
dat=preprocTable.get(self.h5s[i+1].filename+'-cyc')
dat1=[]
for j in xrange(len(dat)):
if dat[j]!=3.14159265:
dat1.append(dat[j])
dat=dat1
for j in xrange(len(dat)):
dat[j]=str(int(dat[j]))
for k in xrange(10-len(dat[j])):
dat[j]='0'+dat[j]
for j in xrange(len(dat)):
self.cycles.append(dat[j])
self.h5s[i+1].cycle=dat
dat=preprocTable.get(self.h5s[i+1].filename+'-age')
dat1=[]
for j in xrange(len(dat)):
if dat[j]!=3.14159265:
dat1.append(dat[j])
dat=dat1
self.h5s[i+1].age=dat
for j in xrange(len(dat)):
self.ages.append(dat[j])
try:
self.cycles = sorted(self.cycles, cmp=self.numeric_compare)
except TypeError:
print "There was a problem sorting the cycles. You may have problems later. Please consider reloading(h5T) and trying again"
try:
self.ages = sorted(self.ages, cmp=self.numeric_compare)
except TypeError:
None
print self.h5sStarted
t2=t.time()
print "Time: "+str(t2-self.t1)
def run(self):
self.cycles.extend(self.h5s[0].cycle)
self.ages.extend(self.h5s[0].age)
self.hattrs = self.h5s[0].hattr
self.cattrs = self.h5s[0].cattr
self.Tables = self.h5s[0].Table
self.dcols = self.h5s[0].dcol
self.cycle_header = self.h5s[0].cycle_header #This string handles the name of the cycle
try:
self.A = self.h5s[0].A[0]
except IndexError:
print "Sorry, there is no A vector. This can cause problems for reading abundances. Continue..."
try:
self.Z = self.h5s[0].Z[0]
except IndexError:
print "Sorry, there is no Z vector. This can cause problems for reading abundances. Continue... "
try:
self.isomeric_states = self.h5s[0].isomeric_state[0]
except IndexError:
print "Sorry, there is no isomeric state vector. Continue..."
new = self.h5s[0].new # This boolean handles the changes to the cycle nomenclature format
if self.filename.endswith(os.sep):
b = str(self.filename)+str(self.preprocName)
else:
b = str(self.filename)+os.sep+str(self.preprocName)
if self.preprocExists:
preprocTable=ascii_table(self.preprocName,self.filename)
if int(preprocTable.hattrs[0])<len(self.h5files):
self.preprocExists=False
print 'A File was added, rewriteing preprocessor file'
if self.preprocExists:
for i in xrange(len(self.h5files)):
if os.path.basename(self.h5files[i])+'-cyc' not in preprocTable.dcols and self.preprocExists:
print 'A File was renamed, rewriteing preprocessor file'
print preprocTable.dcols[i], os.path.basename(self.h5files[i])+'-cyc'
self.preprocExists=False
if not self.preprocExists and os.path.exists(b):
os.system('rm '+b)
# create list of isotopes stored in this h5 file
try:
for x in xrange(len(self.Tables[0])):
if self.isomeric_states[x] ==1:
self.isotopes.append(self.isos[int(self.Tables[1][x])]+'-' +str(int(self.Tables[0][x])))
else:
self.isotopes.append(self.isos[int(self.Tables[1][x])]+'-' +str(int(self.Tables[0][x]))+\
self.isomerDelimiter+str(self.isomeric_states[x]-1))
except IndexError:
print 'This file does not contain any tables. Isotopic data must be contained elsewhere.'
t1 = time.time()
# create list of elements stored in this h5 file
asaved=''
for atmp in self.Z:
if atmp != asaved:
self.elements.append(self.isos[int(atmp)])
asaved=atmp
thread_list = []
print(self.h5s[0].filename)
for x in xrange(len(self.h5files)-1):
thread_list.append(self.h5s.append(h5File(self.h5files[x+1],False, new)))
print(self.h5s[x+1].filename)
if not self.preprocExists:
self.h5s[x+1].start()
self.h5s[x+1].join()
self.h5sStarted[x+1]=True
#self.h5s[x+1].run()
#print('Active '+ str(threading.active_count()))
# Wait until the threads are done.
#for thread in self.h5s:
# print(thread)
# thread.join()
if not self.preprocExists:
for x in xrange(len(self.h5files)-1):
self.cycles.extend(self.h5s[x+1].cycle)
self.ages.extend(self.h5s[x+1].age)
header=[str(len(self.h5files)),'This is a preprocessor file for the directory: '+str(self.filename),\
'At the time of the creation of this file there were '+str(len(self.h5files))+\
' h5 files.']
try:
self.cycles = sorted(self.cycles, cmp=self.numeric_compare)
except TypeError:
print "There was a problem sorting the cycles. You may have problems later. Please consider reloading(h5T) and trying again"
try:
self.ages = sorted(self.ages, cmp=self.numeric_compare)
except TypeError:
None
print 'Writeing preprocessor files'
data=[]
dcols=[]
length=0
for i in xrange(len(self.h5s)):
print self.h5s[i].filename.rpartition('/')[2]
dcols.append(os.path.basename(self.h5s[i].filename)+'-cyc')
dcols.append(os.path.basename(self.h5s[i].filename)+'-age')
data.append(self.h5s[i].cycle)
data.append(self.h5s[i].age)
if len(self.h5s[i].cycle)>length:
length=len(self.h5s[i].cycle)
if len(self.h5s[i].age)>length:
length=len(self.h5s[i].age)
for i in xrange(len(data)):
for j in xrange(length-len(data[i])):
data[i].append(3.14159265)
write(self.preprocName,header,dcols,data,sldir=self.filename)
else:
print 'Reading preprocessor files'
preprocTable=ascii_table(self.preprocName,self.filename)
for i in xrange(len(self.h5s)-1):
dat=preprocTable.get(os.path.basename(self.h5s[i+1].filename)+'-cyc')
dat1=[]
for j in xrange(len(dat)):
if dat[j]!=3.14159265:
dat1.append(dat[j])
dat=dat1
for j in xrange(len(dat)):
dat[j]=str(int(dat[j]))
for k in xrange(10-len(dat[j])):
dat[j]='0'+dat[j]
for j in xrange(len(dat)):
self.cycles.append(dat[j])
self.h5s[i+1].cycle=dat
dat=preprocTable.get(os.path.basename(self.h5s[i+1].filename)+'-age')
dat1=[]
for j in xrange(len(dat)):
if dat[j]!=3.14159265:
dat1.append(dat[j])
dat=dat1
self.h5s[i+1].age=dat
for j in xrange(len(dat)):
self.ages.append(dat[j])
try:
self.cycles = sorted(self.cycles, cmp=self.numeric_compare)
except TypeError:
print "There was a problem sorting the cycles. You may have problems later. Please consider reloading(h5T) and trying again"
try:
self.ages = sorted(self.ages, cmp=self.numeric_compare)
except TypeError:
None
print 'File search complete.'
t2 = time.time()
print "Total duration is " + str(t2-t1) + " seconds."
return
def continue_h5s(self): #tis is equivilent to the run in h5t.py
if debug:
print "continue_h5s"
self.cycles.extend(self.h5s[0].cycle)
self.ages.extend(self.h5s[0].age)
self.hattrs = self.h5s[0].hattr
self.cattrs = self.h5s[0].cattr
self.Tables = self.h5s[0].Table
self.dcols = self.h5s[0].dcol
self.cycle_header = self.h5s[0].cycle_header #This string handles the name of the cycle
new = self.h5s[0].new # This boolean handles the changes to the cycle nomenclature format
#preproc stuff
if self.filepath.endswith(os.sep):
b = str(self.filepath)+self.preprocName
else:
b = str(self.filepath)+os.sep+self.preprocName
if self.preprocExists:
preprocTable=ascii_table(self.preprocName,self.filepath)
if int(preprocTable.hattrs[0])<len(self.h5files):
self.preprocExists=False
print 'A File was added, rewriteing preprocessor file'
if self.preprocExists:
for i in xrange(len(self.h5files)):
if self.h5files[i]+'-cyc' not in preprocTable.dcols and self.preprocExists:
print 'A File was renamed, rewriteing preprocessor file'
self.preprocExists=False
if not self.preprocExists and os.path.exists(b):
os.system('rm '+b)
# create list of isotopes stored in this h5 file
try:
for x in xrange(len(self.Tables[0])):
self.isotopes.append([self.isos[int(self.Tables[1][x])],str(int(self.Tables[0][x]))])
#print 'new file: ', new, self.isotopes
except IndexError:
print self.Tables, self.h5s[0].Table
self.t1 = t.time()
print "continueing"
if len(self.filepaths) > 1:
for x in range(len(self.filepaths)-1):
self.h5s.append(h5File(self.filepaths[x+1],False, new))
if not self.preprocExists:
self.h5sStarted[x+1]=True
self.h5s[-1].start()
self.connect(self.h5s[-1], qc.SIGNAL('finished()'), self.add_data)
if not self.preprocExists:
print "all done?"
self.connect(self, qc.SIGNAL('finished()'), self.all_done)
else:
self.all_done()
