def main():
"""
NAME
cart_dir.py
DESCRIPTION
converts cartesian coordinates to geomagnetic elements
INPUT (COMMAND LINE ENTRY)
x1 x2 x3
if only two columns, assumes magnitude of unity
OUTPUT
declination inclination magnitude
SYNTAX
cart_dir.py [command line options] [< filename]
OPTIONS
-h prints help message and quits
-i for interactive data entry
-f FILE to specify input filename
-F OFILE to specify output filename (also prints to screen)
"""
ofile=""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
ofile=sys.argv[ind+1]
outfile=open(ofile,'w')
if '-i' in sys.argv:
cont=1
while cont==1:
cart=[]
try:
ans=raw_input('X: [ctrl-D to quit] ')
cart.append(float(ans))
ans=raw_input('Y: ')
cart.append(float(ans))
ans=raw_input('Z: ')
cart.append(float(ans))
except:
print "\n Good-bye \n"
sys.exit()
dir= pmag.cart2dir(cart) # send dir to dir2cart and spit out result
print '%7.1f %7.1f %10.3e'%(dir[0],dir[1],dir[2])
elif '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
input=numpy.loadtxt(file) # read from a file
else:
input = numpy.loadtxt(sys.stdin,dtype=numpy.float) # read from standard input
dir=pmag.cart2dir(input)
for line in dir:
print '%7.1f %7.1f %10.3e'%(line[0],line[1],line[2])
if ofile!="":
outstring='%7.1f %7.1f %10.8e\n' %(line[0],line[1],line[2])
outfile.write(outstring)
def spitout(line):
cart=[] # initialize list for dec,inc,intensity
dat=line.split() # split the data on a space into columns
for element in dat: # step through dec,inc, int
cart.append(float(element)) # append floating point variable to "cart"
dir= pmag.cart2dir(cart) # send cart to cart2dir
print '%7.1f %7.1f %10.3e'%(dir[0],dir[1],dir[2])
return dir
def Rotate_zijderveld(Zdata, rot_declination):
if len(Zdata) == 0:
return ([])
CART_rot = []
for i in range(0, len(Zdata)):
DIR = cart2dir(Zdata[i])
DIR[0] = (DIR[0] - rot_declination) % 360.
CART_rot.append(array(dir2cart(DIR)))
CART_rot = array(CART_rot)
return (CART_rot)
def Rotate_zijderveld(Zdata,rot_declination):
if len(Zdata)==0:
return([])
CART_rot=[]
for i in range(0,len(Zdata)):
DIR=cart2dir(Zdata[i])
DIR[0]=(DIR[0]-rot_declination)%360.
CART_rot.append(array(dir2cart(DIR)))
CART_rot=array(CART_rot)
return(CART_rot)
def plotELL(pars,col,lower,plot): #Modified from PmagPy (Tauxe et al., 2016)
"""
function to calculate points on an ellipse about Pdec,Pdip with angle beta,gamma
"""
#pylab.figure(num=fignum)
Pdec,Pinc,beta,Bdec,Binc,gamma,Gdec,Ginc=pars[0],pars[1],pars[2],pars[3],pars[4],pars[5],pars[6],pars[7]
if beta > 90. or gamma>90:
beta=180.-beta
gamma=180.-beta
Pdec=Pdec-180.
Pinc=-Pinc
beta,gamma=beta*rad,gamma*rad # convert to radians
X_ell,Y_ell,X_up,Y_up,PTS=[],[],[],[],[]
nums=201
xnum=float(nums-1.)/2.
# set up t matrix
t=[[0,0,0],[0,0,0],[0,0,0]]
X=pmag.dir2cart((Pdec,Pinc,1.0)) # convert to cartesian coordintes
if lower==1 and X[2]<0:
for i in range(3):
X[i]=-X[i]
# set up rotation matrix t
t[0][2]=X[0]
t[1][2]=X[1]
t[2][2]=X[2]
X=pmag.dir2cart((Bdec,Binc,1.0))
if lower==1 and X[2]<0:
for i in range(3):
X[i]=-X[i]
t[0][0]=X[0]
t[1][0]=X[1]
t[2][0]=X[2]
X=pmag.dir2cart((Gdec,Ginc,1.0))
if lower==1 and X[2]<0:
for i in range(3):
X[i]=-X[i]
t[0][1]=X[0]
t[1][1]=X[1]
t[2][1]=X[2]
# set up v matrix
v=[0,0,0]
for i in range(nums): # incremental point along ellipse
psi=float(i)*np.pi/xnum
v[0]=np.sin(beta)*np.cos(psi)
v[1]=np.sin(gamma)*np.sin(psi)
v[2]=np.sqrt(1.-v[0]**2 - v[1]**2)
elli=[0,0,0]
# calculate points on the ellipse
for j in range(3):
for k in range(3):
elli[j]=elli[j] + t[j][k]*v[k] # cartesian coordinate j of ellipse
PTS.append(pmag.cart2dir(elli))
R=np.sqrt( 1.-abs(elli[2]))/(np.sqrt(elli[0]**2+elli[1]**2)) # put on an equal area projection
if elli[2]<0:
# for i in range(3): elli[i]=-elli[i]
X_up.append(elli[1]*R)
Y_up.append(elli[0]*R)
else:
X_ell.append(elli[1]*R)
Y_ell.append(elli[0]*R)
if plot==1:
if X_ell!=[]:plt.plot(X_ell,Y_ell,col,linewidth=2,zorder=5)#pylab.plot(X_ell,Y_ell,col,zorder=3)
if X_up!=[]:plt.plot(X_up,Y_up,col,linewidth=2,zorder=5)#pylab.plot(X_up,Y_up,'g-',zorder=3)
#pylab.draw()
else:
return PTS
def main():
"""
NAME
LIVMW_magic.py
DESCRIPTION
converts Liverpool microwave format files to magic_measurements format files
SYNTAX
LIVMW_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify liverpool format input file, required
-usr USER: identify user, default is ""
-ins INST: identify instrument, e.g., LIV-TRISTAN, LIV-OLD14GHZ, default is ""
-loc LOCNAME : specify location/study name, required
-F FILE: specify output file, default is magic_measurements.txt
-Fsa FILE: specify er_samples formatted file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-sit Site_name : specify site name for this specimen
-unc measurement units are uncalibrated (default is uAm^2)
-B PHI THETA: dc lab field phi, theta, default is 0, 90
-ncn NCON: specify naming convention - required if -sit not specified
Sample naming convention:
do not use if -sit option used!
[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 same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
"""
# initialize some stuff
version_num = pmag.get_version()
noave = 0
methcode, instcode = "", ""
phi, theta, peakfield, labfield = 0, 0, 0, 0
pMRM, MD, samp_con, Z, site = 0, 0, "6", "", ""
er_location_name = ""
citation = "This study"
args = sys.argv
methcode = "LP-NO" # NRM
specnum, measnum = 1, 1
powt_max = 0
ErSamps, Samps = [], []
#
# get command line arguments
#
dirpath = "."
meas_file, samp_file = dirpath + "/magic_measurements.txt", dirpath + "/er_samples.txt"
user = ""
unc = 0
if "-WD" in args:
ind = args.index("-WD")
dirpath = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if "-ins" in args:
ind = args.index("-ins")
instcode = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = dirpath + "/" + args[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
samp_file = dirpath + "/" + samp_file
try:
open(samp_file, "rU")
ErSamps, file_type = pmag.magic_read(samp_file)
print "sample information will be appended to new er_samples.txt file"
except:
print "er_samples.txt file does not exist"
print "sample information will be stored in new er_samples.txt file"
if "-f" in args:
ind = args.index("-f")
magfile = args[ind + 1]
magfile = dirpath + "/" + magfile
try:
input = open(magfile, "rU")
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-B" in args:
ind = args.index("-B")
phi = args[ind + 1]
theta = args[ind + 2]
else:
phi, theta = "0.", "90."
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0:
specnum = -specnum
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-unc" in args:
unc = 1
if "-sit" in args:
ind = args.index("-sit")
site = args[ind + 1]
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 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"
sys.exit()
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"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if samp_con == "6" and site == "":
print "you must either specify a naming convention, or a site name"
print main.__doc__
sys.exit()
MagRecs = []
if len(ErSamps) > 1:
for samp in ErSamps:
if samp["er_sample_name"] not in Samps:
Samps.append(samp["er_sample_name"])
Data = input.readlines()
if 1: # never mind
for line in Data:
if len(line) > 1:
rec = line.split(",")
MagRec = {}
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["treatment_ac_field"] = "0"
MagRec["treatment_dc_field"] = "0"
MagRec["treatment_dc_field_phi"] = ""
MagRec["treatment_dc_field_theta"] = ""
MagRec["treatment_mw_integral"] = ""
meas_type = "LT-NO"
MagRec["er_specimen_name"] = rec[0][1:-1]
MagRec["er_location_name"] = er_location_name
if specnum != 0:
MagRec["er_sample_name"] = rec[0][1:-1][:specnum]
else:
MagRec["er_sample_name"] = rec[0][1:-1]
if site == "":
site = pmag.parse_site(MagRec["er_sample_name"], samp_con, Z)
MagRec["er_site_name"] = site
MagRec["treatment_mw_power"] = rec[2]
MagRec["treatment_mw_time"] = rec[3]
powt = int(float(MagRec["treatment_mw_power"]) * (float(MagRec["treatment_mw_time"])))
MagRec["treatment_mw_energy"] = "%7.1f" % (powt)
if powt > powt_max:
powt_max = powt
treat = rec[1].strip('"').upper()
if treat == "Z": # in zero field
meas_type = "LT-M-Z" # as opposed to LT-MV-Z
if powt < powt_max:
meas_type = "LT-PMRM-Z"
elif treat == "A": # in zero field
meas_type = "LT-M-I" # as opposed to LT-MV-I
labfield = float(rec[10]) * 1e-6 # assuming uT, convert to T
MagRec["treatment_dc_field"] = "%8.3e" % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"] = phi # labfield phi
MagRec["treatment_dc_field_theta"] = theta # labfield theta
if powt < powt_max:
meas_type = "LT-PMRM-I"
if len(rec) > 10:
MagRec["treatment_mw_integral"] = rec[10]
if unc == 0:
MagRec["measurement_magn_moment"] = "%10.3e" % (float(rec[4]) * 1e-6) # moment in Am^2 (from uAm^2)
if unc == 1:
MagRec["measurement_magnitude"] = rec[4] # uncalibrated moment
cart = []
cart.append(float(rec[7]))
cart.append(float(rec[8]))
cart.append(float(rec[9]))
dir = pmag.cart2dir(cart)
MagRec["measurement_dec"] = "%9.3f" % (dir[0])
MagRec["measurement_inc"] = "%9.3f" % (dir[1])
MagRec["magic_instrument_codes"] = instcode
MagRec["magic_method_codes"] = meas_type
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "%i" % (measnum)
MagRec["magic_experiment_name"] = MagRec["er_specimen_name"] + ":" + methcode
measnum += 1
MagRecs.append(MagRec)
if MagRec["er_sample_name"] not in Samps: # add this puppy to the list in er_samples.txt
Samps.append(MagRec["er_sample_name"])
ErSamp = {}
ErSamp["er_sample_name"] = Samps[-1]
ErSamp["er_location_name"] = MagRec["er_location_name"]
ErSamp["er_site_name"] = site
ErSamp["er_citation_names"] = "This study"
gdec = float(rec[5])
ginc = float(rec[6])
az, pl = pmag.get_azpl(dir[0], dir[1], gdec, ginc)
ErSamp["sample_azimuth"] = "%7.1f" % az
ErSamp["sample_dip"] = "%7.1f" % pl
ErSamps.append(ErSamp)
MagOuts = pmag.mw_measurements_methods(MagRecs)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "measurements put in ", meas_file
pmag.magic_write(samp_file, ErSamps, "er_samples")
print "sample names put in ", samp_file
def main(command_line=True, **kwargs):
"""
NAME
IODP_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
IODP_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace('-', ' -')
new_line = new_line.replace(' ', ' ')
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if '-' in i[1:]:
lead_char = '-' if i[0] == '-' else ''
if lead_char:
v = i[1:].split('-')
else:
v = i.split('-')
new_line.append(lead_char + v[0])
new_line.append('-' + v[1])
else:
new_line.append(i)
new_line = (' '.join(new_line)) + '\n'
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave=0
volume=2.5**3 #default volume is a 2.5cm cube
inst=""
samp_con,Z='5',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
version_num=pmag.get_version()
dir_path='.'
MagRecs=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
mag_file = ''
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-fsa' in args:
ind = args.index("-fsa")
samp_file = args[ind+1]
if samp_file[0]!='/':
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
except:
print samp_file,' not found: '
print ' download csv file and import to MagIC with IODP_samples_magic.py'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args:
noave=1
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file', '')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split('-')
else:
Z = ''
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print "You must provide an IODP_jr6 format file"
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(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(os.path.join(input_dir_path, 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(magfile)
if not os.path.exists(samp_file):
print 'samp_file', samp_file
print "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
return False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
#os.rename('temp.txt', mag_file)
#data = open(mag_file, 'rU').readlines()
data=pd.read_csv(temp, delim_whitespace=True,header=None)
os.remove(temp)
samples,filetype = pmag.magic_read(samp_file)
data.columns=['specname','step','negz','y','x','expon','sample_azimuth','sample_dip','sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],-data['negz']]).transpose()
dir= pmag.cart2dir(cart).transpose()
data['measurement_dec']=dir[0]
data['measurement_inc']=dir[1]
data['measurement_magn_volume']=dir[2]*(10.0**data['expon']) # A/m - data in A/m
data['measurement_flag']='g'
data['measurement_standard']='u'
data['measurement_number']='1'
data['measurement_temp']='273'
data['er_location_name']=er_location_name
for rowNum, row in data.iterrows():
MagRec={}
spec_text_id=row['specname'].split('_')[1]
SampRecs=pmag.get_dictitem(samples,'er_sample_alternatives',spec_text_id,'has') # retrieve sample record for this specimen
if len(SampRecs)>0: # found one
MagRec['er_specimen_name']=SampRecs[0]['er_sample_name']
MagRec['er_sample_name']=MagRec['er_specimen_name']
MagRec['er_site_name']=MagRec['er_specimen_name']
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["treatment_ac_field"]='0'
volume=float(SampRecs[0]['sample_volume'])
moment=row['measurement_magn_volume'] * volume
MagRec["measurement_magn_moment"]=str(moment)
MagRec["measurement_magn_volume"]=str(row['measurement_magn_volume'])
MagRec["measurement_dec"]='%7.1f'%(row['measurement_dec'])
MagRec["measurement_inc"]='%7.1f'%(row['measurement_inc'])
if row['step'] == 'NRM':
meas_type="LT-NO"
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MagRec["treatment_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:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0:3]=='ARM': #
meas_type="LT-AF-I"
treat=float(row['step'][3:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"]='%8.3e' %(50e-6) # assume 50uT DC field
MagRec["measurement_description"]='Assumed DC field - actual unknown'
elif row['step'][0:3]=='IRM': #
meas_type="LT-IRM"
treat=float(row['step'][3:])
MagRec["treatment_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
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
else:
print 'sample name not found: ',row['specname']
MagOuts=pmag.measurements_methods(MagRecs,noave)
file_created, error_message = pmag.magic_write(meas_file,MagOuts,'magic_measurements')
if file_created:
return True, meas_file
else:
return False, 'Results not written to file'
def main(command_line=True, **kwargs):
"""
NAME
BGC_magic.py
DESCRIPTION
converts Berkeley Geochronology Center (BGC) format files to magic_measurements format files
SYNTAX
BGC_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-loc LOCNAME : specify location/study name
-site SITENAME : specify site name
-A: don't average replicate measurements
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-v NUM : specify the volume in cc of the sample, default 2.5^3cc. Will use vol in data file if volume!=0 in file.
INPUT
BGC paleomag format file
"""
# initialize some stuff
noave = 0
volume = 0.025 ** 3 # default volume is a 2.5cm cube
# inst=""
# samp_con,Z='1',""
# missing=1
# demag="N"
er_location_name = "unknown"
er_site_name = "unknown"
# citation='This study'
args = sys.argv
meth_code = "LP-NO"
# specnum=1
version_num = pmag.get_version()
mag_file = ""
dir_path = "."
MagRecs = []
SampOuts = []
samp_file = "er_samples.txt"
meas_file = "magic_measurements.txt"
meth_code = ""
#
# get command line arguments
#
if command_line:
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
if "-ID" in sys.argv:
ind = sys.argv.index("-ID")
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if "-F" in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
# try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
# except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if "-f" in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-site" in args:
ind = args.index("-site")
er_site_name = args[ind + 1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
# samp_con='5'
if "-v" in args:
ind = args.index("-v")
volume = float(args[ind + 1]) * 1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get("dir_path", ".")
input_dir_path = kwargs.get("input_dir_path", dir_path)
output_dir_path = dir_path
meas_file = kwargs.get("meas_file", "magic_measurements.txt")
mag_file = kwargs.get("mag_file")
samp_file = kwargs.get("samp_file", "er_samples.txt")
er_location_name = kwargs.get("er_location_name", "")
er_site_name = kwargs.get("er_site_name", "")
noave = kwargs.get("noave", 0) # default (0) 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:
# convert cm^3 to m^3
volume *= 1e-6
# format variables
if not mag_file:
return False, "You must provide a BCG format file"
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSampRec = {}
# parse data
# Open up the BGC file and read the header information
print "mag_file in BGC_magic", mag_file
pre_data = open(mag_file, "rU")
line = pre_data.readline()
line_items = line.split(" ")
sample_name = line_items[2]
sample_name = sample_name.replace("\n", "")
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split("\t")
sample_azimuth = float(line_items[1])
sample_dip = 90.0 - float(line_items[2])
sample_bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
sample_lon = line_items[5]
sample_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)
# print "\ndata\n", data
cart = np.array([data["X"], data["Y"], data["Z"]]).transpose()
direction = pmag.cart2dir(cart).transpose()
data["measurement_dec"] = direction[0]
data["measurement_inc"] = direction[1]
data["measurement_magn_moment"] = direction[2] * 1000 * volume # the data are in EMU - this converts to Am^2
data["measurement_magn_volume"] = direction[2] * 1000 # EMU - data converted to A/m
# DGEOs, IGEOs = [], []
# print "len(data)=",len(data)
# for ind in range(len(data)):
# dgeo,igeo=pmag.dogeo(data.ix[ind]['measurement_dec'],data.ix[ind]['measurement_inc'],90-sample_azimuth,sample_dip)
# DGEOs.append(dgeo)
# IGEOs.append(igeo)
# data['specimen_dec']=DGEOs
# data['specimen_inc']=IGEOs
# data['specimen_tilt']='1'
# print "data specimn_dec=",DGEOs
# print "data specimn_inc=",IGEOs
# Configure the er_sample table
ErSampRec["er_sample_name"] = sample_name
ErSampRec["sample_azimuth"] = sample_azimuth
ErSampRec["sample_dip"] = sample_dip
ErSampRec["sample_bed_dip_direction"] = sample_bed_azimuth
ErSampRec["sample_bed_dip"] = sample_bed_dip
ErSampRec["sample_lat"] = sample_lat
ErSampRec["sample_lon"] = sample_lon
ErSampRec["magic_method_codes"] = meth_code
ErSampRec["er_location_name"] = er_location_name
ErSampRec["er_site_name"] = er_site_name
ErSampRec["er_citation_names"] = "This study"
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec = {}
MagRec["measurement_description"] = "Date: " + str(row["Date"]) + " Time: " + str(row["Time"])
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["er_site_name"] = er_site_name
MagRec["er_sample_name"] = sample_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "1"
MagRec["er_specimen_name"] = sample_name
MagRec["treatment_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"])
MagRec["treatment_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"])
MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin
else:
print "measurement type unknown:", row["DM Type"], " in row ", rowNum
MagRec["measurement_magn_moment"] = str(row["measurement_magn_moment"])
MagRec["measurement_magn_volume"] = str(row["measurement_magn_volume"])
MagRec["measurement_dec"] = str(row["measurement_dec"])
MagRec["measurement_inc"] = str(row["measurement_inc"])
MagRec["magic_method_codes"] = meas_type
MagRec["measurement_csd"] = "0.0" # added due to magic.write error
MagRec["measurement_positions"] = "1" # added due to magic.write error
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file, SampOuts, "er_samples")
print "sample orientations put in ", samp_file
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "results put in ", meas_file
print "exit!"
return True, meas_file
def main():
"""
NAME
UR_jr6_magic.py
DESCRIPTION
converts University of Rome JR6 format files to magic_measurements format files
SYNTAX
UR_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-A : don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM:SO-SUN]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-SUN orientations are from a sun compass
SO-MAG orientations are from a magnetic compass
SO-MAG-CMD orientations declination corrected magnetic compass
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[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 same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
[9] ODP naming convention
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num=pmag.get_version()
er_location_name=""
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
specnum=0
sampmeths='FS-FD:SO-POM:SO-SUN'
samp_con,Z="4","2"
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
meas_file=dir_path+'/'+'magic_measurements.txt'
samp_file=dir_path+'/'+'er_samples.txt'
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+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"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "-mcd" in args:
ind=args.index("-mcd")
sampmeths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
filelist=os.listdir(dir_path) # read in list of files to import
samples=[]
MagRecs,SampRecs=[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
parts=file.split('.')
if parts[1].upper()=='JR6':
print 'processing: ',file
treatment_type,treatment_value,user="","",""
inst="UR-JR6"
input=open(dir_path+'/'+file,'rU').readlines()
for line in input:
newline=line.replace('-',' -')
rec=newline.split()
MagRec,SampRec={},{}
specimen=rec[0]
if specnum!=0:
SampRec['er_sample_name']=specimen[:specnum]
else:
SampRec['er_sample_name']=specimen
er_site_name=pmag.parse_site(SampRec['er_sample_name'],samp_con,Z)
SampRec['er_site_name']=er_site_name
SampRec['er_location_name']=er_location_name
for key in SampRec.keys():MagRec[key]=SampRec[key]
SampRec['sample_azimuth']=rec[7]
SampRec['sample_dip']='-'+rec[8]
SampRec['sample_bed_dip_direction']=rec[9]
SampRec['sample_bed_dip']=rec[10]
SampRec['magic_method_codes']=sampmeths
MagRec['er_specimen_name']=specimen
MagRec['er_analyst_mail_names']=user
MagRec['magic_software_packages']=version_num
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec['magic_method_codes']='LT-NO'
if rec[2]=='C':
temp=float(rec[1])+273.
if temp>298:
MagRec["treatment_temp"]='%8.3e' % (temp) # room temp in kelvin
MagRec['magic_method_codes']='LT-T-Z'
else: # measurement is in oe
AC=float(rec[1])*1e-4 # convert to tesla
if AC!=0.:
MagRec["treatment_ac_field"]='%8.3e' %(AC)
MagRec['magic_method_codes']='LT-AF-Z'
vol=10.8*1e-6 # standard Roma lab volume
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
mexp=10**(float(rec[6]))
x,y,z=mexp*float(rec[3]),mexp*float(rec[4]),mexp*float(rec[5])
Cart=[x,y,z]
Dir=pmag.cart2dir(Cart)
MagRec['measurement_dec']='%7.1f'%(Dir[0])
MagRec['measurement_inc']='%7.1f'%(Dir[1])
MagRec['measurement_magn_volume']='%8.3e'%(Dir[2])
MagRec['measurement_magn_moment']='%8.3e'%(Dir[2]*vol)
MagRec['measurement_description']='converted A/m to Am^2 using volume of '+str(vol)+' m^3'
MagRecs.append(MagRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print 'samples stored in ',samp_file
Fixed=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def average_duplicates(duplicates):
'''
avarage replicate measurements.
'''
carts_s,carts_g,carts_t=[],[],[]
for rec in duplicates:
moment=float(rec['moment'])
if 'dec_s' in rec.keys() and 'inc_s' in rec.keys():
if rec['dec_s']!="" and rec['inc_s']!="":
dec_s=float(rec['dec_s'])
inc_s=float(rec['inc_s'])
cart_s=pmag.dir2cart([dec_s,inc_s,moment])
carts_s.append(cart_s)
if 'dec_g' in rec.keys() and 'inc_g' in rec.keys():
if rec['dec_g']!="" and rec['inc_g']!="":
dec_g=float(rec['dec_g'])
inc_g=float(rec['inc_g'])
cart_g=pmag.dir2cart([dec_g,inc_g,moment])
carts_g.append(cart_g)
if 'dec_t' in rec.keys() and 'inc_t' in rec.keys():
if rec['dec_t']!="" and rec['inc_t']!="":
dec_t=float(rec['dec_t'])
inc_t=float(rec['inc_t'])
cart_t=pmag.dir2cart([dec_t,inc_t,moment])
carts_t.append(cart_t)
if len(carts_s)>0:
carts=scipy.array(carts_s)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_s="%.2f"%mean_dir[0]
mean_inc_s="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_s,mean_inc_s="",""
if len(carts_g)>0:
carts=scipy.array(carts_g)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_g="%.2f"%mean_dir[0]
mean_inc_g="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_g,mean_inc_g="",""
if len(carts_t)>0:
carts=scipy.array(carts_t)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_t="%.2f"%mean_dir[0]
mean_inc_t="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_t,mean_inc_t="",""
meanrec={}
for key in duplicates[0].keys():
if key in ['dec_s','inc_s','dec_g','inc_g','dec_t','inc_t','moment']:
continue
else:
meanrec[key]=duplicates[0][key]
meanrec['dec_s']=mean_dec_s
meanrec['dec_g']=mean_dec_g
meanrec['dec_t']=mean_dec_t
meanrec['inc_s']=mean_inc_s
meanrec['inc_g']=mean_inc_g
meanrec['inc_t']=mean_inc_t
meanrec['moment']=mean_moment
return meanrec
def main(command_line=True, **kwargs):
"""
NAME
IODP_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
IODP_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, "rU")
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace("-", " -")
new_line = new_line.replace(" ", " ")
new_data.append(new_line)
new_file = open(new_filename, "w")
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, "rU")
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if "-" in i[1:]:
lead_char = "-" if i[0] == "-" else ""
if lead_char:
v = i[1:].split("-")
else:
v = i.split("-")
new_line.append(lead_char + v[0])
new_line.append("-" + v[1])
else:
new_line.append(i)
new_line = (" ".join(new_line)) + "\n"
new_data.append(new_line)
new_file = open(new_filename, "w")
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave = 0
volume = 2.5 ** 3 # default volume is a 2.5cm cube
inst = ""
samp_con, Z = "5", ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = "This study"
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
dir_path = "."
MagRecs = []
samp_file = "er_samples.txt"
meas_file = "magic_measurements.txt"
mag_file = ""
#
# get command line arguments
#
if command_line:
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
if "-ID" in sys.argv:
ind = sys.argv.index("-ID")
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if "-F" in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = args[ind + 1]
if samp_file[0] != "/":
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file, "rU")
ErSamps, file_type = pmag.magic_read(samp_file)
except:
print samp_file, " not found: "
print " download csv file and import to MagIC with IODP_samples_magic.py"
if "-f" in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args:
noave = 1
if not command_line:
dir_path = kwargs.get("dir_path", ".")
input_dir_path = kwargs.get("input_dir_path", dir_path)
output_dir_path = dir_path
meas_file = kwargs.get("meas_file", "magic_measurements.txt")
mag_file = kwargs.get("mag_file", "")
samp_file = kwargs.get("samp_file", "er_samples.txt")
specnum = kwargs.get("specnum", 1)
samp_con = kwargs.get("samp_con", "1")
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split("-")
else:
Z = ""
er_location_name = kwargs.get("er_location_name", "")
noave = kwargs.get("noave", 0) # default (0) means DO average
meth_code = kwargs.get("meth_code", "LP-NO")
# format variables
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print "You must provide an IODP_jr6 format file"
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(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
),
)
if not os.path.exists(samp_file):
print "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(
input_dir_path
)
return (
False,
"Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(
input_dir_path
),
)
# parse data
temp = os.path.join(output_dir_path, "temp.txt")
fix_separation(mag_file, temp)
samples, filetype = pmag.magic_read(samp_file)
lines = open(temp, "rU").readlines()
os.remove(temp)
for line in lines:
MagRec = {}
line = line.split()
spec_text_id = line[0].split("_")[1]
SampRecs = pmag.get_dictitem(samples, "er_sample_alternatives", spec_text_id, "has")
if len(SampRecs) > 0: # found one
MagRec["er_specimen_name"] = SampRecs[0]["er_sample_name"]
MagRec["er_sample_name"] = MagRec["er_specimen_name"]
MagRec["er_site_name"] = MagRec["er_specimen_name"]
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "1"
MagRec["treatment_ac_field"] = "0"
volume = float(SampRecs[0]["sample_volume"])
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
MagRec["measurement_magn_moment"] = str(moment)
MagRec["measurement_magn_volume"] = str(magn_volume) # str(direction[2] * (10.0 ** expon))
MagRec["measurement_dec"] = "%7.1f" % (direction[0])
MagRec["measurement_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:])
MagRec["treatment_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:])
MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin
elif step[0:3] == "ARM": #
meas_type = "LT-AF-I"
treat = float(row["step"][3:])
MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"] = "%8.3e" % (50e-6) # assume 50uT DC field
MagRec["measurement_description"] = "Assumed DC field - actual unknown"
elif step[0:3] == "IRM": #
meas_type = "LT-IRM"
treat = float(step[3:])
MagRec["treatment_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
MagRec["magic_method_codes"] = meas_type
MagRecs.append(MagRec.copy())
else:
print "sample name not found: ", row["specname"]
MagOuts = pmag.measurements_methods(MagRecs, noave)
file_created, error_message = pmag.magic_write(meas_file, MagOuts, "magic_measurements")
if file_created:
return True, meas_file
else:
return False, "Results not written to file"
def main():
"""
NAME
IPG_magic.py
DESCRIPTION
converts PMD (IPG - PaleoMac) format files to magic_measurements format files
SYNTAX
IPG_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify naming convention
Sample naming convention:
[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 same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
IPG-PMD format files
"""
# initialize some stuff
noave = 0
methcode, inst = "", ""
samp_con, Z = "1", ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = "This study"
args = sys.argv
methcode = "LP-NO"
specnum = -1
MagRecs = []
version_num = pmag.get_version()
Samps = [] # keeps track of sample orientations
DIspec = []
MagFiles = []
#
# get command line arguments
#
user = ""
mag_file = ""
dir_path = "."
ErSamps = []
SampOuts = []
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
samp_file = dir_path + "/er_samples.txt"
meas_file = dir_path + "/magic_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = dir_path + "/" + args[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = dir_path + "/" + args[ind + 1]
try:
open(samp_file, "rU")
ErSamps, file_type = pmag.magic_read(samp_file)
print "sample information will be appended to ", samp_file
except:
print samp_file, " not found: sample information will be stored in new er_samples.txt file"
samp_file = dir_path + "/er_samples.txt"
if "-f" in args:
ind = args.index("-f")
mag_file = dir_path + "/" + args[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0:
specnum = -specnum
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 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"
sys.exit()
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"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args:
noave = 1
data = open(mag_file, "rU").readlines() # read in data from file
for line in data:
rec = line.split()
if "E-" not in rec[1] and "E+" not in rec[1]: # new specimen
er_specimen_name = rec[0]
ErSampRec, ErSiteRec = {}, {} # make a sample record
if specnum != 0:
er_sample_name = rec[0][:specnum]
else:
er_sample_name = rec[0]
if len(ErSamps) > 0: # need to copy existing
for samp in ErSamps:
if samp["er_sample_name"] == er_sample_name:
ErSampRec = samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con) < 6:
er_site_name = pmag.parse_site(er_sample_name, samp_con, Z)
else:
if "er_site_name" in ErSampRec.keys():
er_site_name = ErSampREc["er_site_name"]
if "er_location_name" in ErSampRec.keys():
er_location_name = ErSampREc["er_location_name"]
ErSampRec["er_sample_name"] = er_sample_name
ErSampRec["sample_azimuth"] = rec[1]
dip = -float(rec[2])
ErSampRec["sample_dip"] = "%7.1f" % (dip)
ErSampRec["sample_bed_dip_direction"] = "%7.1f" % (float(rec[3]) + 90.0)
ErSampRec["sample_bed_dip"] = rec[4]
if "er_location_name" not in ErSampRec.keys():
ErSampRec["er_location_name"] = er_location_name
if "er_site_name" not in ErSampRec.keys():
ErSampRec["er_site_name"] = er_site_name
if "er_citation_names" not in ErSampRec.keys():
ErSampRec["er_citation_names"] = "This study"
if "magic_method_codes" not in ErSampRec.keys():
ErSampRec["magic_method_codes"] = "SO-NO"
SampOuts.append(ErSampRec)
elif rec[0][0] == "N" or rec[0][0] == "T" or rec[0][0] == "M":
if len(rec) > 1: # skip blank lines at bottom
MagRec = {}
# MagRec['measurement_date']=measdate
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["er_site_name"] = er_site_name
MagRec["er_sample_name"] = er_sample_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "1"
MagRec["er_specimen_name"] = er_specimen_name
if rec[0] == "NRM":
meas_type = "LT-NO"
elif rec[0][0] == "M":
meas_type = "LT-AF-Z"
elif rec[0][0] == "T":
meas_type = "LT-T-Z"
else:
print "measurement type unknown"
sys.exit()
X = [float(rec[1]), float(rec[2]), float(rec[3])]
Vec = pmag.cart2dir(X)
MagRec["measurement_magn_moment"] = "%10.3e" % (Vec[2]) # Am^2
# MagRec["measurement_magn_volume"]=rec[4] # A/m
MagRec["measurement_dec"] = "%7.1f" % (Vec[0])
MagRec["measurement_inc"] = "%7.1f" % (Vec[1])
MagRec["treatment_ac_field"] = "0"
if meas_type != "LT-NO":
treat = float(rec[0][1:])
else:
treat = 0
if meas_type == "LT-AF-Z":
MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla
elif meas_type == "LT-T-Z":
MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin
MagRec["magic_method_codes"] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "results put in ", meas_file
pmag.magic_write(samp_file, SampOuts, "er_samples")
print "sample orientations put in ", samp_file
def main():
"""
NAME
orientation_magic.py
DESCRIPTION
takes tab delimited field notebook information and converts to MagIC formatted tables
SYNTAX
orientation_magic.py [command line options]
OPTIONS
-f FILE: specify input file, default is: orient.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output site location file, default is: er_sites.txt
-app append/update these data in existing er_samples.txt, er_sites.txt files
-ocn OCON: specify orientation convention, default is #1 below
-dcn DCON [DEC]: specify declination convention, default is #1 below
if DCON = 2, you must supply the declination correction
-BCN don't correct bedding_dip_dir for magnetic declination -already corrected
-ncn NCON: specify naming convention: default is #1 below
-a: averages all bedding poles and uses average for all samples: default is NO
-gmt HRS: specify hours to subtract from local time to get GMT: default is 0
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
INPUT FORMAT
Input files must be tab delimited and have in the first line:
tab location_name
Note: The "location_name" will facilitate searching in the MagIC database. Data from different
"locations" should be put in separate files. The definition of a "location" is rather loose.
Also this is the word 'tab' not a tab, which will be indicated by '\t'.
The second line has the names of the columns (tab delimited), e.g.:
site_name sample_name mag_azimuth field_dip date lat long sample_lithology sample_type sample_class shadow_angle hhmm stratigraphic_height bedding_dip_direction bedding_dip GPS_baseline image_name image_look image_photographer participants method_codes site_description sample_description GPS_Az, sample_igsn, sample_texture, sample_cooling_rate, cooling_rate_corr, cooling_rate_mcd
Notes:
1) column order doesn't matter but the NAMES do.
2) sample_name, sample_lithology, sample_type, sample_class, lat and long are required. all others are optional.
3) If subsequent data are the same (e.g., date, bedding orientation, participants, stratigraphic_height),
you can leave the field blank and the program will fill in the last recorded information. BUT if you really want a blank stratigraphic_height, enter a '-1'. These will not be inherited and must be specified for each entry: image_name, look, photographer or method_codes
4) hhmm must be in the format: hh:mm and the hh must be in 24 hour time.
date must be mm/dd/yy (years < 50 will be converted to 20yy and >50 will be assumed 19yy)
5) image_name, image_look and image_photographer are colon delimited lists of file name (e.g., IMG_001.jpg) image look direction and the name of the photographer respectively. If all images had same look and photographer, just enter info once. The images will be assigned to the site for which they were taken - not at the sample level.
6) participants: Names of who helped take the samples. These must be a colon delimited list.
7) method_codes: Special method codes on a sample level, e.g., SO-GT5 which means the orientation is has an uncertainty of >5 degrees
for example if it broke off before orienting....
8) GPS_Az is the place to put directly determined GPS Azimuths, using, e.g., points along the drill direction.
9) sample_cooling_rate is the cooling rate in K per Ma
10) int_corr_cooling_rate
11) cooling_rate_mcd: data adjustment method code for cooling rate correction; DA-CR-EG is educated guess; DA-CR-PS is percent estimated from pilot samples; DA-CR-TRM is comparison between 2 TRMs acquired with slow and rapid cooling rates.
is the percent cooling rate factor to apply to specimens from this sample, DA-CR-XX is the method code
Orientation convention:
Samples are oriented in the field with a "field arrow" and measured in the laboratory with a "lab arrow". The lab arrow is the positive X direction of the right handed coordinate system of the specimen measurements. The lab and field arrows may not be the same. In the MagIC database, we require the orientation (azimuth and plunge) of the X direction of the measurements (lab arrow). Here are some popular conventions that convert the field arrow azimuth (mag_azimuth in the orient.txt file) and dip (field_dip in orient.txt) to the azimuth and plunge of the laboratory arrow (sample_azimuth and sample_dip in er_samples.txt). The two angles, mag_azimuth and field_dip are explained below.
[1] Standard Pomeroy convention of azimuth and hade (degrees from vertical down)
of the drill direction (field arrow). lab arrow azimuth= sample_azimuth = mag_azimuth;
lab arrow dip = sample_dip =-field_dip. i.e. the lab arrow dip is minus the hade.
[2] Field arrow is the strike of the plane orthogonal to the drill direction,
Field dip is the hade of the drill direction. Lab arrow azimuth = mag_azimuth-90
Lab arrow dip = -field_dip
[3] Lab arrow is the same as the drill direction;
hade was measured in the field.
Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
[4] lab azimuth and dip are same as mag_azimuth, field_dip : use this for unoriented samples too
[5] Same as AZDIP convention explained below -
azimuth and inclination of the drill direction are mag_azimuth and field_dip;
lab arrow is as in [1] above.
lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
[1] Use the IGRF value at the lat/long and date supplied [default]
[2] Will supply declination correction
[3] mag_az is already corrected in file
[4] Correct mag_az but not bedding_dip_dir
Sample naming convention:
[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 site_name column in the orient.txt format input file
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in er_samples.txt and er_sites.txt - will overwrite any existing files
"""
#
# initialize variables
#
stratpos=""
args=sys.argv
date,lat,lon="","","" # date of sampling, latitude (pos North), longitude (pos East)
bed_dip,bed_dip_dir="",""
participantlist=""
Lats,Lons=[],[] # list of latitudes and longitudes
SampOuts,SiteOuts,ImageOuts=[],[],[] # lists of Sample records and Site records
samplelist,sitelist,imagelist=[],[],[]
samp_con,Z,average_bedding,DecCorr="1",1,"0",0.
newbaseline,newbeddir,newbeddip="","",""
meths=''
delta_u="0"
sclass,lithology,type="","",""
newclass,newlith,newtype='','',''
user=""
BPs=[]# bedding pole declinations, bedding pole inclinations
#
#
dir_path,AddTo='.',0
if "-WD" in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
orient_file,samp_file,or_con,corr = dir_path+"/orient.txt",dir_path+"/er_samples.txt","1","1"
site_file=dir_path+"/er_sites.txt"
image_file=dir_path+"/er_images.txt"
SampRecs,SiteRecs,ImageRecs=[],[],[]
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind=args.index("-f")
orient_file=dir_path+'/'+sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+sys.argv[ind+1]
if "-Fsi" in args:
ind=args.index("-Fsi")
site_file=dir_path+'/'+sys.argv[ind+1]
if '-app' in args:
AddTo=1
try:
SampRecs,file_type=pmag.magic_read(samp_file)
print 'sample data to be appended to: ', samp_file
except:
print 'problem with existing file: ',samp_file, ' will create new.'
try:
SiteRecs,file_type=pmag.magic_read(site_file)
print 'site data to be appended to: ',site_file
except:
print 'problem with existing file: ',site_file,' will create new.'
try:
ImageRecs,file_type=pmag.magic_read(image_file)
print 'image data to be appended to: ',image_file
except:
print 'problem with existing file: ',image_file,' will create new.'
if "-ocn" in args:
ind=args.index("-ocn")
or_con=sys.argv[ind+1]
if "-dcn" in args:
ind=args.index("-dcn")
corr=sys.argv[ind+1]
if corr=="2":
DecCorr=float(sys.argv[ind+2])
elif corr=="3":
DecCorr=0.
if '-BCN' in args:
BedCorr=0
else:
BedCorr=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+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"
sys.exit()
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"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "-gmt" in args:
ind=args.index("-gmt")
delta_u=(sys.argv[ind+1])
if "-mcd" in args:
ind=args.index("-mcd")
meths=(sys.argv[ind+1])
if "-a" in args: average_bedding="1"
#
# read in file to convert
#
OrData,location_name=pmag.magic_read(orient_file)
#
# step through the data sample by sample
#
for OrRec in OrData:
if 'mag_azimuth' not in OrRec.keys():OrRec['mag_azimuth']=""
if 'field_dip' not in OrRec.keys():OrRec['field_dip']=""
if OrRec['mag_azimuth']==" ":OrRec["mag_azimuth"]=""
if OrRec['field_dip']==" ":OrRec["field_dip"]=""
if 'sample_description' in OrRec.keys():
sample_description=OrRec['sample_description']
else:
sample_description=""
if 'sample_igsn' in OrRec.keys():
sample_igsn=OrRec['sample_igsn']
else:
sample_igsn=""
if 'sample_texture' in OrRec.keys():
sample_texture=OrRec['sample_texture']
else:
sample_texture=""
if 'sample_cooling_rate' in OrRec.keys():
sample_cooling_rate=OrRec['sample_cooling_rate']
else:
sample_cooling_rate=""
if 'cooling_rate_corr' in OrRec.keys():
cooling_rate_corr=OrRec['cooling_rate_corr']
if 'cooling_rate_mcd' in OrRec.keys():
cooling_rate_mcd=OrRec['cooling_rate_mcd']
else:
cooling_rate_mcd='DA-CR'
else:
cooling_rate_corr=""
cooling_rate_mcd=""
sample_orientation_flag='g'
if 'sample_orientation_flag' in OrRec.keys():
if OrRec['sample_orientation_flag']=='b' or OrRec["mag_azimuth"]=="":
sample_orientation_flag='b'
methcodes=meths # initialize method codes
if meths!='':
if 'method_codes' in OrRec.keys() and OrRec['method_codes'].strip()!="":methcodes=methcodes+":"+OrRec['method_codes'] # add notes
else:
if 'method_codes' in OrRec.keys() and OrRec['method_codes'].strip()!="":methcodes=OrRec['method_codes'] # add notes
codes=methcodes.replace(" ","").split(":")
MagRec={}
MagRec["er_location_name"]=location_name
MagRec["er_citation_names"]="This study"
MagRec['sample_orientation_flag']=sample_orientation_flag
MagRec['sample_igsn']=sample_igsn
MagRec['sample_texture']=sample_texture
MagRec['sample_cooling_rate']=sample_cooling_rate
MagRec['cooling_rate_corr']=cooling_rate_corr
MagRec['cooling_rate_mcd']=cooling_rate_mcd
#
# parse information common to all orientation methods
#
MagRec["er_sample_name"]=OrRec["sample_name"]
if "IGSN" in OrRec.keys():
MagRec["sample_igsn"]=OrRec["IGSN"]
else:
MagRec["sample_igsn"]=""
MagRec["sample_height"],MagRec["sample_bed_dip_direction"],MagRec["sample_bed_dip"]="","",""
if "er_sample_alternatives" in OrRec.keys():MagRec["er_sample_alternatives"]=OrRec["sample_alternatives"]
sample=OrRec["sample_name"]
if OrRec['mag_azimuth']=="" and OrRec['field_dip']!="":
OrRec['mag_azimuth']='999'
if OrRec["mag_azimuth"]!="":
labaz,labdip=pmag.orient(float(OrRec["mag_azimuth"]),float(OrRec["field_dip"]),or_con)
if labaz<0:labaz+=360.
else:
labaz,labdip="",""
if OrRec['mag_azimuth']=='999':labaz=""
if "GPS_baseline" in OrRec.keys() and OrRec['GPS_baseline']!="":newbaseline=OrRec["GPS_baseline"]
if newbaseline!="":baseline=float(newbaseline)
if 'participants' in OrRec.keys() and OrRec['participants']!="" and OrRec['participants']!=participantlist:
participantlist=OrRec['participants']
MagRec['er_scientist_mail_names']=participantlist
newlat=OrRec["lat"]
if newlat!="":lat=float(newlat)
if lat=="":
print "No latitude specified for ! ",sample
sys.exit()
MagRec["sample_lat"]='%11.5f'%(lat)
newlon=OrRec["long"]
if newlon!="":lon=float(newlon)
if lon=="":
print "No longitude specified for ! ",sample
sys.exit()
MagRec["sample_lon"]='%11.5f'%(lon)
if 'bedding_dip_direction' in OrRec.keys(): newbeddir=OrRec["bedding_dip_direction"]
if newbeddir!="":bed_dip_dir=OrRec['bedding_dip_direction']
if 'bedding_dip' in OrRec.keys(): newbeddip=OrRec["bedding_dip"]
if newbeddip!="":bed_dip=OrRec['bedding_dip']
MagRec["sample_bed_dip"]=bed_dip
MagRec["sample_bed_dip_direction"]=bed_dip_dir
if "sample_class" in OrRec.keys():newclass=OrRec["sample_class"]
if newclass!="":sclass=newclass
if sclass=="": sclass="Not Specified"
MagRec["sample_class"]=sclass
if "sample_lithology" in OrRec.keys():newlith=OrRec["sample_lithology"]
if newlith!="":lithology=newlith
if lithology=="": lithology="Not Specified"
MagRec["sample_lithology"]=lithology
if "sample_type" in OrRec.keys():newtype=OrRec["sample_type"]
if newtype!="":type=newtype
if type=="": type="Not Specified"
MagRec["sample_type"]=type
if labdip!="":
MagRec["sample_dip"]='%7.1f'%labdip
else:
MagRec["sample_dip"]=""
if "date" in OrRec.keys():
newdate=OrRec["date"]
if newdate!="":date=newdate
mmddyy=date.split('/')
yy=int(mmddyy[2])
if yy>50:
yy=1900+yy
else:
yy=2000+yy
decimal_year=yy+float(mmddyy[0])/12
sample_date='%i:%s:%s'%(yy,mmddyy[0],mmddyy[1])
MagRec["sample_date"]=sample_date
if labaz!="":
MagRec["sample_azimuth"]='%7.1f'%(labaz)
else:
MagRec["sample_azimuth"]=""
if "stratigraphic_height" in OrRec.keys():
if OrRec["stratigraphic_height"]!="":
MagRec["sample_height"]=OrRec["stratigraphic_height"]
stratpos=OrRec["stratigraphic_height"]
elif OrRec["stratigraphic_height"]=='-1':
MagRec["sample_height"]="" # make empty
else:
MagRec["sample_height"]=stratpos # keep last record if blank
#
if corr=="1" and MagRec['sample_azimuth']!="": # get magnetic declination (corrected with igrf value)
x,y,z,f=pmag.doigrf(lon,lat,0,decimal_year)
Dir=pmag.cart2dir( (x,y,z))
DecCorr=Dir[0]
if "bedding_dip" in OrRec.keys():
if OrRec["bedding_dip"]!="":
MagRec["sample_bed_dip"]=OrRec["bedding_dip"]
bed_dip=OrRec["bedding_dip"]
else:
MagRec["sample_bed_dip"]=bed_dip
else: MagRec["sample_bed_dip"]='0'
if "bedding_dip_direction" in OrRec.keys():
if OrRec["bedding_dip_direction"]!="" and BedCorr==1:
dd=float(OrRec["bedding_dip_direction"])+DecCorr
if dd>360.:dd=dd-360.
MagRec["sample_bed_dip_direction"]='%7.1f'%(dd)
dip_dir=MagRec["sample_bed_dip_direction"]
else:
MagRec["sample_bed_dip_direction"]=OrRec['bedding_dip_direction']
else: MagRec["sample_bed_dip_direction"]='0'
if average_bedding!="0": BPs.append([float(MagRec["sample_bed_dip_direction"]),float(MagRec["sample_bed_dip"])-90.,1.])
if MagRec['sample_azimuth']=="" and MagRec['sample_dip']=="":
MagRec["sample_declination_correction"]=''
methcodes=methcodes+':SO-NO'
MagRec["magic_method_codes"]=methcodes
MagRec['sample_description']=sample_description
#
# work on the site stuff too
if 'site_name' in OrRec.keys():
site=OrRec['site_name']
else:
site=pmag.parse_site(OrRec["sample_name"],samp_con,Z) # parse out the site name
MagRec["er_site_name"]=site
site_description="" # overwrite any prior description
if 'site_description' in OrRec.keys() and OrRec['site_description']!="":
site_description=OrRec['site_description'].replace(",",";")
if "image_name" in OrRec.keys():
images=OrRec["image_name"].split(":")
if "image_look" in OrRec.keys():
looks=OrRec['image_look'].split(":")
else:
looks=[]
if "image_photographer" in OrRec.keys():
photographers=OrRec['image_photographer'].split(":")
else:
photographers=[]
for image in images:
if image !="" and image not in imagelist:
imagelist.append(image)
ImageRec={}
ImageRec['er_image_name']=image
ImageRec['image_type']="outcrop"
ImageRec['image_date']=sample_date
ImageRec['er_citation_names']="This study"
ImageRec['er_location_name']=location_name
ImageRec['er_site_name']=MagRec['er_site_name']
k=images.index(image)
if len(looks)>k:
ImageRec['er_image_description']="Look direction: "+looks[k]
elif len(looks)>=1:
ImageRec['er_image_description']="Look direction: "+looks[-1]
else:
ImageRec['er_image_description']="Look direction: unknown"
if len(photographers)>k:
ImageRec['er_photographer_mail_names']=photographers[k]
elif len(photographers)>=1:
ImageRec['er_photographer_mail_names']=photographers[-1]
else:
ImageRec['er_photographer_mail_names']="unknown"
ImageOuts.append(ImageRec)
if site not in sitelist:
sitelist.append(site) # collect unique site names
SiteRec={}
SiteRec["er_site_name"]=site
SiteRec["site_definition"]="s"
SiteRec["er_location_name"]=location_name
SiteRec["er_citation_names"]="This study"
SiteRec["site_lat"]=MagRec["sample_lat"]
SiteRec["site_lon"]=MagRec["sample_lon"]
SiteRec["site_height"]=MagRec["sample_height"]
SiteRec["site_class"]=MagRec["sample_class"]
SiteRec["site_lithology"]=MagRec["sample_lithology"]
SiteRec["site_type"]=MagRec["sample_type"]
SiteRec["site_description"]=site_description
SiteOuts.append(SiteRec)
if sample not in samplelist:
samplelist.append(sample)
if MagRec['sample_azimuth']!="": # assume magnetic compass only
MagRec['magic_method_codes']=MagRec['magic_method_codes']+':SO-MAG'
MagRec['magic_method_codes']=MagRec['magic_method_codes'].strip(":")
SampOuts.append(MagRec)
if MagRec['sample_azimuth']!="" and corr!='3':
az=labaz+DecCorr
if az>360.:az=az-360.
CMDRec={}
for key in MagRec.keys():
CMDRec[key]=MagRec[key] # make a copy of MagRec
CMDRec["sample_azimuth"]='%7.1f'%(az)
CMDRec["magic_method_codes"]=methcodes+':SO-CMD-NORTH'
CMDRec["magic_method_codes"]=CMDRec['magic_method_codes'].strip(':')
CMDRec["sample_declination_correction"]='%7.1f'%(DecCorr)
if corr=='1':
CMDRec['sample_description']=sample_description+':Declination correction calculated from IGRF'
else:
CMDRec['sample_description']=sample_description+':Declination correction supplied by user'
CMDRec["sample_description"]=CMDRec['sample_description'].strip(':')
SampOuts.append(CMDRec)
if "mag_az_bs" in OrRec.keys() and OrRec["mag_az_bs"] !="" and OrRec["mag_az_bs"]!=" ":
SRec={}
for key in MagRec.keys():
SRec[key]=MagRec[key] # make a copy of MagRec
labaz=float(OrRec["mag_az_bs"])
az=labaz+DecCorr
if az>360.:az=az-360.
SRec["sample_azimuth"]='%7.1f'%(az)
SRec["sample_declination_correction"]='%7.1f'%(DecCorr)
SRec["magic_method_codes"]=methcodes+':SO-SIGHT-BACK:SO-CMD-NORTH'
SampOuts.append(SRec)
#
# check for suncompass data
#
if "shadow_angle" in OrRec.keys() and OrRec["shadow_angle"]!="": # there are sun compass data
if delta_u=="":
delta_u=raw_input("Enter hours to SUBTRACT from time for GMT: [0] ")
if delta_u=="":delta_u="0"
SunRec,sundata={},{}
shad_az=float(OrRec["shadow_angle"])
sundata["date"]='%i:%s:%s:%s'%(yy,mmddyy[0],mmddyy[1],OrRec["hhmm"])
# if eval(delta_u)<0:
# MagRec["sample_time_zone"]='GMT'+delta_u+' hours'
# else:
# MagRec["sample_time_zone"]='GMT+'+delta_u+' hours'
sundata["delta_u"]=delta_u
sundata["lon"]='%7.1f'%(lon)
sundata["lat"]='%7.1f'%(lat)
sundata["shadow_angle"]=OrRec["shadow_angle"]
sundec=pmag.dosundec(sundata)
for key in MagRec.keys():
SunRec[key]=MagRec[key] # make a copy of MagRec
SunRec["sample_azimuth"]='%7.1f'%(sundec)
SunRec["sample_declination_correction"]=''
SunRec["magic_method_codes"]=methcodes+':SO-SUN'
SunRec["magic_method_codes"]=SunRec['magic_method_codes'].strip(':')
SampOuts.append(SunRec)
#
# check for differential GPS data
#
if "prism_angle" in OrRec.keys() and OrRec["prism_angle"]!="": # there are diff GPS data
GPSRec={}
for key in MagRec.keys():
GPSRec[key]=MagRec[key] # make a copy of MagRec
prism_angle=float(OrRec["prism_angle"])
laser_angle=float(OrRec["laser_angle"])
if OrRec["GPS_baseline"]!="": baseline=float(OrRec["GPS_baseline"]) # new baseline
gps_dec=baseline+laser_angle+prism_angle-90.
while gps_dec>360.:
gps_dec=gps_dec-360.
while gps_dec<0:
gps_dec=gps_dec+360.
for key in MagRec.keys():
GPSRec[key]=MagRec[key] # make a copy of MagRec
GPSRec["sample_azimuth"]='%7.1f'%(gps_dec)
GPSRec["sample_declination_correction"]=''
GPSRec["magic_method_codes"]=methcodes+':SO-GPS-DIFF'
SampOuts.append(GPSRec)
if "GPS_Az" in OrRec.keys() and OrRec["GPS_Az"]!="": # there are differential GPS Azimuth data
GPSRec={}
for key in MagRec.keys():
GPSRec[key]=MagRec[key] # make a copy of MagRec
GPSRec["sample_azimuth"]='%7.1f'%(float(OrRec["GPS_Az"]))
GPSRec["sample_declination_correction"]=''
GPSRec["magic_method_codes"]=methcodes+':SO-GPS-DIFF'
SampOuts.append(GPSRec)
if average_bedding!="0":
fpars=pmag.fisher_mean(BPs)
print 'over-writing all bedding with average '
Samps=[]
for rec in SampOuts:
if average_bedding!="0":
rec['sample_bed_dip_direction']='%7.1f'%(fpars['dec'])
rec['sample_bed_dip']='%7.1f'%(fpars['inc']+90.)
Samps.append(rec)
else:
Samps.append(rec)
for rec in SampRecs:
if rec['er_sample_name'] not in samplelist: # overwrite prior for this sample
Samps.append(rec)
for rec in SiteRecs:
if rec['er_site_name'] not in sitelist: # overwrite prior for this sample
SiteOuts.append(rec)
for rec in ImageRecs:
if rec['er_image_name'] not in imagelist: # overwrite prior for this sample
ImageOuts.append(rec)
print 'saving data...'
SampsOut,keys=pmag.fillkeys(Samps)
Sites,keys=pmag.fillkeys(SiteOuts)
pmag.magic_write(samp_file,SampsOut,"er_samples")
pmag.magic_write(site_file,Sites,"er_sites")
print "Data saved in ", samp_file,' and ',site_file
if len(ImageOuts)>0:
Images,keys=pmag.fillkeys(ImageOuts)
pmag.magic_write(image_file,Images,"er_images")
print "Image info saved in ",image_file
def main(command_line=True, **kwargs):
"""
NAME
PMD_magic.py
DESCRIPTION
converts PMD (Enkin) format files to magic_measurements format files
SYNTAX
PMD_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify naming convention
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
Sample naming convention:
[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 same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
PMD format files
"""
# initialize some stuff
noave=0
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
DIspec=[]
MagFiles=[]
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
print samp_con
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
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"
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, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
# parse data
data=open(mag_file,'rU').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.
er_specimen_name=rec[0]
ErSampRec,ErSiteRec={},{} # make a sample record
if specnum!=0:
er_sample_name=rec[0][:specnum]
else:
er_sample_name=rec[0]
if len(ErSamps)>0: # need to copy existing
for samp in ErSamps:
if samp['er_sample_name']==er_sample_name:
ErSampRec=samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con)<6:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
else:
if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampREc['er_site_name']
if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampREc['er_location_name']
az_ind=rec.index('a=')+1
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['er_sample_description']=comment
ErSampRec['sample_azimuth']=rec[az_ind]
dip_ind=rec.index('b=')+1
dip=-float(rec[dip_ind])
ErSampRec['sample_dip']='%7.1f'%(dip)
strike_ind=rec.index('s=')+1
ErSampRec['sample_bed_dip_direction']='%7.1f'%(float(rec[strike_ind])+90.)
bd_ind=rec.index('d=')+1
ErSampRec['sample_bed_dip']=rec[bd_ind]
v_ind=rec.index('v=')+1
vol=rec[v_ind][:-3]
date=rec[-2]
time=rec[-1]
ErSampRec['magic_method_codes']=meth_code
if 'er_location_name' not in ErSampRec.keys():ErSampRec['er_location_name']=er_location_name
if 'er_site_name' not in ErSampRec.keys():ErSampRec['er_site_name']=er_site_name
if 'er_citation_names' not in ErSampRec.keys():ErSampRec['er_citation_names']='This study'
if 'magic_method_codes' not in ErSampRec.keys():ErSampRec['magic_method_codes']='SO-NO'
SampOuts.append(ErSampRec)
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
MagRec={}
MagRec['measurement_description']='Date: '+date+' '+time
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
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)
MagRec["measurement_magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MagRec["measurement_magn_volume"]=rec[4] # A/m
MagRec["measurement_dec"]='%7.1f'%(Vec[0])
MagRec["measurement_inc"]='%7.1f'%(Vec[1])
MagRec["treatment_ac_field"]='0'
if meas_type!='LT-NO':
treat=float(rec[0][1:])
else:
treat=0
if meas_type=="LT-AF-Z":
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif meas_type=="LT-T-Z":
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
pmag.magic_write(samp_file,SampOuts,'er_samples')
print "sample orientations put in ",samp_file
return True, meas_file
def main():
"""
NAME
UU_magic.py
DESCRIPTION
takes Fort Hoofddijk (University of Utrecht) format magnetometer files and converts them to magic_measurements and er_samples.txt
SYNTAX
UU_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-fpos FILE: specify stratigraphic position file (.saf format)
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-ncn NCON: specify naming convention: default is #1 below
-ocn OCON: specify orientation convention, default is #1 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
INPUT FORMAT
Input files must be colon delimited:
"file_name", "instrument"
"specimen name","",az,pl,vol(cc),strike,dip
treatment,X,Y,Z,CSD,"yy-mm-dd","hh:mm"
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-dip
i.e., dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -dip
i.e., mag_azimuth is strike and dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = dip-90
e.g. dip is degrees from horizontal of drill direction
[4] Lab arrow azimuth = mag_azimuth; Lab arrow dip = dip
[5] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-dip
[6] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az is already corrected in file
Sample naming convention:
[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 same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
uu_file,samp_file,or_con,corr,meas_file = "","er_samples.txt","1","1","magic_measurements.txt"
pos_file=""
specnum=-1
args=sys.argv
bed_dip,bed_dip_dir="",""
samp_con,Z,average_bedding="1",1,"0"
meths='FS-FD:SO-POM'
sclass,lithology,type="","",""
user,inst="",""
or_con='1'
corr=="3"
DecCorr=0.
location_name="unknown"
#
#
dir_path='.'
if '-WD' in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind=args.index("-f")
uu_file=sys.argv[ind+1]
d=uu_file.split('.')
if d[1].upper()=="AF":demag="AF"
if d[1].upper()=="TH":demag="T"
if "-fpos" in args:
ind=args.index("-fpos")
pos_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
meas_file=sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-ocn" in args:
ind=args.index("-ocn")
or_con=sys.argv[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+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"
sys.exit()
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"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "-mcd" in args:
ind=args.index("-mcd")
meths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
location_name=(sys.argv[ind+1])
if "-spc" in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
#
#
uu_file=dir_path+'/'+uu_file
samp_file=dir_path+'/'+samp_file
meas_file=dir_path+'/'+meas_file
if pos_file!="":pos_file=dir_path+'/'+pos_file
samplist=[]
try:
SampOut,file_type=pmag.magic_read(samp_file)
for rec in SampOut:
if rec['er_sample_name'] not in samplist: samplist.append(rec['er_sample_name'])
except:
SampOut=[]
PosData=[]
if pos_file != "":
p=open(pos_file,'rU')
PosIn=p.readlines()
p.close()
for line in PosIn:
srec=line.split()[0].split(',')
Prec={'er_site_name':srec[0],'sample_height':srec[1]}
PosData.append(Prec)
infile=open(uu_file,'rU')
Data=infile.readlines()
infile.close()
MagRecs=[]
header=Data[0].split(',')
if inst=="":inst=header[1].strip('"')
if inst=='2G DC':
inst=="FH-2GDC" # Dc Squid machine at Fort Hoofddijk
else:
inst=""
newsamp=1
for k in range(1,len(Data)-1): # step through file, skipping header and "END" statement
line=Data[k].split('\n')[0]
rec=line.split(',')
if newsamp==1 and rec[0].lower()!='end':
newsamp=0
specname=rec[0].strip('"') # take off quotation marks
if specnum!=0:
sample=specname[:specnum]
else:
sample=specname
site=pmag.parse_site(sample,samp_con,Z) # parse out the site name
SampRec={}
SampRec["er_sample_name"]=sample
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
labaz,labdip=pmag.orient(float(rec[2]),float(rec[3]),or_con)
bed_dip=float(rec[6])
if bed_dip!=0:
bed_dip_dir=float(rec[5])+90. # assume dip to right of strike
if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360.
else:
bed_dip_dir=float(rec[5])
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"]='%7.1f'%(bed_dip)
SampRec["sample_bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
vol=float(rec[4])*1e-6
SampRec["sample_volume"]='%10.3e'%(vol) # convert cc into m^3
SampRec["sample_class"]=sclass
SampRec["sample_lithology"]=lithology
SampRec["sample_type"]=type
SampRec["magic_method_codes"]=meths
SampRec["er_site_name"]=site
#
# find position data
#
if PosData!=[]:
for srec in PosData:
if srec['er_site_name']==site:
SampRec['sample_height']=srec['sample_height']
break
if sample not in samplist:
samplist.append(sample)
SampOut.append(SampRec)
elif rec[0]=='9999': # end of this specimen
k=k+1 # move on
newsamp=1
elif rec[0].lower()!='end' and rec[0]!="": # got some data
line=Data[k].split('\n')[0]
rec=line.split(',')
MagRec={}
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=specname
MagRec["er_sample_name"]=sample
MagRec["er_site_name"]=site
MagRec["er_location_name"]=location_name
MagRec["measurement_csd"]=rec[4]
cart=[]
cart.append(-float(rec[2])) # appending x,y,z from data record
cart.append(float(rec[3]))
cart.append(-float(rec[1]))
Dir=pmag.cart2dir(cart)
MagRec["measurement_magn_volume"]='%10.3e'% (float(Dir[2])*1e-6) # moment in A/m (from 10^-6 A/m)
MagRec["measurement_magn_moment"]='%10.3e'% (float(Dir[2])*vol*1e-6) # moment in Am^2
MagRec["measurement_dec"]='%7.1f'%(Dir[0])
MagRec["measurement_inc"]='%7.1f'%(Dir[1])
MagRec["magic_instrument_codes"]=inst
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
MagRec["treatment_ac_field"]='%8.3e' %(float(rec[0])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (float(rec[0])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec['magic_method_codes']=meas_type
# date=rec[5].strip('"').split('-')
# time=rec[6].strip('"')
# if int(date[0])<50: # assume this century
# yyyy='20'+date[0]
# else:
# yyyy='19'+date[0] # assume last century
# dstring=yyyy+':'+date[1]+':'+date[2]+":"+time
# MagRec['measurement_date']=dstring
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,0)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "Measurements put in ",meas_file
pmag.magic_write(samp_file,SampOut,"er_samples")
print "Sample orientation info saved in ", samp_file
print "Good bye"
def main():
"""
NAME
ani_depthplot.py
DESCRIPTION
plots tau, V3_inc, P and chi versus core_depth
SYNTAX
ani_depthplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input rmag_anisotropy format file from magic
-fb FILE: specify input magic_measurements format file from magic
-fsa FILE: specify input er_samples format file from magic
-fa FILE: specify input er_ages format file from magic
-d min max [in m] depth range to plot
-ds [mcd,mbsf], specify depth scale, default is mbsf
-sav save plot without review
-fmt specfiy format for figures - default is svg
DEFAULTS:
Anisotropy file: rmag_anisotropy.txt
Bulk susceptibility file: magic_measurements.txt
Samples file: er_samples.txt
"""
fmt='.svg'
dir_path="./"
pcol=3
verbose=pmagplotlib.verbose
plots=0
age_file=""
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
ani_file=dir_path+'/rmag_anisotropy.txt'
meas_file=dir_path+'/magic_measurements.txt'
samp_file=dir_path+'/er_samples.txt'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
ani_file=dir_path+'/'+sys.argv[ind+1]
if '-fb' in sys.argv:
ind=sys.argv.index('-fb')
meas_file=dir_path+'/'+sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index('-fsa')
samp_file=dir_path+'/'+sys.argv[ind+1]
if '-fa' in sys.argv:
print main.__doc__
print 'only -fsa OR -fa - not both'
sys.exit()
elif '-fa' in sys.argv:
ind=sys.argv.index('-fa')
age_file=dir_path+"/"+sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
dmin,dmax=-1,-1
if '-d' in sys.argv:
ind=sys.argv.index('-d')
dmin=float(sys.argv[ind+1])
dmax=float(sys.argv[ind+2])
if '-ds' in sys.argv and 'mcd' in sys.argv: # sets depth scale to meters composite depth (as opposed to meters below sea floor)
depth_scale='sample_composite_depth'
elif age_file=="":
depth_scale='sample_core_depth'
else:
depth_scale='age'
if '-sav' in sys.argv:
plots=1
verbose=0
#
# get data read in
isbulk=0 # tests if there are bulk susceptibility measurements
AniData,file_type=pmag.magic_read(ani_file) # read in tensor elements
if age_file=="":
Samps,file_type=pmag.magic_read(samp_file) # read in sample depth info from er_sample.txt format file
else:
Samps,file_type=pmag.magic_read(age_file) # read in sample age info from er_ages.txt format file
age_unit=Samps[0]['age_unit']
for s in Samps:s['er_sample_name']=s['er_sample_name'].upper() # change to upper case for every sample name
Meas,file_type=pmag.magic_read(meas_file)
if file_type=='magic_measurements':isbulk=1
Data=[]
Bulks=[]
BulkDepths=[]
for rec in AniData:
samprecs=pmag.get_dictitem(Samps,'er_sample_name',rec['er_sample_name'].upper(),'T') # look for depth record for this sample
sampdepths=pmag.get_dictitem(samprecs,depth_scale,'','F') # see if there are non-blank depth data
if dmax!=-1:
sampdepths=pmag.get_dictitem(sampdepths,depth_scale,dmax,'max') # fishes out records within depth bounds
sampdepths=pmag.get_dictitem(sampdepths,depth_scale,dmin,'min')
if len(sampdepths)>0: # if there are any....
rec['core_depth'] = sampdepths[0][depth_scale] # set the core depth of this record
Data.append(rec) # fish out data with core_depth
if isbulk: # if there are bulk data
chis=pmag.get_dictitem(Meas,'er_specimen_name',rec['er_specimen_name'],'T')
chis=pmag.get_dictitem(chis,'measurement_chi_volume','','F') # get the non-zero values for this specimen
if len(chis)>0: # if there are any....
Bulks.append(1e6*float(chis[0]['measurement_chi_volume'])) # put in microSI
BulkDepths.append(float(sampdepths[0][depth_scale]))
if len(Bulks)>0: # set min and max bulk values
bmin=min(Bulks)
bmax=max(Bulks)
xlab="Depth (m)"
if len(Data)>0:
location=Data[0]['er_location_name']
else:
print 'no data to plot'
sys.exit()
# collect the data for plotting tau and V3_inc
Depths,Tau1,Tau2,Tau3,V3Incs,P=[],[],[],[],[],[]
Axs=[] # collect the plot ids
if len(Bulks)>0: pcol+=1
s1=pmag.get_dictkey(Data,'anisotropy_s1','f') # get all the s1 values from Data as floats
s2=pmag.get_dictkey(Data,'anisotropy_s2','f')
s3=pmag.get_dictkey(Data,'anisotropy_s3','f')
s4=pmag.get_dictkey(Data,'anisotropy_s4','f')
s5=pmag.get_dictkey(Data,'anisotropy_s5','f')
s6=pmag.get_dictkey(Data,'anisotropy_s6','f')
Depths=pmag.get_dictkey(Data,'core_depth','f')
Ss=numpy.array([s1,s4,s5,s4,s2,s6,s5,s6,s3]).transpose() # make an array
Ts=numpy.reshape(Ss,(len(Ss),3,-1)) # and re-shape to be n-length array of 3x3 sub-arrays
for k in range(len(Depths)):
tau,Evecs= pmag.tauV(Ts[k]) # get the sorted eigenvalues and eigenvectors
v3=pmag.cart2dir(Evecs[2])[1] # convert to inclination of the minimum eigenvector
V3Incs.append(v3)
Tau1.append(tau[0])
Tau2.append(tau[1])
Tau3.append(tau[2])
P.append(tau[0]/tau[2])
if len(Depths)>0:
if dmax==-1:
dmax=max(Depths)
dmin=min(Depths)
tau_max=max(Tau1)
tau_min=min(Tau3)
P_max=max(P)
P_min=min(P)
#dmax=dmax+.05*dmax
#dmin=dmin-.05*dmax
pylab.figure(1,figsize=(10,8)) # make the figure
version_num=pmag.get_version()
pylab.figtext(.02,.01,version_num) # attach the pmagpy version number
ax=pylab.subplot(1,pcol,1) # make the first column
Axs.append(ax)
ax.plot(Tau1,Depths,'rs')
ax.plot(Tau2,Depths,'b^')
ax.plot(Tau3,Depths,'ko')
ax.axis([tau_min,tau_max,dmax,dmin])
ax.set_xlabel('Eigenvalues')
if depth_scale=='sample_core_depth':
ax.set_ylabel('Depth (mbsf)')
elif depth_scale=='age':
ax.set_ylabel('Age ('+age_unit+')')
else:
ax.set_ylabel('Depth (mcd)')
ax2=pylab.subplot(1,pcol,2) # make the second column
ax2.plot(P,Depths,'rs')
ax2.axis([P_min,P_max,dmax,dmin])
ax2.set_xlabel('P')
ax2.set_title(location)
Axs.append(ax2)
ax3=pylab.subplot(1,pcol,3)
Axs.append(ax3)
ax3.plot(V3Incs,Depths,'ko')
ax3.axis([0,90,dmax,dmin])
ax3.set_xlabel('V3 Inclination')
if pcol==4:
ax4=pylab.subplot(1,pcol,4)
Axs.append(ax4)
ax4.plot(Bulks,BulkDepths,'bo')
ax4.axis([bmin-1,bmax+1,dmax,dmin])
ax4.set_xlabel('Bulk Susc. (uSI)')
for x in Axs:pmagplotlib.delticks(x) # this makes the x-tick labels more reasonable - they were overcrowded using the defaults
figname=location+'_ani-depthplot'+fmt
if verbose:
pylab.draw()
ans=raw_input("S[a]ve plot? Return to quit ")
if ans=='a':
pylab.savefig(figname)
print 'Plot saved as ',figname
elif plots:
pylab.savefig(figname)
print 'Plot saved as ',figname
sys.exit()
else:
print "No data points met your criteria - try again"
def plotELL(pars,col,lower,plot):
"""
function to calculate points on an ellipse about Pdec,Pdip with angle beta,gamma
"""
rad=np.pi/180.
Pdec,Pinc,beta,Bdec,Binc,gamma,Gdec,Ginc=pars[0],pars[1],pars[2],pars[3],pars[4],pars[5],pars[6],pars[7]
if beta > 90. or gamma>90:
beta=180.-beta
gamma=180.-beta
Pdec=Pdec-180.
Pinc=-Pinc
beta,gamma=beta*rad,gamma*rad # convert to radians
X_ell,Y_ell,X_up,Y_up,PTS=[],[],[],[],[]
nums=201
xnum=float(nums-1.)/2.
# set up t matrix
t=[[0,0,0],[0,0,0],[0,0,0]]
X=pmag.dir2cart((Pdec,Pinc,1.0)) # convert to cartesian coordintes
if lower==1 and X[2]<0:
for i in range(3):
X[i]=-X[i]
# set up rotation matrix t
t[0][2]=X[0]
t[1][2]=X[1]
t[2][2]=X[2]
X=pmag.dir2cart((Bdec,Binc,1.0))
if lower==1 and X[2]<0:
for i in range(3):
X[i]=-X[i]
t[0][0]=X[0]
t[1][0]=X[1]
t[2][0]=X[2]
X=pmag.dir2cart((Gdec,Ginc,1.0))
if lower==1 and X[2]<0:
for i in range(3):
X[i]=-X[i]
t[0][1]=X[0]
t[1][1]=X[1]
t[2][1]=X[2]
# set up v matrix
v=[0,0,0]
for i in range(nums): # incremental point along ellipse
psi=float(i)*np.pi/xnum
v[0]=np.sin(beta)*np.cos(psi)
v[1]=np.sin(gamma)*np.sin(psi)
v[2]=np.sqrt(1.-v[0]**2 - v[1]**2)
elli=[0,0,0]
# calculate points on the ellipse
for j in range(3):
for k in range(3):
elli[j]=elli[j] + t[j][k]*v[k] # cartesian coordinate j of ellipse
PTS.append(pmag.cart2dir(elli))
R=np.sqrt( 1.-abs(elli[2]))/(np.sqrt(elli[0]**2+elli[1]**2)) # put on an equal area projection
if elli[2]<0:
# for i in range(3): elli[i]=-elli[i]
X_up.append(elli[1]*R)
Y_up.append(elli[0]*R)
# Adding None values stops plotting of an additional straight line
# between the points where the ellipse crosses the edge of the stereonet
X_ell.append(None)
Y_ell.append(None)
else:
X_ell.append(elli[1]*R)
Y_ell.append(elli[0]*R)
if plot==1:
if X_ell!=[]:plt.plot(X_ell,Y_ell,color=col, linewidth=2, zorder=6)
if X_up!=[]:plt.plot(X_up,Y_up,color=col,linewidth=2,linestyle=':')
else:
return PTS
def dokent(data, NN): #From PmagPy (Tauxe et al., 2016)
"""
gets Kent parameters for data ([D,I],N)
"""
X, kpars = [], {}
N = len(data)
if N < 2:
return kpars
#
# get fisher mean and convert to co-inclination (theta)/dec (phi) in radians
#
fpars = pmag.fisher_mean(data)
pbar = fpars["dec"] * np.pi / 180.
tbar = (90. - fpars["inc"]) * np.pi / 180.
#
# initialize matrices
#
H = [[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]]
w = [[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]]
b = [[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]]
gam = [[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]]
xg = []
#
# set up rotation matrix H
#
H = [[
np.cos(tbar) * np.cos(pbar), -np.sin(pbar),
np.sin(tbar) * np.cos(pbar)
], [
np.cos(tbar) * np.sin(pbar),
np.cos(pbar),
np.sin(pbar) * np.sin(tbar)
], [-np.sin(tbar), 0., np.cos(tbar)]]
#
# get cartesian coordinates of data
#
for rec in data:
X.append(pmag.dir2cart([rec[0], rec[1], 1.]))
#
# put in T matrix
#
T = pmag.Tmatrix(X)
for i in range(3):
for j in range(3):
T[i][j] = old_div(T[i][j], float(NN))
#
# compute B=H'TH
#
for i in range(3):
for j in range(3):
for k in range(3):
w[i][j] += T[i][k] * H[k][j]
for i in range(3):
for j in range(3):
for k in range(3):
b[i][j] += H[k][i] * w[k][j]
#
# choose a rotation w about North pole to diagonalize upper part of B
#
psi = 0.5 * np.arctan(2. * b[0][1] / (b[0][0] - b[1][1]))
w = [[np.cos(psi), -np.sin(psi), 0], [np.sin(psi),
np.cos(psi), 0], [0., 0., 1.]]
for i in range(3):
for j in range(3):
gamtmp = 0.
for k in range(3):
gamtmp += H[i][k] * w[k][j]
gam[i][j] = gamtmp
for i in range(N):
xg.append([0., 0., 0.])
for k in range(3):
xgtmp = 0.
for j in range(3):
xgtmp += gam[j][k] * X[i][j]
xg[i][k] = xgtmp
# compute asymptotic ellipse parameters
#
xmu, sigma1, sigma2 = 0., 0., 0.
for i in range(N):
xmu += xg[i][2]
sigma1 = sigma1 + xg[i][0]**2
sigma2 = sigma2 + xg[i][1]**2
xmu = old_div(xmu, float(N))
sigma1 = old_div(sigma1, float(N))
sigma2 = old_div(sigma2, float(N))
g = -2.0 * np.log(0.05) / (float(NN) * xmu**2)
if np.sqrt(sigma1 * g) < 1:
eta = np.arcsin(np.sqrt(sigma1 * g))
if np.sqrt(sigma2 * g) < 1:
zeta = np.arcsin(np.sqrt(sigma2 * g))
if np.sqrt(sigma1 * g) >= 1.:
eta = old_div(np.pi, 2.)
if np.sqrt(sigma2 * g) >= 1.:
zeta = old_div(np.pi, 2.)
#
# convert Kent parameters to directions,angles
#
kpars["dec"] = fpars["dec"]
kpars["inc"] = fpars["inc"]
kpars["n"] = NN
ZDir = pmag.cart2dir([gam[0][1], gam[1][1], gam[2][1]])
EDir = pmag.cart2dir([gam[0][0], gam[1][0], gam[2][0]])
kpars["Zdec"] = ZDir[0]
kpars["Zinc"] = ZDir[1]
kpars["Edec"] = EDir[0]
kpars["Einc"] = EDir[1]
if kpars["Zinc"] < 0:
kpars["Zinc"] = -kpars["Zinc"]
kpars["Zdec"] = (kpars["Zdec"] + 180.) % 360.
if kpars["Einc"] < 0:
kpars["Einc"] = -kpars["Einc"]
kpars["Edec"] = (kpars["Edec"] + 180.) % 360.
kpars["Zeta"] = zeta * 180. / np.pi
kpars["Eta"] = eta * 180. / np.pi
return kpars
def main():
"""
NAME
igrf.py
DESCRIPTION
This program calculates igrf field values
using the routine of Malin and Barraclough (1981)
based on d/igrfs from 1900 to 2010.
between 1900 and 1000BCE, it uses CALS3K.4 or ARCH3K.1
Prior to 1000BCE, it uses CALS10k-4b
Calculates reference field vector at specified location and time.
SYNTAX
igrf.py [-h] [-i] -f FILE [< filename]
OPTIONS:
-h prints help message and quits
-i for interactive data entry
-f FILE specify file name with input data
-F FILE specify output file name
-ages MIN MAX INCR: specify age minimum in years (+/- AD), maximum and increment, default is line by line
-loc LAT LON; specify location, default is line by line
-alt ALT; specify altitude in km, default is sealevel (0)
-plt; make a plot of the time series
-fmt [pdf,jpg,eps,svg] specify format for output figure (default is svg)
-mod [arch3k,cals3k] specify model for 3ka to 1900 AD, default is cals3k.4b
INPUT FORMAT
interactive entry:
date: decimal year
alt: altitude in km
lat: positive north
lon: positive east
for file entry:
space delimited string: date alt lat long
OUTPUT FORMAT
Declination Inclination Intensity (nT) date alt lat long
"""
plt,fmt=0,'svg'
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if len(sys.argv)!=0 and '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-mod' in sys.argv:
ind=sys.argv.index('-mod')
mod3k=sys.argv[ind+1]
else: mod3k=''
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
input=numpy.loadtxt(file)
elif '-i' in sys.argv:
while 1:
try:
line=[]
line.append(float(raw_input("Decimal year: <cntrl-D to quit> ")))
alt=raw_input("Elevation in km [0] ")
if alt=="":alt="0"
line.append(float(alt))
line.append(float(raw_input("Latitude (positive north) ")))
line.append(float(raw_input("Longitude (positive east) ")))
if mod3k=='':
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0])
else:
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0],mod3k=mod3k)
Dir=pmag.cart2dir((x,y,z))
print '%7.1f %7.1f %8.0f'%(Dir[0],Dir[1],f)
except EOFError:
print "\n Good-bye\n"
sys.exit()
elif '-ages' in sys.argv:
ind=sys.argv.index('-ages')
agemin=float(sys.argv[ind+1])
agemax=float(sys.argv[ind+2])
ageincr=float(sys.argv[ind+3])
if '-loc' in sys.argv:
ind=sys.argv.index('-loc')
lat=float(sys.argv[ind+1])
lon=float(sys.argv[ind+2])
else:
print "must specify lat/lon if using age range option"
sys.exit()
if '-alt' in sys.argv:
ind=sys.argv.index('-alt')
alt=float(sys.argv[ind+1])
else: alt=0
ages=numpy.arange(agemin,agemax,ageincr)
lats=numpy.ones(len(ages))*lat
lons=numpy.ones(len(ages))*lon
alts=numpy.ones(len(ages))*alt
input=numpy.array([ages,alts,lats,lons]).transpose()
else:
input=numpy.loadtxt(sys.stdin,dtype=numpy.float)
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=sys.argv[ind+1]
out=open(outfile,'w')
else:outfile=""
if '-plt' in sys.argv:
plt=1
import matplotlib
matplotlib.use("TkAgg")
import pylab
pylab.ion()
Ages,Decs,Incs,Ints,VADMs=[],[],[],[],[]
for line in input:
if mod3k=='':
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0])
else:
x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0],mod3k=mod3k)
Dir=pmag.cart2dir((x,y,z))
if outfile!="":
out.write('%7.1f %7.1f %8.0f %7.1f %7.1f %7.1f %7.1f\n'%(Dir[0],Dir[1],f,line[0],line[1],line[2],line[3]))
elif plt:
Ages.append(line[0])
if Dir[0]>180: Dir[0]=Dir[0]-360.0
Decs.append(Dir[0])
Incs.append(Dir[1])
Ints.append(f*1e-3)
VADMs.append(pmag.b_vdm(f*1e-9,line[2])*1e-21)
else:
print '%7.1f %7.1f %8.0f %7.1f %7.1f %7.1f %7.1f'%(Dir[0],Dir[1],f,line[0],line[1],line[2],line[3])
if plt:
fig=pylab.figure(num=1,figsize=(7,9))
fig.add_subplot(411)
pylab.plot(Ages,Decs)
pylab.ylabel('Declination ($^{\circ}$)')
fig.add_subplot(412)
pylab.plot(Ages,Incs)
pylab.ylabel('Inclination ($^{\circ}$)')
fig.add_subplot(413)
pylab.plot(Ages,Ints)
pylab.ylabel('Intensity ($\mu$T)')
fig.add_subplot(414)
pylab.plot(Ages,VADMs)
pylab.ylabel('VADMs (ZAm$^2$)')
pylab.xlabel('Ages')
pylab.draw()
ans=raw_input("S[a]ve to save figure, <Return> to quit ")
if ans=='a':
pylab.savefig('igrf.'+fmt)
print 'Figure saved as: ','igrf.'+fmt
sys.exit()
def plotELL(pars, col, lower, plot):
"""
function to calculate points on an ellipse about Pdec,Pdip with angle beta,gamma
"""
rad = np.pi / 180.
Pdec, Pinc, beta, Bdec, Binc, gamma, Gdec, Ginc = pars[0], pars[1], pars[
2], pars[3], pars[4], pars[5], pars[6], pars[7]
if beta > 90. or gamma > 90:
beta = 180. - beta
gamma = 180. - beta
Pdec = Pdec - 180.
Pinc = -Pinc
beta, gamma = beta * rad, gamma * rad # convert to radians
X_ell, Y_ell, X_up, Y_up, PTS = [], [], [], [], []
nums = 201
xnum = float(nums - 1.) / 2.
# set up t matrix
t = [[0, 0, 0], [0, 0, 0], [0, 0, 0]]
X = pmag.dir2cart((Pdec, Pinc, 1.0)) # convert to cartesian coordintes
if lower == 1 and X[2] < 0:
for i in range(3):
X[i] = -X[i]
# set up rotation matrix t
t[0][2] = X[0]
t[1][2] = X[1]
t[2][2] = X[2]
X = pmag.dir2cart((Bdec, Binc, 1.0))
if lower == 1 and X[2] < 0:
for i in range(3):
X[i] = -X[i]
t[0][0] = X[0]
t[1][0] = X[1]
t[2][0] = X[2]
X = pmag.dir2cart((Gdec, Ginc, 1.0))
if lower == 1 and X[2] < 0:
for i in range(3):
X[i] = -X[i]
t[0][1] = X[0]
t[1][1] = X[1]
t[2][1] = X[2]
# set up v matrix
v = [0, 0, 0]
for i in range(nums): # incremental point along ellipse
psi = float(i) * np.pi / xnum
v[0] = np.sin(beta) * np.cos(psi)
v[1] = np.sin(gamma) * np.sin(psi)
v[2] = np.sqrt(1. - v[0]**2 - v[1]**2)
elli = [0, 0, 0]
# calculate points on the ellipse
for j in range(3):
for k in range(3):
elli[j] = elli[j] + t[j][k] * v[
k] # cartesian coordinate j of ellipse
PTS.append(pmag.cart2dir(elli))
R = np.sqrt(1. - abs(elli[2])) / (np.sqrt(elli[0]**2 + elli[1]**2)
) # put on an equal area projection
if elli[2] < 0:
# for i in range(3): elli[i]=-elli[i]
X_up.append(elli[1] * R)
Y_up.append(elli[0] * R)
# Adding None values stops plotting of an additional straight line
# between the points where the ellipse crosses the edge of the stereonet
X_ell.append(None)
Y_ell.append(None)
else:
X_ell.append(elli[1] * R)
Y_ell.append(elli[0] * R)
if plot == 1:
if X_ell != []:
plt.plot(X_ell, Y_ell, color=col, linewidth=2, zorder=6)
if X_up != []:
plt.plot(X_up, Y_up, color=col, linewidth=2, linestyle=':')
else:
return PTS
def calculate_aniso_parameters(B,K):
aniso_parameters={}
S_bs=dot(B,K)
# normalize by trace
trace=S_bs[0]+S_bs[1]+S_bs[2]
S_bs=S_bs/trace
s1,s2,s3,s4,s5,s6=S_bs[0],S_bs[1],S_bs[2],S_bs[3],S_bs[4],S_bs[5]
s_matrix=[[s1,s4,s6],[s4,s2,s5],[s6,s5,s3]]
# calculate eigen vector,
t,evectors=eig(s_matrix)
# sort vectors
t=list(t)
t1=max(t)
ix_1=t.index(t1)
t3=min(t)
ix_3=t.index(t3)
for tt in range(3):
if t[tt]!=t1 and t[tt]!=t3:
t2=t[tt]
ix_2=t.index(t2)
v1=[evectors[0][ix_1],evectors[1][ix_1],evectors[2][ix_1]]
v2=[evectors[0][ix_2],evectors[1][ix_2],evectors[2][ix_2]]
v3=[evectors[0][ix_3],evectors[1][ix_3],evectors[2][ix_3]]
DIR_v1=pmag.cart2dir(v1)
DIR_v2=pmag.cart2dir(v2)
DIR_v3=pmag.cart2dir(v3)
aniso_parameters['anisotropy_s1']="%f"%s1
aniso_parameters['anisotropy_s2']="%f"%s2
aniso_parameters['anisotropy_s3']="%f"%s3
aniso_parameters['anisotropy_s4']="%f"%s4
aniso_parameters['anisotropy_s5']="%f"%s5
aniso_parameters['anisotropy_s6']="%f"%s6
aniso_parameters['anisotropy_degree']="%f"%(t1/t3)
aniso_parameters['anisotropy_t1']="%f"%t1
aniso_parameters['anisotropy_t2']="%f"%t2
aniso_parameters['anisotropy_t3']="%f"%t3
aniso_parameters['anisotropy_v1_dec']="%.1f"%DIR_v1[0]
aniso_parameters['anisotropy_v1_inc']="%.1f"%DIR_v1[1]
aniso_parameters['anisotropy_v2_dec']="%.1f"%DIR_v2[0]
aniso_parameters['anisotropy_v2_inc']="%.1f"%DIR_v2[1]
aniso_parameters['anisotropy_v3_dec']="%.1f"%DIR_v3[0]
aniso_parameters['anisotropy_v3_inc']="%.1f"%DIR_v3[1]
# modified from pmagpy:
if len(K)/3==9 or len(K)/3==6 or len(K)/3==15:
n_pos=len(K)/3
tmpH = Matrices[n_pos]['tmpH']
a=s_matrix
S=0.
comp=zeros((n_pos*3),'f')
for i in range(n_pos):
for j in range(3):
index=i*3+j
compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2]
comp[index]=compare
for i in range(n_pos*3):
d=K[i]/trace - comp[i] # del values
S+=d*d
nf=float(n_pos*3-6) # number of degrees of freedom
if S >0:
sigma=math.sqrt(S/nf)
hpars=pmag.dohext(nf,sigma,[s1,s2,s3,s4,s5,s6])
aniso_parameters['anisotropy_sigma']="%f"%sigma
aniso_parameters['anisotropy_ftest']="%f"%hpars["F"]
aniso_parameters['anisotropy_ftest12']="%f"%hpars["F12"]
aniso_parameters['anisotropy_ftest23']="%f"%hpars["F23"]
aniso_parameters['result_description']="Critical F: %s"%(hpars['F_crit'])
aniso_parameters['anisotropy_F_crit']="%f"%float(hpars['F_crit'])
aniso_parameters['anisotropy_n']=n_pos
return(aniso_parameters)
