/
storage.py
149 lines (123 loc) · 4.92 KB
/
storage.py
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import tables as pytables
from numarray import array, NewAxis
from units import G_0
def read_legend_values(table):
legend_by = getattr(table.attrs,'legend_by',None)
if legend_by:
return sorted(set([ x[legend_by] for x in table.iterrows() ]))
else:
return [ None ]
def read_scan_value(table,legend_value=None):
legend_by = getattr(table.attrs,'legend_by',None)
def rows():
if legend_by and legend_value:
return table.where(getattr(table.cols,legend_by) == legend_value)
else:
return table.iterrows()
scan_by = table.attrs.scan_by
energy = array([ x[scan_by] for x in rows() ])
return energy
def read_energy(table,legend_value):
legend_by = getattr(table.attrs,'legend_by',None)
def rows():
if legend_by:
return table.where(getattr(table.cols,legend_by) == legend_value)
else:
return table.iterrows()
energy = array([ x['energy'] for x in rows() ])
return energy
def read_transmission(table,legend_value,read_err=True):
legend_by = getattr(table.attrs,'legend_by',None)
def rows():
if legend_by:
return table.where(getattr(table.cols,legend_by) == legend_value)
else:
return table.iterrows()
if hasattr(table.cols,'samples'):
samples = array([ abs(x['samples']) for x in rows() ])
transmission_sum = array([ x['transmission_sum'] for x in rows() ])
if len(transmission_sum.shape) > len(samples.shape):
samples = samples[:,NewAxis]
transmission_avg = transmission_sum / samples
if read_err and hasattr(table.cols,'transmission_sqsum'):
transmission_sqsum = array([ x['transmission_sqsum'] for x in rows() ])
transmission_var = abs(transmission_sqsum/samples - transmission_avg**2)
# abs is needed for cases where var==0 mathematically, and therefore possibly
# var<0 numerically
transmission_stdev = transmission_var**0.5
transmission_err = transmission_stdev/(samples**0.5)
else:
transmission_err = None
else:
transmission_avg = array([ x['transmission'] for x in rows() ])
if read_err and hasattr(intable.cols,'transmission_err'):
transmission_err = array([ x['transmission_err'] for x in rows() ])
else:
transmission_err = None
return transmission_avg, transmission_err
def read_samples(table):
samples = [ x['samples'] for x in table.iterrows() if x['samples'] > 1 ]
return min(samples),max(samples)
def read_conductance(table,legend_value,read_err=True):
legend_by = getattr(table.attrs,'legend_by',None)
def rows():
if legend_by:
return table.where(getattr(table.cols,legend_by) == legend_value)
else:
return table.iterrows()
conductance_avg = array([ x['conductance'] for x in rows() ]) * G_0
if read_err and hasattr(table.cols,'conductance_err'):
conductance_err = array([ x['conductance_err'] for x in rows() ]) * G_0
else:
conductance_err = None
return conductance_avg, conductance_err
def get_timestamp():
import time
return time.strftime("%Y%m%d-%H%M%S",time.localtime())
def get_directory():
import os
return os.getenv('DDIR','.')
def get_pathnames(prefix = '.*',suffix = '.h5'):
import sys, os, re
namepatterns = []
pathnames = []
ddir = get_directory()
for arg in sys.argv[1:]:
if arg.endswith('.py'):
pass
elif arg.startswith('-'):
pass
elif arg.endswith(suffix):
pathnames += [arg]
else:
namepatterns += [arg]
if pathnames == [] and namepatterns == []:
namepatterns = [r'.*']
for namepattern in namepatterns:
regexp = re.compile(prefix+"-........-......-"+namepattern+suffix.replace('.',r'\.')+"$")
# regexp = re.compile(prefix+r"-........-......-"+namefragment+suffix.replace('.',r'\.')+"$")
names = [ n for n in os.listdir(ddir) if regexp.match(n) ]
if len(names) == 0:
raise LookupError, "No "+prefix+"-...-" + namepattern + suffix + " file found in directory '" + ddir + "'"
names.sort()
pathnames = [ ddir + "/" + name for name in names ]
return pathnames
def get_pathname(*args,**kwargs):
names = get_pathnames(*args,**kwargs)
if len(names) != 1:
print names
raise "Exactly one file should be selected!"
return names[0]
def create_new_file(prefix = None,suffix = '.h5'):
import sys
if len(sys.argv) == 1:
pathname = 'tryout.h5'
h5file = pytables.openFile(pathname,mode='w')
else:
datapath = get_directory()
filename = get_timestamp() + "-" + sys.argv[1] + ".h5"
if prefix:
filename = prefix + '-' + filename
pathname = datapath + "/" + filename
h5file = pytables.openFile(pathname,mode='a')
return h5file