def main():
"""
NAME
odp_dcs_magic.py
DESCRIPTION
converts ODP discrete sample format files to magic_measurements format files
SYNTAX
odp_dsc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-A : don't average replicate measurements
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-A" in args: noave=1
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
else:
samp_file=dir_path+'/'+samp_file
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
spec_file=dir_path+'/'+spec_file
site_file=dir_path+'/'+site_file
meas_file=dir_path+'/'+meas_file
filelist=os.listdir(dir_path) # read in list of files to import
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs=[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
if file[-3:].lower()=='dsc':
print('processing: ',file)
MagRec,SpecRec,SampRec={},{},{}
treatment_type,treatment_value,user="","",""
inst="ODP-SRM"
input=open(dir_path+'/'+file,'r').readlines()
IDs=file.split('_') # splits on underscores
pieces=IDs[0].split('-')
expedition=pieces[0]
location=pieces[1]
if file[0]!='_':
while len(pieces[2])<4:pieces[2]='0'+pieces[2] # pad core to be 3 characters
specimen=""
else:
specimen="test"
for piece in pieces:
specimen=specimen+piece+'-'
specimen=specimen[:-1]
alt_spec=IDs[1] # alternate specimen is second field in field name
# set up specimen record for Er_specimens table
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_sample_name']=specimen
SpecRec['er_citation_names']=citation
for key in list(SpecRec.keys()):SampRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
SpecRec['er_specimen_name']=specimen
SampRec['er_specimen_names']=specimen
for key in list(SpecRec.keys()):MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names']=user
MagRec['magic_method_codes']='LT-NO'
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]=0.
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
SpecRec['er_specimen_alternatives']=alt_spec
vol=7e-6 # assume 7 cc samples
datestamp=input[1].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
date=mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]
MagRec["measurement_date"]=date
for k in range(len(input)):
fields= input[k].split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="AF"
if "Anhysteretic Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-I'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="ARM"
if "Isothermal Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-IRM'
inst=inst+':ODP-IMP' # measured on shipboard ASC IMPULSE magnetizer
treatment_type="IRM"
if "treatment_value" in fields[0]:
values=fields[1].split(',')
value=values[0]
if value!=" \n":
if treatment_type=="AF":
treatment_value=float(value)*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif treatment_type=="IRM":
treatment_value=float(value)*1e-3
MagRec["treatment_dc_field"]='%8.3e'%(treatment_value) # IRM treat mT => T
if treatment_type=="ARM":
treatment_value=float(value)*1e-3
dc_value=float(values[1])*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
MagRec["treatment_dc_field"]='%8.3e'%(dc_value) # DC mT => T
if 'user' in fields[0]:
user=fields[-1]
MagRec["er_analyst_mail_names"]=user
if 'sample_orientation' in fields[0]:
MagRec["measurement_description"]=fields[-1]
MagRec["measurement_standard"]='u' # assume all data are "good"
if 'sample_area' in fields[0]: vol=float(fields[1])*1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids']=fields[1] # run number is the LIMS measurement number
MagRec['external_database_names']='LIMS'
if input[k][0:7]=='<MULTI>':
rec=input[k+1].split(',') # list of data
for item in rec:
items=item.split('=')
if items[0].strip()=='demag_level' and treatment_value=="" :
treat= float(items[1])
if treat!=0:
MagRec['magic_method_codes']='LT-AF-Z'
inst=inst+':ODP-SRM-AF'
MagRec["treatment_ac_field"]=treat*1e-3 # AF demag in treat mT => T
if items[0].strip()=='inclination_w_tray_w_bkgrd': MagRec['measurement_inc']=items[1]
if items[0].strip()=='declination_w_tray_w_bkgrd': MagRec['measurement_dec']=items[1]
if items[0].strip()=='intensity_w_tray_w_bkgrd': MagRec['measurement_magn_moment']='%8.3e'%(float(items[1])*vol) # convert intensity from A/m to Am^2 using vol
if items[0].strip()=='x_stdev':MagRec['measurement_x_sd']=items[1]
if items[0].strip()=='y_stdev':MagRec['measurement_y_sd']=items[1]
if items[0].strip()=='z_stdev':MagRec['measurement_sd_z']=items[1]
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
MagOuts=pmag.sort_diclist(MagRecs,'treatment_ac_field')
for MagRec in MagOuts:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec["treatment_ac_field"]) # convert to string
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print('samples stored in ',samp_file)
pmag.magic_write(samp_file,SampRecs,'er_samples')
print('specimens stored in ',spec_file)
Fixed=pmag.measurements_methods(MagOuts,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print('data stored in ',meas_file)
def main():
"""
NAME
odp_dcs_magic.py
DESCRIPTION
converts ODP discrete sample format files to magic_measurements format files
SYNTAX
odp_dsc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-A : don't average replicate measurements
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num = pmag.get_version()
meas_file = 'magic_measurements.txt'
spec_file = 'er_specimens.txt'
samp_file = 'er_samples.txt'
site_file = 'er_sites.txt'
ErSpecs, ErSamps, ErSites, ErLocs, ErCits = [], [], [], [], []
MagRecs = []
citation = "This study"
dir_path, demag = '.', 'NRM'
args = sys.argv
noave = 0
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-A" in args: noave = 1
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsp' in args:
ind = args.index("-Fsp")
spec_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = dir_path + '/' + args[ind + 1]
ErSamps, file_type = pmag.magic_read(samp_file)
else:
samp_file = dir_path + '/' + samp_file
if '-LP' in args:
ind = args.index("-LP")
codelist = args[ind + 1]
codes = codelist.split(':')
if "AF" in codes:
demag = 'AF'
if '-dc' not in args: methcode = "LT-AF-Z"
if '-dc' in args: methcode = "LT-AF-I"
if "T" in codes:
demag = "T"
if '-dc' not in args: methcode = "LT-T-Z"
if '-dc' in args: methcode = "LT-T-I"
if "I" in codes:
methcode = "LP-IRM"
if "S" in codes:
demag = "S"
methcode = "LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield = labfield
ans = input("DC lab field for ARM step: [50uT] ")
if ans == "":
arm_labfield = 50e-6
else:
arm_labfield = float(ans) * 1e-6
ans = input("temperature for total trm step: [600 C] ")
if ans == "":
trm_peakT = 600 + 273 # convert to kelvin
else:
trm_peakT = float(ans) + 273 # convert to kelvin
if "G" in codes: methcode = "LT-AF-G"
if "D" in codes: methcode = "LT-AF-D"
if "TRM" in codes:
demag = "T"
trm = 1
if demag == "T" and "ANI" in codes:
methcode = "LP-AN-TRM"
if demag == "AF" and "ANI" in codes:
methcode = "LP-AN-ARM"
if labfield == 0: labfield = 50e-6
if peakfield == 0: peakfield = .180
spec_file = dir_path + '/' + spec_file
site_file = dir_path + '/' + site_file
meas_file = dir_path + '/' + meas_file
filelist = os.listdir(dir_path) # read in list of files to import
specimens, samples, sites = [], [], []
MagRecs, SpecRecs, SampRecs = [], [], []
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
if file[-3:].lower() == 'dsc':
print('processing: ', file)
MagRec, SpecRec, SampRec = {}, {}, {}
treatment_type, treatment_value, user = "", "", ""
inst = "ODP-SRM"
input = open(dir_path + '/' + file, 'r').readlines()
IDs = file.split('_') # splits on underscores
pieces = IDs[0].split('-')
expedition = pieces[0]
location = pieces[1]
if file[0] != '_':
while len(pieces[2]) < 4:
pieces[2] = '0' + pieces[2] # pad core to be 3 characters
specimen = ""
else:
specimen = "test"
for piece in pieces:
specimen = specimen + piece + '-'
specimen = specimen[:-1]
alt_spec = IDs[
1] # alternate specimen is second field in field name
# set up specimen record for Er_specimens table
SpecRec['er_expedition_name'] = expedition
SpecRec['er_location_name'] = location
SpecRec['er_site_name'] = specimen
SpecRec['er_sample_name'] = specimen
SpecRec['er_citation_names'] = citation
for key in list(SpecRec.keys()):
SampRec[key] = SpecRec[key]
SampRec['sample_azimuth'] = '0'
SampRec['sample_dip'] = '0'
SampRec['magic_method_codes'] = 'FS-C-DRILL-IODP:SP-SS-C:SO-V'
SpecRec['er_specimen_name'] = specimen
SampRec['er_specimen_names'] = specimen
for key in list(SpecRec.keys()):
MagRec[key] = SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names'] = user
MagRec['magic_method_codes'] = 'LT-NO'
MagRec['magic_software_packages'] = version_num
MagRec["treatment_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"] = 0.
MagRec["treatment_dc_field"] = '0'
MagRec["treatment_dc_field_phi"] = '0'
MagRec["treatment_dc_field_theta"] = '0'
MagRec["measurement_flag"] = 'g' # assume all data are "good"
MagRec["measurement_standard"] = 'u' # assume all data are "good"
MagRec["measurement_csd"] = '' # set csd to blank
SpecRec['er_specimen_alternatives'] = alt_spec
vol = 7e-6 # assume 7 cc samples
datestamp = input[1].split() # date time is second line of file
mmddyy = datestamp[0].split('/') # break into month day year
date = mmddyy[2] + ':' + mmddyy[0] + ":" + mmddyy[
1] + ':' + datestamp[1]
MagRec["measurement_date"] = date
for k in range(len(input)):
fields = input[k].split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst = inst + ':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type = "AF"
if "Anhysteretic Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-I'
inst = inst + ':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type = "ARM"
if "Isothermal Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-IRM'
inst = inst + ':ODP-IMP' # measured on shipboard ASC IMPULSE magnetizer
treatment_type = "IRM"
if "treatment_value" in fields[0]:
values = fields[1].split(',')
value = values[0]
if value != " \n":
if treatment_type == "AF":
treatment_value = float(value) * 1e-3
MagRec[
"treatment_ac_field"] = treatment_value # AF demag in treat mT => T
elif treatment_type == "IRM":
treatment_value = float(value) * 1e-3
MagRec["treatment_dc_field"] = '%8.3e' % (
treatment_value) # IRM treat mT => T
if treatment_type == "ARM":
treatment_value = float(value) * 1e-3
dc_value = float(values[1]) * 1e-3
MagRec[
"treatment_ac_field"] = treatment_value # AF demag in treat mT => T
MagRec["treatment_dc_field"] = '%8.3e' % (
dc_value) # DC mT => T
if 'user' in fields[0]:
user = fields[-1]
MagRec["er_analyst_mail_names"] = user
if 'sample_orientation' in fields[0]:
MagRec["measurement_description"] = fields[-1]
MagRec[
"measurement_standard"] = 'u' # assume all data are "good"
if 'sample_area' in fields[0]:
vol = float(
fields[1]
) * 1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids'] = fields[
1] # run number is the LIMS measurement number
MagRec['external_database_names'] = 'LIMS'
if input[k][0:7] == '<MULTI>':
rec = input[k + 1].split(',') # list of data
for item in rec:
items = item.split('=')
if items[0].strip(
) == 'demag_level' and treatment_value == "":
treat = float(items[1])
if treat != 0:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst = inst + ':ODP-SRM-AF'
MagRec[
"treatment_ac_field"] = treat * 1e-3 # AF demag in treat mT => T
if items[0].strip() == 'inclination_w_tray_w_bkgrd':
MagRec['measurement_inc'] = items[1]
if items[0].strip() == 'declination_w_tray_w_bkgrd':
MagRec['measurement_dec'] = items[1]
if items[0].strip() == 'intensity_w_tray_w_bkgrd':
MagRec['measurement_magn_moment'] = '%8.3e' % (
float(items[1]) * vol
) # convert intensity from A/m to Am^2 using vol
if items[0].strip() == 'x_stdev':
MagRec['measurement_x_sd'] = items[1]
if items[0].strip() == 'y_stdev':
MagRec['measurement_y_sd'] = items[1]
if items[0].strip() == 'z_stdev':
MagRec['measurement_sd_z'] = items[1]
MagRec['magic_instrument_codes'] = inst
MagRec['measurement_number'] = '1'
MagRec['measurement_positions'] = ''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
MagOuts = pmag.sort_diclist(MagRecs, 'treatment_ac_field')
for MagRec in MagOuts:
MagRec["treatment_ac_field"] = '%8.3e' % (MagRec["treatment_ac_field"]
) # convert to string
pmag.magic_write(spec_file, SpecRecs, 'er_specimens')
if len(SampRecs) > 0:
SampOut, keys = pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file, SampOut, 'er_samples')
print('samples stored in ', samp_file)
pmag.magic_write(samp_file, SampRecs, 'er_samples')
print('specimens stored in ', spec_file)
Fixed = pmag.measurements_methods(MagOuts, noave)
pmag.magic_write(meas_file, Fixed, 'magic_measurements')
print('data stored in ', meas_file)
def main(command_line=True, **kwargs):
"""
NAME
iodp_dscr_magic.py
DESCRIPTION
converts ODP LIMS discrete sample format files to magic_measurements format files
SYNTAX
iodp_descr_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-A : don't average replicate measurements
INPUTS
IODP discrete sample .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
csv_file=''
MagRecs,Specs=[],[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
# get command line args
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if "-A" in args: noave=1
if '-f' in args:
ind=args.index("-f")
csv_file=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path # rename dir_path after input_dir_path is set
noave = kwargs.get('noave', 0) # default (0) is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
# format variables
meas_file= os.path.join(output_dir_path, meas_file)
if csv_file=="":
filelist=os.listdir(input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist=[csv_file]
# parsing the data
file_found = False
for file in filelist: # parse each file
if file[-3:].lower()=='csv':
file_found = True
print 'processing: ',file
input=open(file,'rU').readlines()
keys=input[0].replace('\n','').split(',') # splits on underscores
interval_key="Offset (cm)"
demag_key="Demag level (mT)"
offline_demag_key="Treatment Value (mT or °C)"
offline_treatment_type="Treatment type"
run_key="Test No."
if "Inclination background + tray corrected (deg)" in keys: inc_key="Inclination background + tray corrected (deg)"
if "Inclination background & tray corrected (deg)" in keys: inc_key="Inclination background & tray corrected (deg)"
if "Declination background + tray corrected (deg)" in keys: dec_key="Declination background + tray corrected (deg)"
if "Declination background & tray corrected (deg)" in keys: dec_key="Declination background & tray corrected (deg)"
if "Intensity background + tray corrected (A/m)" in keys: int_key="Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys: int_key="Intensity background & tray corrected (A/m)"
type="Type"
sect_key="Sect"
half_key="A/W"
# need to add volume_key to LORE format!
if "Sample volume (cm^3)" in keys:volume_key="Sample volume (cm^3)"
if "Sample volume (cc)" in keys:volume_key="Sample volume (cc)"
if "Sample volume (cm³)" in keys:volume_key="Sample volume (cm³)"
for line in input[1:]:
InRec={}
for k in range(len(keys)):InRec[keys[k]]=line.split(',')[k]
inst="IODP-SRM"
MagRec={}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
offsets=InRec[interval_key].split('.') # maintain consistency with er_samples convention of using top interval
if len(offsets)==1:
offset=int(offsets[0])
else:
offset=int(offsets[0])-1
#interval=str(offset+1)# maintain consistency with er_samples convention of using top interval
interval=str(offset)# maintain consistency with er_samples convention of using top interval
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[type]+"-"+InRec[sect_key]+'_'+InRec[half_key]+'_'+interval
if specimen not in Specs:Specs.append(specimen)
MagRec['er_expedition_name']=expedition
MagRec['er_location_name']=location
MagRec['er_site_name']=specimen
MagRec['er_citation_names']=citation
MagRec['er_specimen_name']=specimen
MagRec['er_sample_name']=specimen
MagRec['er_site_name']=specimen
# set up measurement record - default is NRM
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='0' # assume all data are "good"
volume=InRec[volume_key]
MagRec["magic_method_codes"]='LT-NO'
sort_by='treatment_ac_field' # set default to AF demag
if InRec[demag_key]!="0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
if sort_by =="treatment_ac_field":
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
else:
MagRec["treatment_ac_field"]=str(treatment_value)# AF demag in treat mT => T
elif offline_treatment_type in InRec.keys() and InRec[offline_treatment_type]!="":
if "Lowrie" in InRec['Comments']:
MagRec['magic_method_codes'] = 'LP-IRM-3D'
treatment_value=float(InRec[offline_demag_key].strip('"'))+273. # convert C => K
MagRec["treatment_temp"]=treatment_value
MagRec["treatment_ac_field"]="0"
sort_by='treatment_temp'
elif 'Isothermal' in InRec[offline_treatment_type]:
MagRec['magic_method_codes'] = 'LT-IRM'
treatment_value=float(InRec[offline_demag_key].strip('"'))*1e-3 # convert mT => T
MagRec["treatment_dc_field"]=treatment_value
MagRec["treatment_ac_field"]="0"
sort_by='treatment_dc_field'
MagRec["measurement_standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_key in InRec.keys():
run_number=InRec[run_key]
MagRec['external_database_ids']=run_number
MagRec['external_database_names']='LIMS'
else:
MagRec['external_database_ids']=""
MagRec['external_database_names']=''
MagRec['measurement_description']='sample orientation: '+InRec['Sample orientation']
MagRec['measurement_inc']=InRec[inc_key].strip('"')
MagRec['measurement_dec']=InRec[dec_key].strip('"')
intens= InRec[int_key].strip('"')
MagRec['measurement_magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if not file_found:
print "No .csv files were found"
return False, "No .csv files were found"
MagOuts=[]
for spec in Specs:
Speclist=pmag.get_dictitem(MagRecs,'er_specimen_name',spec,'T')
sorted=pmag.sort_diclist(Speclist,sort_by)
for rec in sorted:
for key in rec.keys(): rec[key]=str(rec[key])
MagOuts.append(rec)
Fixed=pmag.measurements_methods(MagOuts,noave)
Out,keys=pmag.fillkeys(Fixed)
if pmag.magic_write(meas_file,Out,'magic_measurements'):
print 'data stored in ',meas_file
return True, meas_file
else:
print 'no data found. bad magfile?'
return False, 'no data found. bad magfile?'
