def __init__(self, filename, header):
FileReader.__init__(self, filename, header)
""" Keep track of number of locations and cost of prescriptions
"""
self.__prescription_location_count = 0
self.__prescription_total_cost = 0.0
""" Plugin a method to lookup postcode from practice code
Maintain a dictionary with outer postcodes as keys and actual spend as values
"""
self.__postcode_lookup_method = None
self.__post_codes_by_actual_spend = {}
""" Plugin a method to lookup region from postcode
Compile a regex to look for a particular prescription
Track the cost and prescription count nationally
"""
self.__region_lookup_method = None
self.__average_price_per_region = {}
self.__prescription_count_by_region = {}
self.__prescription_regex = re.compile(r'^Flucloxacillin\s*\w*')
self.__cost_per_prescription = 0
self.__prescription_count = 0
""" Keep track of various anti-depressant prescriptions
"""
self.__antidepressant_prescriptions = 'Fluoxetine Hydrochloride Citalopram Hydrobromide Paroxetine' \
' Hydrochloride Sertraline Hydrochloride Duloxetine Hydrochloride' \
' Venlafaxine Mirtazapine'
self.__antidepressant_prescription_count_by_region = {}
def __init__(self, path):
FileReader.__init__(self, path)
acqs_name = glob.glob( os.path.join(os.path.dirname(path), 'acqu*s') )
self.npts = 1
#First build a dictonary for each dimension in the experiment
self.acq={}
for dim in acqs_name:
if 'acqus' in dim: n = 1
if 'acqu2s' in dim: n = 2
if 'acqu3s' in dim: n = 3
if 'acqu4s' in dim: n = 4
if 'acqu5s' in dim: n = 5
dic = {}
for line in open( dim, 'r' ):
if 'TD=' in line:
dic['TD'] = int(split(line)[-1])
if n==1:
dic['TD'] /= 2
self.pts_in_fid = dic['TD']
else: self.npts *= dic['TD']
elif 'SW_h=' in line: dic['SW_h'] = float(split(line)[-1])
elif 'PULPROG=' in line: dic['PULPROG']= split(line)[-1]
elif 'DTYPA=' in line: dic['DTYPA'] = { 0:'i', 1:'d'}[ int(split(line)[-1])]
elif 'BYTORDA=' in line: dic['BYTORDA']={ 0:'<', 1:'>'}[ int(split(line)[-1])]
elif 'GRPDLY=' in line: dic['GRPDLY']= int(split(line)[-1])
elif 'DECIM=' in line: dic['DECIM']= int(split(line)[-1])
elif 'DSPFVS=' in line: dic['DSPFVS']= int(split(line)[-1])
self.acq[n]=dic
#Now build the format string for reading in the data
self.fmt = '%s%d%s' % (self.acq[1]['BYTORDA'],self.pts_in_fid*2, self.acq[1]['DTYPA'])
#In bruker ser, each block must end at integer of 1024
#check to see what correction is needed
blk_sz = calcsize(self.fmt)
if blk_sz % 1024: self.cor = 1024 - (blk_sz % 1024) #correction needed
else: self.cor = 0 #no correction
#Now prepare for the dreaded digital filtering
if ('GRPDLY' in self.acq[1] ) and self.acq[1]['GRPDLY'] != -1:
digshift = acq[1]['GRPDLY']
else:
indx1,indx2 = self.acq[1]['DECIM'], self.acq[1]['DSPFVS'] - 10
digshift = _brukdigital[indx1][indx2]
self.roll_npts = int(floor(digshift))+1
self.phase = digshift - self.roll_npts
def __init__(self, path):
FileReader.__init__(self, path)
self.binary = open( self.path, 'r' )
self._glb_header_sz = struct.unpack( 'I', self.binary.read(struct.calcsize('I')))[0]
self._local_header_sz = 128
self.binary.seek( self._glb_header_sz )
self.read_headers( )
def __init__(self, path):
FileReader.__init__(self, path)
self.binary = open(self.path, 'r')
self._glb_header_sz = struct.unpack(
'I', self.binary.read(struct.calcsize('I')))[0]
self._local_header_sz = 128
self.binary.seek(self._glb_header_sz)
self.read_headers()
def __init__(self, path):
FileReader.__init__(self, path)
acqs_name = glob.glob(os.path.join(os.path.dirname(path), 'acqu*s'))
self.npts = 1
#First build a dictonary for each dimension in the experiment
self.acq = {}
for dim in acqs_name:
if 'acqus' in dim: n = 1
if 'acqu2s' in dim: n = 2
if 'acqu3s' in dim: n = 3
if 'acqu4s' in dim: n = 4
if 'acqu5s' in dim: n = 5
dic = {}
for line in open(dim, 'r'):
if 'TD=' in line:
dic['TD'] = int(split(line)[-1])
if n == 1:
dic['TD'] /= 2
self.pts_in_fid = dic['TD']
else:
self.npts *= dic['TD']
elif 'SW_h=' in line:
dic['SW_h'] = float(split(line)[-1])
elif 'PULPROG=' in line:
dic['PULPROG'] = split(line)[-1]
elif 'DTYPA=' in line:
dic['DTYPA'] = {0: 'i', 1: 'd'}[int(split(line)[-1])]
elif 'BYTORDA=' in line:
dic['BYTORDA'] = {0: '<', 1: '>'}[int(split(line)[-1])]
elif 'GRPDLY=' in line:
dic['GRPDLY'] = int(split(line)[-1])
elif 'DECIM=' in line:
dic['DECIM'] = int(split(line)[-1])
elif 'DSPFVS=' in line:
dic['DSPFVS'] = int(split(line)[-1])
self.acq[n] = dic
#Now build the format string for reading in the data
self.fmt = '%s%d%s' % (self.acq[1]['BYTORDA'], self.pts_in_fid * 2,
self.acq[1]['DTYPA'])
#In bruker ser, each block must end at integer of 1024
#check to see what correction is needed
blk_sz = calcsize(self.fmt)
if blk_sz % 1024: self.cor = 1024 - (blk_sz % 1024) #correction needed
else: self.cor = 0 #no correction
#Now prepare for the dreaded digital filtering
if ('GRPDLY' in self.acq[1]) and self.acq[1]['GRPDLY'] != -1:
digshift = acq[1]['GRPDLY']
else:
indx1, indx2 = self.acq[1]['DECIM'], self.acq[1]['DSPFVS'] - 10
digshift = _brukdigital[indx1][indx2]
self.roll_npts = int(floor(digshift)) + 1
self.phase = digshift - self.roll_npts
def __init__(self, fn):
FileReader.__init__(self, fn)
self.state = self.STATE_NORMAL
def __init__(self, filename, header):
FileReader.__init__(self, filename, header)
def __init__(self, filename, header):
FileReader.__init__(self, filename, header)
self.__location_to_search = None
self.__location_count = 0
self.__practice_code_to_postcode = {}
def __init__(self, header, filename):
FileReader.__init__(self, header, filename)
self.__postcode_to_region_lookup = {}
self.__regions = []
def __init__(self, fn):
FileReader.__init__(self, fn)
self.state = self.STATE_NORMAL
