def convert(**kwargs):
version_num = pmag.get_version()
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # Loc outfile
mag_file = kwargs.get('mag_file', '') #required
location = kwargs.get('location', 'unknown')
site = kwargs.get('site', '')
samp_con = kwargs.get('samp_con', '1')
specnum = int(kwargs.get('specnum', 0))
timezone = kwargs.get('timestamp', 'US/Pacific')
append = kwargs.get('append', False)
noave = kwargs.get('noave', False) # default False means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume: volume = 0.025**3 #default volume is a 2.5 cm cube, translated to meters cubed
else: volume *= 1e-6 #convert cm^3 to m^3
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=int(samp_con.split("-")[1])
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=int(samp_con.split("-")[1])
samp_con="7"
else: Z=1
# format variables
mag_file = os.path.join(input_dir_path, mag_file)
if not os.path.isfile(mag_file):
print("%s is not a BGC file"%mag_file)
return False, 'You must provide a BCG format file'
# Open up the BGC file and read the header information
print('mag_file in bgc_magic', mag_file)
pre_data = open(mag_file, 'r')
line = pre_data.readline()
line_items = line.split(' ')
specimen = line_items[2]
specimen = specimen.replace('\n', '')
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split('\t')
azimuth = float(line_items[1])
dip = float(line_items[2])
bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
lon = line_items[5]
lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep='\t', header=3, index_col=False)
cart = np.array([data['X'], data['Y'], data['Z']]).transpose()
direction = pmag.cart2dir(cart).transpose()
data['dir_dec'] = direction[0]
data['dir_inc'] = direction[1]
data['magn_moment'] = old_div(direction[2], 1000) # the data are in EMU - this converts to Am^2
data['magn_volume'] = old_div((old_div(direction[2], 1000)), volume) # EMU - data converted to A/m
# Configure the magic_measurements table
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for rowNum, row in data.iterrows():
MeasRec,SpecRec,SampRec,SiteRec,LocRec = {},{},{},{},{}
if specnum!=0:
sample=specimen[:specnum]
else:
sample=specimen
if site=='':
site=pmag.parse_site(sample,samp_con,Z)
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['volume'] = volume
SpecRec['analysts']=user
SpecRec['citations'] = 'This study'
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['azimuth'] = azimuth
SampRec['dip'] = dip
SampRec['bed_dip_direction'] = sample_bed_azimuth
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['analysts']=user
SampRec['citations'] = 'This study'
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec['analysts']=user
SiteRec['citations'] = 'This study'
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['analysts']=user
LocRec['citations'] = 'This study'
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['description'] = 'Date: ' + str(row['Date']) + ' Time: ' + str(row['Time'])
if '.' in row['Date']: datelist = row['Date'].split('.')
elif '/' in row['Date']: datelist = row['Date'].split('/')
elif '-' in row['Date']: datelist = row['Date'].split('-')
else: print("unrecogized date formating on one of the measurement entries for specimen %s"%specimen); datelist=['','','']
if ':' in row['Time']: timelist = row['Time'].split(':')
else: print("unrecogized time formating on one of the measurement entries for specimen %s"%specimen); timelist=['','','']
datelist[2]='19'+datelist[2] if len(datelist[2])<=2 else datelist[2]
dt=":".join([datelist[1],datelist[0],datelist[2],timelist[0],timelist[1],timelist[2]])
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
MeasRec["timestamp"] = timestamp
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = rowNum
MeasRec["specimen"] = specimen
MeasRec["treat_ac_field"] = '0'
if row['DM Val'] == '0':
meas_type = "LT-NO"
elif int(row['DM Type']) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row['DM Val'])
MeasRec["treat_ac_field"] = '%8.3e' %(treat*1e-3) # convert from mT to tesla
elif int(row['DM Type']) == -1:
meas_type = "LT-T-Z"
treat = float(row['DM Val'])
MeasRec["treat_temp"] = '%8.3e' % (treat+273.) # temp in kelvin
else:
print("measurement type unknown:", row['DM Type'], " in row ", rowNum)
MeasRec["magn_moment"] = str(row['magn_moment'])
MeasRec["magn_volume"] = str(row['magn_volume'])
MeasRec["dir_dec"] = str(row['dir_dec'])
MeasRec["dir_inc"] = str(row['dir_inc'])
MeasRec['method_codes'] = meas_type
MeasRec['dir_csd'] = '0.0' # added due to magic.write error
MeasRec['meas_n_orient'] = '1' # added due to magic.write error
MeasRecs.append(MeasRec.copy())
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.write_table_to_file('specimens', custom_name=spec_file, append=append)
con.write_table_to_file('samples', custom_name=samp_file, append=append)
con.write_table_to_file('sites', custom_name=site_file, append=append)
con.write_table_to_file('locations', custom_name=loc_file, append=append)
meas_file = con.write_table_to_file('measurements', custom_name=meas_file, append=append)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
demag = "N"
version_num = pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
mag_file = kwargs.get('mag_file', '')
site = kwargs.get('site', 'unknown')
expedition = kwargs.get('expedition', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', False) # default means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = kwargs.get('volume', 2.5**
3) * 1e-6 #default volume is a 2.5cm cube
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
if not mag_file:
print("-W- You must provide an IODP_jr6 format file")
return False, "You must provide an IODP_jr6 format file"
mag_file = os.path.join(input_dir_path, mag_file)
# validate variables
if not os.path.isfile(mag_file):
print(
'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'
.format(mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(
mag_file)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
infile = open(temp, 'r')
lines = infile.readlines()
infile.close()
try:
os.remove(temp)
except OSError:
print("problem with temp file")
citations = "This Study"
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for line in lines:
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
line = line.split()
spec_text_id = line[0]
specimen = spec_text_id
for dem in ['-', '_']:
if dem in spec_text_id:
sample = dem.join(spec_text_id.split(dem)[:-1])
break
location = expedition + site
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['volume'] = volume
SpecRec['citations'] = citations
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['citations'] = citations
SampRec['azimuth'] = line[6]
SampRec['dip'] = line[7]
SampRec['bed_dip_direction'] = line[8]
SampRec['bed_dip'] = line[9]
SampRec['method_codes'] = meth_code
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations'] = citations
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['citations'] = citations
LocRec['expedition_name'] = expedition
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['specimen'] = specimen
MeasRec["citations"] = citations
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["treat_ac_field"] = '0'
x = float(line[4])
y = float(line[3])
negz = float(line[2])
cart = np.array([x, y, -negz]).transpose()
direction = pmag.cart2dir(cart).transpose()
expon = float(line[5])
magn_volume = direction[2] * (10.0**expon)
moment = magn_volume * volume
MeasRec["magn_moment"] = str(moment)
MeasRec["magn_volume"] = str(
magn_volume) #str(direction[2] * (10.0 ** expon))
MeasRec["dir_dec"] = '%7.1f' % (direction[0])
MeasRec["dir_inc"] = '%7.1f' % (direction[1])
step = line[1]
if step == 'NRM':
meas_type = "LT-NO"
elif step[0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(step[2:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif step[0:2] == 'TD':
meas_type = "LT-T-Z"
treat = float(step[2:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
elif step[0:3] == 'ARM': #
meas_type = "LT-AF-I"
treat = float(row['step'][3:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
MeasRec["treat_dc_field"] = '%8.3e' % (50e-6
) # assume 50uT DC field
MeasRec[
"measurement_description"] = 'Assumed DC field - actual unknown'
elif step[0] == 'A':
meas_type = "LT-AF-Z"
treat = float(step[1:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif step[0] == 'T':
meas_type = "LT-T-Z"
treat = float(step[1:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
elif step[0:3] == 'IRM': #
meas_type = "LT-IRM"
treat = float(step[3:])
MeasRec["treat_dc_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
else:
print('unknown treatment type for ', row)
return False, 'unknown treatment type for ', row
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec.copy())
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return (True, meas_file)
def convert(**kwargs):
# initialize some stuff
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
demag="N"
trm=0
irm=0
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # site outfile
magfile = kwargs.get('magfile', '')
labfield = int(kwargs.get('labfield', 0)) *1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = int(kwargs.get('peakfield', 0))*1e-3
specnum = int(kwargs.get('specnum', 0))
location = kwargs.get('location', 'unknown')
noave = kwargs.get('noave', False) # 0 means "do average", is default
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
arm_labfield = kwargs.get('arm_labfield', 50e-6)
trm_peakT = kwargs.get('trm_peakT', 600+273)
mv = kwargs.get('mv', 'v')
# format/organize variables
if magfile:
try:
infile=open(os.path.join(input_dir_path,magfile),'r')
except IOError:
print("bad mag file name")
return False, "bad mag file name"
else:
print("mag_file field is required option")
return False, "mag_file field is required option"
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("naming convention option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("naming convention option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
else: Z=1
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if not labfield: methcode="LT-AF-Z"
if labfield: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if not labfield: methcode="LT-T-Z"
if labfield: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
irmunits="mT"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
# should use arm_labfield and trm_peakT as well, but these values are currently never asked for
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 coil:
methcode="LP-IRM"
irmunits="V"
if coil not in ["1","2","3"]:
print('not a valid coil specification')
return False, 'not a valid coil specification'
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
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
version_num=pmag.get_version()
# find start of data:
DIspec=[]
Data=infile.readlines()
infile.close()
for k in range(len(Data)):
rec=Data[k].split()
if len(rec)<=2: continue
if rec[0].upper()=="LAT:" and len(rec)>3: lat,lon=rec[1],rec[3]; continue
elif rec[0].upper()=="ID": continue
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
specimen=rec[0]
if specnum!=0:
sample=specimen[:specnum]
else:
sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
if mv=='v':
volume = float(rec[12])
if volume > 0: susc_chi_volume='%10.3e'%(old_div((float(rec[11])*1e-5),volume)) #convert to SI (assume Bartington, 10-5 SI)
else: susc_chi_volume='%10.3e'%(float(rec[11])*1e-5) #convert to SI (assume Bartington, 10-5 SI)
else:
mass = float(rec[12])
if mass > 0: susc_chi_mass='%10.3e'%(old_div((float(rec[11])*1e-5),mass)) #convert to SI (assume Bartington, 10-5 SI)
else: susc_chi_mass='%10.3e'%(float(rec[11])*1e-5) #convert to SI (assume Bartington, 10-5 SI)
print((specimen,sample,site,samp_con,Z))
#fill tables besides measurements
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
if mv=='v':
SpecRec["susc_chi_volume"]=susc_chi_volume
SpecRec["volume"]=volume
else:
SpecRec["susc_chi_mass"]=susc_chi_mass
SpecRec["mass"]=mass
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
#fill measurements
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
meas_type="LT-NO"
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["specimen"]=specimen
# if mv=='v': MeasRec["susc_chi_volume"]=susc_chi_volume
# else: MeasRec["susc_chi_mass"]=susc_chi_mass
MeasRec["dir_csd"]=rec[3]
MeasRec["magn_moment"]='%10.3e'% (float(rec[4])*1e-7)
MeasRec["dir_dec"]=rec[5]
MeasRec["dir_inc"]=rec[6]
MeasRec["citations"]="This study"
if demag=="AF":
if methcode != "LP-AN-ARM":
MeasRec["treat_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MeasRec["treat_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z"
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
else:
meas_type="LT-AF-I"
ipos=int(treat[0])-1
MeasRec["treat_dc_field_phi"]='%7.1f' %(dec[ipos])
MeasRec["treat_dc_field_theta"]='%7.1f'% (inc[ipos])
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="T":
if rec[1][0]==".":rec[1]="0"+rec[1]
treat=rec[1].split('.')
if len(treat)==1:treat.append('0')
MeasRec["treat_temp"]='%8.3e' % (float(rec[1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MeasRec["treat_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
meas_type="LT-T-I" # trm acquisition experiment
MeasRec['method_codes']=meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
# initialize defaults
version_num = pmag.get_version()
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', False) # default is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
volume = kwargs.get('volume', 2.5**
3) * 1e-6 #default volume is a 2.5cm cube
# format variables
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, citations = False, "This Study"
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for fin in filelist: # parse each file
if fin[-3:].lower() == 'csv':
file_found = True
print('processing: ', fin)
indata = open(fin, 'r').readlines()
keys = indata[0].replace('\n',
'').split(',') # splits on underscores
keys = [k.strip('"') for k in keys]
interval_key = "Offset (cm)"
if "Treatment Value (mT or \xc2\xb0C)" in keys:
demag_key = "Treatment Value (mT or \xc2\xb0C)"
elif "Treatment Value" in keys:
demag_key = "Treatment Value"
elif "Treatment Value (mT or °C)" in keys:
demag_key = "Treatment Value (mT or °C)"
elif "Demag level (mT)" in keys:
demag_key = "Demag level (mT)"
else:
print("couldn't find demag level")
if "Treatment type" in keys: treatment_type = "Treatment type"
elif "Treatment Type" in keys: treatment_type = "Treatment Type"
else: treatment_type = ""
run_key = "Test No."
if "Inclination background + tray corrected (deg)" in keys:
inc_key = "Inclination background + tray corrected (deg)"
elif "Inclination background & tray corrected (deg)" in keys:
inc_key = "Inclination background & tray corrected (deg)"
elif "Inclination background & tray corrected (deg)" in keys:
inc_key = "Inclination background & tray corrected (deg)"
elif "Inclination background & drift corrected (deg)" in keys:
inc_key = "Inclination background & drift corrected (deg)"
else:
print("couldn't find inclination")
if "Declination background + tray corrected (deg)" in keys:
dec_key = "Declination background + tray corrected (deg)"
elif "Declination background & tray corrected (deg)" in keys:
dec_key = "Declination background & tray corrected (deg)"
elif "Declination background & tray corrected (deg)" in keys:
dec_key = "Declination background & tray corrected (deg)"
elif "Declination background & drift corrected (deg)" in keys:
dec_key = "Declination background & drift corrected (deg)"
else:
print("couldn't find declination")
if "Intensity background + tray corrected (A/m)" in keys:
int_key = "Intensity background + tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys:
int_key = "Intensity background & tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys:
int_key = "Intensity background & tray corrected (A/m)"
elif "Intensity background & drift corrected (A/m)" in keys:
int_key = "Intensity background & drift corrected (A/m)"
else:
print("couldn't find magnetic moment")
type_val = "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)"
elif "Sample volume (cc)" in keys:
volume_key = "Sample volume (cc)"
elif "Sample volume (cm³)" in keys:
volume_key = "Sample volume (cm³)"
elif "Sample volume (cm\xc2\xb3)" in keys:
volume_key = "Sample volume (cm\xc2\xb3)"
else:
volume_key = ""
for line in indata[1:]:
InRec = {}
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
for k in range(len(keys)):
InRec[keys[k]] = line.split(',')[k].strip('"')
inst = "IODP-SRM"
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_val] + "-" + InRec[
sect_key] + '-' + InRec[half_key] + '-' + str(
InRec[interval_key])
sample = expedition + '-' + location + '-' + InRec[
'Core'] + InRec[type_val]
site = expedition + '-' + location
if volume_key in list(InRec.keys()): volume = InRec[volume_key]
if not InRec[dec_key].strip(
""" " ' """) or not InRec[inc_key].strip(""" " ' """):
print("No dec or inc found for specimen %s, skipping" %
specimen)
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['volume'] = volume
SpecRec['citations'] = citations
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['citations'] = citations
SampRec['azimuth'] = '0'
SampRec['dip'] = '0'
SampRec['method_codes'] = 'FS-C-DRILL-IODP:SO-V'
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else ""
for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations'] = citations
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['citations'] = citations
LocRec['expedition_name'] = expedition
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['specimen'] = specimen
# set up measurement record - default is NRM
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"] = '0'
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
MeasRec["quality"] = 'g' # assume all data are "good"
MeasRec["standard"] = 'u' # assume all data are "good"
MeasRec["dir_csd"] = '0' # assume all data are "good"
MeasRec["method_codes"] = 'LT-NO'
sort_by = 'treat_ac_field' # set default to AF demag
if treatment_type in list(
InRec.keys()) and InRec[treatment_type] != "":
if "AF" in InRec[treatment_type].upper():
MeasRec['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
MeasRec["treat_ac_field"] = str(
treatment_value) # AF demag in treat mT => T
elif "T" in InRec[treatment_type].upper():
MeasRec['method_codes'] = 'LT-T-Z'
inst = inst + ':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value = float(InRec[demag_key].strip(
'"')) + 273 # convert C => K
MeasRec["treat_temp"] = str(treatment_value)
elif "Lowrie" in InRec['Comments']:
MeasRec['method_codes'] = 'LP-IRM-3D'
treatment_value = float(InRec[demag_key].strip(
'"')) + 273. # convert C => K
MeasRec["treat_temp"] = str(treatment_value)
MeasRec["treat_ac_field"] = "0"
sort_by = 'treat_temp'
elif 'Isothermal' in InRec[treatment_type]:
MeasRec['method_codes'] = 'LT-IRM'
treatment_value = float(InRec[demag_key].strip(
'"')) * 1e-3 # convert mT => T
MeasRec["treat_dc_field"] = str(treatment_value)
MeasRec["treat_ac_field"] = "0"
sort_by = 'treat_dc_field'
elif InRec[demag_key] != "0" and InRec[
demag_key] != "": #Assume AF if there is no Treatment typ info
MeasRec['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
MeasRec[
"treat_ac_field"] = treatment_value # AF demag in treat mT => T
MeasRec["standard"] = 'u' # assume all data are "good"
vol = float(volume)
if run_key in list(InRec.keys()):
run_number = InRec[run_key]
MeasRec['external_database_ids'] = {'LIMS': run_number}
else:
MeasRec['external_database_ids'] = ""
MeasRec['description'] = 'sample orientation: ' + InRec[
'Sample orientation']
MeasRec['dir_inc'] = InRec[inc_key].strip('"')
MeasRec['dir_dec'] = InRec[dec_key].strip('"')
intens = InRec[int_key].strip('"')
MeasRec['magn_moment'] = '%8.3e' % (
float(intens) * vol
) # convert intensity from A/m to Am^2 using vol
MeasRec['instrument_codes'] = inst
MeasRec['treat_step_num'] = '1'
MeasRec['meas_n_orient'] = ''
MeasRecs.append(MeasRec)
if not file_found:
print("No .csv files were found")
return False, "No .csv files were found"
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasSort = sorted(
MeasRecs,
lambda x, y=None: int(round(float(x[sort_by]) - float(y[sort_by])))
if y != None else 0)
MeasFixed = pmag.measurements_methods3(MeasSort, noave)
MeasOuts, keys = pmag.fillkeys(MeasFixed)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
"""
"""
#get kwargs
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
lat = kwargs.get('lat', 0)
lon = kwargs.get('lon', 0)
specnum = int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
version_num=pmag.get_version()
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("naming convention option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z = 1
# format variables
mag_file = os.path.join(input_dir_path,mag_file)
meas_file = os.path.join(output_dir_path,meas_file)
spec_file = os.path.join(output_dir_path,spec_file)
samp_file = os.path.join(output_dir_path,samp_file)
site_file = os.path.join(output_dir_path,site_file)
# parse data
data=open(mag_file,'r').readlines() # read in data from file
comment=data[0]
line=data[1].strip()
line=line.replace("=","= ") # make finding orientations easier
rec=line.split() # read in sample orientation, etc.
specimen=rec[0]
SpecRecs,SampRecs,SiteRecs,LocRecs,MeasRecs = [],[],[],[],[]
SpecRec,SampRec,SiteRec,LocRec={},{},{},{} # make a sample record
if specnum!=0:
sample=rec[0][:specnum]
else:
sample=rec[0]
if int(samp_con)<6:
site=pmag.parse_site(sample,samp_con,Z)
else:
if 'site' in list(SampRec.keys()):site=ErSampREc['site']
if 'location' in list(SampRec.keys()):location=ErSampREc['location']
az_ind=rec.index('a=')+1
SampRec['sample']=sample
SampRec['description']=comment
SampRec['azimuth']=rec[az_ind]
dip_ind=rec.index('b=')+1
dip=-float(rec[dip_ind])
SampRec['dip']='%7.1f'%(dip)
strike_ind=rec.index('s=')+1
SampRec['bed_dip_direction']='%7.1f'%(float(rec[strike_ind])+90.)
bd_ind=rec.index('d=')+1
SampRec['bed_dip']=rec[bd_ind]
v_ind=rec.index('v=')+1
vol=rec[v_ind][:-3]
date=rec[-2]
time=rec[-1]
SampRec['method_codes']=meth_code
SampRec['site']=site
SampRec['citations']='This study'
SampRec['method_codes']='SO-NO'
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['citations']='This study'
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations']='This study'
SiteRec['lat'] = lat
SiteRec['lon']= lon
LocRec['location'] = location
LocRec['citations']='This study'
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
SpecRecs.append(SpecRec)
SampRecs.append(SampRec)
SiteRecs.append(SiteRec)
LocRecs.append(LocRec)
for k in range(3,len(data)): # read in data
line=data[k]
rec=line.split()
if len(rec)>1: # skip blank lines at bottom
MeasRec={}
MeasRec['description']='Date: '+date+' '+time
MeasRec["citations"]="This study"
MeasRec['software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["specimen"]=specimen
if rec[0]=='NRM':
meas_type="LT-NO"
elif rec[0][0]=='M' or rec[0][0]=='H':
meas_type="LT-AF-Z"
elif rec[0][0]=='T':
meas_type="LT-T-Z"
else:
print("measurement type unknown")
return False, "measurement type unknown"
X=[float(rec[1]),float(rec[2]),float(rec[3])]
Vec=pmag.cart2dir(X)
MeasRec["magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MeasRec["magn_volume"]=rec[4] # A/m
MeasRec["dir_dec"]='%7.1f'%(Vec[0])
MeasRec["dir_inc"]='%7.1f'%(Vec[1])
MeasRec["treat_ac_field"]='0'
if meas_type!='LT-NO':
treat=float(rec[0][1:])
else:
treat=0
if meas_type=="LT-AF-Z":
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif meas_type=="LT-T-Z":
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
MeasRec['method_codes']=meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
#
# initialize variables
#
bed_dip,bed_dip_dir="",""
sclass,lithology,_type="","",""
DecCorr=0.
months=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec']
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', 'FS-FD:SO-POM')
location = kwargs.get('location', 'unknown')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
user = kwargs.get('user', '')
noave = kwargs.get('noave', 0) # default is DO average
ID = kwargs.get('ID', '')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
# format and fix variables acquired from command line sys.argv or input with **kwargs
if specnum!=0:specnum=-specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
Z = 1
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "6" in samp_con:
print('Naming convention option [6] not currently supported')
return False, 'Naming convention option [6] not currently supported'
#Z=1
#try:
# SampRecs,file_type=pmag.magic_read(os.path.join(input_dir_path, 'er_samples.txt'))
#except:
# print("there is no er_samples.txt file in your input directory - you can't use naming convention #6")
# return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
#if file_type == 'bad_file':
# print("there is no er_samples.txt file in your input directory - you can't use naming convention #6")
# return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
#else: Z=1
if not mag_file:
print("mag file is required input")
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samplist=[]
try:
SampRecs,file_type=pmag.magic_read(samp_file)
except:
SampRecs=[]
MeasRecs,SpecRecs,SiteRecs,LocRecs=[],[],[],[]
try:
f=open(mag_file,'br')
input=str(f.read()).strip("b '")
f.close()
except Exception as ex:
print('ex', ex)
print("bad mag file")
return False, "bad mag file"
firstline,date=1,""
d=input.split('\\xcd')
for line in d:
rec=line.split('\\x00')
if firstline==1:
firstline=0
spec,vol="",1
el=51
while line[el:el+1]!="\\": spec=spec+line[el];el+=1
# check for bad sample name
test=spec.split('.')
date=""
if len(test)>1:
spec=test[0]
kk=24
while line[kk]!='\\x01' and line[kk]!='\\x00':
kk+=1
vcc=line[24:kk]
el=10
while rec[el].strip()!='':el+=1
date,comments=rec[el+7],[]
else:
el=9
while rec[el]!='\\x01':el+=1
vcc,date,comments=rec[el-3],rec[el+7],[]
specname=spec.lower()
print('importing ',specname)
el+=8
while rec[el].isdigit()==False:
comments.append(rec[el])
el+=1
while rec[el]=="":el+=1
az=float(rec[el])
el+=1
while rec[el]=="":el+=1
pl=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip_dir=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip=float(rec[el])
el+=1
while rec[el]=="":el+=1
if rec[el]=='\\x01':
bed_dip=180.-bed_dip
el+=1
while rec[el]=="":el+=1
fold_az=float(rec[el])
el+=1
while rec[el]=="":el+=1
fold_pl=rec[el]
el+=1
while rec[el]=="":el+=1
if rec[el]!="" and rec[el]!='\\x02' and rec[el]!='\\x01':
deccorr=float(rec[el])
az+=deccorr
bed_dip_dir+=deccorr
fold_az+=deccorr
if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360.
if az>=360.:az=az-360.
if fold_az>=360.:fold_az=fold_az-360.
else:
deccorr=0
if specnum!=0:
sample=specname[:specnum]
else:
sample=specname
methods=gmeths.split(':')
if deccorr!="0":
if 'SO-MAG' in methods:del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths = reduce(lambda x,y: x+':'+y, methods)
method_codes=meths
site=pmag.parse_site(sample,samp_con,Z) # parse out the site name
SpecRec,SampRec,SiteRec,LocRec={},{},{},{}
SpecRec["specimen"]=specname
SpecRec["sample"]=sample
if vcc.strip()!="":vol=float(vcc)*1e-6 # convert to m^3 from cc
SpecRec["volumne"]='%10.3e'%(vol) #
SpecRec["geologic_classes"]=sclass
SpecRec["lithologies"]=lithology
SpecRec["geologic_types"]=_type
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec["sample"]=sample
SampRec["site"]=site
labaz,labdip=pmag.orient(az,pl,or_con) # convert to labaz, labpl
SampRec["bed_dip"]='%7.1f'%(bed_dip)
SampRec["bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["dip"]='%7.1f'%(labdip)
SampRec["azimuth"]='%7.1f'%(labaz)
SampRec["azimuth_dec_correction"]='%7.1f'%(deccorr)
SampRec["geologic_classes"]=sclass
SampRec["lithologies"]=lithology
SampRec["geologic_types"]=_type
SampRec["method_codes"]=method_codes
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec["geologic_classes"]=sclass
SiteRec["lithologies"]=lithology
SiteRec["geologic_types"]=_type
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRec["geologic_classes"]=sclass
LocRec["lithologies"]=lithology
LocRec["geologic_types"]=_type
LocRecs.append(LocRec)
else:
MeasRec={}
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
meas_type="LT-NO"
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["specimen"]=specname
el,demag=1,''
treat=rec[el]
if treat[-1]=='C':
demag='T'
elif treat!='NRM':
demag='AF'
el+=1
while rec[el]=="":el+=1
MeasRec["dir_dec"]=rec[el]
cdec=float(rec[el])
el+=1
while rec[el]=="":el+=1
MeasRec["dir_inc"]=rec[el]
cinc=float(rec[el])
el+=1
while rec[el]=="":el+=1
gdec=rec[el]
el+=1
while rec[el]=="":el+=1
ginc=rec[el]
el=skip(2,el,rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MeasRec["magn_moment"]='%10.3e'% (float(rec[el])*1e-3) # moment in Am^2 (from emu)
MeasRec["magn_volume"]='%10.3e'% (float(rec[el])*1e-3/vol) # magnetization in A/m
el=skip(2,el,rec) # skip to xsig
MeasRec["magn_x_sigma"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to ysig
MeasRec["magn_y_sigma"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to zsig
MeasRec["magn_z_sigma"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el+=1 # skip to positions
MeasRec["meas_n_orient"]=rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MeasRec['measurement_date']=dstring
MeasRec["instrument_codes"]=inst
MeasRec["analysts"]=user
MeasRec["citations"]="This study"
MeasRec["method_codes"]=meas_type
if demag=="AF":
MeasRec["treat_ac_field"]='%8.3e' %(float(treat[:-2])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MeasRec["treat_dc_field"]='0'
elif demag=="T":
MeasRec["treat_temp"]='%8.3e' % (float(treat[:-1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MeasRec['method_codes']=meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.write_table_to_file('specimens', custom_name=spec_file)
con.write_table_to_file('samples', custom_name=samp_file)
con.write_table_to_file('sites', custom_name=site_file)
con.write_table_to_file('locations', custom_name=loc_file)
con.write_table_to_file('measurements', custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
"""
EXAMPLE DOCSTRING for function (you would usually put the discription here)
Parameters
-----------
user : colon delimited list of analysts (default : "")
magfile : input magnetometer file (required)
Returns
-----------
type - Tuple : (True or False indicating if conversion was sucessful, meas_file name written)
"""
#get parameters from kwargs.get(parameter_name, default_value)
user = kwargs.get('user', '')
magfile = kwargs.get('magfile')
#do any extra formating you need to variables here
#open magfile to start reading data
try:
infile=open(magfile,'r')
except Exception as ex:
print(("bad file path: ", magfile))
return False, "bad file path"
#Depending on the dataset you may need to read in all data here put it in a list of dictionaries or something here. If you do just replace the "for line in infile.readlines():" bellow with "for d in data:" where data is the structure you put your data into
#define the lists that hold each line of data for their respective tables
SpecRecs,SampRecs,SiteRecs,LocRecs,MeasRecs=[],[],[],[],[]
#itterate over the contence of the file
for line in infile.readlines():
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
#extract data from line and put it in variables
#fill this line of the Specimen table using above variables
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['analysts']=user
SpecRecs.append(SpecRec)
#fill this line of the Sample table using above variables
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['analysts']=user
SampRecs.append(SampRec)
#fill this line of the Site table using above variables
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['analysts']=user
SiteRecs.append(SiteRec)
#fill this line of the Location table using above variables
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['analysts']=user
LocRecs.append(LocRec)
#Fill this line of Meas Table using data in line
MeasRec['analysts']=user
MeasRecs.append(MeasRec)
#close your file object so Python3 doesn't throw an annoying warning
infile.close()
#open a Contribution object
con = nb.Contribution(output_dir_path,read_tables=[])
#Create Magic Tables and add to a contribution
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave) #figures out method codes for measuremet data
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
#write to file
con.write_table_to_file('specimens', custom_name=spec_file)
con.write_table_to_file('samples', custom_name=samp_file)
con.write_table_to_file('sites', custom_name=site_file)
con.write_table_to_file('locations', custom_name=loc_file)
meas_file = con.write_table_to_file('measurements', custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # Loc outfile
magfile = kwargs.get('magfile', '')
datafile = kwargs.get('datafile', '')
specnum = int(kwargs.get('specnum', 0))
labfield = int(kwargs.get('labfield', 0)) * 1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = kwargs.get('peakfield', 0)
if peakfield:
peakfield = float(peakfield) * 1e-3
location = kwargs.get('location', '')
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
CR_cooling_times = kwargs.get('CR_cooling_times', None)
noave = kwargs.get('noave', False)
# format and validate variables
if magfile:
try:
infile = open(os.path.join(input_dir_path, magfile), 'r')
except IOError:
print("bad mag file name")
return False, "bad mag file name"
else:
print("mag_file field is required option")
print(__doc__)
return False, "mag_file field is required option"
if specnum != 0:
specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z = int(samp_con.split("-")[1])
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = int(samp_con.split("-")[1])
samp_con = "7"
else:
Z = 1
if codelist:
codes = codelist.split(':')
else:
print("Must select experiment type (-LP option)")
return False, "Must select experiment type (-LP option)"
if "AF" in codes:
demag = 'AF'
LPcode = "LP-DIR-AF"
if "T" in codes:
demag = "T"
if not labfield: LPcode = "LP-DIR-T"
if labfield: LPcode = "LP-PI-TRM"
if "ANI" in codes:
if not labfield:
print("missing lab field option")
return False, "missing lab field option"
LPcode = "LP-AN-TRM"
if "TRM" in codes:
demag = "T"
LPcode = "LP-TRM"
#trm=1
if "CR" in codes:
demag = "T"
# dc should be in the code
if not labfield:
print("missing lab field option")
return False, "missing lab field option"
LPcode = "LP-CR-TRM" # TRM in different cooling rates
if command_line:
ind = sys.argv.index("-LP")
CR_cooling_times = sys.argv[ind + 2].split(",")
version_num = pmag.get_version()
#--------------------------------------
# Read the file
# Assumption:
# 1. different lab protocolsa are in different files
# 2. measurements are in the correct order
#--------------------------------------
Data = {}
line_no = 0
for line in infile.readlines():
line_no += 1
this_line_data = {}
line_no += 1
instcode = ""
if len(line) < 2:
continue
if line[0] == "#": #HUJI way of marking bad data points
continue
rec = line.strip('\n').split()
specimen = rec[0]
date = rec[2].split("/")
hour = rec[3].split(":")
treatment_type = rec[4]
treatment = rec[5].split(".")
dec_core = rec[6]
inc_core = rec[7]
moment_emu = float(rec[-1])
if specimen not in list(Data.keys()):
Data[specimen] = []
# check duplicate treatments:
# if yes, delete the first and use the second
if len(Data[specimen]) > 0:
if treatment == Data[specimen][-1]['treatment']:
del (Data[specimen][-1])
print(
"-W- Identical treatments in file %s magfile line %i: specimen %s, treatment %s ignoring the first. "
% (magfile, line_no, specimen, ".".join(treatment)))
this_line_data = {}
this_line_data['specimen'] = specimen
this_line_data['date'] = date
this_line_data['hour'] = hour
this_line_data['treatment_type'] = treatment_type
this_line_data['treatment'] = treatment
this_line_data['dec_core'] = dec_core
this_line_data['inc_core'] = inc_core
this_line_data['moment_emu'] = moment_emu
this_line_data['azimuth'] = ''
this_line_data['dip'] = ''
this_line_data['bed_dip_direction'] = ''
this_line_data['bed_dip'] = ''
this_line_data['lat'] = ''
this_line_data['lon'] = ''
this_line_data['volume'] = ''
Data[specimen].append(this_line_data)
infile.close()
print("-I- done reading file %s" % magfile)
if datafile:
dinfile = open(datafile)
for line in dinfile.readlines():
data = line.split()
if len(data) < 8 or data[0] == '': continue
elif data[0] in list(Data.keys()):
for i in range(len(Data[data[0]])):
Data[data[0]][i]['azimuth'] = data[1]
Data[data[0]][i]['dip'] = data[2]
try:
Data[data[0]][i]['bed_dip_direction'] = float(
data[3]) + 90
except ValueError:
Data[data[0]][i]['bed_dip_direction'] = ''
Data[data[0]][i]['bed_dip'] = data[4]
Data[data[0]][i]['lat'] = data[5]
Data[data[0]][i]['lon'] = data[6]
Data[data[0]][i]['volume'] = data[7]
else:
print(
"no specimen %s found in magnetometer data file when reading specimen orientation data file, or data file record for specimen too short"
% data[0])
dinfile.close()
#--------------------------------------
# Convert to MagIC
#--------------------------------------
specimens_list = list(Data.keys())
specimens_list.sort()
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for specimen in specimens_list:
for i in range(len(Data[specimen])):
this_line_data = Data[specimen][i]
methcode = ""
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
specimen = this_line_data['specimen']
if specnum != 0:
sample = this_line_data['specimen'][:specnum]
else:
sample = this_line_data['specimen']
site = pmag.parse_site(sample, samp_con, Z)
if not location:
location = site
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['azimuth'] = this_line_data['azimuth']
SampRec['dip'] = this_line_data['dip']
SampRec['bed_dip_direction'] = this_line_data[
'bed_dip_direction']
SampRec['bed_dip'] = this_line_data['bed_dip']
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else ""
for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = this_line_data['lat']
SiteRec['lon'] = this_line_data['lon']
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['lat_n'] = this_line_data['lat']
LocRec['lon_e'] = this_line_data['lon']
LocRec['lat_s'] = this_line_data['lat']
LocRec['lon_w'] = this_line_data['lon']
LocRecs.append(LocRec)
MeasRec['specimen'] = specimen
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["magn_moment"] = '%10.3e' % (
float(this_line_data['moment_emu']) * 1e-3
) # moment in Am^2 (from emu)
MeasRec["dir_dec"] = this_line_data['dec_core']
MeasRec["dir_inc"] = this_line_data['inc_core']
date = this_line_data['date']
hour = this_line_data['hour']
if len(date[2]) < 4 and float(date[2]) >= 70:
yyyy = "19" + date[2]
elif len(date[2]) < 4 and float(date[2]) < 70:
yyyy = "20" + date[2]
else:
yyyy = date[2]
if len(date[0]) == 1:
date[0] = "0" + date[0]
if len(date[1]) == 1:
date[1] = "0" + date[1]
dt = ":".join([date[0], date[1], yyyy, hour[0], hour[1], "0"])
local = pytz.timezone("America/New_York")
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
MeasRec['analysts'] = user
MeasRec["citations"] = "This study"
MeasRec["instrument_codes"] = "HUJI-2G"
MeasRec["quality"] = "g"
MeasRec["meas_n_orient"] = "1"
MeasRec["standard"] = "u"
MeasRec["description"] = ""
#----------------------------------------
# AF demag
# do not support AARM yet
#----------------------------------------
if demag == "AF":
treatment_type = this_line_data['treatment_type']
# demag in zero field
if LPcode != "LP-AN-ARM":
MeasRec["treat_ac_field"] = '%8.3e' % (
float(this_line_data['treatment'][0]) * 1e-3
) # peak field in tesla
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
if treatment_type == "N":
methcode = "LP-DIR-AF:LT-NO"
elif treatment_type == "A":
methcode = "LP-DIR-AF:LT-AF-Z"
else:
print(
"ERROR in treatment field line %i... exiting until you fix the problem"
% line_no)
print(this_line_data)
return False, "ERROR in treatment field line %i... exiting until you fix the problem" % line_no
# AARM experiment
else:
print(
"Dont supprot AARM in HUJI format yet. sorry... do be DONE"
)
MeasRec["method_codes"] = methcode
MeasRec["experiments"] = specimen + ":" + LPcode
MeasRec["treat_step_num"] = "%i" % i
MeasRec["description"] = ""
MeasRecs.append(MeasRec)
#----------------------------------------
# Thermal:
# Thellier experiment: "IZ", "ZI", "IZZI", pTRM checks
# Thermal demag
# Thermal cooling rate experiment
# Thermal NLT
#----------------------------------------
if demag == "T":
treatment = this_line_data['treatment']
treatment_type = this_line_data['treatment_type']
#----------------------------------------
# Thellier experimet
#----------------------------------------
if LPcode == "LP-PI-TRM": # Thelllier experiment
MeasRec["experiments"] = specimen + ":" + LPcode
methcode = LPcode
if treatment_type == "N" or (
(treatment[1] == '0' or treatment[1] == '00')
and float(treatment[0]) == 0):
LT_code = "LT-NO"
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_temp"] = '273.'
elif treatment[1] == '0' or treatment[1] == '00':
LT_code = "LT-T-Z"
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
MeasRec["treat_dc_field"] = '%8.3e' % (0)
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode = "LP-PI-TRM:LP-PI-TRM-ZI"
for j in range(0, i):
if Data[specimen][j]['treatment'][0] == treatment[
0]:
if Data[specimen][j]['treatment'][
1] == '1' or Data[specimen][j][
'treatment'][1] == '10':
methcode = "LP-PI-TRM:LP-PI-TRM-IZ"
else:
methcode = "LP-PI-TRM:LP-PI-TRM-ZI"
elif treatment[1] == '1' or treatment[1] == '10':
LT_code = "LT-T-I"
MeasRec["treat_dc_field"] = '%8.3e' % (
labfield
) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MeasRec["treat_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode = "LP-PI-TRM:LP-PI-TRM-IZ"
for j in range(0, i):
if Data[specimen][j]['treatment'][0] == treatment[
0]:
if Data[specimen][j]['treatment'][
1] == '0' or Data[specimen][j][
'treatment'][1] == '00':
methcode = "LP-PI-TRM:LP-PI-TRM-ZI"
else:
methcode = "LP-PI-TRM:LP-PI-TRM-IZ"
elif treatment[1] == '2' or treatment[1] == '20':
LT_code = "LT-PTRM-I"
MeasRec["treat_dc_field"] = '%8.3e' % (
labfield
) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MeasRec["treat_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
methcode = "LP-PI-TRM:LP-PI-TRM-IZ"
else:
print(
"ERROR in treatment field line %i... exiting until you fix the problem"
% line_no)
return False, "ERROR in treatment field line %i... exiting until you fix the problem" % line_no
MeasRec["method_codes"] = LT_code + ":" + methcode
MeasRec["treat_step_num"] = "%i" % i
MeasRec["description"] = ""
MeasRecs.append(MeasRec)
#----------------------------------------
# demag experimet
#----------------------------------------
if LPcode == "LP-DIR-T":
MeasRec["experiments"] = specimen + ":" + LPcode
methcode = LPcode
if treatment_type == "N":
LT_code = "LT-NO"
else:
LT_code = "LT-T-Z"
methcode = LPcode + ":" + "LT-T-Z"
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
MeasRec["treat_dc_field"] = '%8.3e' % (0)
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
MeasRec["method_codes"] = LT_code + ":" + methcode
MeasRec["treat_step_num"] = "%i" % i
MeasRec["description"] = ""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# ATRM measurements
# The direction of the magnetization is used to determine the
# direction of the lab field.
#----------------------------------------
if LPcode == "LP-AN-TRM":
MeasRec["experiments"] = specimen + ":" + LPcode
methcode = LPcode
if float(treatment[1]) == 0:
MeasRec["method_codes"] = "LP-AN-TRM:LT-T-Z"
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
MeasRec["treat_dc_field"] = '0'
else:
if float(treatment[1]) == 7:
# alteration check
methcode = "LP-AN-TRM:LT-PTRM-I"
MeasRec["treat_step_num"] = '7' # -z
else:
MeasRec["method_codes"] = "LP-AN-TRM:LT-T-I"
inc = float(MeasRec["dir_inc"])
dec = float(MeasRec["dir_dec"])
if abs(inc) < 45 and (dec < 45 or dec > 315): # +x
tdec, tinc = 0, 0
MeasRec["treat_step_num"] = '1'
if abs(inc) < 45 and (dec < 135 and dec > 45):
tdec, tinc = 90, 0
MeasRec["treat_step_num"] = '2' # +y
if inc > 45:
tdec, tinc = 0, 90
MeasRec["treat_step_num"] = '3' # +z
if abs(inc) < 45 and (dec < 225 and dec > 135):
tdec, tinc = 180, 0
MeasRec["treat_step_num"] = '4' # -x
if abs(inc) < 45 and (dec < 315 and dec > 225):
tdec, tinc = 270, 0
MeasRec["treat_step_num"] = '5' # -y
if inc < -45:
tdec, tinc = 0, -90
MeasRec["treat_step_num"] = '6' # -z
MeasRec["treat_dc_field_phi"] = '%7.1f' % (tdec)
MeasRec["treat_dc_field_theta"] = '%7.1f' % (tinc)
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
MeasRec["treat_dc_field"] = '%8.3e' % (labfield)
MeasRec["description"] = ""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# NLT measurements
# or TRM acquisistion experiment
#----------------------------------------
if LPcode == "LP-TRM":
MeasRec["experiments"] = specimen + ":" + LPcode
MeasRec["method_codes"] = "LP-TRM:LT-T-I"
if float(treatment[1]) == 0:
labfield = 0
else:
labfield = float(float(treatment[1])) * 1e-6
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
MeasRec["treat_dc_field"] = '%8.3e' % (
labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MeasRec["treat_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
MeasRec["treat_step_num"] = "%i" % i
MeasRec["description"] = ""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# Cooling rate experiments
#----------------------------------------
if LPcode == "LP-CR-TRM":
index = int(treatment[1][0])
#print index,"index"
#print CR_cooling_times,"CR_cooling_times"
#print CR_cooling_times[index-1]
#print CR_cooling_times[0:index-1]
if index == 7 or index == 70: # alteration check as final measurement
meas_type = "LT-PTRM-I:LP-CR-TRM"
CR_cooling_time = CR_cooling_times[-1]
else:
meas_type = "LT-T-I:LP-CR-TRM"
CR_cooling_time = CR_cooling_times[index - 1]
MeasRec["method_codes"] = meas_type
MeasRec["experiments"] = specimen + ":" + LPcode
MeasRec["treat_temp"] = '%8.3e' % (
float(treatment[0]) + 273.) # temp in kelvin
MeasRec["treat_dc_field"] = '%8.3e' % (
labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MeasRec["treat_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
MeasRec["treat_step_num"] = "%i" % index
MeasRec[
"description"] = "cooling_rate" + ":" + CR_cooling_time + ":" + "K/min"
#MeasRec["description"]="%.1f minutes per cooling time"%int(CR_cooling_time)
MeasRecs.append(MeasRec)
#continue
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
demag="N"
version_num=pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
mag_file = kwargs.get('mag_file', '')
site = kwargs.get('site', 'unknown')
expedition = kwargs.get('expedition', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', False) # default means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = kwargs.get('volume', 2.5**3)*1e-6#default volume is a 2.5cm cube
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
if not mag_file:
print("-W- You must provide an IODP_jr6 format file")
return False, "You must provide an IODP_jr6 format file"
mag_file = os.path.join(input_dir_path, mag_file)
# validate variables
if not os.path.isfile(mag_file):
print('The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(mag_file)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
infile = open(temp, 'r')
lines = infile.readlines()
infile.close()
try: os.remove(temp)
except OSError: print("problem with temp file")
citations="This Study"
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for line in lines:
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
line = line.split()
spec_text_id = line[0]
specimen = spec_text_id
for dem in ['-','_']:
if dem in spec_text_id:
sample=dem.join(spec_text_id.split(dem)[:-1]); break
location = expedition + site
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['volume'] = volume
SpecRec['citations']=citations
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['citations']=citations
SampRec['azimuth']=line[6]
SampRec['dip']=line[7]
SampRec['bed_dip_direction']=line[8]
SampRec['bed_dip']=line[9]
SampRec['method_codes']=meth_code
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations']= citations
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['citations']=citations
LocRec['expedition_name']=expedition
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['specimen']=specimen
MeasRec["citations"]=citations
MeasRec['software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["treat_ac_field"]='0'
x = float(line[4])
y = float(line[3])
negz = float(line[2])
cart=np.array([x,y,-negz]).transpose()
direction = pmag.cart2dir(cart).transpose()
expon = float(line[5])
magn_volume = direction[2] * (10.0**expon)
moment = magn_volume * volume
MeasRec["magn_moment"]=str(moment)
MeasRec["magn_volume"]=str(magn_volume)#str(direction[2] * (10.0 ** expon))
MeasRec["dir_dec"]='%7.1f'%(direction[0])
MeasRec["dir_inc"]='%7.1f'%(direction[1])
step = line[1]
if step == 'NRM':
meas_type="LT-NO"
elif step[0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(step[2:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif step[0:2] == 'TD':
meas_type="LT-T-Z"
treat=float(step[2:])
MeasRec["treat_temp"]='%8.3e'%(treat+273.) # temp in kelvin
elif step[0:3]=='ARM': #
meas_type="LT-AF-I"
treat=float(row['step'][3:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
MeasRec["treat_dc_field"]='%8.3e' %(50e-6) # assume 50uT DC field
MeasRec["measurement_description"]='Assumed DC field - actual unknown'
elif step[0] == 'A':
meas_type="LT-AF-Z"
treat=float(step[1:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif step[0] == 'T':
meas_type="LT-T-Z"
treat=float(step[1:])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif step[0:3]=='IRM': #
meas_type="LT-IRM"
treat=float(step[3:])
MeasRec["treat_dc_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
else:
print('unknown treatment type for ',row)
return False, 'unknown treatment type for ',row
MeasRec['method_codes']=meas_type
MeasRecs.append(MeasRec.copy())
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return (True, meas_file)
def convert(**kwargs):
"""
"""
#get kwargs
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
lat = kwargs.get('lat', 0)
lon = kwargs.get('lon', 0)
specnum = int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
version_num = pmag.get_version()
if specnum != 0: specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print(
"naming convention option [4] must be in form 4-Z where Z is an integer"
)
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 1
# format variables
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
# parse data
data = open(mag_file, 'r').readlines() # read in data from file
comment = data[0]
line = data[1].strip()
line = line.replace("=", "= ") # make finding orientations easier
rec = line.split() # read in sample orientation, etc.
specimen = rec[0]
SpecRecs, SampRecs, SiteRecs, LocRecs, MeasRecs = [], [], [], [], []
SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {} # make a sample record
if specnum != 0:
sample = rec[0][:specnum]
else:
sample = rec[0]
if int(samp_con) < 6:
site = pmag.parse_site(sample, samp_con, Z)
else:
if 'site' in list(SampRec.keys()): site = ErSampREc['site']
if 'location' in list(SampRec.keys()): location = ErSampREc['location']
az_ind = rec.index('a=') + 1
SampRec['sample'] = sample
SampRec['description'] = comment
SampRec['azimuth'] = rec[az_ind]
dip_ind = rec.index('b=') + 1
dip = -float(rec[dip_ind])
SampRec['dip'] = '%7.1f' % (dip)
strike_ind = rec.index('s=') + 1
SampRec['bed_dip_direction'] = '%7.1f' % (float(rec[strike_ind]) + 90.)
bd_ind = rec.index('d=') + 1
SampRec['bed_dip'] = rec[bd_ind]
v_ind = rec.index('v=') + 1
vol = rec[v_ind][:-3]
date = rec[-2]
time = rec[-1]
SampRec['method_codes'] = meth_code
SampRec['site'] = site
SampRec['citations'] = 'This study'
SampRec['method_codes'] = 'SO-NO'
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['citations'] = 'This study'
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations'] = 'This study'
SiteRec['lat'] = lat
SiteRec['lon'] = lon
LocRec['location'] = location
LocRec['citations'] = 'This study'
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
SpecRecs.append(SpecRec)
SampRecs.append(SampRec)
SiteRecs.append(SiteRec)
LocRecs.append(LocRec)
for k in range(3, len(data)): # read in data
line = data[k]
rec = line.split()
if len(rec) > 1: # skip blank lines at bottom
MeasRec = {}
MeasRec['description'] = 'Date: ' + date + ' ' + time
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["specimen"] = specimen
if rec[0] == 'NRM':
meas_type = "LT-NO"
elif rec[0][0] == 'M' or rec[0][0] == 'H':
meas_type = "LT-AF-Z"
elif rec[0][0] == 'T':
meas_type = "LT-T-Z"
else:
print("measurement type unknown")
return False, "measurement type unknown"
X = [float(rec[1]), float(rec[2]), float(rec[3])]
Vec = pmag.cart2dir(X)
MeasRec["magn_moment"] = '%10.3e' % (Vec[2]) # Am^2
MeasRec["magn_volume"] = rec[4] # A/m
MeasRec["dir_dec"] = '%7.1f' % (Vec[0])
MeasRec["dir_inc"] = '%7.1f' % (Vec[1])
MeasRec["treat_ac_field"] = '0'
if meas_type != 'LT-NO':
treat = float(rec[0][1:])
else:
treat = 0
if meas_type == "LT-AF-Z":
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif meas_type == "LT-T-Z":
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
version_num = pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file')
input_dir_path = kwargs.get('input_dir_path', dir_path)
if input_dir_path == dir_path:
mag_file = pmag.resolve_file_name(mag_file, dir_path)
input_dir_path = os.path.split(mag_file)[0]
output_dir_path = dir_path
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 2.5)) * 1e-6
timezone = kwargs.get('timestamp', 'UTC')
# format variables
mag_file = os.path.join(input_dir_path, mag_file)
if specnum != 0: specnum = -int(specnum)
if samp_con.startswith("4"):
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif samp_con.startswith("7"):
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 1
#create data holders
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
data = pmag.open_file(mag_file)
# remove garbage/blank lines
data = [i for i in data if len(i) >= 5]
if not len(data):
print('No data')
return
n = 0
end = False
# loop through records
while not end:
first_line = data[n].split()
sampleName = first_line[0]
demagLevel = first_line[2]
date = first_line[3] + ":0:0:0"
n += 2
third_line = data[n].split()
if not third_line[0].startswith('SPEC.ANGLES'):
print('third line of a block should start with SPEC.ANGLES')
print(third_line)
return
specimenAngleDec = third_line[1]
specimenAngleInc = third_line[2]
n += 4
while not data[n].startswith('MEAN'):
n += 1
mean_line = data[n]
Mx = mean_line[1]
My = mean_line[2]
Mz = mean_line[3]
n += 1
precision_line = data[n].split()
if not precision_line[0].startswith('Modulus'):
print('precision line should start with "Modulus"')
return
splitExp = precision_line[2].split('A')
intensityVolStr = precision_line[1] + splitExp[0]
intensityVol = float(intensityVolStr)
# check and see if Prec is too big and messes with the parcing.
precisionStr = ''
if len(precision_line) == 6: #normal line
precisionStr = precision_line[5][0:-1]
else:
precisionStr = precision_line[4][0:-1]
precisionPer = float(precisionStr)
precision = intensityVol * precisionPer / 100
while not data[n].startswith('SPEC.'):
n += 1
specimen_line = data[n].split()
specimenDec = specimen_line[2]
specimenInc = specimen_line[3]
n += 1
geographic_line = data[n]
if not geographic_line.startswith('GEOGR'):
geographic_dec = ''
geographic_inc = ''
else:
geographic_line = geographic_line.split()
geographicDec = geographic_line[1]
geographicInc = geographic_line[2]
# Add data to various MagIC data tables.
specimen = sampleName
if specnum != 0: sample = specimen[:specnum]
else: sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec["citations"] = "This study"
SpecRec["analysts"] = user
SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec["citations"] = "This study"
SampRec["analysts"] = user
SampRec['azimuth'] = specimenAngleDec
sample_dip = str(float(specimenAngleInc) -
90.0) #convert to magic orientation
SampRec['dip'] = sample_dip
SampRec['method_codes'] = meth_code
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec["citations"] = "This study"
SiteRec["analysts"] = user
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec["citations"] = "This study"
LocRec["analysts"] = user
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(date, "%m-%d-%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
MeasRec["specimen"] = specimen
MeasRec["timestamp"] = timestamp
MeasRec['description'] = ''
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["treat_ac_field"] = '0'
if demagLevel == 'NRM':
meas_type = "LT-NO"
elif demagLevel[0] == 'A':
if demagLevel[:2] == 'AD':
treat = float(demagLevel[2:])
else:
treat = float(demagLevel[1:])
meas_type = "LT-AF-Z"
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif demagLevel[0] == 'T':
meas_type = "LT-T-Z"
treat = float(demagLevel[1:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
else:
print("measurement type unknown", demagLevel)
return False, "measurement type unknown"
MeasRec["magn_moment"] = str(intensityVol * volume) # Am^2
MeasRec["magn_volume"] = intensityVolStr # A/m
MeasRec["dir_dec"] = specimenDec
MeasRec["dir_inc"] = specimenInc
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
# ignore all the rest of the special characters. Some data files not consistantly formatted.
n += 1
while ((len(data[n]) <= 5 and data[n] != '')
or data[n].startswith('----')):
n += 1
if n >= len(data):
break
if n >= len(data):
# we're done!
end = True
#end of data while loop
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # Loc outfile
magfile = kwargs.get('magfile', '')
datafile = kwargs.get('datafile', '')
specnum = int(kwargs.get('specnum', 0))
labfield = int(kwargs.get('labfield', 0)) *1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = kwargs.get('peakfield', 0)
if peakfield:
peakfield = float(peakfield)*1e-3
location = kwargs.get('location', '')
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
CR_cooling_times = kwargs.get('CR_cooling_times', None)
noave = kwargs.get('noave', False)
# format and validate variables
if magfile:
try:
infile=open(os.path.join(input_dir_path,magfile),'r')
except IOError:
print("bad mag file name")
return False, "bad mag file name"
else:
print("mag_file field is required option")
print(__doc__)
return False, "mag_file field is required option"
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=int(samp_con.split("-")[1])
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=int(samp_con.split("-")[1])
samp_con="7"
else: Z=1
if codelist:
codes=codelist.split(':')
else:
print("Must select experiment type (-LP option)")
return False, "Must select experiment type (-LP option)"
if "AF" in codes:
demag='AF'
LPcode="LP-DIR-AF"
if "T" in codes:
demag="T"
if not labfield: LPcode="LP-DIR-T"
if labfield: LPcode="LP-PI-TRM"
if "ANI" in codes:
if not labfield:
print("missing lab field option")
return False, "missing lab field option"
LPcode="LP-AN-TRM"
if "TRM" in codes:
demag="T"
LPcode="LP-TRM"
#trm=1
if "CR" in codes:
demag="T"
# dc should be in the code
if not labfield:
print("missing lab field option")
return False, "missing lab field option"
LPcode="LP-CR-TRM" # TRM in different cooling rates
if command_line:
ind=sys.argv.index("-LP")
CR_cooling_times=sys.argv[ind+2].split(",")
version_num=pmag.get_version()
#--------------------------------------
# Read the file
# Assumption:
# 1. different lab protocolsa are in different files
# 2. measurements are in the correct order
#--------------------------------------
Data={}
line_no=0
for line in infile.readlines():
line_no+=1
this_line_data={}
line_no+=1
instcode=""
if len(line)<2:
continue
if line[0]=="#": #HUJI way of marking bad data points
continue
rec=line.strip('\n').split()
specimen=rec[0]
date=rec[2].split("/")
hour=rec[3].split(":")
treatment_type=rec[4]
treatment=rec[5].split(".")
dec_core=rec[6]
inc_core=rec[7]
moment_emu=float(rec[-1])
if specimen not in list(Data.keys()):
Data[specimen]=[]
# check duplicate treatments:
# if yes, delete the first and use the second
if len(Data[specimen])>0:
if treatment==Data[specimen][-1]['treatment']:
del(Data[specimen][-1])
print("-W- Identical treatments in file %s magfile line %i: specimen %s, treatment %s ignoring the first. " %(magfile, line_no, specimen,".".join(treatment)))
this_line_data={}
this_line_data['specimen']=specimen
this_line_data['date']=date
this_line_data['hour']=hour
this_line_data['treatment_type']=treatment_type
this_line_data['treatment']=treatment
this_line_data['dec_core']=dec_core
this_line_data['inc_core']=inc_core
this_line_data['moment_emu']=moment_emu
this_line_data['azimuth']=''
this_line_data['dip']=''
this_line_data['bed_dip_direction']=''
this_line_data['bed_dip']=''
this_line_data['lat']=''
this_line_data['lon']=''
this_line_data['volume']=''
Data[specimen].append(this_line_data)
infile.close()
print("-I- done reading file %s"%magfile)
if datafile:
dinfile = open(datafile)
for line in dinfile.readlines():
data = line.split()
if len(data)<8 or data[0]=='': continue
elif data[0] in list(Data.keys()):
for i in range(len(Data[data[0]])):
Data[data[0]][i]['azimuth'] = data[1]
Data[data[0]][i]['dip'] = data[2]
try: Data[data[0]][i]['bed_dip_direction'] = float(data[3])+90
except ValueError: Data[data[0]][i]['bed_dip_direction'] = ''
Data[data[0]][i]['bed_dip'] = data[4]
Data[data[0]][i]['lat'] = data[5]
Data[data[0]][i]['lon'] = data[6]
Data[data[0]][i]['volume'] = data[7]
else:
print("no specimen %s found in magnetometer data file when reading specimen orientation data file, or data file record for specimen too short"%data[0])
dinfile.close()
#--------------------------------------
# Convert to MagIC
#--------------------------------------
specimens_list=list(Data.keys())
specimens_list.sort()
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for specimen in specimens_list:
for i in range(len(Data[specimen])):
this_line_data=Data[specimen][i]
methcode=""
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
specimen=this_line_data['specimen']
if specnum!=0:
sample=this_line_data['specimen'][:specnum]
else:
sample=this_line_data['specimen']
site=pmag.parse_site(sample,samp_con,Z)
if not location:
location=site
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['azimuth'] = this_line_data['azimuth']
SampRec['dip'] = this_line_data['dip']
SampRec['bed_dip_direction'] = this_line_data['bed_dip_direction']
SampRec['bed_dip'] = this_line_data['bed_dip']
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = this_line_data['lat']
SiteRec['lon'] = this_line_data['lon']
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['lat_n'] = this_line_data['lat']
LocRec['lon_e'] = this_line_data['lon']
LocRec['lat_s'] = this_line_data['lat']
LocRec['lon_w'] = this_line_data['lon']
LocRecs.append(LocRec)
MeasRec['specimen'] = specimen
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["magn_moment"]='%10.3e'% (float(this_line_data['moment_emu'])*1e-3) # moment in Am^2 (from emu)
MeasRec["dir_dec"]=this_line_data['dec_core']
MeasRec["dir_inc"]=this_line_data['inc_core']
date=this_line_data['date']
hour=this_line_data['hour']
if len(date[2])<4 and float(date[2])>=70:
yyyy="19"+date[2]
elif len(date[2])<4 and float(date[2])<70:
yyyy="20"+date[2]
else: yyyy=date[2]
if len (date[0])==1:
date[0]="0"+date[0]
if len (date[1])==1:
date[1]="0"+date[1]
dt=":".join([date[0],date[1],yyyy,hour[0],hour[1],"0"])
local = pytz.timezone("America/New_York")
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
MeasRec['analysts']=user
MeasRec["citations"]="This study"
MeasRec["instrument_codes"]="HUJI-2G"
MeasRec["quality"]="g"
MeasRec["meas_n_orient"]="1"
MeasRec["standard"]="u"
MeasRec["description"]=""
#----------------------------------------
# AF demag
# do not support AARM yet
#----------------------------------------
if demag=="AF":
treatment_type=this_line_data['treatment_type']
# demag in zero field
if LPcode != "LP-AN-ARM":
MeasRec["treat_ac_field"]='%8.3e' %(float(this_line_data['treatment'][0])*1e-3) # peak field in tesla
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
if treatment_type=="N":
methcode="LP-DIR-AF:LT-NO"
elif treatment_type=="A":
methcode="LP-DIR-AF:LT-AF-Z"
else:
print("ERROR in treatment field line %i... exiting until you fix the problem" %line_no)
print(this_line_data)
return False, "ERROR in treatment field line %i... exiting until you fix the problem" %line_no
# AARM experiment
else:
print("Dont supprot AARM in HUJI format yet. sorry... do be DONE")
MeasRec["method_codes"]=methcode
MeasRec["experiments"]=specimen+ ":" + LPcode
MeasRec["treat_step_num"]="%i"%i
MeasRec["description"]=""
MeasRecs.append(MeasRec)
#----------------------------------------
# Thermal:
# Thellier experiment: "IZ", "ZI", "IZZI", pTRM checks
# Thermal demag
# Thermal cooling rate experiment
# Thermal NLT
#----------------------------------------
if demag=="T":
treatment=this_line_data['treatment']
treatment_type=this_line_data['treatment_type']
#----------------------------------------
# Thellier experimet
#----------------------------------------
if LPcode == "LP-PI-TRM" : # Thelllier experiment
MeasRec["experiments"]=specimen+ ":" + LPcode
methcode=LPcode
if treatment_type=="N" or ( (treatment[1]=='0' or treatment[1]=='00') and float(treatment[0])==0):
LT_code="LT-NO"
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_temp"]='273.'
elif treatment[1]=='0' or treatment[1]=='00':
LT_code="LT-T-Z"
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["treat_dc_field"]='%8.3e'%(0)
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
for j in range (0,i):
if Data[specimen][j]['treatment'][0] == treatment[0]:
if Data[specimen][j]['treatment'][1] == '1' or Data[specimen][j]['treatment'][1] == '10':
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
else:
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
elif treatment[1]=='1' or treatment[1]=='10':
LT_code="LT-T-I"
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
for j in range (0,i):
if Data[specimen][j]['treatment'][0] == treatment[0]:
if Data[specimen][j]['treatment'][1] == '0' or Data[specimen][j]['treatment'][1] == '00':
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
else:
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
elif treatment[1]=='2' or treatment[1]=='20':
LT_code="LT-PTRM-I"
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
else:
print("ERROR in treatment field line %i... exiting until you fix the problem" %line_no)
return False, "ERROR in treatment field line %i... exiting until you fix the problem" %line_no
MeasRec["method_codes"]=LT_code+":"+methcode
MeasRec["treat_step_num"]="%i"%i
MeasRec["description"]=""
MeasRecs.append(MeasRec)
#----------------------------------------
# demag experimet
#----------------------------------------
if LPcode == "LP-DIR-T" :
MeasRec["experiments"]=specimen+ ":" + LPcode
methcode=LPcode
if treatment_type=="N":
LT_code="LT-NO"
else:
LT_code="LT-T-Z"
methcode=LPcode+":"+"LT-T-Z"
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["treat_dc_field"]='%8.3e'%(0)
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MeasRec["method_codes"]=LT_code+":"+methcode
MeasRec["treat_step_num"]="%i"%i
MeasRec["description"]=""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# ATRM measurements
# The direction of the magnetization is used to determine the
# direction of the lab field.
#----------------------------------------
if LPcode =="LP-AN-TRM":
MeasRec["experiments"]=specimen+ ":" + LPcode
methcode=LPcode
if float(treatment[1])==0:
MeasRec["method_codes"]="LP-AN-TRM:LT-T-Z"
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MeasRec["treat_dc_field"]='0'
else:
if float(treatment[1])==7:
# alteration check
methcode="LP-AN-TRM:LT-PTRM-I"
MeasRec["treat_step_num"]='7'# -z
else:
MeasRec["method_codes"]="LP-AN-TRM:LT-T-I"
inc=float(MeasRec["dir_inc"]);dec=float(MeasRec["dir_dec"])
if abs(inc)<45 and (dec<45 or dec>315): # +x
tdec,tinc=0,0
MeasRec["treat_step_num"]='1'
if abs(inc)<45 and (dec<135 and dec>45):
tdec,tinc=90,0
MeasRec["treat_step_num"]='2' # +y
if inc>45 :
tdec,tinc=0,90
MeasRec["treat_step_num"]='3' # +z
if abs(inc)<45 and (dec<225 and dec>135):
tdec,tinc=180,0
MeasRec["treat_step_num"]='4' # -x
if abs(inc)<45 and (dec<315 and dec>225):
tdec,tinc=270,0
MeasRec["treat_step_num"]='5'# -y
if inc<-45 :
tdec,tinc=0,-90
MeasRec["treat_step_num"]='6'# -z
MeasRec["treat_dc_field_phi"]='%7.1f' %(tdec)
MeasRec["treat_dc_field_theta"]='%7.1f'% (tinc)
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["description"]=""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# NLT measurements
# or TRM acquisistion experiment
#----------------------------------------
if LPcode == "LP-TRM" :
MeasRec["experiments"]=specimen+ ":" + LPcode
MeasRec["method_codes"]="LP-TRM:LT-T-I"
if float(treatment[1])==0:
labfield=0
else:
labfield=float(float(treatment[1]))*1e-6
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MeasRec["treat_step_num"]="%i"%i
MeasRec["description"]=""
MeasRecs.append(MeasRec)
#continue
#----------------------------------------
# Cooling rate experiments
#----------------------------------------
if LPcode =="LP-CR-TRM":
index=int(treatment[1][0])
#print index,"index"
#print CR_cooling_times,"CR_cooling_times"
#print CR_cooling_times[index-1]
#print CR_cooling_times[0:index-1]
if index==7 or index==70: # alteration check as final measurement
meas_type="LT-PTRM-I:LP-CR-TRM"
CR_cooling_time=CR_cooling_times[-1]
else:
meas_type="LT-T-I:LP-CR-TRM"
CR_cooling_time=CR_cooling_times[index-1]
MeasRec["method_codes"]=meas_type
MeasRec["experiments"]=specimen+ ":" + LPcode
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MeasRec["treat_step_num"]="%i"%index
MeasRec["description"]="cooling_rate"+":"+CR_cooling_time+":"+"K/min"
#MeasRec["description"]="%.1f minutes per cooling time"%int(CR_cooling_time)
MeasRecs.append(MeasRec)
#continue
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
version_num = pmag.get_version()
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # Loc outfile
mag_file = kwargs.get('mag_file') #required
location = kwargs.get('location', 'unknown')
site = kwargs.get('site', '')
samp_con = kwargs.get('samp_con', '1')
specnum = int(kwargs.get('specnum', 0))
timezone = kwargs.get('timestamp', 'US/Pacific')
noave = kwargs.get('noave', False) # default False means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 0.025**3 #default volume is a 2.5 cm cube, translated to meters cubed
else:
volume *= 1e-6 #convert cm^3 to m^3
if specnum != 0:
specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z = int(samp_con.split("-")[1])
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = int(samp_con.split("-")[1])
samp_con = "7"
else:
Z = 1
# format variables
if not os.path.isfile(mag_file):
print("%s is not a BGC file" % mag_file)
return False, 'You must provide a BCG format file'
mag_file = os.path.join(input_dir_path, mag_file)
# Open up the BGC file and read the header information
print('mag_file in bgc_magic', mag_file)
pre_data = open(mag_file, 'r')
line = pre_data.readline()
line_items = line.split(' ')
specimen = line_items[2]
specimen = specimen.replace('\n', '')
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split('\t')
azimuth = float(line_items[1])
dip = float(line_items[2])
bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
lon = line_items[5]
lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep='\t', header=3, index_col=False)
cart = np.array([data['X'], data['Y'], data['Z']]).transpose()
direction = pmag.cart2dir(cart).transpose()
data['dir_dec'] = direction[0]
data['dir_inc'] = direction[1]
data['magn_moment'] = old_div(
direction[2], 1000) # the data are in EMU - this converts to Am^2
data['magn_volume'] = old_div((old_div(direction[2], 1000)),
volume) # EMU - data converted to A/m
# Configure the magic_measurements table
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for rowNum, row in data.iterrows():
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
if site == '':
site = pmag.parse_site(sample, samp_con, Z)
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['volume'] = volume
SpecRec['analysts'] = user
SpecRec['citations'] = 'This study'
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['azimuth'] = azimuth
SampRec['dip'] = dip
SampRec['bed_dip_direction'] = sample_bed_azimuth
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['analysts'] = user
SampRec['citations'] = 'This study'
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec['analysts'] = user
SiteRec['citations'] = 'This study'
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['analysts'] = user
LocRec['citations'] = 'This study'
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['description'] = 'Date: ' + str(row['Date']) + ' Time: ' + str(
row['Time'])
if '.' in row['Date']: datelist = row['Date'].split('.')
elif '/' in row['Date']: datelist = row['Date'].split('/')
elif '-' in row['Date']: datelist = row['Date'].split('-')
else:
print(
"unrecogized date formating on one of the measurement entries for specimen %s"
% specimen)
datelist = ['', '', '']
if ':' in row['Time']: timelist = row['Time'].split(':')
else:
print(
"unrecogized time formating on one of the measurement entries for specimen %s"
% specimen)
timelist = ['', '', '']
datelist[2] = '19' + datelist[2] if len(
datelist[2]) <= 2 else datelist[2]
dt = ":".join([
datelist[1], datelist[0], datelist[2], timelist[0], timelist[1],
timelist[2]
])
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
MeasRec["timestamp"] = timestamp
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = rowNum
MeasRec["specimen"] = specimen
MeasRec["treat_ac_field"] = '0'
if row['DM Val'] == '0':
meas_type = "LT-NO"
elif int(row['DM Type']) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row['DM Val'])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif int(row['DM Type']) == -1:
meas_type = "LT-T-Z"
treat = float(row['DM Val'])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
else:
print("measurement type unknown:", row['DM Type'], " in row ",
rowNum)
MeasRec["magn_moment"] = str(row['magn_moment'])
MeasRec["magn_volume"] = str(row['magn_volume'])
MeasRec["dir_dec"] = str(row['dir_dec'])
MeasRec["dir_inc"] = str(row['dir_inc'])
MeasRec['method_codes'] = meas_type
MeasRec['dir_csd'] = '0.0' # added due to magic.write error
MeasRec['meas_n_orient'] = '1' # added due to magic.write error
MeasRecs.append(MeasRec.copy())
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
# initialize defaults
version_num=pmag.get_version()
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', False) # default is DO average
csv_file = kwargs.get('csv_file', '')
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
volume = kwargs.get('volume', 2.5**3)*1e-6#default volume is a 2.5cm cube
# format variables
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,citations = False,"This Study"
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for fin in filelist: # parse each file
if fin[-3:].lower()=='csv':
file_found = True
print('processing: ',fin)
indata=open(fin,'r').readlines()
keys=indata[0].replace('\n','').split(',') # splits on underscores
keys=[k.strip('"') for k in keys]
interval_key="Offset (cm)"
if "Treatment Value (mT or \xc2\xb0C)" in keys:demag_key="Treatment Value (mT or \xc2\xb0C)"
elif "Treatment Value" in keys:demag_key="Treatment Value"
elif "Treatment Value (mT or °C)" in keys:demag_key="Treatment Value (mT or °C)"
elif "Demag level (mT)" in keys:demag_key="Demag level (mT)"
else: print("couldn't find demag level")
if "Treatment type" in keys:treatment_type="Treatment type"
elif "Treatment Type" in keys:treatment_type="Treatment Type"
else: treatment_type=""
run_key="Test No."
if "Inclination background + tray corrected (deg)" in keys: inc_key="Inclination background + tray corrected (deg)"
elif "Inclination background & tray corrected (deg)" in keys: inc_key="Inclination background & tray corrected (deg)"
elif "Inclination background & tray corrected (deg)" in keys:inc_key="Inclination background & tray corrected (deg)"
elif "Inclination background & drift corrected (deg)" in keys:inc_key="Inclination background & drift corrected (deg)"
else: print("couldn't find inclination")
if "Declination background + tray corrected (deg)" in keys: dec_key="Declination background + tray corrected (deg)"
elif "Declination background & tray corrected (deg)" in keys: dec_key="Declination background & tray corrected (deg)"
elif "Declination background & tray corrected (deg)" in keys:dec_key="Declination background & tray corrected (deg)"
elif "Declination background & drift corrected (deg)" in keys:dec_key="Declination background & drift corrected (deg)"
else: print("couldn't find declination")
if "Intensity background + tray corrected (A/m)" in keys: int_key="Intensity background + tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys: int_key="Intensity background & tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys:int_key="Intensity background & tray corrected (A/m)"
elif "Intensity background & drift corrected (A/m)" in keys:int_key="Intensity background & drift corrected (A/m)"
else: print("couldn't find magnetic moment")
type_val="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)"
elif "Sample volume (cc)" in keys:volume_key="Sample volume (cc)"
elif "Sample volume (cm³)" in keys:volume_key="Sample volume (cm³)"
elif "Sample volume (cm\xc2\xb3)" in keys:volume_key="Sample volume (cm\xc2\xb3)"
else: volume_key=""
for line in indata[1:]:
InRec={}
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
for k in range(len(keys)):InRec[keys[k]]=line.split(',')[k].strip('"')
inst="IODP-SRM"
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_val]+"-"+InRec[sect_key]+'-'+InRec[half_key]+'-'+str(InRec[interval_key])
sample = expedition+'-'+location+'-'+InRec['Core']+InRec[type_val]
site = expedition+'-'+location
if volume_key in list(InRec.keys()): volume=InRec[volume_key]
if not InRec[dec_key].strip(""" " ' """) or not InRec[inc_key].strip(""" " ' """):
print("No dec or inc found for specimen %s, skipping"%specimen)
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['volume'] = volume
SpecRec['citations']=citations
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['citations']=citations
SampRec['azimuth']='0'
SampRec['dip']='0'
SampRec['method_codes']='FS-C-DRILL-IODP:SO-V'
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations']=citations
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['citations']=citations
LocRec['expedition_name']=expedition
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['specimen']=specimen
# set up measurement record - default is NRM
MeasRec['software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["quality"]='g' # assume all data are "good"
MeasRec["standard"]='u' # assume all data are "good"
MeasRec["dir_csd"]='0' # assume all data are "good"
MeasRec["method_codes"]='LT-NO'
sort_by='treat_ac_field' # set default to AF demag
if treatment_type in list(InRec.keys()) and InRec[treatment_type]!="":
if "AF" in InRec[treatment_type].upper():
MeasRec['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
MeasRec["treat_ac_field"]=str(treatment_value) # AF demag in treat mT => T
elif "T" in InRec[treatment_type].upper():
MeasRec['method_codes'] = 'LT-T-Z'
inst=inst+':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec[demag_key].strip('"'))+273 # convert C => K
MeasRec["treat_temp"]=str(treatment_value)
elif "Lowrie" in InRec['Comments']:
MeasRec['method_codes'] = 'LP-IRM-3D'
treatment_value=float(InRec[demag_key].strip('"'))+273. # convert C => K
MeasRec["treat_temp"]=str(treatment_value)
MeasRec["treat_ac_field"]="0"
sort_by='treat_temp'
elif 'Isothermal' in InRec[treatment_type]:
MeasRec['method_codes'] = 'LT-IRM'
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
MeasRec["treat_dc_field"]=str(treatment_value)
MeasRec["treat_ac_field"]="0"
sort_by='treat_dc_field'
elif InRec[demag_key]!="0" and InRec[demag_key]!="": #Assume AF if there is no Treatment typ info
MeasRec['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
MeasRec["treat_ac_field"]=treatment_value # AF demag in treat mT => T
MeasRec["standard"]='u' # assume all data are "good"
vol=float(volume)
if run_key in list(InRec.keys()):
run_number=InRec[run_key]
MeasRec['external_database_ids']={'LIMS':run_number}
else:
MeasRec['external_database_ids']=""
MeasRec['description']='sample orientation: '+InRec['Sample orientation']
MeasRec['dir_inc']=InRec[inc_key].strip('"')
MeasRec['dir_dec']=InRec[dec_key].strip('"')
intens= InRec[int_key].strip('"')
MeasRec['magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
MeasRec['instrument_codes']=inst
MeasRec['treat_step_num']='1'
MeasRec['meas_n_orient']=''
MeasRecs.append(MeasRec)
if not file_found:
print("No .csv files were found")
return False, "No .csv files were found"
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasSort=sorted(MeasRecs, lambda x,y=None: int(round(float(x[sort_by])-float(y[sort_by]))) if y!=None else 0)
MeasFixed=pmag.measurements_methods3(MeasSort,noave)
MeasOuts,keys=pmag.fillkeys(MeasFixed)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
version_num = pmag.get_version()
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # site outfile
location = kwargs.get('location', 'unknown')
dmy_flag = kwargs.get('dmy_flag', False)
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
specnum = -int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '2')
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num = samp_con.split("-")[1]
samp_con = "7"
else:
site_num = 1
try:
DC_FIELD = float(kwargs.get('labfield', 0)) * 1e-6
DC_PHI = float(kwargs.get('phi', 0))
DC_THETA = float(kwargs.get('theta', 0))
except ValueError:
raise ValueError(
'problem with your dc parameters. please provide a labfield in microTesla and a phi and theta in degrees.'
)
noave = kwargs.get('noave', False)
dmy_flag = kwargs.get('dmy_flag', False)
meas_n_orient = kwargs.get('meas_n_orient', '8')
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
# parse data
# Open up the Utrecht file and read the header information
AF_or_T = mag_file.split('.')[-1]
data = open(mag_file, 'r')
line = data.readline()
line_items = line.split(',')
operator = line_items[0]
operator = operator.replace("\"", "")
machine = line_items[1]
machine = machine.replace("\"", "")
machine = machine.rstrip('\n')
# print("operator=", operator)
# print("machine=", machine)
#read in measurement data
line = data.readline()
while line != "END" and line != '"END"':
SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}
line_items = line.split(',')
spec_name = line_items[0]
spec_name = spec_name.replace("\"", "")
# print("spec_name=", spec_name)
free_string = line_items[1]
free_string = free_string.replace("\"", "")
# print("free_string=", free_string)
dec = line_items[2]
# print("dec=", dec)
inc = line_items[3]
# print("inc=", inc)
volume = float(line_items[4])
volume = volume * 1e-6 # enter volume in cm^3, convert to m^3
# print("volume=", volume)
bed_plane = line_items[5]
# print("bed_plane=", bed_plane)
bed_dip = line_items[6]
# print("bed_dip=", bed_dip)
# Configure et er_ tables
if specnum == 0: sample_name = spec_name
else: sample_name = spec_name[:specnum]
site = pmag.parse_site(sample_name, samp_con, site_num)
SpecRec['specimen'] = spec_name
SpecRec['sample'] = sample_name
if volume != 0: SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample_name != "" and sample_name not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample_name
SampRec['azimuth'] = dec
SampRec['dip'] = str(float(inc) - 90)
SampRec['bed_dip_direction'] = bed_plane
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['site'] = site
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
#measurement data
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
while line != '9999':
step = items[0]
step = step.split('.')
step_value = step[0]
step_type = ""
if len(step) == 2:
step_type = step[1]
if step_type == '5':
step_value = items[0]
A = float(items[1])
B = float(items[2])
C = float(items[3])
# convert to MagIC coordinates
Z = -A
X = -B
Y = C
cart = array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
magn_moment = direction[
2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
if volume != 0:
magn_volume = direction[
2] * 1.0e-12 / volume # data volume normalized - converted to A/m
# print("magn_moment=", magn_moment)
# print("magn_volume=", magn_volume)
error = items[4]
date = items[5]
date = date.strip('"').replace(' ', '')
if date.count("-") > 0:
date = date.split("-")
elif date.count("/") > 0:
date = date.split("/")
else:
print("date format seperator cannot be identified")
# print(date)
time = items[6]
time = time.strip('"').replace(' ', '')
time = time.split(":")
# print(time)
dt = date[0] + ":" + date[1] + ":" + date[2] + ":" + time[
0] + ":" + time[1] + ":" + "0"
local = pytz.timezone("Europe/Amsterdam")
try:
if dmy_flag:
naive = datetime.datetime.strptime(dt, "%d:%m:%Y:%H:%M:%S")
else:
naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
except ValueError:
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
# print(timestamp)
MeasRec = {}
MeasRec["timestamp"] = timestamp
MeasRec["analysts"] = operator
MeasRec["instrument_codes"] = "Utrecht_" + machine
MeasRec["description"] = "free string = " + free_string
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["experiments"] = location + site + spec_name
MeasRec["treat_step_num"] = location + site + spec_name + items[0]
MeasRec["specimen"] = spec_name
# MeasRec["treat_ac_field"] = '0'
if AF_or_T.lower() == "th":
MeasRec["treat_temp"] = '%8.3e' % (float(step_value) + 273.
) # temp in kelvin
MeasRec['treat_ac_field'] = '0'
lab_treat_type = "T"
else:
MeasRec['treat_temp'] = '273'
MeasRec['treat_ac_field'] = '%10.3e' % (float(step_value) *
1e-3)
lab_treat_type = "AF"
MeasRec['treat_dc_field'] = '0'
if step_value == '0':
meas_type = "LT-NO"
# print("step_type=", step_type)
if step_type == '0' or step_type == '00':
meas_type = "LT-%s-Z" % lab_treat_type
elif step_type == '1' or step_type == '11':
meas_type = "LT-%s-I" % lab_treat_type
MeasRec['treat_dc_field'] = '%1.2e' % DC_FIELD
elif step_type == '2' or step_type == '12':
meas_type = "LT-PTRM-I"
MeasRec['treat_dc_field'] = '%1.2e' % DC_FIELD
elif step_type == '3' or step_type == '13':
meas_type = "LT-PTRM-Z"
# print("meas_type=", meas_type)
MeasRec['treat_dc_field_phi'] = '%1.2f' % DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f' % DC_THETA
MeasRec['method_codes'] = meas_type
MeasRec["magn_moment"] = magn_moment
if volume != 0: MeasRec["magn_volume"] = magn_volume
MeasRec["dir_dec"] = measurement_dec
MeasRec["dir_inc"] = measurement_inc
MeasRec['dir_csd'] = error
MeasRec['meas_n_orient'] = meas_n_orient
# print(MeasRec)
MeasRecs.append(MeasRec)
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
data.close()
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(
MeasRecs, noave) #figures out method codes for measuremet data
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
dec = [315, 225, 180, 135, 45, 90, 270, 270, 270, 90, 180, 180, 0, 0, 0]
inc = [0, 0, 0, 0, 0, -45, -45, 0, 45, 45, 45, -45, -90, -45, 45]
tdec = [0, 90, 0, 180, 270, 0, 0, 90, 0]
tinc = [0, 0, 90, 0, 0, -90, 0, 0, 90]
demag = "N"
trm = 0
irm = 0
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # site outfile
magfile = kwargs.get('magfile', '')
labfield = int(kwargs.get('labfield', 0)) * 1e-6
phi = int(kwargs.get('phi', 0))
theta = int(kwargs.get('theta', 0))
peakfield = int(kwargs.get('peakfield', 0)) * 1e-3
specnum = int(kwargs.get('specnum', 0))
location = kwargs.get('location', 'unknown')
noave = kwargs.get('noave', False) # 0 means "do average", is default
samp_con = kwargs.get('samp_con', '1')
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
arm_labfield = kwargs.get('arm_labfield', 50e-6)
trm_peakT = kwargs.get('trm_peakT', 600 + 273)
mv = kwargs.get('mv', 'v')
# format/organize variables
if magfile:
try:
infile = open(os.path.join(input_dir_path, magfile), 'r')
except IOError:
print("bad mag file name")
return False, "bad mag file name"
else:
print("mag_file field is required option")
return False, "mag_file field is required option"
if specnum != 0: specnum = -specnum
if "4" in samp_con:
if "-" not in samp_con:
print(
"naming convention option [4] must be in form 4-Z where Z is an integer"
)
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif "7" in samp_con:
if "-" not in samp_con:
print(
"naming convention option [7] must be in form 7-Z where Z is an integer"
)
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
else:
Z = 1
codes = codelist.split(':')
if "AF" in codes:
demag = 'AF'
if not labfield: methcode = "LT-AF-Z"
if labfield: methcode = "LT-AF-I"
if "T" in codes:
demag = "T"
if not labfield: methcode = "LT-T-Z"
if labfield: methcode = "LT-T-I"
if "I" in codes:
methcode = "LP-IRM"
irmunits = "mT"
if "S" in codes:
demag = "S"
methcode = "LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield = labfield
# should use arm_labfield and trm_peakT as well, but these values are currently never asked for
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 coil:
methcode = "LP-IRM"
irmunits = "V"
if coil not in ["1", "2", "3"]:
print('not a valid coil specification')
return False, 'not a valid coil specification'
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
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
version_num = pmag.get_version()
# find start of data:
DIspec = []
Data = infile.readlines()
infile.close()
for k in range(len(Data)):
rec = Data[k].split()
if len(rec) <= 2: continue
if rec[0].upper() == "LAT:" and len(rec) > 3:
lat, lon = rec[1], rec[3]
continue
elif rec[0].upper() == "ID":
continue
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
specimen = rec[0]
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
if mv == 'v':
volume = float(rec[12])
if volume > 0:
susc_chi_volume = '%10.3e' % (old_div(
(float(rec[11]) * 1e-5),
volume)) #convert to SI (assume Bartington, 10-5 SI)
else:
susc_chi_volume = '%10.3e' % (
float(rec[11]) * 1e-5
) #convert to SI (assume Bartington, 10-5 SI)
else:
mass = float(rec[12])
if mass > 0:
susc_chi_mass = '%10.3e' % (old_div(
(float(rec[11]) * 1e-5),
mass)) #convert to SI (assume Bartington, 10-5 SI)
else:
susc_chi_mass = '%10.3e' % (
float(rec[11]) * 1e-5
) #convert to SI (assume Bartington, 10-5 SI)
print((specimen, sample, site, samp_con, Z))
#fill tables besides measurements
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
if mv == 'v':
SpecRec["susc_chi_volume"] = susc_chi_volume
SpecRec["volume"] = volume
else:
SpecRec["susc_chi_mass"] = susc_chi_mass
SpecRec["mass"] = mass
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
#fill measurements
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"] = '0'
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
meas_type = "LT-NO"
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["specimen"] = specimen
# if mv=='v': MeasRec["susc_chi_volume"]=susc_chi_volume
# else: MeasRec["susc_chi_mass"]=susc_chi_mass
MeasRec["dir_csd"] = rec[3]
MeasRec["magn_moment"] = '%10.3e' % (float(rec[4]) * 1e-7)
MeasRec["dir_dec"] = rec[5]
MeasRec["dir_inc"] = rec[6]
MeasRec["citations"] = "This study"
if demag == "AF":
if methcode != "LP-AN-ARM":
MeasRec["treat_ac_field"] = '%8.3e' % (float(rec[1]) * 1e-3
) # peak field in tesla
meas_type = "LT-AF-Z"
MeasRec["treat_dc_field"] = '0'
else: # AARM experiment
if treat[1][0] == '0':
meas_type = "LT-AF-Z"
MeasRec["treat_ac_field"] = '%8.3e' % (
peakfield) # peak field in tesla
else:
meas_type = "LT-AF-I"
ipos = int(treat[0]) - 1
MeasRec["treat_dc_field_phi"] = '%7.1f' % (dec[ipos])
MeasRec["treat_dc_field_theta"] = '%7.1f' % (inc[ipos])
MeasRec["treat_dc_field"] = '%8.3e' % (labfield)
MeasRec["treat_ac_field"] = '%8.3e' % (
peakfield) # peak field in tesla
elif demag == "T":
if rec[1][0] == ".": rec[1] = "0" + rec[1]
treat = rec[1].split('.')
if len(treat) == 1: treat.append('0')
MeasRec["treat_temp"] = '%8.3e' % (float(rec[1]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
MeasRec["treat_temp"] = '%8.3e' % (float(treat[0]) + 273.
) # temp in kelvin
if trm == 0: # demag=T and not trmaq
if treat[1][0] == '0':
meas_type = "LT-T-Z"
else:
MeasRec["treat_dc_field"] = '%8.3e' % (
labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MeasRec["treat_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
if treat[1][0] == '1':
meas_type = "LT-T-I" # in-field thermal step
if treat[1][0] == '2':
meas_type = "LT-PTRM-I" # pTRM check
pTRM = 1
if treat[1][0] == '3':
MeasRec[
"treat_dc_field"] = '0' # this is a zero field step
meas_type = "LT-PTRM-MD" # pTRM tail check
else:
meas_type = "LT-T-I" # trm acquisition experiment
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main(**kwargs):
version_num = pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 2.5)) * 1e-6
JR = kwargs.get('JR', False)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
samp_con = '5'
# format variables
tmp_file = mag_file.split(os.extsep)[0] + os.extsep + 'tmp'
mag_file = os.path.join(input_dir_path, mag_file)
if specnum != 0: specnum = -int(specnum)
if samp_con.startswith("4"):
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif samp_con.startswith("7"):
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 1
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data = open(mag_file, 'r')
tmp_data = open(tmp_file, 'w')
if samp_con != '2': fixed_data = pre_data.read().replace('-', ' -')
else:
fixed_data = ""
for line in pre_data.readlines():
entries = line.split()
if len(entries) < 2: continue
fixed_line = entries[0] + ' ' + reduce(
lambda x, y: x + ' ' + y,
[x.replace('-', ' -') for x in entries[1:]])
fixed_data += fixed_line + os.linesep
tmp_data.write(fixed_data)
tmp_data.close()
pre_data.close()
if not JR:
column_names = [
'specimen', 'step', 'x', 'y', 'z', 'expon', 'azimuth', 'dip',
'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2',
'param1', 'param2', 'param3', 'param4', 'dir_csd'
]
else: # measured on the Joides Resolution JR6
column_names = [
'specimen', 'step', 'negz', 'y', 'x', 'expon', 'azimuth', 'dip',
'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2',
'param1', 'param2', 'param3', 'param4', 'dir_csd'
]
data = pd.read_csv(tmp_file,
delim_whitespace=True,
names=column_names,
index_col=False)
if isinstance(data['x'][0], str):
column_names = [
'specimen', 'step', 'step_unit', 'x', 'y', 'z', 'expon', 'azimuth',
'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2',
'param1', 'param2', 'param3', 'param4', 'dir_csd'
]
data = pd.read_csv(tmp_file,
delim_whitespace=True,
names=column_names,
index_col=False)
if JR: data['z'] = -data['negz']
cart = np.array([data['x'], data['y'], data['z']]).transpose()
dir_dat = pmag.cart2dir(cart).transpose()
data['dir_dec'] = dir_dat[0]
data['dir_inc'] = dir_dat[1]
data['magn_moment'] = dir_dat[2] * (
10.0**
data['expon']) * volume # the data are in A/m - this converts to Am^2
data['magn_volume'] = dir_dat[2] * (10.0**data['expon']
) # A/m - data in A/m
data['dip'] = -data['dip']
data['specimen']
# put data into magic tables
MagRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
for rowNum, row in data.iterrows():
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
specimen = row['specimen']
if specnum != 0: sample = specimen[:specnum]
else: sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec["citations"] = "This study"
SpecRec["analysts"] = user
SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec["citations"] = "This study"
SampRec["analysts"] = user
SampRec['azimuth'] = row['azimuth']
SampRec['dip'] = row['dip']
SampRec['bed_dip_direction'] = row['bed_dip_direction']
SampRec['bed_dip'] = row['bed_dip']
SampRec['method_codes'] = meth_code
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec["citations"] = "This study"
SiteRec["analysts"] = user
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec["citations"] = "This study"
LocRec["analysts"] = user
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec["citations"] = "This study"
MeasRec["analysts"] = user
MeasRec["specimen"] = specimen
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["treat_ac_field"] = '0'
if row['step'] == 'NRM':
meas_type = "LT-NO"
elif 'step_unit' in row and row['step_unit'] == 'C':
meas_type = "LT-T-Z"
treat = float(row['step'])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
elif row['step'][0:2] == 'AD':
meas_type = "LT-AF-Z"
treat = float(row['step'][2:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif row['step'][0] == 'A':
meas_type = "LT-AF-Z"
treat = float(row['step'][1:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type = "LT-T-Z"
treat = float(row['step'][2:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
elif row['step'][0] == 'T':
meas_type = "LT-T-Z"
treat = float(row['step'][1:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.) # temp in kelvin
else: # need to add IRM, and ARM options
print("measurement type unknown", row['step'])
return False, "measurement type unknown"
MeasRec["magn_moment"] = str(row['magn_moment'])
MeasRec["magn_volume"] = str(row['magn_volume'])
MeasRec["dir_dec"] = str(row['dir_dec'])
MeasRec["dir_inc"] = str(row['dir_inc'])
MeasRec['method_codes'] = meas_type
MagRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
try:
os.remove(tmp_file)
except (OSError, IOError) as e:
print("couldn't remove temperary fixed JR6 file %s" % tmp_file)
return True, meas_file
def convert(**kwargs):
# initialize some stuff
version_num = pmag.get_version()
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs = [],[],[],[],[]
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
mag_file = kwargs.get('mag_file')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # site outfile
location = kwargs.get('location', 'unknown')
dmy_flag = kwargs.get('dmy_flag', False)
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
#oave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
specnum = -int(kwargs.get('specnum', 0))
samp_con = kwargs.get('samp_con', '2')
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
site_num=samp_con.split("-")[1]
samp_con="7"
else: site_num=1
try:
DC_FIELD = float(kwargs.get('labfield',0))*1e-6
DC_PHI = float(kwargs.get('phi',0))
DC_THETA = float(kwargs.get('theta',0))
except ValueError: raise ValueError('problem with your dc parameters. please provide a labfield in microTesla and a phi and theta in degrees.')
noave = kwargs.get('noave', False)
dmy_flag = kwargs.get('dmy_flag', False)
meas_n_orient = kwargs.get('meas_n_orient', '8')
# format variables
if not mag_file:
return False, 'You must provide a Utrecht formated file'
mag_file = os.path.join(input_dir_path, mag_file)
# parse data
# Open up the Utrecht file and read the header information
AF_or_T = mag_file.split('.')[-1]
data = open(mag_file, 'r')
line = data.readline()
line_items = line.split(',')
operator=line_items[0]
operator=operator.replace("\"","")
machine=line_items[1]
machine=machine.replace("\"","")
machine=machine.rstrip('\n')
# print("operator=", operator)
# print("machine=", machine)
#read in measurement data
line = data.readline()
while line != "END" and line != '"END"':
SpecRec,SampRec,SiteRec,LocRec = {},{},{},{}
line_items = line.split(',')
spec_name=line_items[0]
spec_name=spec_name.replace("\"","")
# print("spec_name=", spec_name)
free_string=line_items[1]
free_string=free_string.replace("\"","")
# print("free_string=", free_string)
dec=line_items[2]
# print("dec=", dec)
inc=line_items[3]
# print("inc=", inc)
volume=float(line_items[4])
volume=volume * 1e-6 # enter volume in cm^3, convert to m^3
# print("volume=", volume)
bed_plane=line_items[5]
# print("bed_plane=", bed_plane)
bed_dip=line_items[6]
# print("bed_dip=", bed_dip)
# Configure et er_ tables
if specnum==0: sample_name = spec_name
else: sample_name = spec_name[:specnum]
site = pmag.parse_site(sample_name,samp_con,site_num)
SpecRec['specimen'] = spec_name
SpecRec['sample'] = sample_name
if volume!=0: SpecRec['volume']=volume
SpecRecs.append(SpecRec)
if sample_name!="" and sample_name not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample_name
SampRec['azimuth'] = dec
SampRec['dip'] = str(float(inc)-90)
SampRec['bed_dip_direction'] = bed_plane
SampRec['bed_dip'] = bed_dip
SampRec['method_codes'] = meth_code
SampRec['site'] = site
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
#measurement data
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
while line != '9999':
step=items[0]
step=step.split('.')
step_value=step[0]
step_type = ""
if len(step) == 2:
step_type=step[1]
if step_type=='5':
step_value = items[0]
A=float(items[1])
B=float(items[2])
C=float(items[3])
# convert to MagIC coordinates
Z=-A
X=-B
Y=C
cart = array([X, Y, Z]).transpose()
direction = pmag.cart2dir(cart).transpose()
measurement_dec = direction[0]
measurement_inc = direction[1]
magn_moment = direction[2] * 1.0e-12 # the data are in pico-Am^2 - this converts to Am^2
if volume!=0:
magn_volume = direction[2] * 1.0e-12 / volume # data volume normalized - converted to A/m
# print("magn_moment=", magn_moment)
# print("magn_volume=", magn_volume)
error = items[4]
date=items[5]
date=date.strip('"').replace(' ','')
if date.count("-") > 0:
date=date.split("-")
elif date.count("/") > 0:
date=date.split("/")
else: print("date format seperator cannot be identified")
# print(date)
time=items[6]
time=time.strip('"').replace(' ','')
time=time.split(":")
# print(time)
dt = date[0] + ":" + date[1] + ":" + date[2] + ":" + time[0] + ":" + time[1] + ":" + "0"
local = pytz.timezone("Europe/Amsterdam")
try:
if dmy_flag: naive = datetime.datetime.strptime(dt, "%d:%m:%Y:%H:%M:%S")
else: naive = datetime.datetime.strptime(dt, "%m:%d:%Y:%H:%M:%S")
except ValueError:
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
# print(timestamp)
MeasRec = {}
MeasRec["timestamp"]=timestamp
MeasRec["analysts"] = operator
MeasRec["instrument_codes"] = "Utrecht_" + machine
MeasRec["description"] = "free string = " + free_string
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["experiments"] = location + site + spec_name
MeasRec["treat_step_num"] = location + site + spec_name + items[0]
MeasRec["specimen"] = spec_name
# MeasRec["treat_ac_field"] = '0'
if AF_or_T.lower() == "th":
MeasRec["treat_temp"] = '%8.3e' % (float(step_value)+273.) # temp in kelvin
MeasRec['treat_ac_field']='0'
lab_treat_type = "T"
else:
MeasRec['treat_temp']='273'
MeasRec['treat_ac_field']='%10.3e'%(float(step_value)*1e-3)
lab_treat_type = "AF"
MeasRec['treat_dc_field']='0'
if step_value == '0':
meas_type = "LT-NO"
# print("step_type=", step_type)
if step_type == '0' or step_type == '00':
meas_type = "LT-%s-Z"%lab_treat_type
elif step_type == '1' or step_type == '11':
meas_type = "LT-%s-I"%lab_treat_type
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
elif step_type == '2' or step_type == '12':
meas_type = "LT-PTRM-I"
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
elif step_type == '3' or step_type == '13':
meas_type = "LT-PTRM-Z"
# print("meas_type=", meas_type)
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['method_codes'] = meas_type
MeasRec["magn_moment"] = magn_moment
if volume!=0: MeasRec["magn_volume"] = magn_volume
MeasRec["dir_dec"] = measurement_dec
MeasRec["dir_inc"] = measurement_inc
MeasRec['dir_csd'] = error
MeasRec['meas_n_orient'] = meas_n_orient
# print(MeasRec)
MeasRecs.append(MeasRec)
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
line = data.readline()
line = line.rstrip("\n")
items = line.split(",")
data.close()
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave) #figures out method codes for measuremet data
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
# unpack keyword args
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
magfile = kwargs.get('magfile', '')
labfield = float(kwargs.get('labfield', 0))*1e-6
labfield_phi = float(kwargs.get('labfield_phi', 0))
labfield_theta = float(kwargs.get('labfield_theta', 0))
experiment = kwargs.get('experiment', '')
cooling_times_list = kwargs.get('cooling_times_list', [])
sample_nc = kwargs.get('sample_nc', [1, 0])
site_nc = kwargs.get('site_nc', [1, 0])
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', False) # False is default, means do average
WD = kwargs.get('WD', '.')
output_dir_path=WD
# format and validate variables
if magfile:
try:
input=open(magfile,'r')
except:
print("bad mag file:",magfile)
return False, "bad mag file"
else:
print("mag_file field is required option")
print(__doc__)
return False, "mag_file field is required option"
if not experiment:
print("-exp is required option. Please provide experiment type of: Demag, PI, ATRM n (n of positions), CR (see below for format), NLT")
print(__doc__)
return False, "-exp is required option"
if experiment=='ATRM':
if command_line:
ind=sys.argv.index("ATRM")
atrm_n_pos=int(sys.argv[ind+1])
else:
atrm_n_pos = 6
if experiment=='AARM':
if command_line:
ind=sys.argv.index("AARM")
aarm_n_pos=int(sys.argv[ind+1])
else:
aarm_n_pos = 6
if experiment=='CR':
if command_line:
ind=sys.argv.index("CR")
cooling_times=sys.argv[ind+1]
cooling_times_list=cooling_times.split(',')
# if not command line, cooling_times_list is already set
#--------------------------------------
# read data from generic file
#--------------------------------------
mag_data=read_generic_file(magfile,not noave)
#--------------------------------------
# for each specimen get the data, and translate it to MagIC format
#--------------------------------------
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
specimens_list=sorted(mag_data.keys())
for specimen in specimens_list:
measurement_running_number=0
this_specimen_treatments=[] # a list of all treatments
MeasRecs_this_specimen=[]
LP_this_specimen=[] # a list of all lab protocols
IZ,ZI=0,0 # counter for IZ and ZI steps
for meas_line in mag_data[specimen]:
#------------------
# trivial MeasRec data
#------------------
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
specimen=meas_line['specimen']
sample=get_upper_level_name(specimen,sample_nc)
site=get_upper_level_name(sample,site_nc)
sample_method_codes=""
azimuth,dip,DipDir,Dip="","","",""
MeasRec['citations']="This study"
MeasRec["specimen"]=specimen
MeasRec['analysts']=user
MeasRec["instrument_codes"]=""
MeasRec["quality"]='g'
MeasRec["treat_step_num"]="%i"%measurement_running_number
MeasRec["magn_moment"]='%10.3e'%(float(meas_line["moment"])*1e-3) # in Am^2
MeasRec["meas_temp"]='273.' # room temp in kelvin
#------------------
# decode treatments from treatment column in the generic file
#------------------
treatment=[]
treatment_code=str(meas_line['treatment']).split(".")
treatment.append(float(treatment_code[0]))
if len(treatment_code)==1:
treatment.append(0)
else:
treatment.append(float(treatment_code[1]))
#------------------
# lab field direction
#------------------
if experiment in ['PI','NLT','CR']:
if float(treatment[1])==0:
MeasRec["treat_dc_field"]="0"
MeasRec["treat_dc_field_phi"]="0"
MeasRec["treat_dc_field_theta"]="0"
elif not labfield:
print("-W- WARNING: labfield (-dc) is a required argument for this experiment type")
return False, "labfield (-dc) is a required argument for this experiment type"
else:
MeasRec["treat_dc_field"]='%8.3e'%(float(labfield))
MeasRec["treat_dc_field_phi"]="%.2f"%(float(labfield_phi))
MeasRec["treat_dc_field_theta"]="%.2f"%(float(labfield_theta))
else:
MeasRec["treat_dc_field"]=""
MeasRec["treat_dc_field_phi"]=""
MeasRec["treat_dc_field_theta"]=""
#------------------
# treatment temperature/peak field
#------------------
if experiment == 'Demag':
if meas_line['treatment_type']=='A':
MeasRec['treat_temp']="273."
MeasRec["treat_ac_field"]="%.3e"%(treatment[0]*1e-3)
elif meas_line['treatment_type']=='N':
MeasRec['treat_temp']="273."
MeasRec["treat_ac_field"]=""
else:
MeasRec['treat_temp']="%.2f"%(treatment[0]+273.)
MeasRec["treat_ac_field"]=""
else:
MeasRec['treat_temp']="%.2f"%(treatment[0]+273.)
MeasRec["treat_ac_field"]=""
#---------------------
# Lab treatment
# Lab protocol
#---------------------
#---------------------
# Lab treatment and lab protocoal for NRM:
#---------------------
if float(meas_line['treatment'])==0:
LT="LT-NO"
LP="" # will be filled later after finishing reading all measurements line
#---------------------
# Lab treatment and lab protocoal for paleointensity experiment
#---------------------
elif experiment =='PI':
LP="LP-PI-TRM"
if treatment[1]==0:
LT="LT-T-Z"
elif treatment[1]==1 or treatment[1]==10: # infield
LT="LT-T-I"
elif treatment[1]==2 or treatment[1]==20: # pTRM check
LT="LT-PTRM-I"
LP=LP+":"+"LP-PI-ALT-PTRM"
elif treatment[1]==3 or treatment[1]==30: # Tail check
LT="LT-PTRM-MD"
LP=LP+":"+"LP-PI-BT-MD"
elif treatment[1]==4 or treatment[1]==40: # Additivity check
LT="LT-PTRM-AC"
LP=LP+":"+"LP-PI-BT-MD"
else:
print("-E- unknown measurement code specimen %s treatmemt %s"%(meas_line['specimen'],meas_line['treatment']))
MeasRec={}
continue
# save all treatment in a list
# we will use this later to distinguidh between ZI / IZ / and IZZI
this_specimen_treatments.append(float(meas_line['treatment']))
if LT=="LT-T-Z":
if float(treatment[0]+0.1) in this_specimen_treatments:
LP=LP+":"+"LP-PI-IZ"
if LT=="LT-T-I":
if float(treatment[0]+0.0) in this_specimen_treatments:
LP=LP+":"+"LP-PI-ZI"
#---------------------
# Lab treatment and lab protocoal for demag experiment
#---------------------
elif "Demag" in experiment:
if meas_line['treatment_type']=='A':
LT="LT-AF-Z"
LP="LP-DIR-AF"
else:
LT="LT-T-Z"
LP="LP-DIR-T"
#---------------------
# Lab treatment and lab protocoal for ATRM experiment
#---------------------
elif experiment in ['ATRM','AARM']:
if experiment=='ATRM':
LP="LP-AN-TRM"
n_pos=atrm_n_pos
if n_pos!=6:
print("the program does not support ATRM in %i position."%n_pos)
continue
if experiment=='AARM':
LP="LP-AN-ARM"
n_pos=aarm_n_pos
if n_pos!=6:
print("the program does not support AARM in %i position."%n_pos)
continue
if treatment[1]==0:
if experiment=='ATRM':
LT="LT-T-Z"
MeasRec['treat_temp']="%.2f"%(treatment[0]+273.)
MeasRec["treat_ac_field"]=""
else:
LT="LT-AF-Z"
MeasRec['treat_temp']="273."
MeasRec["treat_ac_field"]="%.3e"%(treatment[0]*1e-3)
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
else:
if experiment=='ATRM':
if float(treatment[1])==70 or float(treatment[1])==7: # alteration check as final measurement
LT="LT-PTRM-I"
else:
LT="LT-T-I"
else:
LT="LT-AF-I"
MeasRec["treat_dc_field"]='%8.3e'%(float(labfield))
# find the direction of the lab field in two ways:
# (1) using the treatment coding (XX.1=+x, XX.2=+y, XX.3=+z, XX.4=-x, XX.5=-y, XX.6=-z)
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
if treatment[1] < 10:
ipos_code=int(treatment[1])-1
else:
ipos_code=int(old_div(treatment[1],10))-1
# (2) using the magnetization
if meas_line["dec_s"]!="":
DEC=float(meas_line["dec_s"])
INC=float(meas_line["inc_s"])
elif meas_line["dec_g"]!="":
DEC=float(meas_line["dec_g"])
INC=float(meas_line["inc_g"])
elif meas_line["dec_t"]!="":
DEC=float(meas_line["dec_t"])
INC=float(meas_line["inc_t"])
if DEC<0 and DEC>-359:
DEC=360.+DEC
if INC < 45 and INC > -45:
if DEC>315 or DEC<45: ipos_guess=0
if DEC>45 and DEC<135: ipos_guess=1
if DEC>135 and DEC<225: ipos_guess=3
if DEC>225 and DEC<315: ipos_guess=4
else:
if INC >45: ipos_guess=2
if INC <-45: ipos_guess=5
# prefer the guess over the code
ipos=ipos_guess
# check it
if treatment[1]!= 7 and treatment[1]!= 70:
if ipos_guess!=ipos_code:
print("-W- WARNING: check specimen %s step %s, anistropy measurements, coding does not match the direction of the lab field"%(specimen,meas_line['treatment']))
MeasRec["treat_dc_field_phi"]='%7.1f' %(tdec[ipos])
MeasRec["treat_dc_field_theta"]='%7.1f'% (tinc[ipos])
#---------------------
# Lab treatment and lab protocoal for cooling rate experiment
#---------------------
elif experiment == "CR":
cooling_times_list
LP="LP-CR-TRM"
MeasRec["treat_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
if treatment[1]==0:
LT="LT-T-Z"
MeasRec["treat_dc_field"]="0"
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
else:
if treatment[1]==7: # alteration check as final measurement
LT="LT-PTRM-I"
else:
LT="LT-T-I"
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_dc_field_phi"]='%7.1f' % (labfield_phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (labfield_theta) # labfield theta
indx=int(treatment[1])-1
# alteration check matjed as 0.7 in the measurement file
if indx==6:
cooling_time= cooling_times_list[-1]
else:
cooling_time=cooling_times_list[indx]
MeasRec["measurement_description"]="cooling_rate"+":"+cooling_time+":"+"K/min"
#---------------------
# Lab treatment and lab protocoal for NLT experiment
#---------------------
elif 'NLT' in experiment :
print("Dont support yet NLT rate experiment file. Contact [email protected]")
#---------------------
# method_codes for this measurement only
# LP will be fixed after all measurement lines are read
#---------------------
MeasRec["method_codes"]=LT+":"+LP
#--------------------
# deal with specimen orientation and different coordinate system
#--------------------
found_s,found_geo,found_tilt=False,False,False
if "dec_s" in list(meas_line.keys()) and "inc_s" in list(meas_line.keys()):
if meas_line["dec_s"]!="" and meas_line["inc_s"]!="":
found_s=True
MeasRec["dir_dec"]=meas_line["dec_s"]
MeasRec["dir_inc"]=meas_line["inc_s"]
if "dec_g" in list(meas_line.keys()) and "inc_g" in list(meas_line.keys()):
if meas_line["dec_g"]!="" and meas_line["inc_g"]!="":
found_geo=True
if "dec_t" in list(meas_line.keys()) and "inc_t" in list(meas_line.keys()):
if meas_line["dec_t"]!="" and meas_line["inc_t"]!="":
found_tilt=True
#-----------------------------
# specimen coordinates: no
# geographic coordinates: yes
#-----------------------------
if found_geo and not found_s:
MeasRec["dir_dec"]=meas_line["dec_g"]
MeasRec["dir_inc"]=meas_line["inc_g"]
azimuth="0"
dip="0"
#-----------------------------
# specimen coordinates: no
# geographic coordinates: no
#-----------------------------
if not found_geo and not found_s:
print("-E- ERROR: sample %s does not have dec_s/inc_s or dec_g/inc_g. Ignore specimen %s "%(sample,specimen))
break
#-----------------------------
# specimen coordinates: yes
# geographic coordinates: yes
#
# commant: Ron, this need to be tested !!
#-----------------------------
if found_geo and found_s:
cdec,cinc=float(meas_line["dec_s"]),float(meas_line["inc_s"])
gdec,ginc=float(meas_line["dec_g"]),float(meas_line["inc_g"])
az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
azimuth="%.1f"%az
dip="%.1f"%pl
#-----------------------------
# specimen coordinates: yes
# geographic coordinates: no
#-----------------------------
if not found_geo and found_s and "Demag" in experiment:
print("-W- WARNING: missing dip or azimuth for sample %s"%sample)
#-----------------------------
# tilt-corrected coordinates: yes
# geographic coordinates: no
#-----------------------------
if found_tilt and not found_geo:
print("-E- ERROR: missing geographic data for sample %s. Ignoring tilt-corrected data "%sample)
#-----------------------------
# tilt-corrected coordinates: yes
# geographic coordinates: yes
#-----------------------------
if found_tilt and found_geo:
dec_geo,inc_geo=float(meas_line["dec_g"]),float(meas_line["inc_g"])
dec_tilt,inc_tilt=float(meas_line["dec_t"]),float(meas_line["inc_t"])
if dec_geo==dec_tilt and inc_geo==inc_tilt:
DipDir,Dip=0.,0.
else:
DipDir,Dip=pmag.get_tilt(dec_geo,inc_geo,dec_tilt,inc_tilt)
#-----------------------------
# samples method codes
# geographic coordinates: no
#-----------------------------
if found_tilt or found_geo:
sample_method_codes="SO-NO"
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['citations'] = "This study"
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['citations'] = "This study"
SampRec['azimuth'] = azimuth
SampRec['dip'] = dip
SampRec['bed_dip_direction'] = DipDir
SampRec['bed_dip'] = Dip
SampRec['method_codes']=sample_method_codes
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations'] = "This study"
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location'] = location
LocRec['citations'] = "This study"
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRecs_this_specimen.append(MeasRec)
measurement_running_number+=1
#-------
#-------
# after reading all the measurements lines for this specimen
# 1) add experiments
# 2) fix method_codes with the correct lab protocol
#-------
LP_this_specimen=[]
for MeasRec in MeasRecs_this_specimen:
method_codes=MeasRec["method_codes"].split(":")
for code in method_codes:
if "LP" in code and code not in LP_this_specimen:
LP_this_specimen.append(code)
# check IZ/ZI/IZZI
if "LP-PI-ZI" in LP_this_specimen and "LP-PI-IZ" in LP_this_specimen:
LP_this_specimen.remove("LP-PI-ZI")
LP_this_specimen.remove("LP-PI-IZ")
LP_this_specimen.append("LP-PI-BT-IZZI")
# add the right LP codes and fix experiment name
for MeasRec in MeasRecs_this_specimen:
MeasRec["experiments"]=MeasRec["specimen"]+":"+":".join(LP_this_specimen)
method_codes=MeasRec["method_codes"].split(":")
LT=""
for code in method_codes:
if code[:3]=="LT-":
LT=code;
break
MeasRec["method_codes"]=LT+":"+":".join(LP_this_specimen)
MeasRecs.append(MeasRec)
#--
# write tables to file
#--
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
# initialize defaults
version_num=pmag.get_version()
citations="This study"
dir_path,demag='.','NRM'
depth_method='a'
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', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
# format variables
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
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
file_found = False
for f in filelist: # parse each file
if f[-3:].lower()=='csv':
file_found = True
print('processing: ',f)
full_file = os.path.join(input_dir_path, f)
file_input=open(full_file,'r').readlines()
keys=file_input[0].replace('\n','').split(',') # splits on underscores
keys=[k.strip('"') for k in keys]
if "Interval Top (cm) on SHLF" in keys:interval_key="Interval Top (cm) on SHLF"
elif " Interval Bot (cm) on SECT" in keys:interval_key=" Interval Bot (cm) on SECT"
elif "Offset (cm)" in keys: interval_key="Offset (cm)"
else: print("couldn't find interval or offset amount")
if "Top Depth (m)" in keys:depth_key="Top Depth (m)"
elif "CSF-A Top (m)" in keys:depth_key="CSF-A Top (m)"
elif "Depth CSF-A (m)" in keys:depth_key="Depth CSF-A (m)"
else: print("couldn't find depth")
if "CSF-B Top (m)" in keys: comp_depth_key="CSF-B Top (m)" # use this model if available
elif "Depth CSF-B (m)" in keys: comp_depth_key="Depth CSF-B (m)"
else: comp_depth_key=""; print("couldn't find composite depth")
if "Demag level (mT)" in keys:demag_key="Demag level (mT)"
elif "Demag Level (mT)" in keys: demag_key="Demag Level (mT)"
elif "Treatment Value" in keys: demag_key="Treatment Value"
else: print("couldn't find demag type")
if "Inclination (Tray- and Bkgrd-Corrected) (deg)" in keys:inc_key="Inclination (Tray- and Bkgrd-Corrected) (deg)"
elif "Inclination background + tray corrected (deg)" in keys:inc_key="Inclination background + tray corrected (deg)"
elif "Inclination background + tray corrected (\xc2\xb0)" in keys:inc_key="Inclination background + tray corrected (\xc2\xb0)"
elif "Inclination background & tray corrected (deg)" in keys:inc_key="Inclination background & tray corrected (deg)"
elif "Inclination background & tray corrected (deg)" in keys:inc_key="Inclination background & tray corrected (deg)"
elif "Inclination background & drift corrected (deg)" in keys:inc_key="Inclination background & drift corrected (deg)"
else: print("couldn't find inclination")
if "Declination (Tray- and Bkgrd-Corrected) (deg)" in keys:dec_key="Declination (Tray- and Bkgrd-Corrected) (deg)"
elif "Declination background + tray corrected (deg)" in keys:dec_key="Declination background + tray corrected (deg)"
elif "Declination background + tray corrected (\xc2\xb0)" in keys:dec_key="Declination background + tray corrected (\xc2\xb0)"
elif "Declination background & tray corrected (deg)" in keys:dec_key="Declination background & tray corrected (deg)"
elif "Declination background & tray corrected (deg)" in keys:dec_key="Declination background & tray corrected (deg)"
elif "Declination background & drift corrected (deg)" in keys:dec_key="Declination background & drift corrected (deg)"
else: print("couldn't find declination")
if "Intensity (Tray- and Bkgrd-Corrected) (A/m)" in keys:int_key="Intensity (Tray- and Bkgrd-Corrected) (A/m)"
elif "Intensity background + tray corrected (A/m)" in keys:int_key="Intensity background + tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys:int_key="Intensity background & tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys:int_key="Intensity background & tray corrected (A/m)"
elif "Intensity background & drift corrected (A/m)" in keys:int_key="Intensity background & drift corrected (A/m)"
else: print("couldn't find magnetic moment")
if "Core Type" in keys:
core_type="Core Type"
elif "Type" in keys: core_type="Type"
else: print("couldn't find core type")
if 'Run Number' in keys: run_number_key='Run Number'
elif 'Test No.' in keys: run_number_key='Test No.'
else: print("couldn't find run number")
if 'Test Changed On' in keys: date_key='Test Changed On'
elif "Timestamp (UTC)" in keys: date_key="Timestamp (UTC)"
else: print("couldn't find timestamp")
if "Section" in keys: sect_key="Section"
elif "Sect" in keys: sect_key="Sect"
else: print("couldn't find section number")
if 'Section Half' in keys: half_key='Section Half'
elif "A/W" in keys: half_key="A/W"
else: print("couldn't find half number")
if "Text ID" in keys: text_id="Text ID"
elif "Text Id" in keys: text_id="Text Id"
else: print("couldn't find ID number")
for line in file_input[1:]:
InRec={}
test=0
recs=line.split(',')
for k in range(len(keys)):
if len(recs)==len(keys):
InRec[keys[k]]=line.split(',')[k].strip(""" " ' """)
if 'Exp' in list(InRec.keys()) and InRec['Exp']!="": test=1 # get rid of pesky blank lines (why is this a thing?)
if not test: continue
run_number=""
inst="IODP-SRM"
volume='15.59' # set default volume to this
if 'Sample Area (cm?)' in list(InRec.keys()) and InRec['Sample Area (cm?)']!= "": volume=InRec['Sample Area (cm?)']
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
# Maintain backward compatibility for the ever-changing LIMS format (Argh!)
while len(InRec['Core'])<3:
InRec['Core']='0'+InRec['Core']
if "Last Tray Measurment" in list(InRec.keys()) and "SHLF" not in InRec[text_id] or 'dscr' in csv_file : # assume discrete sample
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"-"+InRec[sect_key]+'-'+InRec[half_key]+'-'+str(InRec[interval_key])
else: # mark as continuous measurements
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"_"+InRec[sect_key]+InRec[half_key]+'-'+str(InRec[interval_key])
sample = expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]
site = expedition+'-'+location
if not InRec[dec_key] or not InRec[inc_key]:
print("No dec or inc found for specimen %s, skipping"%specimen); continue
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['citations']=citations
SpecRec['volume'] = volume
SpecRec['specimen_alternatives']=InRec[text_id]
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['citations']=citations
SampRec['azimuth']='0'
SampRec['dip']='0'
SampRec['core_depth']=InRec[depth_key]
if comp_depth_key!='':
SampRec['composite_depth']=InRec[comp_depth_key]
if "SHLF" not in InRec[text_id]:
SampRec['method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
else:
SampRec['method_codes']='FS-C-DRILL-IODP:SO-V'
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations']=citations
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['citations']=citations
LocRec['expedition_name']=expedition
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['specimen'] = specimen
MeasRec['magic_software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]=0
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["quality"]='g' # assume all data are "good"
MeasRec["standard"]='u' # assume all data are "good"
if run_number_key in list(InRec.keys()) and InRec[run_number_key]!= "": run_number=InRec[run_number_key]
datestamp=InRec[date_key].split() # date time is second line of file
if '/' in datestamp[0]:
mmddyy=datestamp[0].split('/') # break into month day year
if len(mmddyy[0])==1: mmddyy[0]='0'+mmddyy[0] # make 2 characters
if len(mmddyy[1])==1: mmddyy[1]='0'+mmddyy[1] # make 2 characters
if len(datestamp[1])==1: datestamp[1]='0'+datestamp[1] # make 2 characters
date=mmddyy[0]+':'+mmddyy[1]+":"+mmddyy[2] +':' +datestamp[1]+":0"
if '-' in datestamp[0]:
mmddyy=datestamp[0].split('-') # break into month day year
date=mmddyy[0]+':'+mmddyy[1]+":"+mmddyy[2] +':' +datestamp[1]+":0"
if len(date.split(":")) > 6: date=date[:-2]
try: utc_dt = datetime.datetime.strptime(date, "%m:%d:%Y:%H:%M:%S")
except ValueError:
utc_dt = datetime.datetime.strptime(date, "%Y:%m:%d:%H:%M:%S")
MeasRec['timestamp']=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
MeasRec["method_codes"]='LT-NO'
if 'Treatment Type' in list(InRec.keys()) and InRec['Treatment Type']!="":
if "AF" in InRec['Treatment Type'].upper():
MeasRec['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
MeasRec["treat_ac_field"]=treatment_value # AF demag in treat mT => T
elif "T" in InRec['Treatment Type'].upper():
MeasRec['method_codes'] = 'LT-T-Z'
inst=inst+':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec['Treatment Value'])+273 # convert C => K
MeasRec["treat_temp"]=treatment_value
elif 'Alternating Frequency' in InRec['Treatment Type']:
MeasRec['method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-DTECH' # measured on shipboard Dtech D2000
treatment_value=float(InRec[demag_key])*1e-3 # convert mT => T
MeasRec["treat_ac_field"]=treatment_value # AF demag in treat mT => T
elif 'Thermal' in InRec['Treatment Type']:
MeasRec['method_codes'] = 'LT-T-Z'
inst=inst+':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec[demag_key])+273 # convert C => K
MeasRec["treat_temp"]='%8.3e'%(treatment_value) #
elif InRec[demag_key]!="0":
MeasRec['method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
try: treatment_value=float(InRec[demag_key])*1e-3 # convert mT => T
except ValueError: print("Couldn't determine treatment value was given treatment value of %s and demag key %s; setting to blank you will have to manually correct this (or fix it)"%(InRec[demag_key], demag_key)); treatment_value=''
MeasRec["treat_ac_field"]=treatment_value # AF demag in treat mT => T
MeasRec["standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_number!="":
MeasRec['external_database_ids']={'LIMS':run_number}
else:
MeasRec['external_database_ids']=""
MeasRec['dir_inc']=InRec[inc_key]
MeasRec['dir_dec']=InRec[dec_key]
intens = InRec[int_key]
try: MeasRec['magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
except ValueError: print("couldn't find magnetic moment for specimen %s and int_key %s; leaving this field blank you'll have to fix this manually"%(specimen, int_key)); MeasRec['magn_moment']=''
MeasRec['instrument_codes']=inst
MeasRec['treat_step_num']='1'
MeasRec['dir_csd']='0'
MeasRec['meas_n_orient']=''
MeasRecs.append(MeasRec)
if not file_found:
print("No .csv files were found")
return (False, "No .csv files were found")
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasSort=sorted(MeasRecs,lambda x,y: int(round(x['treat_ac_field']-y['treat_ac_field'])))
MeasOuts=pmag.measurements_methods3(MeasSort,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return (True, meas_file)
def convert(**kwargs):
version_num = pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 2.5)) * 1e-6
timezone = kwargs.get('timestamp', 'UTC')
# format variables
mag_file = os.path.join(input_dir_path, mag_file)
if specnum != 0: specnum = -int(specnum)
if samp_con.startswith("4"):
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
elif samp_con.startswith("7"):
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
else:
Z = 1
#create data holders
MeasRecs, SpecRecs, SampRecs, SiteRecs, LocRecs = [], [], [], [], []
# parse data
data = open(mag_file, 'r')
line = data.readline()
line = data.readline()
line = data.readline()
while line != '':
parsedLine = line.split()
if len(parsedLine) >= 4:
sampleName = parsedLine[0]
demagLevel = parsedLine[2]
date = parsedLine[3] + ":0:0:0"
line = data.readline()
line = data.readline()
line = data.readline()
line = data.readline()
parsedLine = line.split()
specimenAngleDec = parsedLine[1]
specimenAngleInc = parsedLine[2]
while parsedLine[0] != 'MEAN':
line = data.readline()
parsedLine = line.split()
if len(parsedLine) == 0:
parsedLine = ["Hello"]
Mx = parsedLine[1]
My = parsedLine[2]
Mz = parsedLine[3]
line = data.readline()
line = data.readline()
parsedLine = line.split()
splitExp = parsedLine[2].split('A')
intensityVolStr = parsedLine[1] + splitExp[0]
intensityVol = float(intensityVolStr)
# check and see if Prec is too big and messes with the parcing.
precisionStr = ''
if len(parsedLine) == 6: #normal line
precisionStr = parsedLine[5][0:-1]
else:
precisionStr = parsedLine[4][0:-1]
precisionPer = float(precisionStr)
precision = intensityVol * precisionPer / 100
while parsedLine[0] != 'SPEC.':
line = data.readline()
parsedLine = line.split()
if len(parsedLine) == 0:
parsedLine = ["Hello"]
specimenDec = parsedLine[2]
specimenInc = parsedLine[3]
line = data.readline()
line = data.readline()
parsedLine = line.split()
geographicDec = parsedLine[1]
geographicInc = parsedLine[2]
# Add data to various MagIC data tables.
specimen = sampleName
if specnum != 0: sample = specimen[:specnum]
else: sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
if specimen != "" and specimen not in [
x['specimen'] if 'specimen' in list(x.keys()) else ""
for x in SpecRecs
]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec["citations"] = "This study"
SpecRec["analysts"] = user
SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec["citations"] = "This study"
SampRec["analysts"] = user
SampRec['azimuth'] = specimenAngleDec
sample_dip = str(float(specimenAngleInc) -
90.0) #convert to magic orientation
SampRec['dip'] = sample_dip
SampRec['method_codes'] = meth_code
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else ""
for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec["citations"] = "This study"
SiteRec["analysts"] = user
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec["citations"] = "This study"
LocRec["analysts"] = user
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(date, "%m-%d-%Y:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
timestamp = utc_dt.strftime("%Y-%m-%dT%H:%M:%S") + "Z"
MeasRec["specimen"] = specimen
MeasRec["timestamp"] = timestamp
MeasRec['description'] = ''
MeasRec["citations"] = "This study"
MeasRec['software_packages'] = version_num
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["treat_ac_field"] = '0'
if demagLevel == 'NRM':
meas_type = "LT-NO"
elif demagLevel[0] == 'A':
meas_type = "LT-AF-Z"
treat = float(demagLevel[1:])
MeasRec["treat_ac_field"] = '%8.3e' % (
treat * 1e-3) # convert from mT to tesla
elif demagLevel[0] == 'T':
meas_type = "LT-T-Z"
treat = float(demagLevel[1:])
MeasRec["treat_temp"] = '%8.3e' % (treat + 273.
) # temp in kelvin
else:
print("measurement type unknown", demag_level)
return False, "measurement type unknown"
MeasRec["magn_moment"] = str(intensityVol * volume) # Am^2
MeasRec["magn_volume"] = intensityVolStr # A/m
MeasRec["dir_dec"] = specimenDec
MeasRec["dir_inc"] = specimenInc
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
#read lines till end of record
line = data.readline()
line = data.readline()
line = data.readline()
line = data.readline()
line = data.readline()
# read all the rest of the special characters. Some data files not consistantly formatted.
while (len(line) <= 3 and line != ''):
line = data.readline()
#end of data while loop
data.close()
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
# initialize defaults
version_num=pmag.get_version()
citations="This study"
dir_path,demag='.','NRM'
depth_method='a'
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', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
# format variables
if csv_file=="":
filelist=os.listdir(input_dir_path) # read in list of files to import
else:
filelist=[csv_file]
# parsing the data
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
file_found = False
for f in filelist: # parse each file
year_warning = True
if f[-3:].lower()=='csv':
print('processing:', f)
file_found = True
# get correct full filename and read data
fname = pmag.resolve_file_name(f, input_dir_path)
full_file = open(fname)
file_input=full_file.readlines()
full_file.close()
keys=file_input[0].replace('\n','').split(',') # splits on underscores
keys=[k.strip('"') for k in keys]
if "Interval Top (cm) on SHLF" in keys:interval_key="Interval Top (cm) on SHLF"
elif " Interval Bot (cm) on SECT" in keys:interval_key=" Interval Bot (cm) on SECT"
elif "Offset (cm)" in keys: interval_key="Offset (cm)"
else: print("couldn't find interval or offset amount")
if "Top Depth (m)" in keys:depth_key="Top Depth (m)"
elif "CSF-A Top (m)" in keys:depth_key="CSF-A Top (m)"
elif "Depth CSF-A (m)" in keys:depth_key="Depth CSF-A (m)"
else: print("couldn't find depth")
if "CSF-B Top (m)" in keys: comp_depth_key="CSF-B Top (m)" # use this model if available
elif "Depth CSF-B (m)" in keys: comp_depth_key="Depth CSF-B (m)"
else: comp_depth_key=""; print("couldn't find composite depth")
if "Demag level (mT)" in keys:demag_key="Demag level (mT)"
elif "Demag Level (mT)" in keys: demag_key="Demag Level (mT)"
elif "Treatment Value" in keys: demag_key="Treatment Value"
else: print("couldn't find demag type")
if "Inclination (Tray- and Bkgrd-Corrected) (deg)" in keys:inc_key="Inclination (Tray- and Bkgrd-Corrected) (deg)"
elif "Inclination background + tray corrected (deg)" in keys:inc_key="Inclination background + tray corrected (deg)"
elif "Inclination background + tray corrected (\xc2\xb0)" in keys:inc_key="Inclination background + tray corrected (\xc2\xb0)"
elif "Inclination background & tray corrected (deg)" in keys:inc_key="Inclination background & tray corrected (deg)"
elif "Inclination background & tray corrected (deg)" in keys:inc_key="Inclination background & tray corrected (deg)"
elif "Inclination background & drift corrected (deg)" in keys:inc_key="Inclination background & drift corrected (deg)"
else: print("couldn't find inclination")
if "Declination (Tray- and Bkgrd-Corrected) (deg)" in keys:dec_key="Declination (Tray- and Bkgrd-Corrected) (deg)"
elif "Declination background + tray corrected (deg)" in keys:dec_key="Declination background + tray corrected (deg)"
elif "Declination background + tray corrected (\xc2\xb0)" in keys:dec_key="Declination background + tray corrected (\xc2\xb0)"
elif "Declination background & tray corrected (deg)" in keys:dec_key="Declination background & tray corrected (deg)"
elif "Declination background & tray corrected (deg)" in keys:dec_key="Declination background & tray corrected (deg)"
elif "Declination background & drift corrected (deg)" in keys:dec_key="Declination background & drift corrected (deg)"
else: print("couldn't find declination")
if "Intensity (Tray- and Bkgrd-Corrected) (A/m)" in keys:int_key="Intensity (Tray- and Bkgrd-Corrected) (A/m)"
elif "Intensity background + tray corrected (A/m)" in keys:int_key="Intensity background + tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys:int_key="Intensity background & tray corrected (A/m)"
elif "Intensity background & tray corrected (A/m)" in keys:int_key="Intensity background & tray corrected (A/m)"
elif "Intensity background & drift corrected (A/m)" in keys:int_key="Intensity background & drift corrected (A/m)"
else: print("couldn't find magnetic moment")
if "Core Type" in keys:
core_type="Core Type"
elif "Type" in keys: core_type="Type"
else: print("couldn't find core type")
if 'Run Number' in keys: run_number_key='Run Number'
elif 'Test No.' in keys: run_number_key='Test No.'
else: print("couldn't find run number")
if 'Test Changed On' in keys: date_key='Test Changed On'
elif "Timestamp (UTC)" in keys: date_key="Timestamp (UTC)"
else: print("couldn't find timestamp")
if "Section" in keys: sect_key="Section"
elif "Sect" in keys: sect_key="Sect"
else: print("couldn't find section number")
if 'Section Half' in keys: half_key='Section Half'
elif "A/W" in keys: half_key="A/W"
else: print("couldn't find half number")
if "Text ID" in keys: text_id="Text ID"
elif "Text Id" in keys: text_id="Text Id"
else: print("couldn't find ID number")
for line in file_input[1:]:
InRec={}
test=0
recs=line.split(',')
for k in range(len(keys)):
if len(recs)==len(keys):
InRec[keys[k]]=line.split(',')[k].strip(""" " ' """)
if 'Exp' in list(InRec.keys()) and InRec['Exp']!="": test=1 # get rid of pesky blank lines (why is this a thing?)
if not test: continue
run_number=""
inst="IODP-SRM"
volume='15.59' # set default volume to this
if 'Sample Area (cm?)' in list(InRec.keys()) and InRec['Sample Area (cm?)']!= "": volume=InRec['Sample Area (cm?)']
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
# Maintain backward compatibility for the ever-changing LIMS format (Argh!)
while len(InRec['Core'])<3:
InRec['Core']='0'+InRec['Core']
if "Last Tray Measurment" in list(InRec.keys()) and "SHLF" not in InRec[text_id] or 'dscr' in csv_file : # assume discrete sample
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"-"+InRec[sect_key]+'-'+InRec[half_key]+'-'+str(InRec[interval_key])
else: # mark as continuous measurements
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]+"_"+InRec[sect_key]+InRec[half_key]+'-'+str(InRec[interval_key])
sample = expedition+'-'+location+'-'+InRec['Core']+InRec[core_type]
site = expedition+'-'+location
if not InRec[dec_key] or not InRec[inc_key]:
print("No dec or inc found for specimen %s, skipping"%specimen); continue
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec['citations']=citations
SpecRec['volume'] = volume
SpecRec['specimen_alternatives']=InRec[text_id]
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec['citations']=citations
SampRec['azimuth']='0'
SampRec['dip']='0'
SampRec['core_depth']=InRec[depth_key]
if comp_depth_key!='':
SampRec['composite_depth']=InRec[comp_depth_key]
if "SHLF" not in InRec[text_id]:
SampRec['method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
else:
SampRec['method_codes']='FS-C-DRILL-IODP:SO-V'
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['citations']=citations
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec['citations']=citations
LocRec['expedition_name']=expedition
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec['specimen'] = specimen
MeasRec['magic_software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]=0
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
MeasRec["quality"]='g' # assume all data are "good"
MeasRec["standard"]='u' # assume all data are "good"
if run_number_key in list(InRec.keys()) and InRec[run_number_key]!= "": run_number=InRec[run_number_key]
datestamp=InRec[date_key].split() # date time is second line of file
if '/' in datestamp[0]:
mmddyy=datestamp[0].split('/') # break into month day year
if len(mmddyy[0])==1: mmddyy[0]='0'+mmddyy[0] # make 2 characters
if len(mmddyy[1])==1: mmddyy[1]='0'+mmddyy[1] # make 2 characters
if len(mmddyy[2])==1: mmddyy[2] = '0'+mmddyy[2] # make 2 characters
if len(datestamp[1])==1: datestamp[1]='0'+datestamp[1] # make 2 characters
hour, minute = datestamp[1].split(':')
if len(hour) == 1:
hour = '0' + hour
date=mmddyy[0]+':'+mmddyy[1]+":"+mmddyy[2] +':' + hour + ":" + minute + ":00"
#date=mmddyy[2] + ':'+mmddyy[0]+":"+mmddyy[1] +':' + hour + ":" + minute + ":00"
if '-' in datestamp[0]:
mmddyy=datestamp[0].split('-') # break into month day year
date=mmddyy[0]+':'+mmddyy[1]+":"+mmddyy[2] +':' +datestamp[1]+":0"
if len(date.split(":")) > 6: date=date[:-2]
# try with month:day:year
try:
utc_dt = datetime.datetime.strptime(date, "%m:%d:%Y:%H:%M:%S")
except ValueError:
# try with year:month:day
try:
utc_dt = datetime.datetime.strptime(date, "%Y:%m:%d:%H:%M:%S")
except ValueError:
# if all else fails, assume the year is in the third position
# and try padding with '20'
new_date = pad_year(date, ind=2, warn=year_warning, fname=os.path.split(f)[1])
utc_dt = datetime.datetime.strptime(new_date, "%m:%d:%Y:%H:%M:%S")
# only give warning once per csv file
year_warning = False
MeasRec['timestamp']=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
MeasRec["method_codes"]='LT-NO'
if 'Treatment Type' in list(InRec.keys()) and InRec['Treatment Type']!="":
if "AF" in InRec['Treatment Type'].upper():
MeasRec['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
MeasRec["treat_ac_field"]=treatment_value # AF demag in treat mT => T
elif "T" in InRec['Treatment Type'].upper():
MeasRec['method_codes'] = 'LT-T-Z'
inst=inst+':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec['Treatment Value'])+273 # convert C => K
MeasRec["treat_temp"]=treatment_value
elif 'Alternating Frequency' in InRec['Treatment Type']:
MeasRec['method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-DTECH' # measured on shipboard Dtech D2000
treatment_value=float(InRec[demag_key])*1e-3 # convert mT => T
MeasRec["treat_ac_field"]=treatment_value # AF demag in treat mT => T
elif 'Thermal' in InRec['Treatment Type']:
MeasRec['method_codes'] = 'LT-T-Z'
inst=inst+':IODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec[demag_key])+273 # convert C => K
MeasRec["treat_temp"]='%8.3e'%(treatment_value) #
elif InRec[demag_key]!="0":
MeasRec['method_codes'] = 'LT-AF-Z'
inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF
try: treatment_value=float(InRec[demag_key])*1e-3 # convert mT => T
except ValueError: print("Couldn't determine treatment value was given treatment value of %s and demag key %s; setting to blank you will have to manually correct this (or fix it)"%(InRec[demag_key], demag_key)); treatment_value=''
MeasRec["treat_ac_field"]=treatment_value # AF demag in treat mT => T
MeasRec["standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_number!="":
MeasRec['external_database_ids']={'LIMS':run_number}
else:
MeasRec['external_database_ids']=""
MeasRec['dir_inc']=InRec[inc_key]
MeasRec['dir_dec']=InRec[dec_key]
intens = InRec[int_key]
try: MeasRec['magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
except ValueError: print("couldn't find magnetic moment for specimen %s and int_key %s; leaving this field blank you'll have to fix this manually"%(specimen, int_key)); MeasRec['magn_moment']=''
MeasRec['instrument_codes']=inst
MeasRec['treat_step_num']='1'
MeasRec['dir_csd']='0'
MeasRec['meas_n_orient']=''
MeasRecs.append(MeasRec)
if not file_found:
print("No .csv files were found")
return (False, "No .csv files were found")
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
#MeasSort=sorted(MeasRecs,key=lambda x: (x['specimen'], float(x['treat_ac_field'])))
#MeasSort=sorted(MeasRecs,key=lambda x: float(x['treat_ac_field']))
#MeasOuts=pmag.measurements_methods3(MeasSort,noave)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.write_table_to_file('specimens', custom_name=spec_file)
con.write_table_to_file('samples', custom_name=samp_file)
con.write_table_to_file('sites', custom_name=site_file)
con.write_table_to_file('locations', custom_name=loc_file)
con.write_table_to_file('measurements', custom_name=meas_file)
return (True, meas_file)
def convert(**kwargs):
# initialize some stuff
methcode="LP-NO"
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD=0,0
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
missing=1
demag="N"
citations='This study'
fmt='old'
Samps=[]
trm=0
irm=0
#get args
user = kwargs.get('user', '')
dir_path = kwargs.get('dir_path', '.')
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file', '')
labfield = kwargs.get('labfield', '')
if labfield:
labfield = float(labfield) *1e-6
else:
labfield = 0
phi = kwargs.get('phi', 0)
if phi:
phi = float(phi)
else:
phi = 0
theta = kwargs.get('theta', 0)
if theta:
theta=float(theta)
else:
theta = 0
peakfield = kwargs.get('peakfield', 0)
if peakfield:
peakfield=float(peakfield) *1e-3
else:
peakfield = 0
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
samp_infile = kwargs.get('samp_infile', '')
syn = kwargs.get('syn', 0)
institution = kwargs.get('institution', '')
syntype = kwargs.get('syntype', '')
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 0)
codelist = kwargs.get('codelist', '')
coil = kwargs.get('coil', '')
cooling_rates = kwargs.get('cooling_rates', '')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
timezone = kwargs.get('timezone', 'UTC')
# make sure all initial values are correctly set up (whether they come from the command line or a GUI)
if samp_infile:
Samps, file_type = pmag.magic_read(samp_infile)
if coil:
coil = str(coil)
methcode="LP-IRM"
irmunits = "V"
if coil not in ["1","2","3"]:
print(__doc__)
print('not a valid coil specification')
return False, '{} is not a valid coil specification'.format(coil)
if mag_file:
lines = pmag.open_file(mag_file)
if not lines:
print("you must provide a valid mag_file")
return False, "you must provide a valid mag_file"
if not mag_file:
print(__doc__)
print("mag_file field is required option")
return False, "mag_file field is required option"
if specnum!=0:
specnum=-specnum
if "4" == samp_con[0]:
if "-" not in samp_con:
print("naming convention option [4] must be in form 4-Z where Z is an integer")
print('---------------')
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" == samp_con[0]:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z = 0
if codelist:
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in sys.argv: methcode="LT-AF-Z"
if'-dc' in sys.argv: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in sys.argv: methcode="LT-T-Z"
if '-dc' in sys.argv: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
irmunits="mT"
if "I3d" in codes:
methcode="LT-T-Z:LP-IRM-3D"
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 "CR" in codes:
demag="T"
cooling_rate_experiment=1
if command_line:
ind=sys.argv.index("CR")
cooling_rates=sys.argv[ind+1]
cooling_rates_list=cooling_rates.split(',')
else:
cooling_rates_list=str(cooling_rates).split(',')
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="T" and "CR" in codes:
methcode="LP-CR-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
MeasRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
version_num=pmag.get_version()
##################################
for line in lines:
instcode=""
if len(line)>2:
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
MeasRec['software_packages']=version_num
MeasRec["description"]=""
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
meas_type="LT-NO"
rec=line.split()
try: float(rec[0]); print("No specimen name for line #%d in the measurement file"%lines.index(line)); continue
except ValueError: pass
if rec[1]==".00":rec[1]="0.00"
treat=rec[1].split('.')
if methcode=="LP-IRM":
if irmunits=='mT':
labfield=float(treat[0])*1e-3
else:
labfield=pmag.getfield(irmunits,coil,treat[0])
if rec[1][0]!="-":
phi,theta=0.,90.
else:
phi,theta=0.,-90.
meas_type="LT-IRM"
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
if len(rec)>6:
code1=rec[6].split(';') # break e.g., 10/15/02;7:45 indo date and time
if len(code1)==2: # old format with AM/PM
missing=0
code2=code1[0].split('/') # break date into mon/day/year
code3=rec[7].split(';') # break e.g., AM;C34;200 into time;instr/axes/measuring pos;number of measurements
yy=int(code2[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(code2[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(code2[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if code3[0]=="PM":hh=hh+12
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
dt=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00"
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
MeasRec["timestamp"]=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
if inst=="":
if code3[1][0]=='C':instcode='SIO-bubba'
if code3[1][0]=='G':instcode='SIO-flo'
else:
instcode=''
MeasRec["meas_n_orient"]=code3[1][2]
elif len(code1)>2: # newest format (cryo7 or later)
if "LP-AN-ARM" not in methcode:labfield=0
fmt='new'
date=code1[0].split('/') # break date into mon/day/year
yy=int(date[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(date[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(date[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else:
min=str(min)
dt=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00"
local = pytz.timezone(timezone)
naive = datetime.datetime.strptime(dt, "%Y:%m:%d:%H:%M:%S")
local_dt = local.localize(naive, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
MeasRec["timestamp"]=utc_dt.strftime("%Y-%m-%dT%H:%M:%S")+"Z"
if inst=="":
if code1[6][0]=='C':
instcode='SIO-bubba'
if code1[6][0]=='G':
instcode='SIO-flo'
else:
instcode=''
if len(code1)>1:
MeasRec["meas_n_orient"]=code1[6][2]
else:
MeasRec["meas_n_orient"]=code1[7] # takes care of awkward format with bubba and flo being different
if user=="":user=code1[5]
if code1[2][-1]=='C':
demag="T"
if code1[4]=='microT' and float(code1[3])!=0. and "LP-AN-ARM" not in methcode: labfield=float(code1[3])*1e-6
if code1[2]=='mT' and methcode!="LP-IRM":
demag="AF"
if code1[4]=='microT' and float(code1[3])!=0.: labfield=float(code1[3])*1e-6
if code1[4]=='microT' and labfield!=0. and meas_type!="LT-IRM":
phi,theta=0.,-90.
if demag=="T": meas_type="LT-T-I"
if demag=="AF": meas_type="LT-AF-I"
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
if code1[4]=='' or labfield==0. and meas_type!="LT-IRM":
if demag=='T':meas_type="LT-T-Z"
if demag=="AF":meas_type="LT-AF-Z"
MeasRec["treat_dc_field"]='0'
if syn==0:
specimen=rec[0]
MeasRec["specimen"]=specimen
if specnum!=0:
sample=rec[0][:specnum]
else:
sample=rec[0]
if samp_infile and Samps: # if samp_infile was provided AND yielded sample data
samp=pmag.get_dictitem(Samps,'sample',sample,'T')
if len(samp)>0:
location=samp[0]["location"]
site=samp[0]["site"]
else:
location=''
site=''
else:
site=pmag.parse_site(sample,samp_con,Z)
if location!='' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
if site!='' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]:
SiteRec['location'] = location
SiteRec['site'] = site
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if sample!='' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]:
SampRec['site'] = site
SampRec['sample'] = sample
SampRecs.append(SampRec)
if specimen!='' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]:
SpecRec["specimen"]=specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
else:
specimen=rec[0]
MeasRec["specimen"]=specimen
if specnum!=0:
sample=rec[0][:specnum]
else:
sample=rec[0]
site=pmag.parse_site(sample,samp_con,Z)
if location!='' and location not in [x['location'] if 'location' in list(x.keys()) else '' for x in LocRecs]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lat_s'] = lat
LocRec['lon_e'] = lon
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
if site!='' and site not in [x['site'] if 'site' in list(x.keys()) else '' for x in SiteRecs]:
SiteRec['location'] = location
SiteRec['site'] = site
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if sample!='' and sample not in [x['sample'] if 'sample' in list(x.keys()) else '' for x in SampRecs]:
SampRec['site'] = site
SampRec['sample'] = sample
SampRecs.append(SampRec)
if specimen!='' and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else '' for x in SpecRecs]:
SpecRec["specimen"]=specimen
SpecRec['sample'] = sample
SpecRecs.append(SpecRec)
SampRec["institution"]=institution
SampRec["material_type"]=syntype
if float(rec[1])==0:
pass
elif demag=="AF":
if methcode != "LP-AN-ARM":
MeasRec["treat_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
if meas_type=="LT-AF-Z": MeasRec["treat_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z:LP-AN-ARM:"
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MeasRec["treat_dc_field"]='%8.3e'%(0)
if labfield!=0 and methcode!="LP-AN-ARM": print("Warning - inconsistency in mag file with lab field - overriding file with 0")
else:
meas_type="LT-AF-I:LP-AN-ARM"
ipos=int(treat[0])-1
MeasRec["treat_dc_field_phi"]='%7.1f' %(dec[ipos])
MeasRec["treat_dc_field_theta"]='%7.1f'% (inc[ipos])
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="T" and methcode == "LP-AN-TRM":
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-AN-TRM"
MeasRec["treat_dc_field"]='%8.3e'%(0)
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
else:
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-AN-TRM"
else:
meas_type="LT-T-I:LP-AN-TRM"
# find the direction of the lab field in two ways:
# (1) using the treatment coding (XX.1=+x, XX.2=+y, XX.3=+z, XX.4=-x, XX.5=-y, XX.6=-z)
ipos_code=int(treat[1][0])-1
# (2) using the magnetization
DEC=float(rec[4])
INC=float(rec[5])
if INC < 45 and INC > -45:
if DEC>315 or DEC<45: ipos_guess=0
if DEC>45 and DEC<135: ipos_guess=1
if DEC>135 and DEC<225: ipos_guess=3
if DEC>225 and DEC<315: ipos_guess=4
else:
if INC >45: ipos_guess=2
if INC <-45: ipos_guess=5
# prefer the guess over the code
ipos=ipos_guess
MeasRec["treat_dc_field_phi"]='%7.1f' %(tdec[ipos])
MeasRec["treat_dc_field_theta"]='%7.1f'% (tinc[ipos])
# check it
if ipos_guess!=ipos_code and treat[1][0]!='7':
print("-E- ERROR: check specimen %s step %s, ATRM measurements, coding does not match the direction of the lab field!"%(rec[0],".".join(list(treat))))
elif demag=="S": # Shaw experiment
if treat[1][1]=='0':
if int(treat[0])!=0:
MeasRec["treat_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z" # first AF
else:
meas_type="LT-NO"
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='0'
elif treat[1][1]=='1':
if int(treat[0])==0:
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MeasRec["treat_dc_field"]='%8.3e'%(arm_labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='2':
if int(treat[0])==0:
MeasRec["treat_ac_field"]='0'
MeasRec["treat_dc_field"]='%8.3e'%(trm_labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
MeasRec["treat_temp"]='%8.3e' % (trm_peakT)
meas_type="LT-T-I"
else:
MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='3':
if int(treat[0])==0:
MeasRec["treat_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MeasRec["treat_dc_field"]='%8.3e'%(arm_labfield)
MeasRec["treat_dc_field_phi"]='%7.1f'%(phi)
MeasRec["treat_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MeasRec["treat_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MeasRec["treat_dc_field"]='0'
meas_type="LT-AF-Z"
# Cooling rate experient # added by rshaar
elif demag=="T" and methcode == "LP-CR-TRM":
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-CR-TRM"
MeasRec["treat_dc_field"]='%8.3e'%(0)
MeasRec["treat_dc_field_phi"]='0'
MeasRec["treat_dc_field_theta"]='0'
else:
MeasRec["treat_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-CR-TRM"
else:
meas_type="LT-T-I:LP-CR-TRM"
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
indx=int(treat[1][0])-1
# alteration check matjed as 0.7 in the measurement file
if indx==6:
cooling_time= cooling_rates_list[-1]
else:
cooling_time=cooling_rates_list[indx]
MeasRec["description"]="cooling_rate"+":"+cooling_time+":"+"K/min"
elif demag!='N':
if len(treat)==1:treat.append('0')
MeasRec["treat_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MeasRec["treat_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
labfield=float(treat[1])*1e-6
MeasRec["treat_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MeasRec["treat_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MeasRec["treat_dc_field_theta"]='%7.1f' % (theta) # labfield theta
meas_type="LT-T-I:LP-TRM" # trm acquisition experiment
MeasRec["dir_csd"]=rec[2]
MeasRec["magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
MeasRec["dir_dec"]=rec[4]
MeasRec["dir_inc"]=rec[5]
MeasRec["instrument_codes"]=instcode
MeasRec["analysts"]=user
MeasRec["citations"]=citations
if "LP-IRM-3D" in methcode : meas_type=methcode
#MeasRec["method_codes"]=methcode.strip(':')
MeasRec["method_codes"]=meas_type
MeasRec["quality"]='g'
if 'std' in rec[0]:
MeasRec["standard"]='s'
else:
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
#print MeasRec['treat_temp']
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
# create MagIC tables
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
# write MagIC tables to file
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
"""
Converts CIT formated Magnetometer data into MagIC format for Analysis and contribution to the MagIC database
Parameters
-----------
dir_path : directory to output files to (default : current directory)
user : colon delimited list of analysts (default : "")
magfile : magnetometer file (.sam) to convert to MagIC (required)
meas_file : measurement file name to output (default : measurements.txt)
spec_file : specimen file name to output (default : specimens.txt)
samp_file : sample file name to output (default : samples.txt)
site_file : site file name to output (default : site.txt)
loc_file : location file name to output (default : locations.txt)
locname : location name
methods : colon delimited list of sample method codes. full list here (https://www2.earthref.org/MagIC/method-codes) (default : SO-MAG
specnum : number of terminal characters that identify a specimen
norm : is volume or mass normalization using cgs or si units (options : cc,m3,g,kg) (default : cc)
oersted : demag step vales are in Oersted
noave : average measurement data or not. False is average, True is don't average. (default : False)
samp_con : sample naming convention options as follows:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in sitename column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
input_dir_path : if you did not supply a full path with magfile you can put the directory the magfile is in here
meas_n_orient : Number of different orientations in measurement (default : 8)
labfield : DC_FIELD in microTesla (default : 0)
phi : DC_PHI in degrees (default : 0)
theta : DC_THETA in degrees (default : 0)
Returns
-----------
type - Tuple : (True or False indicating if conversion was sucessful, meas_file name written)
"""
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
locname = kwargs.get('locname', 'unknown')
sitename = kwargs.get('sitename', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
oersted = kwargs.get('oersted', False) # mT (oe/10) is the default value
noave = kwargs.get('noave', False) # False means do average
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path',os.path.split(magfile)[0])
meas_n_orient = kwargs.get('meas_n_orient','8')
output_dir_path = dir_path
try:
DC_FIELD = float(kwargs.get('labfield',0))*1e-6
DC_PHI = float(kwargs.get('phi',0))
DC_THETA = float(kwargs.get('theta',0))
except ValueError: raise ValueError('problem with your dc parameters. please provide a labfield in microTesla and a phi and theta in degrees.')
yn = ''
if DC_FIELD==0 and DC_PHI==0 and DC_THETA==0: GET_DC_PARAMS=True
else: GET_DC_PARAMS=False
if locname=='' or locname==None: locname = 'unknown'
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z=1
#get file names and open magfile to start reading data
if input_dir_path=='': input_dir_path='.'
magfile = os.path.join(input_dir_path, magfile)
FIRST_GET_DC=True
try:
file_input=open(magfile,'r')
except IOError as ex:
print(("bad sam file name: ", magfile))
return False, "bad sam file name"
File = file_input.readlines()
file_input.close()
if len(File) == 1: File = File[0].split('\r'); File = [x+"\r\n" for x in File]
#define initial variables
SpecRecs,SampRecs,SiteRecs,LocRecs,MeasRecs=[],[],[],[],[]
sids,ln,format,citations=[],0,'CIT',"This study"
formats=['CIT','2G','APP','JRA']
if File[ln].strip()=='CIT': ln+=1
LocRec={}
LocRec["location"]=locname
LocRec["citations"]=citations
LocRec['analysts']=user
comment=File[ln]
if comment=='CIT':
format=comment
ln+=1
comment=File[ln]
print(comment)
ln+=1
specimens,samples,sites=[],[],[]
if format=='CIT':
line=File[ln].split()
site_lat=line[0]
site_lon=line[1]
LocRec["lat_n"]=site_lat
LocRec["lon_e"]=site_lon
LocRec["lat_s"]=site_lat
LocRec["lon_w"]=site_lon
LocRecs.append(LocRec)
Cdec=float(line[2])
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
if rec == []: continue
specimen=rec[0]
specimens.append(specimen)
for specimen in specimens:
SpecRec,SampRec,SiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
if sitename: site=sitename
else: site=pmag.parse_site(sample,samp_con,Z)
SpecRec['specimen']=specimen
SpecRec['sample']=sample
SpecRec['citations']=citations
SpecRec['analysts']=user
SampRec['sample']=sample
SampRec['site']=site
SampRec['citations']=citations
SampRec['method_codes']=methods
SampRec['azimuth_dec_correction']='%7.1f'%(Cdec)
SampRec['analysts']=user
SiteRec['site']=site
SiteRec['location']=locname
SiteRec['citations']=citations
SiteRec['lat']=site_lat
SiteRec['lon']=site_lon
SiteRec['analysts']=user
f=open(os.path.join(input_dir_path,specimen),'r')
Lines=f.readlines()
f.close()
comment=""
line=Lines[0].split()
if len(line)>2:
comment=line[2]
info=Lines[1].split()
volmass=float(info[-1])
if volmass==1.0:
print('Warning: Specimen volume set to 1.0.')
print('Warning: If volume/mass really is 1.0, set volume/mass to 1.001')
print('Warning: specimen method code LP-NOMAG set.')
SpecRec['weight']=""
SpecRec['volume']=""
SpecRec['method_codes']='LP-NOMAG'
elif norm=="gm":
SpecRec['volume']=''
SpecRec['weight']='%10.3e'%volmass*1e-3
elif norm=="kg":
SpecRec['volume']=''
SpecRec['weight']='%10.3e'*volmass
elif norm=="cc":
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass*1e-6)
elif norm=="m3":
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass)
else:
print('Warning: Unknown normalization unit ', norm, '. Using default of cc')
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass*1e-6)
dip=float(info[-2])
dip_direction=float(info[-3])+Cdec+90.
sample_dip=-float(info[-4])
sample_azimuth=float(info[-5])+Cdec-90.
if len(info)>5:
SampRec['height']=info[-6]
else:
SampRec['height']='0'
SampRec['azimuth']='%7.1f'%(sample_azimuth)
SampRec['dip']='%7.1f'%(sample_dip)
SampRec['bed_dip']='%7.1f'%(dip)
SampRec['bed_dip_direction']='%7.1f'%(dip_direction)
SampRec['geologic_classes']=''
SampRec['geologic_types']=''
SampRec['lithologies']=''
if Cdec!=0 or Cdec!="":
SampRec['method_codes']='SO-CMD-NORTH'
else:
SampRec['method_codes']='SO-MAG'
for line in Lines[2:len(Lines)]:
if line == '\n': continue
MeasRec=SpecRec.copy()
MeasRec.pop('sample')
MeasRec['analysts']=user
# Remove volume and weight as they do not exits in the magic_measurement table
del MeasRec["volume"]
del MeasRec["weight"]
if line[3:6]==' ' : # USGS files have blank for an AF demag value when measurement is the NRM. njarboe
line = 'NRM' + line[3:]
treat_type=line[0:3]
if treat_type[1] == '.':
treat_type = 'NRM'
treat=line[2:6]
try: float(treat)
except ValueError:
treat=line[3:6]
if treat.split()=='': treat='0'
try: float(treat)
except ValueError: treat = line.split()[1]
if treat_type.startswith('NRM'):
MeasRec['method_codes']='LT-NO'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('LT') or treat_type.upper().startswith('LN2'):
MeasRec['method_codes']='LT-LT-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='77'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('AF') or treat_type.startswith('MAF'):
MeasRec['method_codes']='LT-AF-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treat_ac_field']='0'
else:
try: MeasRec['treat_ac_field']='%10.3e'%(float(treat)*1e-3)
except ValueError as e: print(os.path.join(input_dir_path,specimen)); raise e
if MeasRec['treat_ac_field']!='0':
MeasRec['treat_ac_field']='%10.3e'%(float(MeasRec['treat_ac_field'])/10)
elif treat_type.startswith('ARM'):
MeasRec['method_codes']="LP-ARM"
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treat_ac_field']='0'
else:
MeasRec['method_codes']="LP-ARM-AFD"
MeasRec['treat_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('IRM'):
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']="LT-IRM"
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('TT'):
MeasRec['method_codes']='LT-T-Z'
MeasRec['meas_temp']='273'
if treat.strip() == '':
MeasRec['treat_temp']='273'
else:
MeasRec['treat_temp']='%7.1f'%(float(treat)+273)
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '0': #assume decimal IZZI format 0 field thus can hardcode the dc fields
MeasRec['method_codes']='LT-T-Z'
MeasRec['meas_temp']='273'
try: MeasRec['treat_temp']=str(int(treat_type) + 273)
except ValueError as e: print(specimen); raise e
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '1': #assume decimal IZZI format in constant field
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-T-I'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '2': #assume decimal IZZI format PTRM step
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-PTRM-I'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '3': #assume decimal IZZI format PTRM tail check
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-PTRM-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
else:
print("trouble with your treatment steps")
MeasRec['dir_dec']=line[46:51]
MeasRec['dir_inc']=line[52:58]
# Some MIT files have and extra digit in the exponent of the magnetude.
# That makes those files not compliant with the cit measurement file spec.
# Not sure if we should just print an error message and exit. For now we accept the file and fix it.
# The first digit of the exponent, which should always be zero, is cut out of the line if column 39 is not ' '
if line[39] != ' ': line = line[0:37] + line[38:]
M='%8.2e'%(float(line[31:39])*volmass*1e-3) # convert to Am2
MeasRec['magn_moment']=M
MeasRec['dir_csd']='%7.1f'%(eval(line[41:46]))
MeasRec["meas_n_orient"]=meas_n_orient
MeasRec['standard']='u'
if len(line)>60:
MeasRec['instrument_codes']=line[85:].strip('\n \r \t "')
MeasRec['magn_x_sigma']='%8.2e'%(float(line[58:67])*1e-8) #(convert e-5emu to Am2)
MeasRec['magn_y_sigma']='%8.2e'%(float(line[67:76])*1e-8)
MeasRec['magn_z_sigma']='%8.2e'%(float(line[76:85])*1e-8)
MeasRecs.append(MeasRec)
SpecRecs.append(SpecRec)
if sample not in samples:
samples.append(sample)
SampRecs.append(SampRec)
if site not in sites:
sites.append(site)
SiteRecs.append(SiteRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
"""
Converts CIT formated Magnetometer data into MagIC format for Analysis and contribution to the MagIC database
Parameters
-----------
dir_path : directory to output files to (default : current directory)
user : colon delimited list of analysts (default : "")
magfile : magnetometer file (.sam) to convert to MagIC (required)
meas_file : measurement file name to output (default : measurements.txt)
spec_file : specimen file name to output (default : specimens.txt)
samp_file : sample file name to output (default : samples.txt)
site_file : site file name to output (default : site.txt)
loc_file : location file name to output (default : locations.txt)
locname : location name
methods : colon delimited list of sample method codes. full list here (https://www2.earthref.org/MagIC/method-codes) (default : SO-MAG
specnum : number of terminal characters that identify a specimen
norm : is volume or mass normalization using cgs or si units (options : cc,m3,g,kg) (default : cc)
noave : average measurement data or not. False is average, True is don't average. (default : False)
samp_con : sample naming convention options as follows:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in sitename column in the orient.txt format input file -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
input_dir_path : if you did not supply a full path with magfile you can put the directory the magfile is in here
meas_n_orient : Number of different orientations in measurement (default : 8)
labfield : DC_FIELD in microTesla (default : 0)
phi : DC_PHI in degrees (default : 0)
theta : DC_THETA in degrees (default : 0)
Returns
-----------
type - Tuple : (True or False indicating if conversion was sucessful, meas_file name written)
"""
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
locname = kwargs.get('locname', 'unknown')
sitename = kwargs.get('sitename', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
noave = kwargs.get('noave', False) # False means do average
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path',os.path.split(magfile)[0])
meas_n_orient = kwargs.get('meas_n_orient','8')
output_dir_path = dir_path
try:
DC_FIELD = float(kwargs.get('labfield',0))*1e-6
DC_PHI = float(kwargs.get('phi',0))
DC_THETA = float(kwargs.get('theta',0))
except ValueError: raise ValueError('problem with your dc parameters. please provide a labfield in microTesla and a phi and theta in degrees.')
yn = ''
if DC_FIELD==0 and DC_PHI==0 and DC_THETA==0: GET_DC_PARAMS=True
else: GET_DC_PARAMS=False
if locname=='' or locname==None: locname = 'unknown'
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z=1
#get file names and open magfile to start reading data
if input_dir_path=='': input_dir_path='.'
magfile = os.path.join(input_dir_path, magfile)
FIRST_GET_DC=True
try:
file_input=open(magfile,'r')
except IOError as ex:
print(("bad sam file name: ", magfile))
return False, "bad sam file name"
File = file_input.readlines()
file_input.close()
if len(File) == 1: File = File[0].split('\r'); File = [x+"\r\n" for x in File]
#define initial variables
SpecRecs,SampRecs,SiteRecs,LocRecs,MeasRecs=[],[],[],[],[]
sids,ln,format,citations=[],0,'CIT',"This study"
formats=['CIT','2G','APP','JRA']
if File[ln].strip()=='CIT': ln+=1
LocRec={}
LocRec["location"]=locname
LocRec["citations"]=citations
LocRec['analysts']=user
comment=File[ln]
if comment=='CIT':
format=comment
ln+=1
comment=File[ln]
print(comment)
ln+=1
specimens,samples,sites=[],[],[]
if format=='CIT':
line=File[ln].split()
site_lat=line[0]
site_lon=line[1]
LocRec["lat_n"]=site_lat
LocRec["lon_e"]=site_lon
LocRec["lat_s"]=site_lat
LocRec["lon_w"]=site_lon
LocRecs.append(LocRec)
Cdec=float(line[2])
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
if rec == []: continue
specimen=rec[0]
specimens.append(specimen)
for specimen in specimens:
SpecRec,SampRec,SiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
if sitename: site=sitename
else: site=pmag.parse_site(sample,samp_con,Z)
SpecRec['specimen']=specimen
SpecRec['sample']=sample
SpecRec['citations']=citations
SpecRec['analysts']=user
SampRec['sample']=sample
SampRec['site']=site
SampRec['citations']=citations
SampRec['method_codes']=methods
SampRec['azimuth_dec_correction']='%7.1f'%(Cdec)
SampRec['analysts']=user
SiteRec['site']=site
SiteRec['location']=locname
SiteRec['citations']=citations
SiteRec['lat']=site_lat
SiteRec['lon']=site_lon
SiteRec['analysts']=user
f=open(os.path.join(input_dir_path,specimen),'r')
Lines=f.readlines()
f.close()
comment=""
line=Lines[0].split()
if len(line)>2:
comment=line[2]
info=Lines[1].split()
volmass=float(info[-1])
if volmass==1.0:
print('Warning: Specimen volume set to 1.0.')
print('Warning: If volume/mass really is 1.0, set volume/mass to 1.001')
print('Warning: specimen method code LP-NOMAG set.')
SpecRec['weight']=""
SpecRec['volume']=""
SpecRec['method_codes']='LP-NOMAG'
elif norm=="gm":
SpecRec['volume']=''
SpecRec['weight']='%10.3e'%volmass*1e-3
elif norm=="kg":
SpecRec['volume']=''
SpecRec['weight']='%10.3e'*volmass
elif norm=="cc":
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass*1e-6)
elif norm=="m3":
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass)
else:
print('Warning: Unknown normalization unit ', norm, '. Using default of cc')
SpecRec['weight']=""
SpecRec['volume']='%10.3e'%(volmass*1e-6)
dip=float(info[-2])
dip_direction=float(info[-3])+Cdec+90.
sample_dip=-float(info[-4])
sample_azimuth=float(info[-5])+Cdec-90.
if len(info)>5:
SampRec['height']=info[-6]
else:
SampRec['height']='0'
SampRec['azimuth']='%7.1f'%(sample_azimuth)
SampRec['dip']='%7.1f'%(sample_dip)
SampRec['bed_dip']='%7.1f'%(dip)
SampRec['bed_dip_direction']='%7.1f'%(dip_direction)
SampRec['geologic_classes']=''
SampRec['geologic_types']=''
SampRec['lithologies']=''
if Cdec!=0 or Cdec!="":
SampRec['method_codes']='SO-CMD-NORTH'
else:
SampRec['method_codes']='SO-MAG'
for line in Lines[2:len(Lines)]:
if line == '\n': continue
MeasRec=SpecRec.copy()
MeasRec.pop('sample')
MeasRec['analysts']=user
# Remove volume and weight as they do not exits in the magic_measurement table
del MeasRec["volume"]
del MeasRec["weight"]
if line[3:6]==' ' : # USGS files have blank for an AF demag value when measurement is the NRM. njarboe
line = 'NRM' + line[3:]
treat_type=line[0:3]
if treat_type[1] == '.':
treat_type = 'NRM'
treat=line[2:6]
try: float(treat)
except ValueError:
treat=line[3:6]
if treat.split()=='': treat='0'
try: float(treat)
except ValueError: treat = line.split()[1]
if treat_type.startswith('NRM'):
MeasRec['method_codes']='LT-NO'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('LT') or treat_type.upper().startswith('LN2'):
MeasRec['method_codes']='LT-LT-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='77'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('AF') or treat_type.startswith('MAF'):
MeasRec['method_codes']='LT-AF-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treat_ac_field']='0'
else:
try: MeasRec['treat_ac_field']='%10.3e'%(float(treat)*1e-3)
except ValueError as e: print(os.path.join(input_dir_path,specimen)); raise e
elif treat_type.startswith('ARM'):
MeasRec['method_codes']="LP-ARM"
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
if treat.strip() == '':
MeasRec['treat_ac_field']='0'
else:
MeasRec['method_codes']="LP-ARM-AFD"
MeasRec['treat_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.startswith('IRM'):
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']="LT-IRM"
MeasRec['meas_temp']='273'
MeasRec['treat_temp']='273'
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif treat_type.startswith('TT'):
MeasRec['method_codes']='LT-T-Z'
MeasRec['meas_temp']='273'
if treat.strip() == '':
MeasRec['treat_temp']='273'
else:
MeasRec['treat_temp']='%7.1f'%(float(treat)+273)
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '0': #assume decimal IZZI format 0 field thus can hardcode the dc fields
MeasRec['method_codes']='LT-T-Z'
MeasRec['meas_temp']='273'
try: MeasRec['treat_temp']=str(int(treat_type) + 273)
except ValueError as e: print(specimen); raise e
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '1': #assume decimal IZZI format in constant field
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-T-I'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '2': #assume decimal IZZI format PTRM step
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-PTRM-I'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='%1.2e'%DC_FIELD
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
elif line[4] == '3': #assume decimal IZZI format PTRM tail check
if GET_DC_PARAMS: GET_DC_PARAMS, FIRST_GET_DC, yn, DC_FIELD, DC_PHI, DC_THETA = get_dc_params(FIRST_GET_DC,specimen,treat_type,yn)
MeasRec['method_codes']='LT-PTRM-Z'
MeasRec['meas_temp']='273'
MeasRec['treat_temp']=str(int(treat_type) + 273)
MeasRec['treat_dc_field']='0'
MeasRec['treat_dc_field_phi'] = '%1.2f'%DC_PHI
MeasRec['treat_dc_field_theta'] = '%1.2f'%DC_THETA
MeasRec['treat_ac_field']='0'
else:
print("trouble with your treatment steps")
MeasRec['dir_dec']=line[46:51]
MeasRec['dir_inc']=line[52:58]
# Some MIT files have and extra digit in the exponent of the magnetude.
# That makes those files not compliant with the cit measurement file spec.
# Not sure if we should just print an error message and exit. For now we accept the file and fix it.
# The first digit of the exponent, which should always be zero, is cut out of the line if column 39 is not ' '
if line[39] != ' ': line = line[0:37] + line[38:]
M='%8.2e'%(float(line[31:39])*volmass*1e-3) # convert to Am2
MeasRec['magn_moment']=M
MeasRec['dir_csd']='%7.1f'%(eval(line[41:46]))
MeasRec["meas_n_orient"]=meas_n_orient
MeasRec['standard']='u'
if len(line)>60:
MeasRec['instrument_codes']=line[85:].strip('\n \r \t "')
MeasRec['magn_x_sigma']='%8.2e'%(float(line[58:67])*1e-8) #(convert e-5emu to Am2)
MeasRec['magn_y_sigma']='%8.2e'%(float(line[67:76])*1e-8)
MeasRec['magn_z_sigma']='%8.2e'%(float(line[76:85])*1e-8)
MeasRecs.append(MeasRec)
SpecRecs.append(SpecRec)
if sample not in samples:
samples.append(sample)
SampRecs.append(SampRec)
if site not in sites:
sites.append(site)
SiteRecs.append(SiteRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
#
# initialize variables
#
bed_dip, bed_dip_dir = "", ""
sclass, lithology, _type = "", "", ""
DecCorr = 0.
months = [
'Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct',
'Nov', 'Dec'
]
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
meas_file = kwargs.get('meas_file', 'measurements.txt')
spec_file = kwargs.get('spec_file', 'specimens.txt')
samp_file = kwargs.get('samp_file', 'samples.txt')
site_file = kwargs.get('site_file', 'sites.txt')
loc_file = kwargs.get('loc_file', 'locations.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', 'FS-FD:SO-POM')
location = kwargs.get('location', 'unknown')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
user = kwargs.get('user', '')
noave = kwargs.get('noave', 0) # default is DO average
ID = kwargs.get('ID', '')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
# format and fix variables acquired from command line sys.argv or input with **kwargs
if specnum != 0: specnum = -specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
Z = 1
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if "6" in samp_con:
print('Naming convention option [6] not currently supported')
return False, 'Naming convention option [6] not currently supported'
#Z=1
#try:
# SampRecs,file_type=pmag.magic_read(os.path.join(input_dir_path, 'er_samples.txt'))
#except:
# print("there is no er_samples.txt file in your input directory - you can't use naming convention #6")
# return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
#if file_type == 'bad_file':
# print("there is no er_samples.txt file in your input directory - you can't use naming convention #6")
# return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
#else: Z=1
if not mag_file:
print("mag file is required input")
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samplist = []
try:
SampRecs, file_type = pmag.magic_read(samp_file)
except:
SampRecs = []
MeasRecs, SpecRecs, SiteRecs, LocRecs = [], [], [], []
try:
f = open(mag_file, 'br')
input = str(f.read()).strip("b '")
f.close()
except Exception as ex:
print('ex', ex)
print("bad mag file")
return False, "bad mag file"
firstline, date = 1, ""
d = input.split('\\xcd')
for line in d:
rec = line.split('\\x00')
if firstline == 1:
firstline = 0
spec, vol = "", 1
el = 51
while line[el:el + 1] != "\\":
spec = spec + line[el]
el += 1
# check for bad sample name
test = spec.split('.')
date = ""
if len(test) > 1:
spec = test[0]
kk = 24
while line[kk] != '\\x01' and line[kk] != '\\x00':
kk += 1
vcc = line[24:kk]
el = 10
while rec[el].strip() != '':
el += 1
date, comments = rec[el + 7], []
else:
el = 9
while rec[el] != '\\x01':
el += 1
vcc, date, comments = rec[el - 3], rec[el + 7], []
specname = spec.lower()
print('importing ', specname)
el += 8
while rec[el].isdigit() == False:
comments.append(rec[el])
el += 1
while rec[el] == "":
el += 1
az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
pl = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip_dir = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip = float(rec[el])
el += 1
while rec[el] == "":
el += 1
if rec[el] == '\\x01':
bed_dip = 180. - bed_dip
el += 1
while rec[el] == "":
el += 1
fold_az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
fold_pl = rec[el]
el += 1
while rec[el] == "":
el += 1
if rec[el] != "" and rec[el] != '\\x02' and rec[el] != '\\x01':
deccorr = float(rec[el])
az += deccorr
bed_dip_dir += deccorr
fold_az += deccorr
if bed_dip_dir >= 360: bed_dip_dir = bed_dip_dir - 360.
if az >= 360.: az = az - 360.
if fold_az >= 360.: fold_az = fold_az - 360.
else:
deccorr = 0
if specnum != 0:
sample = specname[:specnum]
else:
sample = specname
methods = gmeths.split(':')
if deccorr != "0":
if 'SO-MAG' in methods: del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths = reduce(lambda x, y: x + ':' + y, methods)
method_codes = meths
site = pmag.parse_site(sample, samp_con,
Z) # parse out the site name
SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}
SpecRec["specimen"] = specname
SpecRec["sample"] = sample
if vcc.strip() != "":
vol = float(vcc) * 1e-6 # convert to m^3 from cc
SpecRec["volumne"] = '%10.3e' % (vol) #
SpecRec["geologic_classes"] = sclass
SpecRec["lithologies"] = lithology
SpecRec["geologic_types"] = _type
SpecRecs.append(SpecRec)
if sample != "" and sample not in [
x['sample'] if 'sample' in list(x.keys()) else ""
for x in SampRecs
]:
SampRec["sample"] = sample
SampRec["site"] = site
labaz, labdip = pmag.orient(az, pl,
or_con) # convert to labaz, labpl
SampRec["bed_dip"] = '%7.1f' % (bed_dip)
SampRec["bed_dip_direction"] = '%7.1f' % (bed_dip_dir)
SampRec["dip"] = '%7.1f' % (labdip)
SampRec["azimuth"] = '%7.1f' % (labaz)
SampRec["azimuth_dec_correction"] = '%7.1f' % (deccorr)
SampRec["geologic_classes"] = sclass
SampRec["lithologies"] = lithology
SampRec["geologic_types"] = _type
SampRec["method_codes"] = method_codes
SampRecs.append(SampRec)
if site != "" and site not in [
x['site'] if 'site' in list(x.keys()) else ""
for x in SiteRecs
]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRec["geologic_classes"] = sclass
SiteRec["lithologies"] = lithology
SiteRec["geologic_types"] = _type
SiteRecs.append(SiteRec)
if location != "" and location not in [
x['location'] if 'location' in list(x.keys()) else ""
for x in LocRecs
]:
LocRec['location'] = location
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRec["geologic_classes"] = sclass
LocRec["lithologies"] = lithology
LocRec["geologic_types"] = _type
LocRecs.append(LocRec)
else:
MeasRec = {}
MeasRec["treat_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"] = '%8.3e' % (273) # room temp in kelvin
MeasRec["treat_ac_field"] = '0'
MeasRec["treat_dc_field"] = '0'
MeasRec["treat_dc_field_phi"] = '0'
MeasRec["treat_dc_field_theta"] = '0'
meas_type = "LT-NO"
MeasRec["quality"] = 'g'
MeasRec["standard"] = 'u'
MeasRec["treat_step_num"] = '1'
MeasRec["specimen"] = specname
el, demag = 1, ''
treat = rec[el]
if treat[-1] == 'C':
demag = 'T'
elif treat != 'NRM':
demag = 'AF'
el += 1
while rec[el] == "":
el += 1
MeasRec["dir_dec"] = rec[el]
cdec = float(rec[el])
el += 1
while rec[el] == "":
el += 1
MeasRec["dir_inc"] = rec[el]
cinc = float(rec[el])
el += 1
while rec[el] == "":
el += 1
gdec = rec[el]
el += 1
while rec[el] == "":
el += 1
ginc = rec[el]
el = skip(2, el, rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MeasRec["magn_moment"] = '%10.3e' % (float(rec[el]) * 1e-3
) # moment in Am^2 (from emu)
MeasRec["magn_volume"] = '%10.3e' % (float(rec[el]) * 1e-3 / vol
) # magnetization in A/m
el = skip(2, el, rec) # skip to xsig
MeasRec["magn_x_sigma"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el = skip(3, el, rec) # skip to ysig
MeasRec["magn_y_sigma"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el = skip(3, el, rec) # skip to zsig
MeasRec["magn_z_sigma"] = '%10.3e' % (float(rec[el]) * 1e-3
) # convert from emu
el += 1 # skip to positions
MeasRec["meas_n_orient"] = rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MeasRec['measurement_date']=dstring
MeasRec["instrument_codes"] = inst
MeasRec["analysts"] = user
MeasRec["citations"] = "This study"
MeasRec["method_codes"] = meas_type
if demag == "AF":
MeasRec["treat_ac_field"] = '%8.3e' % (float(treat[:-2]) * 1e-3
) # peak field in tesla
meas_type = "LT-AF-Z"
MeasRec["treat_dc_field"] = '0'
elif demag == "T":
MeasRec["treat_temp"] = '%8.3e' % (float(treat[:-1]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
MeasRec['method_codes'] = meas_type
MeasRecs.append(MeasRec)
con = nb.Contribution(output_dir_path, read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts = pmag.measurements_methods3(MeasRecs, noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.write_table_to_file('specimens', custom_name=spec_file)
con.write_table_to_file('samples', custom_name=samp_file)
con.write_table_to_file('sites', custom_name=site_file)
con.write_table_to_file('locations', custom_name=loc_file)
con.write_table_to_file('measurements', custom_name=meas_file)
return True, meas_file
def convert(**kwargs):
"""
EXAMPLE DOCSTRING for function (you would usually put the discription here)
Parameters
-----------
user : colon delimited list of analysts (default : "")
magfile : input magnetometer file (required)
Returns
-----------
type - Tuple : (True or False indicating if conversion was sucessful, meas_file name written)
"""
#get parameters from kwargs.get(parameter_name, default_value)
user = kwargs.get('user', '')
magfile = kwargs.get('magfile')
#do any extra formating you need to variables here
#open magfile to start reading data
try:
infile=open(magfile,'r')
except Exception as ex:
print(("bad file path: ", magfile))
return False, "bad file path"
#Depending on the dataset you may need to read in all data here put it in a list of dictionaries or something here. If you do just replace the "for line in infile.readlines():" bellow with "for d in data:" where data is the structure you put your data into
#define the lists that hold each line of data for their respective tables
SpecRecs,SampRecs,SiteRecs,LocRecs,MeasRecs=[],[],[],[],[]
#itterate over the contence of the file
for line in infile.readlines():
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
#extract data from line and put it in variables
#fill this line of the Specimen table using above variables
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['analysts']=user
SpecRecs.append(SpecRec)
#fill this line of the Sample table using above variables
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['analysts']=user
SampRecs.append(SampRec)
#fill this line of the Site table using above variables
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['analysts']=user
SiteRecs.append(SiteRec)
#fill this line of the Location table using above variables
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['analysts']=user
LocRecs.append(LocRec)
#Fill this line of Meas Table using data in line
MeasRec['analysts']=user
MeasRecs.append(MeasRec)
#close your file object so Python3 doesn't throw an annoying warning
infile.close()
#open a Contribution object
con = nb.Contribution(output_dir_path,read_tables=[])
#Create Magic Tables and add to a contribution
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave) #figures out method codes for measuremet data
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
#write to file
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
return True, meas_file
def main(**kwargs):
version_num=pmag.get_version()
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'sites.txt') # site outfile
loc_file = kwargs.get('loc_file', 'locations.txt') # location outfile
mag_file = kwargs.get('mag_file')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
location = kwargs.get('location', 'unknown')
lat = kwargs.get('lat', '')
lon = kwargs.get('lon', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 2.5))* 1e-6
JR = kwargs.get('JR', False)
if JR:
if meth_code == "LP-NO":
meth_code = ""
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
samp_con='5'
# format variables
tmp_file = mag_file.split(os.extsep)[0]+os.extsep+'tmp'
mag_file = os.path.join(input_dir_path, mag_file)
if specnum!=0: specnum=-int(specnum)
if samp_con.startswith("4"):
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
elif samp_con.startswith("7"):
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
else: Z=1
# parse data
# fix .jr6 file so that there are spaces between all the columns.
pre_data=open(mag_file, 'r')
tmp_data=open(tmp_file, 'w')
if samp_con!='2': fixed_data=pre_data.read().replace('-',' -')
else:
fixed_data=""
for line in pre_data.readlines():
entries=line.split()
if len(entries)<2: continue
fixed_line = entries[0] + ' ' + reduce(lambda x,y: x+' '+y, [x.replace('-',' -') for x in entries[1:]])
fixed_data += fixed_line+os.linesep
tmp_data.write(fixed_data)
tmp_data.close()
pre_data.close()
if not JR:
column_names=['specimen', 'step', 'x', 'y', 'z', 'expon', 'azimuth', 'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2', 'param3', 'param4', 'dir_csd']
else: # measured on the Joides Resolution JR6
column_names=['specimen', 'step', 'negz', 'y', 'x', 'expon', 'azimuth', 'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2', 'param3', 'param4', 'dir_csd']
data=pd.read_csv(tmp_file, delim_whitespace=True, names=column_names, index_col=False)
if isinstance(data['x'][0],str):
column_names=['specimen', 'step', 'step_unit', 'x', 'y', 'z', 'expon', 'azimuth', 'dip', 'bed_dip_direction', 'bed_dip', 'bed_dip_dir2', 'bed_dip2', 'param1', 'param2', 'param3', 'param4', 'dir_csd']
data=pd.read_csv(tmp_file, delim_whitespace=True, names=column_names, index_col=False)
if JR: data['z']=-data['negz']
cart=np.array([data['x'],data['y'],data['z']]).transpose()
dir_dat= pmag.cart2dir(cart).transpose()
data['dir_dec']=dir_dat[0]
data['dir_inc']=dir_dat[1]
data['magn_moment']=dir_dat[2]*(10.0**data['expon'])*volume # the data are in A/m - this converts to Am^2
data['magn_volume']=dir_dat[2]*(10.0**data['expon']) # A/m - data in A/m
data['dip']=-data['dip']
data['specimen']
# put data into magic tables
MagRecs,SpecRecs,SampRecs,SiteRecs,LocRecs=[],[],[],[],[]
for rowNum, row in data.iterrows():
MeasRec,SpecRec,SampRec,SiteRec,LocRec={},{},{},{},{}
specimen=row['specimen']
if specnum!=0: sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
if specimen!="" and specimen not in [x['specimen'] if 'specimen' in list(x.keys()) else "" for x in SpecRecs]:
SpecRec['specimen'] = specimen
SpecRec['sample'] = sample
SpecRec["citations"]="This study"
SpecRec["analysts"]=user
SpecRec['volume'] = volume
SpecRecs.append(SpecRec)
if sample!="" and sample not in [x['sample'] if 'sample' in list(x.keys()) else "" for x in SampRecs]:
SampRec['sample'] = sample
SampRec['site'] = site
SampRec["citations"]="This study"
SampRec["analysts"]=user
SampRec['azimuth'] = row['azimuth']
SampRec['dip'] = row['dip']
SampRec['bed_dip_direction'] = row['bed_dip_direction']
SampRec['bed_dip'] = row['bed_dip']
SampRec['method_codes']=meth_code
SampRecs.append(SampRec)
if site!="" and site not in [x['site'] if 'site' in list(x.keys()) else "" for x in SiteRecs]:
SiteRec['site'] = site
SiteRec['location'] = location
SiteRec["citations"]="This study"
SiteRec["analysts"]=user
SiteRec['lat'] = lat
SiteRec['lon'] = lon
SiteRecs.append(SiteRec)
if location!="" and location not in [x['location'] if 'location' in list(x.keys()) else "" for x in LocRecs]:
LocRec['location']=location
LocRec["citations"]="This study"
LocRec["analysts"]=user
LocRec['lat_n'] = lat
LocRec['lon_e'] = lon
LocRec['lat_s'] = lat
LocRec['lon_w'] = lon
LocRecs.append(LocRec)
MeasRec["citations"]="This study"
MeasRec["analysts"]=user
MeasRec["specimen"]=specimen
MeasRec['software_packages']=version_num
MeasRec["treat_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["meas_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["quality"]='g'
MeasRec["standard"]='u'
MeasRec["treat_step_num"]='1'
MeasRec["treat_ac_field"]='0'
if row['step'] == 'NRM':
meas_type="LT-NO"
elif 'step_unit' in row and row['step_unit']=='C':
meas_type="LT-T-Z"
treat=float(row['step'])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'A':
meas_type="LT-AF-Z"
treat=float(row['step'][1:])
MeasRec["treat_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0] == 'T':
meas_type="LT-T-Z"
treat=float(row['step'][1:])
MeasRec["treat_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else: # need to add IRM, and ARM options
print("measurement type unknown", row['step'])
return False, "measurement type unknown"
MeasRec["magn_moment"]=str(row['magn_moment'])
MeasRec["magn_volume"]=str(row['magn_volume'])
MeasRec["dir_dec"]=str(row['dir_dec'])
MeasRec["dir_inc"]=str(row['dir_inc'])
MeasRec['method_codes']=meas_type
MagRecs.append(MeasRec)
con = nb.Contribution(output_dir_path,read_tables=[])
con.add_magic_table_from_data(dtype='specimens', data=SpecRecs)
con.add_magic_table_from_data(dtype='samples', data=SampRecs)
con.add_magic_table_from_data(dtype='sites', data=SiteRecs)
con.add_magic_table_from_data(dtype='locations', data=LocRecs)
MeasOuts=pmag.measurements_methods3(MeasRecs,noave)
con.add_magic_table_from_data(dtype='measurements', data=MeasOuts)
con.tables['specimens'].write_magic_file(custom_name=spec_file)
con.tables['samples'].write_magic_file(custom_name=samp_file)
con.tables['sites'].write_magic_file(custom_name=site_file)
con.tables['locations'].write_magic_file(custom_name=loc_file)
con.tables['measurements'].write_magic_file(custom_name=meas_file)
try: os.remove(tmp_file)
except (OSError,IOError) as e: print("couldn't remove temperary fixed JR6 file %s"%tmp_file)
return True, meas_file