def get_data_model():
"""
try to grab the up to date data model document from the EarthRef site.
if that fails, try to get the data model document from the PmagPy directory on the user's computer.
if that fails, return False.
data_model is a set of nested dictionaries that looks like this:
{'magic_contributions':
{'group_userid': {'data_status': 'Optional', 'data_type': 'String(10)'}, 'activate': {'data_status': 'Optional', 'data_type': 'String(1)'}, ....},
'er_synthetics':
{'synthetic_type': {'data_status': 'Required', 'data_type': 'String(50)'}, 'er_citation_names': {'data_status': 'Required', 'data_type': 'List(500)'}, ...},
....
}
the top level keys are the file types.
the second level keys are the possible headers for that file type.
the third level keys are data_type and data_status for that header.
"""
print "-I- getting data model, please be patient"
url = 'http://earthref.org/services/MagIC-data-model.txt'
offline = True # always get cached data model, as 2.5 is now static
try:
data = urllib2.urlopen(url)
except urllib2.URLError:
print '-W- Unable to fetch data model online\nTrying to use cached data model instead'
offline = True
except httplib.BadStatusLine:
print '-W- Website: {} not responding\nTrying to use cached data model instead'.format(url)
offline = True
if offline:
data = get_data_offline()
data_model, file_type = pmag.magic_read(None, data)
if file_type in ('bad file', 'empty_file'):
print '-W- Unable to read online data model.\nTrying to use cached data model instead'
data = get_data_offline()
data_model, file_type = pmag.magic_read(None, data)
ref_dicts = [d for d in data_model if d['column_nmb'] != '>>>>>>>>>>']
file_types = [d['field_name'] for d in data_model if d['column_nmb'] == 'tab delimited']
file_types.insert(0, file_type)
complete_ref = {}
dictionary = {}
n = 0
for d in ref_dicts:
if d['field_name'] in file_types:
complete_ref[file_types[n]] = dictionary
n += 1
dictionary = {}
else:
dictionary[d['field_name_oracle']] = {'data_type': d['data_type'], 'data_status': d['data_status']}
return complete_ref
def get_data_model():
"""
try to grab the up to date data model document from the EarthRef site.
if that fails, try to get the data model document from the PmagPy directory on the user's computer.
if that fails, return False.
data_model is a set of nested dictionaries that looks like this:
{'magic_contributions':
{'group_userid': {'data_status': 'Optional', 'data_type': 'String(10)'}, 'activate': {'data_status': 'Optional', 'data_type': 'String(1)'}, ....},
'er_synthetics':
{'synthetic_type': {'data_status': 'Required', 'data_type': 'String(50)'}, 'er_citation_names': {'data_status': 'Required', 'data_type': 'List(500)'}, ...},
....
}
the top level keys are the file types.
the second level keys are the possible headers for that file type.
the third level keys are data_type and data_status for that header.
"""
print "-I- getting data model, please be patient"
url = 'http://earthref.org/services/MagIC-data-model.txt'
offline = False
try:
data = urllib2.urlopen(url)
except urllib2.URLError:
print '-W- Unable to fetch data model online\nTrying to use cached data model instead'
offline = True
except httplib.BadStatusLine:
print '-W- Website: {} not responding\nTrying to use cached data model instead'.format(url)
offline = True
if offline:
data = get_data_offline()
data_model, file_type = pmag.magic_read(None, data)
if file_type in ('bad file', 'empty_file'):
print '-W- Unable to read online data model.\nTrying to use cached data model instead'
data = get_data_offline()
data_model, file_type = pmag.magic_read(None, data)
ref_dicts = [d for d in data_model if d['column_nmb'] != '>>>>>>>>>>']
file_types = [d['field_name'] for d in data_model if d['column_nmb'] == 'tab delimited']
file_types.insert(0, file_type)
complete_ref = {}
dictionary = {}
n = 0
for d in ref_dicts:
if d['field_name'] in file_types:
complete_ref[file_types[n]] = dictionary
n += 1
dictionary = {}
else:
dictionary[d['field_name_oracle']] = {'data_type': d['data_type'], 'data_status': d['data_status']}
return complete_ref
def main():
"""
NAME
change_case_magic.py
DESCRIPTION
picks out key and converts to upper or lower case
SYNTAX
change_case_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-F FILE: specify output magic format file , default is to overwrite input file
-keys KEY1:KEY2 specify colon delimited list of keys to convert
-[U,l] : specify [U]PPER or [l]ower case, default is lower
"""
dir_path = "./"
change = "l"
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-f" in sys.argv:
ind = sys.argv.index("-f")
magic_file = dir_path + "/" + sys.argv[ind + 1]
else:
print main.__doc__
sys.exit()
if "-F" in sys.argv:
ind = sys.argv.index("-F")
out_file = dir_path + "/" + sys.argv[ind + 1]
else:
out_file = magic_file
if "-keys" in sys.argv:
ind = sys.argv.index("-keys")
grab_keys = sys.argv[ind + 1].split(":")
else:
print main.__doc__
sys.exit()
if "-U" in sys.argv:
change = "U"
#
#
# get data read in
Data, file_type = pmag.magic_read(magic_file)
if len(Data) > 0:
for grab_key in grab_keys:
for rec in Data:
if change == "l":
rec[grab_key] = rec[grab_key].lower()
else:
rec[grab_key] = rec[grab_key].upper()
else:
print "bad file name"
pmag.magic_write(out_file, Data, file_type)
def get_data(self):
Data = {}
Data_hierarchy = {}
Data_hierarchy["locations"] = {}
Data_hierarchy["sites"] = {}
Data_hierarchy["samples"] = {}
Data_hierarchy["specimens"] = {}
Data_hierarchy["sample_of_specimen"] = {}
Data_hierarchy["site_of_specimen"] = {}
Data_hierarchy["site_of_sample"] = {}
Data_hierarchy["location_of_specimen"] = {}
Data_hierarchy["location_of_sample"] = {}
Data_hierarchy["location_of_site"] = {}
try:
meas_data, file_type = pmag.magic_read(self.WD + "/magic_measurements.txt")
except:
print "-E- ERROR: Cant read magic_measurement.txt file. File is corrupted."
return {}, {}
sids = pmag.get_specs(meas_data) # samples ID's
for s in sids:
if s not in Data.keys():
Data[s] = {}
for rec in meas_data:
s = rec["er_specimen_name"]
sample = rec["er_sample_name"]
site = rec["er_site_name"]
location = rec["er_location_name"]
if sample not in Data_hierarchy["samples"].keys():
Data_hierarchy["samples"][sample] = []
if site not in Data_hierarchy["sites"].keys():
Data_hierarchy["sites"][site] = []
if location not in Data_hierarchy["locations"].keys():
Data_hierarchy["locations"][location] = []
if s not in Data_hierarchy["samples"][sample]:
Data_hierarchy["samples"][sample].append(s)
if sample not in Data_hierarchy["sites"][site]:
Data_hierarchy["sites"][site].append(sample)
if site not in Data_hierarchy["locations"][location]:
Data_hierarchy["locations"][location].append(site)
Data_hierarchy["specimens"][s] = sample
Data_hierarchy["sample_of_specimen"][s] = sample
Data_hierarchy["site_of_specimen"][s] = site
Data_hierarchy["site_of_sample"][sample] = site
Data_hierarchy["location_of_specimen"][s] = location
Data_hierarchy["location_of_sample"][sample] = location
Data_hierarchy["location_of_site"][site] = location
return (Data, Data_hierarchy)
def main():
"""
NAME
extract_methods.py
DESCRIPTION
reads in a magic table and creates a file with method codes
SYNTAX
extract_methods.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify magic format input file, default is magic_measurements.txt
-F FILE: specify method code output file, default is magic_methods.txt
"""
citation='This study'
args=sys.argv
outfile='magic_methods.txt'
infile='magic_measurements.txt'
#
# get command line arguments
#
dir_path='.'
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if '-F' in args:
ind=args.index("-F")
outfile=args[ind+1]
if '-f' in args:
ind=args.index("-f")
infile=args[ind+1]
infile=dir_path+'/'+infile
outfile=dir_path+'/'+outfile
data,file_type=pmag.magic_read(infile)
MethRecs=[]
methods=[]
for rec in data:
meths=rec['magic_method_codes'].split(":")
for meth in meths:
if meth not in methods:
MethRec={}
methods.append(meth)
MethRec['magic_method_code']=meth
MethRecs.append(MethRec)
pmag.magic_write(outfile,MethRecs,'magic_methods')
def main():
"""
NAME
grab_magic_key.py
DESCRIPTION
picks out key and saves to file
SYNTAX
grab_magic_key.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-key KEY: specify key to print to standard output
"""
dir_path="./"
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
magic_file=dir_path+'/'+sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
if '-key' in sys.argv:
ind=sys.argv.index('-key')
grab_key=sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
#
#
# get data read in
Data,file_type=pmag.magic_read(magic_file)
if len(Data)>0:
for rec in Data: print rec[grab_key]
else:
print 'bad file name'
def main():
"""
ODP_fix_sample_names.py
DESCRIPTION:
pads core to three digits and makes upper case
OPTIONS:
-f FILE, input ODP magic file for sample name conversion
"""
dir_path='.'
if '-WD' in sys.argv:
ind=sys.argv.index("-WD")
dir_path=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index("-f")
infile=dir_path+'/'+sys.argv[ind+1]
else:
print "must specify -f input_file"
sys.exit()
Data,file_type=pmag.magic_read(infile)
Fixed=[]
for rec in Data:
pieces=rec['er_specimen_name'].split('-')
if len(pieces)==6:
while len(pieces[2])<4:pieces[2]='0'+pieces[2] # pad core to be 3 characters
specimen=""
for piece in pieces:
specimen=specimen+piece+'-'
specimen=specimen[:-1].upper()
rec['er_specimen_name']=specimen
rec['er_sample_name']=specimen
rec['er_site_name']=specimen
rec['er_location_name']=pieces[1]
rec['er_expedition_name']=pieces[0]
Fixed.append(rec)
else:
print 'problem with this data record: ',rec['er_specimen_name']
print 'deleting from file ', infile
pmag.magic_write(infile,Fixed,file_type)
print 'new specimen names written to: ',infile
def get_Data(magic_file):
#------------------------------------------------
# Read magic measurement file and sort to blocks
#------------------------------------------------
Data={}
try:
meas_data,file_type=pmag.magic_read(magic_file)
except:
print "-E- ERROR: Cant read magic_measurement.txt file. File is corrupted."
return Data
# get list of unique specimen names
#sids=pmag.get_specs(meas_data) # samples ID's
for rec in meas_data:
s=rec["er_specimen_name"]
method_codes= rec["magic_method_codes"].strip('\n')
method_codes.replace(" ","")
methods=method_codes.split(":")
if "LP-AN-TRM" in methods:
if s not in Data.keys():
Data[s]={}
if 'atrmblock' not in Data[s].keys():
Data[s]['atrmblock']=[]
Data[s]['atrmblock'].append(rec)
if "LP-AN-ARM" in methods:
if s not in Data.keys():
Data[s]={}
if 'aarmblock' not in Data[s].keys():
Data[s]['aarmblock']=[]
Data[s]['aarmblock'].append(rec)
return (Data)
def main():
"""
NAME
eqarea_magic.py
DESCRIPTION
makes equal area projections from declination/inclination data
SYNTAX
eqarea_magic.py [command line options]
INPUT
takes magic formatted pmag_results, pmag_sites, pmag_samples or pmag_specimens
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic,default='pmag_results.txt'
supported types=[magic_measurements,pmag_specimens, pmag_samples, pmag_sites, pmag_results, magic_web]
-obj OBJ: specify level of plot [all, sit, sam, spc], default is all
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is geographic, unspecified assumed geographic
-fmt [svg,png,jpg] format for output plots
-ell [F,K,B,Be,Bv] plot Fisher, Kent, Bingham, Bootstrap ellipses or Boostrap eigenvectors
-c plot as colour contour
-sav save plot and quit quietly
NOTE
all: entire file; sit: site; sam: sample; spc: specimen
"""
FIG = {} # plot dictionary
FIG['eqarea'] = 1 # eqarea is figure 1
in_file, plot_key, coord, crd = 'pmag_results.txt', 'all', "0", 'g'
plotE, contour = 0, 0
dir_path = '.'
fmt = 'svg'
verbose = pmagplotlib.verbose
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
pmagplotlib.plot_init(FIG['eqarea'], 5, 5)
if '-f' in sys.argv:
ind = sys.argv.index("-f")
in_file = dir_path + "/" + sys.argv[ind + 1]
if '-obj' in sys.argv:
ind = sys.argv.index('-obj')
plot_by = sys.argv[ind + 1]
if plot_by == 'all': plot_key = 'all'
if plot_by == 'sit': plot_key = 'er_site_name'
if plot_by == 'sam': plot_key = 'er_sample_name'
if plot_by == 'spc': plot_key = 'er_specimen_name'
if '-c' in sys.argv: contour = 1
plots = 0
if '-sav' in sys.argv:
plots = 1
verbose = 0
if '-ell' in sys.argv:
plotE = 1
ind = sys.argv.index('-ell')
ell_type = sys.argv[ind + 1]
if ell_type == 'F': dist = 'F'
if ell_type == 'K': dist = 'K'
if ell_type == 'B': dist = 'B'
if ell_type == 'Be': dist = 'BE'
if ell_type == 'Bv':
dist = 'BV'
FIG['bdirs'] = 2
pmagplotlib.plot_init(FIG['bdirs'], 5, 5)
if '-crd' in sys.argv:
ind = sys.argv.index("-crd")
crd = sys.argv[ind + 1]
if crd == 's': coord = "-1"
if crd == 'g': coord = "0"
if crd == 't': coord = "100"
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
Dec_keys = ['site_dec', 'sample_dec', 'specimen_dec', 'measurement_dec', 'average_dec', 'none']
Inc_keys = ['site_inc', 'sample_inc', 'specimen_inc', 'measurement_inc', 'average_inc', 'none']
Tilt_keys = ['tilt_correction', 'site_tilt_correction', 'sample_tilt_correction', 'specimen_tilt_correction',
'none']
Dir_type_keys = ['', 'site_direction_type', 'sample_direction_type', 'specimen_direction_type']
Name_keys = ['er_specimen_name', 'er_sample_name', 'er_site_name', 'pmag_result_name']
data, file_type = pmag.magic_read(in_file)
if file_type == 'pmag_results' and plot_key != "all": plot_key = plot_key + 's' # need plural for results table
if verbose:
print len(data), ' records read from ', in_file
#
#
# find desired dec,inc data:
#
dir_type_key = ''
#
# get plotlist if not plotting all records
#
plotlist = []
if plot_key != "all":
plots = pmag.get_dictitem(data, plot_key, '', 'F')
for rec in plots:
if rec[plot_key] not in plotlist:
plotlist.append(rec[plot_key])
plotlist.sort()
else:
plotlist.append('All')
for plot in plotlist:
if verbose: print plot
DIblock = []
GCblock = []
SLblock, SPblock = [], []
title = plot
mode = 1
dec_key, inc_key, tilt_key, name_key, k = "", "", "", "", 0
if plot != "All":
odata = pmag.get_dictitem(data, plot_key, plot, 'T')
else:
odata = data # data for this obj
for dec_key in Dec_keys:
Decs = pmag.get_dictitem(odata, dec_key, '', 'F') # get all records with this dec_key not blank
if len(Decs) > 0: break
for inc_key in Inc_keys:
Incs = pmag.get_dictitem(Decs, inc_key, '', 'F') # get all records with this inc_key not blank
if len(Incs) > 0: break
for tilt_key in Tilt_keys:
if tilt_key in Incs[0].keys(): break # find the tilt_key for these records
if tilt_key == 'none': # no tilt key in data, need to fix this with fake data which will be unknown tilt
tilt_key = 'tilt_correction'
for rec in Incs: rec[tilt_key] = ''
cdata = pmag.get_dictitem(Incs, tilt_key, coord, 'T') # get all records matching specified coordinate system
if coord == '0': # geographic
udata = pmag.get_dictitem(Incs, tilt_key, '', 'T') # get all the blank records - assume geographic
if len(cdata) == 0: crd = ''
if len(udata) > 0:
for d in udata: cdata.append(d)
crd = crd + 'u'
for name_key in Name_keys:
Names = pmag.get_dictitem(cdata, name_key, '', 'F') # get all records with this name_key not blank
if len(Names) > 0: break
for dir_type_key in Dir_type_keys:
Dirs = pmag.get_dictitem(cdata, dir_type_key, '', 'F') # get all records with this direction type
if len(Dirs) > 0: break
if dir_type_key == "": dir_type_key = 'direction_type'
locations, site, sample, specimen = "", "", "", ""
for rec in cdata: # pick out the data
if 'er_location_name' in rec.keys() and rec['er_location_name'] != "" and rec[
'er_location_name'] not in locations: locations = locations + rec['er_location_name'].replace("/",
"") + "_"
if 'er_location_names' in rec.keys() and rec['er_location_names'] != "":
locs = rec['er_location_names'].split(':')
for loc in locs:
if loc not in locations: locations = locations + loc.replace("/", "") + '_'
if plot_key == 'er_site_name' or plot_key == 'er_sample_name' or plot_key == 'er_specimen_name':
site = rec['er_site_name']
if plot_key == 'er_sample_name' or plot_key == 'er_specimen_name':
sample = rec['er_sample_name']
if plot_key == 'er_specimen_name':
specimen = rec['er_specimen_name']
if plot_key == 'er_site_names' or plot_key == 'er_sample_names' or plot_key == 'er_specimen_names':
site = rec['er_site_names']
if plot_key == 'er_sample_names' or plot_key == 'er_specimen_names':
sample = rec['er_sample_names']
if plot_key == 'er_specimen_names':
specimen = rec['er_specimen_names']
if dir_type_key not in rec.keys() or rec[dir_type_key] == "": rec[dir_type_key] = 'l'
if 'magic_method_codes' not in rec.keys(): rec['magic_method_codes'] = ""
DIblock.append([float(rec[dec_key]), float(rec[inc_key])])
SLblock.append([rec[name_key], rec['magic_method_codes']])
if rec[tilt_key] == coord and rec[dir_type_key] != 'l' and rec[dec_key] != "" and rec[inc_key] != "":
GCblock.append([float(rec[dec_key]), float(rec[inc_key])])
SPblock.append([rec[name_key], rec['magic_method_codes']])
if len(DIblock) == 0 and len(GCblock) == 0:
if verbose: print "no records for plotting"
sys.exit()
if verbose:
for k in range(len(SLblock)):
print '%s %s %7.1f %7.1f' % (SLblock[k][0], SLblock[k][1], DIblock[k][0], DIblock[k][1])
for k in range(len(SPblock)):
print '%s %s %7.1f %7.1f' % (SPblock[k][0], SPblock[k][1], GCblock[k][0], GCblock[k][1])
if len(DIblock) > 0:
if contour == 0:
pmagplotlib.plotEQ(FIG['eqarea'], DIblock, title)
else:
pmagplotlib.plotEQcont(FIG['eqarea'], DIblock)
else:
pmagplotlib.plotNET(FIG['eqarea'])
if len(GCblock) > 0:
for rec in GCblock: pmagplotlib.plotC(FIG['eqarea'], rec, 90., 'g')
if plotE == 1:
ppars = pmag.doprinc(DIblock) # get principal directions
nDIs, rDIs, npars, rpars = [], [], [], []
for rec in DIblock:
angle = pmag.angle([rec[0], rec[1]], [ppars['dec'], ppars['inc']])
if angle > 90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist == 'B': # do on whole dataset
etitle = "Bingham confidence ellipse"
bpars = pmag.dobingham(DIblock)
for key in bpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (bpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (bpars[key])
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist == 'F':
etitle = "Fisher confidence cone"
if len(nDIs) > 2:
fpars = pmag.fisher_mean(nDIs)
for key in fpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (fpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (fpars[key])
mode += 1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign = abs(fpars['inc']) / fpars['inc']
npars.append(fpars['inc'] - isign * 90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec'] + 90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs) > 2:
fpars = pmag.fisher_mean(rDIs)
if verbose: print "mode ", mode
for key in fpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (fpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (fpars[key])
mode += 1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign = abs(fpars['inc']) / fpars['inc']
rpars.append(fpars['inc'] - isign * 90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec'] + 90.) # Beta dec
rpars.append(0.) #Beta inc
if dist == 'K':
etitle = "Kent confidence ellipse"
if len(nDIs) > 3:
kpars = pmag.dokent(nDIs, len(nDIs))
if verbose: print "mode ", mode
for key in kpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (kpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (kpars[key])
mode += 1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs) > 3:
kpars = pmag.dokent(rDIs, len(rDIs))
if verbose: print "mode ", mode
for key in kpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (kpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (kpars[key])
mode += 1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if dist == 'BE':
if len(nDIs) > 5:
BnDIs = pmag.di_boot(nDIs)
Bkpars = pmag.dokent(BnDIs, 1.)
if verbose: print "mode ", mode
for key in Bkpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (Bkpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (Bkpars[key])
mode += 1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs) > 5:
BrDIs = pmag.di_boot(rDIs)
Bkpars = pmag.dokent(BrDIs, 1.)
if verbose: print "mode ", mode
for key in Bkpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (Bkpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (Bkpars[key])
mode += 1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
etitle = "Bootstrapped confidence ellipse"
elif dist == 'BV':
sym = {'lower': ['o', 'c'], 'upper': ['o', 'g'], 'size': 3, 'edgecolor': 'face'}
if len(nDIs) > 5:
BnDIs = pmag.di_boot(nDIs)
pmagplotlib.plotEQsym(FIG['bdirs'], BnDIs, 'Bootstrapped Eigenvectors', sym)
if len(rDIs) > 5:
BrDIs = pmag.di_boot(rDIs)
if len(nDIs) > 5: # plot on existing plots
pmagplotlib.plotDIsym(FIG['bdirs'], BrDIs, sym)
else:
pmagplotlib.plotEQ(FIG['bdirs'], BrDIs, 'Bootstrapped Eigenvectors')
if dist == 'B':
if len(nDIs) > 3 or len(rDIs) > 3: pmagplotlib.plotCONF(FIG['eqarea'], etitle, [], npars, 0)
elif len(nDIs) > 3 and dist != 'BV':
pmagplotlib.plotCONF(FIG['eqarea'], etitle, [], npars, 0)
if len(rDIs) > 3:
pmagplotlib.plotCONF(FIG['eqarea'], etitle, [], rpars, 0)
elif len(rDIs) > 3 and dist != 'BV':
pmagplotlib.plotCONF(FIG['eqarea'], etitle, [], rpars, 0)
if verbose: pmagplotlib.drawFIGS(FIG)
#
files = {}
locations = locations[:-1]
for key in FIG.keys():
filename = 'LO:_' + locations + '_SI:_' + site + '_SA:_' + sample + '_SP:_' + specimen + '_CO:_' + crd + '_TY:_' + key + '_.' + fmt
files[key] = filename
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['eq'] = 'Equal Area Plot'
FIG = pmagplotlib.addBorders(FIG, titles, black, purple)
pmagplotlib.saveP(FIG, files)
elif verbose:
ans = raw_input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == "q": sys.exit()
if ans == "a":
pmagplotlib.saveP(FIG, files)
if plots:
pmagplotlib.saveP(FIG, files)
def main():
"""
NAME
pick_AC_specimens.py
DESCRIPTION
finds whether anisotropy correction yeilds more tightly
grouped intensities than uncorrected data.
picks either all corrected or all uncorrected data and
puts in pmag_specimen format file
SYNTAX
pick_AC_specimens.py [-h][-i][-fu TFILE][-fc AFILE][-F FILE]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-fu TFILE uncorrected pmag_specimen format file with thellier interpretations
created by thellier_magic_redo.py
-fc AFILE anisotropy corrected pmag_specimen format file
created by thellier_magic_redo.py
-fcr CRIT pmag_criteria.txt format file with acceptance criteria
-opt SIG use the optimizer_thelpars.txt file for criteria
-F FILE pmag_specimens format output file with "best" set of data
DEFAULTS
TFILE: thellier_specimens.txt
AFILE: AC_specimens.txt
FILE: pmag_specimens.txt
"""
tspec="thellier_specimens.txt"
aspec="AC_specimens.txt"
ofile="pmag_specimens.txt"
critfile="pmag_criteria.txt"
ACSamplist,Samplist,sigmin=[],[],10000
GoodSamps,SpecOuts=[],[]
P={'cdf':1}
pmagplotlib.plot_init(P['cdf'],5,5)
# get arguments from command line
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-fu' in sys.argv:
ind=sys.argv.index('-fu')
tspec=sys.argv[ind+1]
if '-fc' in sys.argv:
ind=sys.argv.index('-fc')
aspec=sys.argv[ind+1]
if '-fcr' in sys.argv:
ind=sys.argv.index('-fcr')
critfile=sys.argv[ind+1]
if '-opt' in sys.argv:
ind=sys.argv.index('-opt')
critfile='optimum_thelpars.txt'
sigcutoff=sys.argv[ind+1]
if '-F' in sys.argv:
ind=sys.argv.index('-F')
ofile=sys.argv[ind+1]
if '-i' in sys.argv:
file=raw_input(" thellier_specimnens.txt file [thellier_specimens.txt]: ")
if file!="":tfile=file
file=raw_input(" AC_specimnens.txt file [AC_specimens.txt]: ")
if file!="":afile=file
file=raw_input(" pmag_specimnens.txt file [pmag_specimens.txt]: ")
if file!="":ofile=file
# read in pmag_specimens file
Specs,file_type=pmag.magic_read(tspec)
Speclist=pmag.get_specs(Specs)
ACSpecs,file_type=pmag.magic_read(aspec)
ACspeclist=pmag.get_specs(ACSpecs)
Crits,file_type=pmag.magic_read(critfile)
keys=['specimen_int_mad','specimen_drats','specimen_fvds','specimen_b_beta','specimen_Z','specimen_md','specimen_dang']
accept={}
for crit in Crits:
if critfile!='optimum_thelpars.txt':
if crit['pmag_criteria_code']=='IE-SPEC':
for key in keys: accept[key]=float(crit[key]) # assign acceptance criteria
break
else:
if float(crit['sample_int_sigma_perc'])==float(sigcutoff):
for key in keys: accept[key]=float(crit[key])
Diff=[]
for aspec in ACSpecs:
grade,kill=pmag.grade(aspec,accept)
if grade==len(accept):
print 'AC: ',aspec["er_specimen_name"],'%i'%(1e6*float(aspec["specimen_int"]))
aint=(1e6*float(aspec["specimen_int"]))
for spec in Specs:
if spec["er_specimen_name"]==aspec['er_specimen_name']:
print 'UC: ',spec["er_specimen_name"],'%i'%(1e6*float(spec["specimen_int"]))
int=(1e6*float(spec["specimen_int"]))
Diff.append(100.*abs(aint-int)/aint)
x,s=pmag.gausspars(Diff)
print x,s
Diff.sort()
print Diff[0],Diff[-1]
pmagplotlib.plotCDF(P['cdf'],Diff,'% Difference','r')
pmagplotlib.drawFIGS(P)
raw_input()
def main():
"""
NAME
magic_select.py
DESCRIPTION
picks out records and dictitem options saves to magic_special file
SYNTAX
magic_select.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-F FILE: specify output magic format file
-key KEY string [T,F,has, not, eval,min,max]
returns records where the value of the key either:
matches exactly the string (T)
does not match the string (F)
contains the string (has)
does not contain the string (not)
the value equals the numerical value of the string (eval)
the value is greater than the numerical value of the string (min)
the value is less than the numerical value of the string (max)
NOTES
for age range:
use KEY: age (converts to Ma, takes mid point of low, high if no value for age.
for paleolat:
use KEY: model_lat (uses lat, if age<5 Ma, else, model_lat, or attempts calculation from average_inc if no model_lat.) returns estimate in model_lat key
"""
dir_path="."
flag=''
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
magic_file=dir_path+'/'+sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=dir_path+'/'+sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
if '-key' in sys.argv:
ind=sys.argv.index('-key')
grab_key=sys.argv[ind+1]
v=sys.argv[ind+2]
flag=sys.argv[ind+3]
else:
print main.__doc__
print '-key is required'
sys.exit()
#
# get data read in
Data,file_type=pmag.magic_read(magic_file)
if grab_key =='age':
grab_key='average_age'
Data=pmag.convert_ages(Data)
if grab_key =='model_lat':
Data=pmag.convert_lat(Data)
Data=pmag.convert_ages(Data)
Selection=pmag.get_dictitem(Data,grab_key,v,flag)
if len(Selection)>0:
pmag.magic_write(outfile,Selection,file_type)
print len(Selection),' records written to ',outfile
else:
print 'no data matched your criteria'
def main():
"""
NAME
FLA_magic.py
DESCRIPTION
import data files from the Univ. Florida, Gainesvile format to magic
SYNTAX
FLA_magic.py
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
meas_type,methcode,instcode,experiment_name,izzi="LT-NO","","","",0
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,ispec=0,0,0
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
er_location_name=raw_input("Enter the location name for this study, or <return> for none ")
if er_location_name=="":
er_sites_file=raw_input("Enter site location file name, or <return> for none ")
if er_sites_file=="":
er_location_name="none"
else:
site_locations,file_type=pmag.magic_read(er_sites_file)
magfile=raw_input("Enter florida measurement filename for processing ")
print "Enter whether [A]F or [T]hermal de-(re)magnetization "
ans=raw_input(" <return> for NRMs only ")
inst=""
methcode="LT-NO"
if ans=="A":
inst="UFG-AF"
methcode="LT-AF-Z"
if ans=="T":
inst="UFG-thermal"
methcode="LT-T-Z"
if ans=="":methcode="LT-NO"
input=open(magfile,'r')
MagRecs=[]
for line in input.readlines():
print line
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"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e' %(labfield) # lab field in tesla
MagRec["treatment_dc_field_phi"]='%7.1f' %(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'% (theta)
rec=line.split()
MagRec["er_specimen_name"]=rec[0]
MagRec["er_sample_name"]=rec[0]
sitetmp=rec[0].split('.') # Florida naming convention splits on '.' between site and sample
MagRec["er_site_name"]=sitetmp[0]
MagRec["er_location_name"]="none"
if er_location_name!="":
MagRec["er_location_name"]=er_location_name
else:
for site in site_locations:
if site["er_site_name"] == MagRec["er_site_name"]:
MagRec["er_location_name"]=site["er_location_name"]
if inst=="UFG-AF":
MagRec["treatment_ac_field"]='%8.3e' % ( float(rec[1])*1e-4) # AF field in tesla from Oersted in Florida convention
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
else:
MagRec["treatment_temp"]='%8.3e' % (float(rec[1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec["measurement_magn_moment"]='%10.3e'% ((float(rec[4])/100)*1e-5) # moment in Am^2 (from 50xA/m and assuming 5cc sample in Florida convention)
MagRec["measurement_dec"]=rec[7]
MagRec["measurement_inc"]=rec[8]
MagRec["magic_method_codes"]=meas_type
MagRecs.append(MagRec)
output=raw_input("Filename for output [magic_measurements.txt] ")
if output=="":output="magic_measurements.txt"
MagOuts=pmag.measurements_methods(MagRecs,0)
pmag.magic_write(output,MagOuts,'magic_measurements')
print "results put in ",output
def main():
"""
NAME
thellier_magic.py
DESCRIPTION
plots Thellier-Thellier, allowing interactive setting of bounds
and customizing of selection criteria. Saves and reads interpretations
from a pmag_specimen formatted table, default: thellier_specimens.txt
SYNTAX
thellier_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEAS, set magic_measurements input file
-fsp PRIOR, set pmag_specimen prior interpretations file
-fan ANIS, set rmag_anisotropy file for doing the anisotropy corrections
-fcr CRIT, set criteria file for grading.
-fmt [svg,png,jpg], format for images - default is svg
-sav, saves plots with out review (default format)
-spc SPEC, plots single specimen SPEC, saves plot with specified format
with optional -b bounds adn quits
-b BEG END: sets bounds for calculation
BEG: starting step for slope calculation
END: ending step for slope calculation
-z use only z component difference for pTRM calculation
DEFAULTS
MEAS: magic_measurements.txt
REDO: thellier_redo
CRIT: NONE
PRIOR: NONE
OUTPUT
figures:
ALL: numbers refer to temperature steps in command line window
1) Arai plot: closed circles are zero-field first/infield
open circles are infield first/zero-field
triangles are pTRM checks
squares are pTRM tail checks
VDS is vector difference sum
diamonds are bounds for interpretation
2) Zijderveld plot: closed (open) symbols are X-Y (X-Z) planes
X rotated to NRM direction
3) (De/Re)Magnetization diagram:
circles are NRM remaining
squares are pTRM gained
4) equal area projections:
green triangles are pTRM gained direction
red (purple) circles are lower(upper) hemisphere of ZI step directions
blue (cyan) squares are lower(upper) hemisphere IZ step directions
5) Optional: TRM acquisition
6) Optional: TDS normalization
command line window:
list is: temperature step numbers, temperatures (C), Dec, Inc, Int (units of magic_measuements)
list of possible commands: type letter followed by return to select option
saving of plots creates .svg format files with specimen_name, plot type as name
"""
#
# initializations
#
meas_file,critout,inspec="magic_measurements.txt","","thellier_specimens.txt"
first=1
inlt=0
version_num=pmag.get_version()
TDinit,Tinit,field,first_save=0,0,-1,1
user,comment,AniSpec,locname="",'',"",""
ans,specimen,recnum,start,end=0,0,0,0,0
plots,pmag_out,samp_file,style=0,"","","svg"
verbose=pmagplotlib.verbose
fmt='.'+style
#
# default acceptance criteria
#
accept=pmag.default_criteria(0)[0] # set the default criteria
#
# parse command line options
#
Zdiff,anis=0,0
spc,BEG,END="","",""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
inspec=sys.argv[ind+1]
if '-fan' in sys.argv:
ind=sys.argv.index('-fan')
anisfile=sys.argv[ind+1]
anis=1
anis_data,file_type=pmag.magic_read(anisfile)
if verbose: print "Anisotropy data read in from ", anisfile
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-sav' in sys.argv:
plots=1
verbose=0
if '-z' in sys.argv: Zdiff=1
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
spc=sys.argv[ind+1]
if '-b' in sys.argv:
ind=sys.argv.index('-b')
BEG=int(sys.argv[ind+1])
END=int(sys.argv[ind+2])
if '-fcr' in sys.argv:
ind=sys.argv.index('-fcr')
critout=sys.argv[ind+1]
crit_data,file_type=pmag.magic_read(critout)
if file_type!='pmag_criteria':
if verbose: print 'bad pmag_criteria file, using no acceptance criteria'
accept=pmag.default_criteria(1)[0]
else:
if verbose: print "Acceptance criteria read in from ", critout
accept={'pmag_criteria_code':'ACCEPTANCE','er_citation_names':'This study'}
for critrec in crit_data:
if 'sample_int_sigma_uT' in critrec.keys(): # accommodate Shaar's new criterion
critrec['sample_int_sigma']='%10.3e'%(eval(critrec['sample_int_sigma_uT'])*1e-6)
for key in critrec.keys():
if key not in accept.keys() and critrec[key]!='':
accept[key]=critrec[key]
try:
open(inspec,'rU')
PriorRecs,file_type=pmag.magic_read(inspec)
if file_type != 'pmag_specimens':
print file_type
print file_type,inspec," is not a valid pmag_specimens file "
sys.exit()
for rec in PriorRecs:
if 'magic_software_packages' not in rec.keys():rec['magic_software_packages']=""
except IOError:
PriorRecs=[]
if verbose:print "starting new specimen interpretation file: ",inspec
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
backup=0
# define figure numbers for arai, zijderveld and
# de-,re-magization diagrams
AZD={}
AZD['deremag'], AZD['zijd'],AZD['arai'],AZD['eqarea']=1,2,3,4
pmagplotlib.plot_init(AZD['arai'],5,5)
pmagplotlib.plot_init(AZD['zijd'],5,5)
pmagplotlib.plot_init(AZD['deremag'],5,5)
pmagplotlib.plot_init(AZD['eqarea'],5,5)
#
#
#
# get list of unique specimen names
#
CurrRec=[]
sids=pmag.get_specs(meas_data)
# get plots for specimen s - default is just to step through arai diagrams
#
if spc!="": specimen =sids.index(spc)
while specimen < len(sids):
methcodes=[]
if verbose:
print sids[specimen],specimen+1, 'of ', len(sids)
MeasRecs=[]
s=sids[specimen]
datablock,trmblock,tdsrecs=[],[],[]
PmagSpecRec={}
if first==0:
for key in keys:PmagSpecRec[key]="" # make sure all new records have same set of keys
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["specimen_correction"]='u'
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"]==s:
MeasRecs.append(rec)
if "magic_method_codes" not in rec.keys():
rec["magic_method_codes"]=""
methods=rec["magic_method_codes"].split(":")
meths=[]
for meth in methods:
meths.append(meth.strip()) # take off annoying spaces
methods=""
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip())
methods=methods+meth+":"
methods=methods[:-1]
rec["magic_method_codes"]=methods
if "LP-PI-TRM" in meths: datablock.append(rec)
if "LP-TRM" in meths: trmblock.append(rec)
if "LP-TRM-TD" in meths: tdsrecs.append(rec)
if len(trmblock)>2 and inspec!="":
if Tinit==0:
Tinit=1
AZD['TRM']=5
pmagplotlib.plot_init(AZD['TRM'],5,5)
elif Tinit==1: # clear the TRM figure if not needed
pmagplotlib.clearFIG(AZD['TRM'])
if len(tdsrecs)>2:
if TDinit==0:
TDinit=1
AZD['TDS']=6
pmagplotlib.plot_init(AZD['TDS'],5,5)
elif TDinit==1: # clear the TDS figure if not needed
pmagplotlib.clearFIG(AZD['TDS'])
if len(datablock) <4:
if backup==0:
specimen+=1
if verbose:
print 'skipping specimen - moving forward ', s
else:
specimen-=1
if verbose:
print 'skipping specimen - moving backward ', s
#
# collect info for the PmagSpecRec dictionary
#
else:
rec=datablock[0]
PmagSpecRec["er_citation_names"]="This study"
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
locname=rec['er_location_name'].replace('/','-')
if "er_expedition_name" in rec.keys():PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
if "magic_instrument_codes" not in rec.keys():rec["magic_instrument_codes"]=""
PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]
PmagSpecRec["measurement_step_unit"]="K"
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
meths=rec["magic_method_codes"].split()
# sort data into types
araiblock,field=pmag.sortarai(datablock,s,Zdiff)
first_Z=araiblock[0]
GammaChecks=araiblock[5]
if len(first_Z)<3:
if backup==0:
specimen+=1
if verbose:
print 'skipping specimen - moving forward ', s
else:
specimen-=1
if verbose:
print 'skipping specimen - moving backward ', s
else:
backup=0
zijdblock,units=pmag.find_dmag_rec(s,meas_data)
recnum=0
if verbose:
print "index step Dec Inc Int Gamma"
for plotrec in zijdblock:
if GammaChecks!="":
gamma=""
for g in GammaChecks:
if g[0]==plotrec[0]-273:
gamma=g[1]
break
if gamma!="":
print '%i %i %7.1f %7.1f %8.3e %7.1f' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3],gamma)
else:
print '%i %i %7.1f %7.1f %8.3e ' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3])
recnum += 1
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
if verbose:pmagplotlib.drawFIGS(AZD)
if len(tdsrecs)>2: # a TDS experiment
tdsblock=[] # make a list for the TDS data
Mkeys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measuruement_magn_mass']
mkey,k="",0
while mkey=="" and k<len(Mkeys)-1: # find which type of intensity
key= Mkeys[k]
if key in tdsrecs[0].keys() and tdsrecs[0][key]!="": mkey=key
k+=1
if mkey=="":break # get outta here
Tnorm=""
for tdrec in tdsrecs:
meths=tdrec['magic_method_codes'].split(":")
for meth in meths: meth.replace(" ","") # strip off potential nasty spaces
if 'LT-T-I' in meths and Tnorm=="": # found first total TRM
Tnorm=float(tdrec[mkey]) # normalize by total TRM
tdsblock.append([273,zijdblock[0][3]/Tnorm,1.]) # put in the zero step
if 'LT-T-Z' in meths and Tnorm!="": # found a LP-TRM-TD demag step, now need complementary LT-T-Z from zijdblock
step=float(tdrec['treatment_temp'])
Tint=""
if mkey!="":
Tint=float(tdrec[mkey])
if Tint!="":
for zrec in zijdblock:
if zrec[0]==step: # found matching
tdsblock.append([step,zrec[3]/Tnorm,Tint/Tnorm])
break
if len(tdsblock)>2:
pmagplotlib.plotTDS(AZD['TDS'],tdsblock,s+':LP-PI-TDS:')
if verbose:pmagplotlib(drawFIGS(AZD))
else:
print "Something wrong here"
if anis==1: # look up anisotropy data for this specimen
AniSpec=""
for aspec in anis_data:
if aspec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
AniSpec=aspec
if verbose: print 'Found anisotropy record...'
break
if inspec !="":
if verbose: print 'Looking up saved interpretation....'
found = 0
for k in range(len(PriorRecs)):
try:
if PriorRecs[k]["er_specimen_name"]==s:
found =1
CurrRec.append(PriorRecs[k])
for j in range(len(zijdblock)):
if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_min"]):start=j
if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_max"]):end=j
pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,start,end,accept)
pars['measurement_step_unit']="K"
pars['experiment_type']='LP-PI-TRM'
del PriorRecs[k] # put in CurrRec, take out of PriorRecs
if errcode!=1:
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
if verbose:
print 'Saved interpretation: '
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose)
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(AZD)
if len(trmblock)>2:
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
PmagSpecRec['specimen_int']=NLpars['banc']
if verbose:
print 'Banc= ',float(NLpars['banc'])*1e6
pmagplotlib.drawFIGS(AZD)
mpars=pmag.domean(araiblock[1],start,end,'DE-BFL')
if verbose:
print 'pTRM direction= ','%7.1f'%(mpars['specimen_dec']),' %7.1f'%(mpars['specimen_inc']),' MAD:','%7.1f'%(mpars['specimen_mad'])
if AniSpec!="":
CpTRM=pmag.Dir_anis_corr([mpars['specimen_dec'],mpars['specimen_inc']],AniSpec)
AniSpecRec=pmag.doaniscorr(PmagSpecRec,AniSpec)
if verbose:
print 'Anisotropy corrected TRM direction= ','%7.1f'%(CpTRM[0]),' %7.1f'%(CpTRM[1])
print 'Anisotropy corrected intensity= ',float(AniSpecRec['specimen_int'])*1e6
else:
print 'error on specimen ',s
except:
pass
if verbose and found==0: print ' None found :( '
if spc!="":
if BEG!="":
pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,BEG,END,accept)
pars['measurement_step_unit']="K"
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
pars['specimen_grade']='' # ungraded
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(AZD)
if len(trmblock)>2:
if inlt==0:
inlt=1
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
files={}
for key in AZD.keys():
files[key]=s+'_'+key+fmt
pmagplotlib.saveP(AZD,files)
sys.exit()
if verbose:
ans='b'
while ans != "":
print """
s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit:
"""
ans=raw_input('Return for next specimen \n')
if ans=="":
specimen +=1
if ans=="d":
save_redo(PriorRecs,inspec)
CurrRec=[]
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
if verbose:pmagplotlib.drawFIGS(AZD)
if ans=='a':
files={}
for key in AZD.keys():
files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_s_TY:_'+key+fmt
pmagplotlib.saveP(AZD,files)
ans=""
if ans=='q':
print "Good bye"
sys.exit()
if ans=='p':
specimen =specimen -1
backup = 1
ans=""
if ans=='s':
keepon=1
spec=raw_input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
specimen =sids.index(spec)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if spec in sids[qq]:tmplist.append(sids[qq])
print specimen," not found, but this was: "
print tmplist
spec=raw_input('Select one or try again\n ')
ans=""
if ans=='b':
if end==0 or end >=len(zijdblock):end=len(zijdblock)-1
GoOn=0
while GoOn==0:
answer=raw_input('Enter index of first point for calculation: ['+str(start)+'] ')
try:
start=int(answer)
answer=raw_input('Enter index of last point for calculation: ['+str(end)+'] ')
end=int(answer)
if start >=0 and start <len(zijdblock)-2 and end >0 and end <len(zijdblock) or start>=end:
GoOn=1
else:
print "Bad endpoints - try again! "
start,end=0,len(zijdblock)
except ValueError:
print "Bad endpoints - try again! "
start,end=0,len(zijdblock)
s=sids[specimen]
pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,start,end,accept)
pars['measurement_step_unit']="K"
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',0)
PmagSpecRec['specimen_scat']=pars['specimen_scat']
PmagSpecRec['specimen_frac']='%5.3f'%(pars['specimen_frac'])
PmagSpecRec['specimen_gmax']='%5.3f'%(pars['specimen_gmax'])
PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"])
PmagSpecRec["measurement_step_unit"]="K"
PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"])
PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"])
PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"])
PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"])
PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"])
PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"])
PmagSpecRec["specimen_grade"]=pars["specimen_grade"]
if pars["method_codes"]!="":
tmpcodes=pars["method_codes"].split(":")
for t in tmpcodes:
if t.strip() not in methcodes:methcodes.append(t.strip())
PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"]='-1'
PmagSpecRec["specimen_direction_type"]='l'
PmagSpecRec["direction_type"]='l' # this is redundant, but helpful - won't be imported
PmagSpecRec["specimen_int_dang"]='%7.1f '%(pars["specimen_int_dang"])
PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"])
PmagSpecRec["specimen_drat"]='%7.1f '%(pars["specimen_drat"])
PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"])
PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"]))
if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]=""
PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:methcodes.append("IE-TT")
methods=""
for meth in methcodes:
methods=methods+meth+":"
PmagSpecRec["magic_method_codes"]=methods[:-1]
PmagSpecRec["specimen_description"]=comment
PmagSpecRec["magic_software_packages"]=version_num
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(AZD)
if len(trmblock)>2:
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
if verbose:
print 'Non-linear TRM corrected intensity= ',float(NLpars['banc'])*1e6
if verbose:pmagplotlib.drawFIGS(AZD)
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose)
saveit=raw_input("Save this interpretation? [y]/n \n")
if saveit!='n':
PriorRecs.append(PmagSpecRec) # put back an interpretation
specimen+=1
save_redo(PriorRecs,inspec)
ans=""
elif plots==1:
specimen+=1
if fmt != ".pmag":
files={}
for key in AZD.keys():
files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_s_TY:_'+key+'_'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['deremag']='DeReMag Plot'
titles['zijd']='Zijderveld Plot'
titles['arai']='Arai Plot'
AZD = pmagplotlib.addBorders(AZD,titles,black,purple)
pmagplotlib.saveP(AZD,files)
# pmagplotlib.combineFigs(s,files,3)
else: # save in pmag format
script="grep "+s+" output.mag | thellier -mfsi"
script=script+' %8.4e'%(field)
min='%i'%((pars["measurement_step_min"]-273))
Max='%i'%((pars["measurement_step_max"]-273))
script=script+" "+min+" "+Max
script=script+" |plotxy;cat mypost >>thellier.ps\n"
pltf.write(script)
pmag.domagicmag(outf,MeasRecs)
if len(CurrRec)>0:
for rec in CurrRec:
PriorRecs.append(rec)
CurrRec=[]
if plots!=1 and verbose:
ans=raw_input(" Save last plot? 1/[0] ")
if ans=="1":
if fmt != ".pmag":
files={}
for key in AZD.keys():
files[key]=s+'_'+key+fmt
pmagplotlib.saveP(AZD,files)
else:
print "\n Good bye\n"
sys.exit()
if len(CurrRec)>0:PriorRecs.append(CurrRec) # put back an interpretation
if len(PriorRecs)>0:
save_redo(PriorRecs,inspec)
print 'Updated interpretations saved in ',inspec
if verbose:
print "Good bye"
def main():
"""
NAME
chi_magic.py
DESCRIPTION
plots magnetic susceptibility as a function of frequency and temperature and AC field
SYNTAX
chi_magic.py [command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of FILE and temperature step
-f FILE, specify magic_measurements format file
-T IND, specify temperature step to plot
-e EXP, specify experiment name to plot
DEFAULTS
FILE: magic_measurements.txt
IND: first
SPEC: step through one by one
"""
cont,FTinit,BTinit,k="",0,0,0
meas_file="magic_measurements.txt"
spec=""
Tind,cont=0,""
EXP=""
fmt='svg' # default image type for saving
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-i' in sys.argv:
file=raw_input("Input magic_measurements file name? [magic_measurements.txt] ")
if file!="":meas_file=file
if '-e' in sys.argv:
ind=sys.argv.index('-e')
EXP=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-T' in sys.argv:
ind=sys.argv.index('-T')
Tind=int(sys.argv[ind+1])
#
meas_data,file_type=pmag.magic_read(meas_file)
#
# get list of unique experiment names
#
# initialize some variables (a continuation flag, plot initialization flags and the experiment counter
experiment_names=[]
for rec in meas_data:
if rec['magic_experiment_name'] not in experiment_names:experiment_names.append(rec['magic_experiment_name'])
#
# hunt through by experiment name
if EXP!="":
try:
k=experiment_names.index(EXP)
except:
print "Bad experiment name"
sys.exit()
while k < len(experiment_names):
e=experiment_names[k]
if EXP=="":print e, k+1 , 'out of ',len(experiment_names)
#
# initialize lists of data, susceptibility, temperature, frequency and field
X,T,F,B=[],[],[],[]
for rec in meas_data:
methcodes=rec['magic_method_codes']
meths=methcodes.strip().split(':')
if rec['magic_experiment_name']==e and "LP-X" in meths: # looking for chi measurement
if 'measurement_temp' not in rec.keys():rec['measurement_temp']='300' # set defaults
if 'measurement_freq' not in rec.keys():rec['measurement_freq']='0' # set defaults
if 'measurement_lab_field_ac' not in rec.keys():rec['measurement_lab_field_ac']='0' # set default
X.append(float(rec['measurement_x']))
T.append(float(rec['measurement_temp']))
F.append(float(rec['measurement_freq']))
B.append(float(rec['measurement_lab_field_ac']))
#
# get unique list of Ts,Fs, and Bs
#
Ts,Fs,Bs=[],[],[]
for k in range(len(X)): # hunt through all the measurements
if T[k] not in Ts:Ts.append(T[k]) # append if not in list
if F[k] not in Fs:Fs.append(F[k])
if B[k] not in Bs:Bs.append(B[k])
Ts.sort() # sort list of temperatures, frequencies and fields
Fs.sort()
Bs.sort()
if '-x' in sys.argv:
k=len(experiment_names)+1 # just plot the one
else:
k+=1 # increment experiment number
#
# plot chi versus T and F holding B constant
#
plotnum=1 # initialize plot number to 1
if len(X)>2: # if there are any data to plot, continue
b=Bs[-1] # keeping field constant and at maximum
XTF=[] # initialize list of chi versus Temp and freq
for f in Fs: # step through frequencies sequentially
XT=[] # initialize list of chi versus temp
for kk in range(len(X)): # hunt through all the data
if F[kk]==f and B[kk]==b: # select data with given freq and field
XT.append([X[kk],T[kk]]) # append to list
XTF.append(XT) # append list to list of frequencies
if len(XT)>1: # if there are any temperature dependent data
pmagplotlib.plot_init(plotnum,5,5) # initialize plot
pmagplotlib.plotXTF(plotnum,XTF,Fs,e,b) # call the plotting function
pmagplotlib.drawFIGS({'fig':plotnum})
plotnum+=1 # increment plot number
f=Fs[0] # set frequency to minimum
XTB=[] # initialize list if chi versus Temp and field
for b in Bs: # step through field values
XT=[] # initial chi versus temp list for this field
for kk in range(len(X)): # hunt through all the data
if F[kk]==f and B[kk]==b: # select data with given freq and field
XT.append([X[kk],T[kk]]) # append to list
XTB.append(XT)
if len(XT)>1: # if there are any temperature dependent data
pmagplotlib.plot_init(plotnum,5,5) # set up plot
pmagplotlib.plotXTB(plotnum,XTB,Bs,e,f) # call the plotting function
pmagplotlib.drawFIGS({'fig':plotnum})
plotnum+=1 # increment plot number
if '-i' in sys.argv:
for ind in range(len(Ts)): # print list of temperatures available
print ind,int(Ts[ind])
cont=raw_input("Enter index of desired temperature step, s[a]ve plots, [return] to quit ")
if cont=='a':
files={}
PLTS={}
for p in range(1,plotnum):
key=str(p)
files[key]=e+'_'+key+'.'+fmt
PLTS[key]=key
pmagplotlib.saveP(PLTS,files)
cont=raw_input("Enter index of desired temperature step, s[a]ve plots, [return] to quit ")
if cont=="":cont='q'
while cont!="q":
if '-i' in sys.argv:Tind=int(cont) # set temperature index
b=Bs[-1] # set field to max available
XF=[] # initial chi versus frequency list
for kk in range(len(X)): # hunt through the data
if T[kk]==Ts[Tind] and B[kk]==b: # if temperature and field match,
XF.append([X[kk],F[kk]]) # append the data
if len(XF)>1: # if there are any data to plot
if FTinit==0: # if not already initialized, initialize plot
pmagplotlib.plot_init(plotnum,5,5)
FTinit=1
XFplot=plotnum
plotnum+=1 # increment plotnum
pmagplotlib.plotXFT(XFplot,XF,Ts[Tind],e,b)
else:
print '\n *** Skipping susceptibitily-frequency plot as a function of temperature *** \n'
f=Fs[0] # set frequency to minimum available
XB=[] # initialize chi versus field list
for kk in range(len(X)): # hunt through the data
if T[kk]==Ts[Tind] and F[kk]==f: # if temperature and field match those desired
XB.append([X[kk],B[kk]]) # append the data to list
if len(XB)>1: # if there are any data
if BTinit==0: # if plot not already initialized
pmagplotlib.plot_init(plotnum,5,5) # do it
BTinit=1
pmagplotlib.plotXBT(plotnum,XB,Ts[Tind],e,f) # and call plotting function
else:
print 'Skipping susceptibitily - AC field plot as a function of temperature'
if '-i' in sys.argv:
for ind in range(len(Ts)): # just in case you forgot, print out a new list of temperatures
print ind,int(Ts[ind])
cont=raw_input("Enter index of next temperature step, s[a]ve plots, [return] to quit ") # ask for new temp
if cont=="":sys.exit()
if cont=='a':
files={}
PLTS={}
for p in range(1,plotnum):
key=str(p)
files[key]=e+'_'+key+'.'+fmt
PLTS[key]=p
pmagplotlib.saveP(PLTS,files)
cont=raw_input("Enter index of desired temperature step, s[a]ve plots, [return] to quit ")
if cont=="":sys.exit()
else:
ans=raw_input("enter s[a]ve to save files, [return] to quit ")
if ans=='a':
files={}
PLTS={}
for p in range(1,plotnum):
key=str(p)
files[key]=e+'_'+key+'.'+fmt
PLTS[key]=p
pmagplotlib.saveP(PLTS,files)
sys.exit()
else:
sys.exit()
def main():
"""
NAME
zeq_magic_redo.py
DESCRIPTION
Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file
SYNTAX
zeq_magic_redo.py [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-F: specify output file, default is zeq_specimens.txt
-fre REDO: specify redo file, default is "zeq_redo"
-fsa SAMPFILE: specify er_samples format file, default is "er_samples.txt"
-A : don't average replicate measurements, default is yes
-crd [s,g,t] :
specify coordinate system [s,g,t] [default is specimen coordinates]
are specimen, geographic, and tilt corrected respectively
NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
INPUTS
zeq_redo format file is:
specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM] step_min step_max component_name[A,B,C]
"""
dir_path='.'
INCL=["LT-NO","LT-AF-Z","LT-T-Z","LT-M-Z"] # looking for demag data
beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0
user,doave,comment= "",1,""
geo,tilt=0,0
version_num=pmag.get_version()
args=sys.argv
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
meas_file,pmag_file,mk_file= dir_path+"/"+"magic_measurements.txt",dir_path+"/"+"zeq_specimens.txt",dir_path+"/"+"zeq_redo"
samp_file,coord=dir_path+"/"+"er_samples.txt",""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-A" in args:doave=0
if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
if "-f" in args:
ind=args.index("-f")
meas_file=dir_path+'/'+sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
pmag_file=dir_path+'/'+sys.argv[ind+1]
if "-fre" in args:
ind=args.index("-fre")
mk_file=dir_path+"/"+args[ind+1]
try:
mk_f=open(mk_file,'rU')
except:
print "Bad redo file"
sys.exit()
mkspec,skipped=[],[]
speclist=[]
for line in mk_f.readlines():
tmp=line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+sys.argv[ind+1]
if "-crd" in args:
ind=args.index("-crd")
coord=sys.argv[ind+1]
if coord=="g":geo,tilt=1,0
if coord=="t":geo,tilt=1,1
#
# now get down to bidness
if geo==1:
samp_data,file_type=pmag.magic_read(samp_file)
if file_type != 'er_samples':
print file_type
print "This is not a valid er_samples file "
sys.exit()
# set orientation priorities
SO_methods=[]
for rec in samp_data:
if "magic_method_codes" in rec:
methlist=rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
SO_priorities=pmag.set_priorities(SO_methods,0)
#
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
#
# sort the specimen names
#
k = 0
print 'Processing ',len(speclist), ' specimens - please wait'
PmagSpecs=[]
while k < len(speclist):
s=speclist[k]
recnum=0
PmagSpecRec={}
method_codes,inst_codes=[],[]
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth=[]
for rec in meas_data: # copy of vital stats to PmagSpecRec from first spec record in demag block
skip=1
if rec["er_specimen_name"]==s:
methods=rec["magic_method_codes"].split(":")
if len(set(methods) & set(INCL))>0:
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["magic_software_packages"]=version_num
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
PmagSpecRec["er_citation_names"]="This study"
if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"]=""
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
if "magic_instrument_codes" not in rec.keys(): rec["magic_instrument_codes"]=""
inst=rec['magic_instrument_codes'].split(":")
for I in inst:
if I not in inst_codes: # copy over instruments
inst_codes.append(I)
meths=rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:meas_meth.append(meth)
if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="T"
if "LP-DIR-AF" not in method_codes:method_codes.append("LP-DIR-AF")
if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="K"
if "LP-DIR-T" not in method_codes:method_codes.append("LP-DIR-T")
if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="J"
if "LP-DIR-M" not in method_codes:method_codes.append("LP-DIR-M")
if PmagSpecRec=={}:
print 'no data found for specimen: ',s
print 'delete from zeq_redo input file...., then try again'
sys.exit()
#
#
data,units=pmag.find_dmag_rec(s,meas_data)
#
datablock=data
noskip=1
if len(datablock) <2 or s not in speclist :
noskip=0
k+=1
# print 'skipping ', s,len(datablock)
if noskip:
#
# find replicate measurements at given treatment step and average them
#
# step_meth,avedata=pmag.vspec(data)
#
# if len(avedata) != len(datablock):
# if doave==1:
# method_codes.append("DE-VM")
# datablock=avedata
#
# do geo or stratigraphic correction now
#
if geo==1:
# find top priority orientation method
redo,p=1,0
if len(SO_methods)<=1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="": method_codes.append(az_type)
redo=0
while redo==1:
if p>=len(SO_priorities):
print "no orientation data for ",s
orient["sample_azimuth"]=""
orient["sample_dip"]=""
method_codes.append("SO-NO")
redo=0
else:
az_type=SO_methods[SO_methods.index(SO_priorities[p])]
orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="":
method_codes.append(az_type)
redo=0
p+=1
#
# if tilt selected, get stratigraphic correction
#
tiltblock,geoblock=[],[]
for rec in datablock:
if "sample_azimuth" in orient.keys() and orient["sample_azimuth"]!="":
d_geo,i_geo=pmag.dogeo(rec[1],rec[2],orient["sample_azimuth"],orient["sample_dip"])
geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5]])
if tilt==1 and "sample_bed_dip_direction" in orient.keys():
d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,orient["sample_bed_dip_direction"],orient["sample_bed_dip"])
tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5]])
elif tilt==1:
if PmagSpecRec["er_sample_name"] not in skipped:
print 'no tilt correction for ', PmagSpecRec["er_sample_name"],' skipping....'
skipped.append(PmagSpecRec["er_sample_name"])
else:
if PmagSpecRec["er_sample_name"] not in skipped:
print 'no geographic correction for ', PmagSpecRec["er_sample_name"],' skipping....'
skipped.append(PmagSpecRec["er_sample_name"])
#
# get beg_pca, end_pca, pca
if PmagSpecRec['er_sample_name'] not in skipped:
compnum=-1
for spec in mkspec:
if spec[0]==s:
CompRec={}
for key in PmagSpecRec.keys():CompRec[key]=PmagSpecRec[key]
compnum+=1
calculation_type=spec[1]
beg=float(spec[2])
end=float(spec[3])
if len(spec)>4:
comp_name=spec[4]
else:
comp_name=string.uppercase[compnum]
CompRec['specimen_comp_name']=comp_name
if beg < float(datablock[0][0]):beg=float(datablock[0][0])
if end > float(datablock[-1][0]):end=float(datablock[-1][0])
for l in range(len(datablock)):
if datablock[l][0]==beg:beg_pca=l
if datablock[l][0]==end:end_pca=l
if geo==1 and tilt==0:
mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='0'
if geo==1 and tilt==1:
mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='100'
if geo==0 and tilt==0:
mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='-1'
if mpars["specimen_direction_type"]=="Error":
pass
else:
CompRec["measurement_step_min"]='%8.3e '%(datablock[beg_pca][0])
try:
CompRec["measurement_step_max"]='%8.3e '%(datablock[end_pca][0] )
except:
print 'error in end_pca ',PmagSpecRec['er_specimen_name']
CompRec["specimen_correction"]='u'
if calculation_type!='DE-FM':
CompRec["specimen_mad"]='%7.1f '%(mpars["specimen_mad"])
CompRec["specimen_alpha95"]=""
else:
CompRec["specimen_mad"]=""
CompRec["specimen_alpha95"]='%7.1f '%(mpars["specimen_alpha95"])
CompRec["specimen_n"]='%i '%(mpars["specimen_n"])
CompMeths=[]
for meth in method_codes:
if meth not in CompMeths:CompMeths.append(meth)
if calculation_type not in CompMeths:CompMeths.append(calculation_type)
if geo==1: CompMeths.append("DA-DIR-GEO")
if tilt==1: CompMeths.append("DA-DIR-TILT")
if "DE-BFP" not in calculation_type:
CompRec["specimen_direction_type"]='l'
else:
CompRec["specimen_direction_type"]='p'
CompRec["magic_method_codes"]=""
if len(CompMeths) != 0:
methstring=""
for meth in CompMeths:
methstring=methstring+ ":" +meth
CompRec["magic_method_codes"]=methstring.strip(':')
CompRec["specimen_description"]=comment
if len(inst_codes) != 0:
inststring=""
for inst in inst_codes:
inststring=inststring+ ":" +inst
CompRec["magic_instrument_codes"]=inststring.strip(':')
PmagSpecs.append(CompRec)
k+=1
pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
print "Recalculated specimen data stored in ",pmag_file
def main():
"""
NAME
scalc_magic.py
DESCRIPTION
calculates Sb from pmag_results files
SYNTAX
scalc_magic -h [command line options]
INPUT
takes magic formatted pmag_results table
pmag_result_name must start with "VGP: Site"
must have average_lat if spin axis is reference
OPTIONS
-h prints help message and quits
-f FILE: specify input results file, default is 'pmag_results.txt'
-c cutoff: specify VGP colatitude cutoff value
-k cutoff: specify kappa cutoff
-crd [s,g,t]: specify coordinate system, default is geographic
-v : use the VanDammme criterion
-a: use antipodes of reverse data: default is to use only normal
-C: use all data without regard to polarity
-r: use reverse data only
-p: do relative to principle axis
-b: do bootstrap confidence bounds
OUTPUT:
if option -b used: N, S_B, lower and upper bounds
otherwise: N, S_B, cutoff
"""
in_file='pmag_results.txt'
coord,kappa,cutoff="0",1.,90.
nb,anti,spin,v,boot=1000,0,1,0,0
coord_key='tilt_correction'
rev=0
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-c' in sys.argv:
ind=sys.argv.index('-c')
cutoff=float(sys.argv[ind+1])
if '-k' in sys.argv:
ind=sys.argv.index('-k')
kappa=float(sys.argv[ind+1])
if '-crd' in sys.argv:
ind=sys.argv.index("-crd")
coord=sys.argv[ind+1]
if coord=='s':coord="-1"
if coord=='g':coord="0"
if coord=='t':coord="100"
if '-a' in sys.argv: anti=1
if '-C' in sys.argv: cutoff=180. # no cutoff
if '-r' in sys.argv: rev=1
if '-p' in sys.argv: spin=0
if '-v' in sys.argv: v=1
if '-b' in sys.argv: boot=1
data,file_type=pmag.magic_read(in_file)
#
#
# find desired vgp lat,lon, kappa,N_site data:
#
#
#
A,Vgps,Pvgps=180.,[],[]
VgpRecs=pmag.get_dictitem(data,'vgp_lat','','F') # get all non-blank vgp latitudes
VgpRecs=pmag.get_dictitem(VgpRecs,'vgp_lon','','F') # get all non-blank vgp longitudes
SiteRecs=pmag.get_dictitem(VgpRecs,'data_type','i','T') # get VGPs (as opposed to averaged)
SiteRecs=pmag.get_dictitem(SiteRecs,coord_key,coord,'T') # get right coordinate system
for rec in SiteRecs:
if anti==1:
if 90.-abs(float(rec['vgp_lat']))<=cutoff and float(rec['average_k'])>=kappa:
if float(rec['vgp_lat'])<0:
rec['vgp_lat']='%7.1f'%(-1*float(rec['vgp_lat']))
rec['vgp_lon']='%7.1f'%(float(rec['vgp_lon'])-180.)
Vgps.append(rec)
Pvgps.append([float(rec['vgp_lon']),float(rec['vgp_lat'])])
elif rev==0: # exclude normals
if 90.-(float(rec['vgp_lat']))<=cutoff and float(rec['average_k'])>=kappa:
Vgps.append(rec)
Pvgps.append([float(rec['vgp_lon']),float(rec['vgp_lat'])])
else: # include normals
if 90.-abs(float(rec['vgp_lat']))<=cutoff and float(rec['average_k'])>=kappa:
if float(rec['vgp_lat'])<0:
rec['vgp_lat']='%7.1f'%(-1*float(rec['vgp_lat']))
rec['vgp_lon']='%7.1f'%(float(rec['vgp_lon'])-180.)
Vgps.append(rec)
Pvgps.append([float(rec['vgp_lon']),float(rec['vgp_lat'])])
if spin==0: # do transformation to pole
ppars=pmag.doprinc(Pvgps)
for vgp in Vgps:
vlon,vlat=pmag.dodirot(float(vgp['vgp_lon']),float(vgp['vgp_lat']),ppars['dec'],ppars['inc'])
vgp['vgp_lon']=vlon
vgp['vgp_lat']=vlat
vgp['average_k']="0"
S_B= pmag.get_Sb(Vgps)
A=cutoff
if v==1:
thetamax,A=181.,180.
vVgps,cnt=[],0
for vgp in Vgps:vVgps.append(vgp) # make a copy of Vgps
while thetamax>A:
thetas=[]
A=1.8*S_B+5
cnt+=1
for vgp in vVgps:thetas.append(90.-(float(vgp['vgp_lat'])))
thetas.sort()
thetamax=thetas[-1]
if thetamax<A:break
nVgps=[]
for vgp in vVgps:
if 90.-(float(vgp['vgp_lat']))<thetamax:nVgps.append(vgp)
vVgps=[]
for vgp in nVgps:vVgps.append(vgp)
S_B= pmag.get_Sb(vVgps)
Vgps=[]
for vgp in vVgps:Vgps.append(vgp) # make a new Vgp list
SBs=[]
if boot==1:
for i in range(nb): # now do bootstrap
BVgps=[]
if i%100==0: print i,' out of ',nb
for k in range(len(Vgps)):
ind=random.randint(0,len(Vgps)-1)
random.jumpahead(int(ind*1000))
BVgps.append(Vgps[ind])
SBs.append(pmag.get_Sb(BVgps))
SBs.sort()
low=int(.025*nb)
high=int(.975*nb)
print len(Vgps),'%7.1f _ %7.1f ^ %7.1f %7.1f'%(S_B,SBs[low],SBs[high],A)
else:
print len(Vgps),'%7.1f %7.1f '%(S_B,A)
def main():
"""
ODP_samples_magic.py
OPTIONS:
-f FILE, input csv file
-Fsa FILE, output er_samples.txt file for updating, default is to overwrite er_samples.txt`
"""
samp_out="er_samples.txt"
dir_path='.'
if "-WD" in sys.argv:
ind=sys.argv.index("-WD")
dir_path=sys.argv[ind+1]
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index("-f")
samp_file=sys.argv[ind+1]
else:
print "must specify -f samp_file"
sys.exit()
samp_file=dir_path+'/'+samp_file
Samps=[]
if '-Fsa' in sys.argv:
ind=sys.argv.index("-Fsa")
samp_out=dir_path+'/'+sys.argv[ind+1]
Samps,file_type=pmag.magic_read(samp_out)
print len(Samps), ' read in from: ',samp_out
input=open(samp_file,"rU").readlines()
keys=input[0].replace('\n','').split(',')
ErSamples,samples=[],[]
for line in input[1:]:
ODPRec,SampRec={},{}
rec=line.replace('\n','').split(',')
for k in range(len(keys)):ODPRec[keys[k]]=rec[k]
SampRec['er_sample_alternatives']=ODPRec['Text Id']
label=ODPRec['Label Id'].split()
if len(label)>1 and 'PMAG' not in label[0]:
interval=label[1].split('/')[0]
pieces=label[0].split('-')
core=pieces[2]
while len(core)<4:core='0'+core
SampRec['magic_method_codes']='FS-C-DRILL-IODP:FS-SS-C:SO-V'
SampRec['er_sample_name']=pieces[0]+'-'+pieces[1]+'-'+core+'-'+pieces[3]+'-'+pieces[4]+'-'+interval
SampRec['er_site_name']=SampRec['er_sample_name']
pieces=SampRec['er_sample_name'].split('-')
SampRec['er_expedition_name']=pieces[0]
SampRec['er_location_name']=pieces[1]
SampRec['er_citation_names']="This study"
SampRec['sample_dip']="0"
SampRec['sample_azimuth']="0"
SampRec['sample_core_depth']=ODPRec['Top Depth (m)']
dates=ODPRec['Sample Date Logged'].split()
mmddyy=dates[0].split('/')
yyyy='20'+mmddyy[2]
mm=mmddyy[0]
if len(mm)==1:mm='0'+mm
dd=mmddyy[1]
if len(dd)==1:dd='0'+dd
date=yyyy+':'+mm+':'+dd+':'+dates[1]+":00.00"
SampRec['sample_date']=date
ErSamples.append(SampRec)
samples.append(SampRec['er_sample_name'])
if len(Samps)>0:
for samp in Samps:
if samp['er_sample_name'] not in samples:
ErSamples.append(samp)
Recs,keys=pmag.fillkeys(ErSamples)
pmag.magic_write(samp_out,Recs,'er_samples')
print('sample information written to er_samples.txt')
def main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or the file
exported by the MagIC v2.2 console software (downloaded from the MagIC database
or output by the Console on your PC).
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
"""
dir_path='.'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-i' in sys.argv:
file=raw_input("Magic txt file for unpacking? ")
elif '-f' in sys.argv:
ind=sys.argv.index("-f")
file=sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
f=open(dir_path+'/'+file,'rU')
File=f.readlines()
LN=0
type_list=[]
filenum=0
while LN<len(File)-1:
line=File[LN]
file_type=line.split('\t')[1]
file_type=file_type.lower()
if file_type=='delimited':file_type=Input[skip].split('\t')[2]
if file_type[-1]=="\n":file_type=file_type[:-1]
print 'working on: ',repr(file_type)
if file_type not in type_list:
type_list.append(file_type)
else:
filenum+=1
LN+=1
line=File[LN]
keys=line.replace('\n','').split('\t')
LN+=1
Recs=[]
while LN<len(File):
line=File[LN]
if line[:4]==">>>>" and len(Recs)>0:
if filenum==0:
outfile=dir_path+"/"+file_type.strip()+'.txt'
else:
outfile=dir_path+"/"+file_type.strip()+'_'+str(filenum)+'.txt'
NewRecs=[]
for rec in Recs:
if 'magic_method_codes' in rec.keys():
meths=rec['magic_method_codes'].split(":")
if len(meths)>0:
methods=""
for meth in meths: methods=methods+meth.strip()+":" # get rid of nasty spaces!!!!!!
rec['magic_method_codes']=methods[:-1]
NewRecs.append(rec)
pmag.magic_write(outfile,Recs,file_type)
print file_type," data put in ",outfile
if file_type =='pmag_specimens' and 'magic_measurements.txt' in File and 'measurement_step_min' in File and 'measurement_step_max' in File: # sort out zeq_specimens and thellier_specimens
os.system('mk_redo.py')
os.system('zeq_magic_redo.py')
os.system('thellier_magic_redo.py')
type_list.append('zeq_specimens')
type_list.append('thellier_specimens')
Recs=[]
LN+=1
break
else:
rec=line.split('\t')
Rec={}
if len(rec)==len(keys):
for k in range(len(rec)):
Rec[keys[k]]=rec[k]
Recs.append(Rec)
else:
print 'WARNING: problem in file with line: '
print line
print 'skipping....'
LN+=1
if len(Recs)>0:
if filenum==0:
outfile=dir_path+"/"+file_type.strip()+'.txt'
else:
outfile=dir_path+"/"+file_type.strip()+'_'+str(filenum)+'.txt'
NewRecs=[]
for rec in Recs:
if 'magic_method_codes' in rec.keys():
meths=rec['magic_method_codes'].split(":")
if len(meths)>0:
methods=""
for meth in meths: methods=methods+meth.strip()+":" # get rid of nasty spaces!!!!!!
rec['magic_method_codes']=methods[:-1]
NewRecs.append(rec)
pmag.magic_write(outfile,Recs,file_type)
print file_type," data put in ",outfile
# look through locations table and create separate directories for each location
locs,locnum=[],1
if 'er_locations' in type_list:
locs,file_type=pmag.magic_read(dir_path+'/er_locations.txt')
if len(locs)>0: # at least one location
for loc in locs:
print 'location_'+str(locnum)+": ",loc['er_location_name']
lpath=dir_path+'/Location_'+str(locnum)
locnum+=1
try:
os.mkdir(lpath)
except:
print 'directory ',lpath,' already exists - overwrite everything [y/n]?'
ans=raw_input()
if ans=='n':sys.exit()
for f in type_list:
print 'unpacking: ',dir_path+'/'+f+'.txt'
recs,file_type=pmag.magic_read(dir_path+'/'+f+'.txt')
print len(recs),' read in'
if 'results' not in f:
lrecs=pmag.get_dictitem(recs,'er_location_name',loc['er_location_name'],'T')
if len(lrecs)>0:
pmag.magic_write(lpath+'/'+f+'.txt',lrecs,file_type)
print len(lrecs),' stored in ',lpath+'/'+f+'.txt'
else:
lrecs=pmag.get_dictitem(recs,'er_location_names',loc['er_location_name'],'T')
if len(lrecs)>0:
pmag.magic_write(lpath+'/'+f+'.txt',lrecs,file_type)
print len(lrecs),' stored in ',lpath+'/'+f+'.txt'
def main():
"""
NAME
kly4s_magic.py
DESCRIPTION
converts files generated by SIO kly4S labview program to MagIC formated
files for use with PmagPy plotting software
SYNTAX
kly4s_magic.py -h [command line options]
OPTIONS
-h: prints the help message and quits
-i: allows interactive input of input/output filenames
-f FILE: specify .ams input file name
-fad AZDIP: specify AZDIP file with orientations, will create er_samples.txt file
-fsa SFILE: specify existing er_samples.txt file with orientation information
-fsp SPFILE: specify existing er_specimens.txt file for appending
-F MFILE: specify magic_measurements output file
-Fa AFILE: specify rmag_anisotropy output file
-ocn ORCON: specify orientation convention: default is #3 below -only with AZDIP file
-usr USER: specify who made the measurements
-loc LOC: specify location name for study
-ins INST: specify instrument used
-spc SPEC: specify number of characters to specify specimen from sample
-ncn NCON: specify naming convention: default is #1 below
DEFAULTS
MFILE: magic_measurements.txt
AFILE: rmag_anisotropy.txt
SPFILE: create new er_specimen.txt file
USER: ""
LOC: "unknown"
INST: "SIO-KLY4S"
SPEC: 1 specimen name is same as sample (if SPEC is 1, sample is all but last character)
NOTES:
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] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] all others you will have to either customize your
self or e-mail [email protected] for help.
Orientation convention:
[1] Lab arrow azimuth= azimuth; Lab arrow dip=-dip
i.e., dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = azimuth-90; Lab arrow dip = -dip
i.e., azimuth is strike and dip is hade
[3] Lab arrow azimuth = azimuth; Lab arrow dip = dip-90
e.g. dip is degrees from horizontal of drill direction
[4] Lab arrow azimuth = azimuth; Lab arrow dip = dip
[5] Lab arrow azimuth = azimuth; Lab arrow dip = 90-dip
[6] all others you will have to either customize your
self or e-mail [email protected] for help.
"""
citation='This study'
cont=0
ask=0
samp_con,Z="1",1
or_con="3" # see orientation_magic.py help message
inst,specnum="SIO-KLY4S",0
AniRecs,SpecRecs,SampRecs,MeasRecs=[],[],[],[]
user,locname,specfile="","unknown","er_specimens.txt"
AppSpec=0
sampfile,measfile='','magic_measurements.txt'
anisfile='rmag_anisotropy.txt'
azdipfile=""
dir_path='.'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-usr' in sys.argv:
ind=sys.argv.index('-usr')
user=sys.argv[ind+1]
if '-ocn' in sys.argv:
ind=sys.argv.index('-ocn')
or_con=sys.argv[ind+1]
if "-ncn" in sys.argv:
ind=sys.argv.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 3-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if '-f' in sys.argv:
ind=sys.argv.index('-f')
amsfile=sys.argv[ind+1]
else:
print main.__doc__
print 'must specify ascii input file '
sys.exit()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
measfile=sys.argv[ind+1]
if '-Fa' in sys.argv:
ind=sys.argv.index('-Fa')
anisfile=sys.argv[ind+1]
if '-Fr' in sys.argv:
ind=sys.argv.index('-Fr')
routput=sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index('-fsa')
sampfile=sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
specfile=sys.argv[ind+1]
AppSpec=1
if '-fad' in sys.argv:
ind=sys.argv.index('-fad')
azdipfile=dir_path+"/"+sys.argv[ind+1]
azfile=open(azdipfile,'rU')
AzDipDat=azfile.readlines()
if '-loc' in sys.argv:
ind=sys.argv.index('-loc')
locname=sys.argv[ind+1]
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
specnum=-(int(sys.argv[ind+1]))
#if specnum!=0:specnum=-specnum
specfile=dir_path+'/'+specfile
sampfile=dir_path+'/'+sampfile
measfile=dir_path+'/'+measfile
anisfile=dir_path+'/'+anisfile
amsfile=dir_path+'/'+amsfile
try:
input=open(amsfile,'rU')
except:
print 'Error opening file: ', amsfile
sys.exit()
SpecRecs,speclist=[],[]
if AppSpec==1:
try:
SpecRecs,filetype=pmag.magic_read(specfile) # append new records to existing
if len(SpecRecs)>0:
for spec in SpecRecs:
if spec['er_specimen_name'] not in speclist:speclist.append(spec['er_specimen_name'])
except IOError:
print 'trouble opening ',specfile
Data=input.readlines()
samps=[]
if sampfile!=dir_path+'/':
samps,file_type=pmag.magic_read(sampfile)
SO_methods=[]
for rec in samps:
if "magic_method_codes" in rec.keys():
methlist=rec["magic_method_codes"].replace(" ","").split(":")
for meth in methlist:
if "SO" in meth and "SO-POM" not in meth and "SO-GT5" not in meth and "SO-ASC" not in meth and "SO-BAD" not in meth:
if meth not in SO_methods: SO_methods.append(meth)
#
SO_priorities=pmag.set_priorities(SO_methods,ask)
for line in Data:
rec=line.split()
if len(rec)>0:
AniRec,SpecRec,SampRec,SiteRec,MeasRec={},{},{},{},{}
specname=rec[0]
if specnum!=0:
sampname=specname[:specnum]
else:
sampname=specname
site=pmag.parse_site(sampname,samp_con,Z)
AniRec['er_location_name']=locname
AniRec['er_citation_names']="This study"
AniRec['magic_instrument_codes']=inst
method_codes=['LP-X','AE-H','LP-AN-MS']
AniRec['magic_experiment_name']=specname+":"+"LP-AN-MS"
AniRec['er_analyst_mail_names']=user
AniRec['er_site_name']=site
AniRec['er_sample_name']=sampname
AniRec['er_specimen_name']=specname
labaz,labdip,bed_dip_direction,bed_dip="","","",""
if azdipfile!="":
for key in AniRec.keys():SampRec[key]=AniRec[key]
for oline in AzDipDat: # look for exact match first
orec=oline.replace('\n','').split()
if orec[0].upper() in specname.upper(): # we have a match
labaz,labdip=pmag.orient(float(orec[1]),float(orec[2]),or_con)
bed_dip_direction=float(orec[3])-90. # assume dip to right of strike
bed_dip=float(orec[4])
break
if labaz=="": # found no exact match - now look at sample level
for oline in AzDipDat:
orec=oline.split()
if orec[0].upper() == sampname.upper(): # we have a match
labaz,labdip=pmag.orient(float(orec[1]),float(orec[2]),or_con)
bed_dip_direction=float(orec[3])-90. # assume dip to right of strike
bed_dip=float(orec[4])
break
if labaz=="": # found no exact match - now look at sample level
print 'found no orientation data - will use specimen coordinates'
raw_input("<return> to continue")
else:
for key in AniRec.keys():SampRec[key]=AniRec[key]
SampRec['sample_azimuth']='%7.1f'%(labaz)
SampRec['sample_dip']='%7.1f'%(labdip)
SampRec['sample_bed_dip_direction']='%7.1f'%(bed_dip_direction)
SampRec['sample_bed_dip']='%7.1f'%(bed_dip)
SampRecs.append(SampRec)
elif sampfile!=dir_path+'/':
redo,p=1,0
orient={}
if len(SO_methods)==1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(AniRec["er_sample_name"],samps,az_type)
if orient['sample_azimuth']!="":
method_codes.append(az_type)
else:
print "no orientation data for ",AniRec["er_sample_name"],labaz
orient["sample_azimuth"]=""
orient["sample_dip"]=""
orient["sample_bed_dip_direction"]=""
orient["sample_bed_dip"]=""
noorient=1
method_codes.append("SO-NO")
redo=0
redo=0
while redo==1:
if p>=len(SO_priorities):
print "no orientation data for ",AniRec["er_sample_name"],labaz
orient["sample_azimuth"]=""
orient["sample_dip"]=""
orient["sample_bed_dip_direction"]=""
orient["sample_bed_dip"]=""
noorient=1
method_codes.append("SO-NO")
redo=0
else:
az_type=SO_methods[SO_methods.index(SO_priorities[p])]
orient=pmag.find_samp_rec(AniRec["er_sample_name"],samps,az_type)
if orient["sample_azimuth"] !="":
method_codes.append(az_type)
redo=0
noorient=0
p+=1
if orient['sample_azimuth']!="":labaz=float(orient['sample_azimuth'])
if orient['sample_dip']!="":labdip=float(orient['sample_dip'])
if "sample_bed_dip_direction" in orient.keys() and orient['sample_bed_dip_direction']!="": bed_dip_direction=float(orient['sample_bed_dip_direction'])
if "sample_bed_dip" in orient.keys() and orient['sample_bed_dip']!="": sample_bed_dip=float(orient['sample_bed_dip'])
for key in AniRec.keys():SpecRec[key]=AniRec[key]
for key in AniRec.keys():MeasRec[key]=AniRec[key]
AniRec['anisotropy_type']="AMS"
AniRec['anisotropy_n']="192"
AniRec['anisotropy_s1']=rec[1]
AniRec['anisotropy_s2']=rec[2]
AniRec['anisotropy_s3']=rec[3]
AniRec['anisotropy_s4']=rec[4]
AniRec['anisotropy_s5']=rec[5]
AniRec['anisotropy_s6']=rec[6]
AniRec['anisotropy_sigma']=rec[7]
AniRec['anisotropy_tilt_correction']='-1'
AniRec['anisotropy_unit']='Normalized by trace'
SpecRec['specimen_volume']='%8.3e'%(1e-6*float(rec[12])) # volume from cc to m^3
MeasRec['measurement_flag']='g' # good
MeasRec['measurement_standard']='u' # unknown
date=rec[14].split('/')
if int(date[2])>80:
date[2]='19'+date[2]
else:
date[2]='20'+date[2]
datetime=date[2]+':'+date[0]+':'+date[1]+":"
datetime=datetime+rec[15]
MeasRec['measurement_number']='1'
MeasRec['measurement_date']=datetime
MeasRec['measurement_lab_field_ac']='%8.3e'%(4*math.pi*1e-7*float(rec[11])) # convert from A/m to T
MeasRec['measurement_temp']="300" # assumed room T in kelvin
MeasRec['measurement_chi_volume']=rec[8]
MeasRec['measurement_description']='Bulk measurement'
MeasRec['magic_method_codes']='LP-X'
if SpecRec['er_specimen_name'] not in speclist: # add to list
speclist.append(SpecRec['er_specimen_name'])
SpecRecs.append(SpecRec)
MeasRecs.append(MeasRec)
methods=""
for meth in method_codes:
methods=methods+meth+":"
AniRec["magic_method_codes"]=methods[:-1] # get rid of annoying spaces in Anthony's export files
AniRecs.append(AniRec)
if labaz!="": # have orientation info
AniRecG,AniRecT={},{}
for key in AniRec.keys():AniRecG[key]=AniRec[key]
for key in AniRec.keys():AniRecT[key]=AniRec[key]
sbar=[]
sbar.append(float(AniRec['anisotropy_s1']))
sbar.append(float(AniRec['anisotropy_s2']))
sbar.append(float(AniRec['anisotropy_s3']))
sbar.append(float(AniRec['anisotropy_s4']))
sbar.append(float(AniRec['anisotropy_s5']))
sbar.append(float(AniRec['anisotropy_s6']))
sbarg=pmag.dosgeo(sbar,labaz,labdip)
AniRecG["anisotropy_s1"]='%12.10f'%(sbarg[0])
AniRecG["anisotropy_s2"]='%12.10f'%(sbarg[1])
AniRecG["anisotropy_s3"]='%12.10f'%(sbarg[2])
AniRecG["anisotropy_s4"]='%12.10f'%(sbarg[3])
AniRecG["anisotropy_s5"]='%12.10f'%(sbarg[4])
AniRecG["anisotropy_s6"]='%12.10f'%(sbarg[5])
AniRecG["anisotropy_tilt_correction"]='0'
AniRecs.append(AniRecG)
if bed_dip!="" and bed_dip!=0: # have tilt correction
sbart=pmag.dostilt(sbarg,bed_dip_direction,bed_dip)
AniRecT["anisotropy_s1"]='%12.10f'%(sbart[0])
AniRecT["anisotropy_s2"]='%12.10f'%(sbart[1])
AniRecT["anisotropy_s3"]='%12.10f'%(sbart[2])
AniRecT["anisotropy_s4"]='%12.10f'%(sbart[3])
AniRecT["anisotropy_s5"]='%12.10f'%(sbart[4])
AniRecT["anisotropy_s6"]='%12.10f'%(sbart[5])
AniRecT["anisotropy_tilt_correction"]='100'
AniRecs.append(AniRecT)
pmag.magic_write(anisfile,AniRecs,'rmag_anisotropy')
pmag.magic_write(measfile,MeasRecs,'magic_measurements')
pmag.magic_write(specfile,SpecRecs,'er_specimens')
print 'anisotropy data saved in ',anisfile
print 'measurement data saved in ',measfile
if AppSpec==1:
print 'new specimen information added to ',specfile
else:
print 'specimen information saved in new ',specfile
if azdipfile!="":
sampfile='er_samples.txt'
pmag.magic_write(sampfile,SampRecs,'er_samples')
print 'sample data saved in ',sampfile
def main():
"""
NAME
UCSC_leg_magic.py
DESCRIPTION
converts UCSC legacy format files to magic_measurements format files
SYNTAX
UCSC_leg_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
-fin INDEX: specify index file for reading whole directory: default is index.txt
-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
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] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] all others you will have to either customize your
self or e-mail [email protected] for help.
INPUT
Format of UCSC legacy files:
Spec Treat CDec CInc GDec GInc SDec SInc Int [optional A95]
Treat is HX where X is AF field in Oe, TX where X is T in C, or NRM
Intensity assumed to be total moment in (emu/cc) with a 10cc specimen volume
CDec: Declination in specimen coordinate system
CInc: Declination in specimen coordinate system
GDec: Declination in geographic coordinate system
GInc: Declination in geographic coordinate system
SDec: Declination in stratigraphic coordinate system
SInc: Declination in stratigraphic coordinate system
index file: must be formatted:
FILENAME SITE
"""
# initialize some stuff
noave=0
methcode,inst="",""
samp_con,Z='4',3
missing=1
demag="N"
er_location_name=""
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=""
ind_file=""
dir_path='.'
ErSamps,ErSites=[],[]
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
samp_file=dir_path+'/er_samples.txt'
site_file=dir_path+'/er_sites.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 '-Fsi' in args:
ind=args.index("-Fsi")
site_file=dirpath+'.'+args[ind+1]
try:
open(site_file,'rU')
ErSites,file_type=pmag.magic_read(site_file)
print 'site information will be appended to ', site_file
except:
print site_file,' not found: site information will be stored in new er_sites.txt file'
site_file=dir_path+'/er_sites.txt'
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dirpath+'/'+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=args[ind+1]
site=mag_file.split('.')[0]
magfile=dir_path+'/'+mag_file
try:
input=open(magfile,'rU')
MagFiles.append([magfile,site])
except:
print "bad input file name"
sys.exit()
elif '-fin' in args:
ind=args.index("-fin")
ind_file=args[ind+1]
ind_file=dir_path+'/'+ind_file
try:
index_file=open(ind_file,'rU')
except:
print "bad index file name"
sys.exit()
elif '-fin' not in args:
ind_file=dir_path+'/index.txt'
try:
index_file=open(ind_file,'rU')
except:
print "bad index file name"
sys.exit()
if ind_file!="":
Files=index_file.readlines()
for file in Files:
rec=file.split()
MagFiles.append(rec)
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]
else:
print "-loc is required option"
print main.__doc__
sys.exit()
if "-A" in args: noave=1
Sites=[]
for file in MagFiles:
site=file[1] # attach site name either from file name or from index file
if site not in Sites:
Sites.append(site)
ErSiteRec={'er_location_name': er_location_name,'er_site_name':site,'er_citation_names':citation,'site_definition':'s','site_lat':'','site_lon':"",'site_class':"",'site_lithology':"",'site_type':""}
ErSites.append(ErSiteRec)
print 'processing file: ',file[0],' for site: ',site
data=open(dir_path+'/'+file[0],'rU').readlines() # read in data from file
firstrec=data[0].split()
if firstrec[0]=='FILE': # this file has a header, must look for start of data
for k in range(len(data)):
if data[k][0]=='-': break
else:
k=-1
while k<len(data)-1:
k+=1
line=data[k]
if len(line)>2: # skip stupid terminal lines
line=line.replace(' T ',' T') # make columns consistent
line=line.replace(' H ',' H') # make columns consistent
line=line.replace(' T ',' T') # make columns consistent
line=line.replace(' H ',' H') # make columns consistent
rec=line.split()
if len(rec)<2: break # skip junk
MagRec={}
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'
meas_type="LT-NO"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=rec[0]
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
# site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[8])*1e-4) # # int is in emu/cc; assuming 10cc, this converts to Am^2
#
if samp_file!="" and MagRec["er_sample_name"] not in Samps: # create er_samples.txt file with these data
cdec,cinc=float(rec[2]),float(rec[3])
gdec,ginc=float(rec[4]),float(rec[5])
az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
bdec,binc=float(rec[6]),float(rec[7])
if rec[4]!=rec[6] and rec[5]!=rec[7]:
dipdir,dip=pmag.get_tilt(gdec,ginc,bdec,binc)
else:
dipdir,dip=0,0
ErSampRec={}
ErSampRec['er_citation_names']='This study'
ErSampRec['er_location_name']=MagRec['er_location_name']
ErSampRec['er_site_name']=MagRec['er_site_name']
ErSampRec['er_sample_name']=MagRec['er_sample_name']
ErSampRec['sample_azimuth']='%7.1f'%(az)
ErSampRec['sample_dip']='%7.1f'%(pl)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dipdir)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_description']='az,pl,dip_dir and dip recalculated from [c,g,b][dec,inc] in UCSC legacy file'
ErSampRec['magic_method_codes']='SO-NO'
ErSamps.append(ErSampRec)
Samps.append(ErSampRec['er_sample_name'])
MagRec["measurement_dec"]=rec[2]
MagRec["measurement_inc"]=rec[3]
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
demag=rec[1][0]
if demag!='N':
treat=float(rec[1][1:])
else:
treat=0
if demag=="H":
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-4) # convert from oe to tesla
meas_type="LT-AF-Z"
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
meas_type="LT-T-Z"
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,ErSamps,'er_samples')
print "sample orientations put in ",samp_file
pmag.magic_write(site_file,ErSites,'er_sites')
print "site names put in ",site_file
def main():
"""
NAME
strip_magic.py
DESCRIPTION
plots various parameters versus depth or age
SYNTAX
strip_magic.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic,default='pmag_results.txt'
supported types=[pmag_specimens, pmag_samples, pmag_sites, pmag_results, magic_web]
-obj [sit,sam,all]: specify object to site,sample,all for pmag_result table, default is all
-fmt [svg,png,jpg], format for images - default is svg
-x [age,pos]: specify whether age or stratigraphic position
-y [dec,inc,int,chi,lat,lon,vdm,vadm]
(lat and lon are VGP lat and lon)
-Iex: plot the expected inc at lat - only available for results with lat info in file
-ts TS amin amax: plot the GPTS for the time interval between amin and amax (numbers in Ma)
TS: [ck95, gts04]
-mcd method_code, specify method code, default is first one encountered
NOTES
when x and/or y are not specified, a list of possibilities will be presented to the user for choosing
"""
xaxis,xplotind,yplotind="",0,0 # (0 for strat pos)
yaxis,Xinc="", ""
obj='all'
supported=['pmag_specimens', 'pmag_samples', 'pmag_sites', 'pmag_results','magic_web']
Depth_keys=['specimen_core_depth','specimen_height','specimen_elevation','specimen_composite_depth', 'sample_core_depth','sample_height','sample_elevation','sample_composite_depth', 'site_core_depth','site_height','site_elevation','site_composite_depth','average_height']
Age_keys=['specimen_inferred_age','sample_inferred_age','site_inferred_age','average_age']
Unit_keys={'specimen_inferred_age':'specimen_inferred_age_unit','sample_inferred_age':'sample_inferred_age_unit','site_inferred_age':'site_inferred_age_unit','average_age':'average_age_unit'}
Dec_keys=['measurement_dec','specimen_dec','sample_dec','site_dec','average_dec']
Inc_keys=['measurement_inc','specimen_inc','sample_inc','site_inc','average_inc']
Int_keys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass','specimen_int','specimen_int_rel','sample_int','sample_int_rel','site_int','site_int_rel','average_int','average_int_rel']
Chi_keys=['measurement_chi_volume','measurement_chi_mass']
Lat_keys=['sample_lat','site_lat','average_lat']
VLat_keys=['vgp_lat']
VLon_keys=['vgp_lon']
Vdm_keys=['vdm']
Vadm_keys=['vadm']
X_keys=[Age_keys,Depth_keys]
Y_keys=[Dec_keys,Inc_keys,Int_keys,Chi_keys,VLat_keys,VLon_keys,Vdm_keys,Vadm_keys]
method,fmt="",'svg'
FIG={'strat':1}
plotexp,pTS=0,0
dir_path="./"
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
res_file=dir_path+'/pmag_results.txt'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
res_file=dir_path+'/'+sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
obj=sys.argv[ind+1]
if '-x' in sys.argv:
ind=sys.argv.index('-x')
xaxis=sys.argv[ind+1]
if '-y' in sys.argv:
ind=sys.argv.index('-y')
yaxis=sys.argv[ind+1]
if yaxis=='dec':ykeys=Dec_keys
if yaxis=='inc':ykeys=Inc_keys
if yaxis=='int':ykeys=Int_keys
if yaxis=='chi':ykeys=Chi_keys
if yaxis=='lat':ykeys=VLat_keys
if yaxis=='lon':ykeys=VLon_keys
if yaxis=='vdm':ykeys=Vdm_keys
if yaxis=='vadm':ykeys=Vadm_keys
if '-mcd' in sys.argv:
ind=sys.argv.index('-mcd')
method=sys.argv[ind+1]
if '-ts' in sys.argv:
ind=sys.argv.index('-ts')
ts=sys.argv[ind+1]
amin=float(sys.argv[ind+2])
amax=float(sys.argv[ind+3])
pTS=1
if '-Iex' in sys.argv: plotexp=1
#
#
# get data read in
Results,file_type=pmag.magic_read(res_file)
if file_type not in supported:
print "Unsupported file type, try again"
sys.exit()
PltObjs=['all']
if file_type=='pmag_results': # find out what to plot
for rec in Results:
resname=rec['pmag_result_name'].split()
if 'Sample' in resname and 'sam' not in PltObjs:PltObjs.append('sam')
if 'Site' in resname and 'sit' not in PltObjs:PltObjs.append('sit')
methcodes=[]
if "magic_method_codes" in Results[0].keys(): # need to know all the measurement types from method_codes
for rec in Results:
meths=rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in methcodes and 'LP' in meth: methcodes.append(meth.strip()) # look for the lab treatments
#
# initialize some variables
X_unit="" # Unit for age or depth plotting (meters if depth)
Xplots,Yplots=[],[]
Xunits=[]
yplotind,xplotind=0,0
#
# step through possible plottable keys
#
if xaxis=="" or yaxis=="":
for key in Results[0].keys():
for keys in X_keys:
for xkeys in keys:
if key in xkeys:
for ResRec in Results:
if ResRec[key]!="":
Xplots.append(key) # only plot something if there is something to plot!
break
for keys in Y_keys:
for pkeys in keys:
if key in pkeys:
for ResRec in Results:
if ResRec[key]!="":
Yplots.append(key)
break
X,Y=[],[]
for plt in Xplots:
if plt in Age_keys and 'age' not in X: X.append('age')
if plt in Depth_keys and 'pos' not in X:X.append('pos')
for plt in Yplots:
if plt in Dec_keys and 'dec' not in Y:Y.append('dec')
if plt in Inc_keys and 'inc' not in Y:Y.append('inc')
if plt in Int_keys and 'int' not in Y:Y.append('int')
if plt in Chi_keys and 'chi' not in Y:Y.append('chi')
if plt in VLat_keys and 'lat' not in Y:Y.append('lat')
if plt in VLon_keys and 'lon' not in Y:Y.append('lon')
if plt in Vadm_keys and 'vadm' not in Y:Y.append('vadm')
if plt in Vdm_keys and 'vdm' not in Y:Y.append('vdm')
if file_type=='pmag_results':
print 'available objects for plotting: ',PltObjs
print 'available X plots: ',X
print 'available Y plots: ',Y
print 'available method codes: ',methcodes
f=open(dir_path+'/.striprc','w')
for x in X:
f.write('x:'+x+'\n')
for y in Y:
f.write('y:'+y+'\n')
for m in methcodes:
f.write('m:'+m+'\n')
for obj in PltObjs:
f.write('obj:'+obj+'\n')
sys.exit()
if plotexp==1:
for lkey in Lat_keys:
for key in Results[0].keys():
if key==lkey:
lat=float(Results[0][lkey])
Xinc=[pmag.pinc(lat),-pmag.pinc(lat)]
break
if Xinc=="":
print 'can not plot expected inc for site - lat unknown'
if method!="" and method not in methcodes:
print 'your method not available, but these are: '
print methcodes
print 'use ',methocodes[0],'? ^D to quit'
if xaxis=='age':
for akey in Age_keys:
for key in Results[0].keys():
if key==akey:
Xplots.append(key)
Xunits.append(Unit_keys[key])
if xaxis=='pos':
for dkey in Depth_keys:
for key in Results[0].keys():
if key==dkey:
Xplots.append(key)
if len(Xplots)==0:
print 'desired X axis information not found'
sys.exit()
if xaxis=='age':age_unit=Results[0][Xunits[0]]
if len(Xplots)>1:
print 'multiple X axis keys found, using: ',Xplots[xplotind]
for ykey in ykeys:
for key in Results[0].keys():
if key==ykey:Yplots.append(key)
if len(Yplots)==0:
print 'desired Y axis information not found'
sys.exit()
if len(Yplots)>1:
print 'multiple Y axis keys found, using: ',Yplots[yplotind]
# check if age or depth info
if len(Xplots)==0:
print "Must have either age or height info to plot "
sys.exit()
#
# check for variable to plot
#
#
# determine X axis (age or depth)
#
if xaxis=="age": plotind="1"
if method=="":method=methcodes[0]
if xaxis=='pos':
xlab="Stratigraphic Height (meters)"
else:
xlab="Age ("+age_unit+")"
Xkey=Xplots[xplotind]
Ykey=Yplots[yplotind]
ylab=Ykey
#
# collect the data for plotting
XY=[]
isign=1.
# if float(Results[0][Xkey])/float(Results[-1][Xkey])>0 and float(Results[0][Xkey])<0:
# isign=-1. # x axis all same sign and negative, take positive (e.g.,for depth in core)
# xlab="Stratigraphic Position (meters)"
# else:
# isign=1.
for rec in Results:
if "magic_method_codes" in rec.keys():
meths=rec["magic_method_codes"].split(":")
if method in meths: # make sure it is desired lab treatment step
if obj=='all' and rec[Xkey].strip()!="":
XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
elif rec[Xkey].strip()!="":
name=rec['pmag_result_name'].split()
if obj=='sit' and "Site" in name: XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
if obj=='sam' and "Sample" in name: XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
elif method =="":
if obj=='all' and rec[Xkey].strip()!="":
XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
elif rec[Xkey].strip()!="":
name=rec['pmag_result_name'].split()
if obj=='sit' and "Site" in name: XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
if obj=='sam' and "Sample" in name: XY.append([isign*float(rec[Xkey]),float(rec[Ykey])])
else:
print "Something wrong with your plotting choices"
break
XY.sort()
title=""
if "er_locations_names" in Results[0].keys(): title=Results[0]["er_location_names"]
if "er_locations_name" in Results[0].keys(): title=Results[0]["er_location_name"]
labels=[xlab,ylab,title]
pmagplotlib.plot_init(FIG['strat'],10,5)
pmagplotlib.plotSTRAT(FIG['strat'],XY,labels) # plot them
if plotexp==1: pmagplotlib.plotHs(FIG['strat'],Xinc,'b','--')
if yaxis=='inc' or yaxis=='lat':
pmagplotlib.plotHs(FIG['strat'],[0],'b','-')
pmagplotlib.plotHs(FIG['strat'],[-90,90],'g','-')
if pTS==1:
FIG['ts']=2
pmagplotlib.plot_init(FIG['ts'],10,5)
pmagplotlib.plotTS(FIG['ts'],[amin,amax],ts)
files={}
for key in FIG.keys():
files[key]=key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
files={}
files['strat']=xaxis+'_'+yaxis+'_.'+fmt
files['ts']='ts.'+fmt
titles={}
titles['strat']='Depth/Time Series Plot'
titles['ts']='Time Series Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
ans=raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(FIG,files)
def main():
"""
NAME
thellier_magic_redo.py
DESCRIPTION
Calculates paleointensity parameters for thellier-thellier type data using bounds
stored in the "redo" file
SYNTAX
thellier_magic_redo [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-fcr CRIT, set criteria for grading
-f IN: specify input file, default is magic_measurements.txt
-fre REDO: specify redo file, default is "thellier_redo"
-F OUT: specify output file, default is thellier_specimens.txt
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
-CR PERC TYPE: apply a blanket cooling rate correction if none supplied in the er_samples.txt file
PERC should be a percentage of original (say reduce to 90%)
TYPE should be one of the following:
EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs)
-ANI: perform anisotropy correction
-fsa SAMPFILE: er_samples.txt file with cooling rate correction information, default is NO CORRECTION
-Fcr CRout: specify pmag_specimen format file for cooling rate corrected data
-fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt
-Fac ACout: specify pmag_specimen format file for anisotropy corrected data
default is AC_specimens.txt
-fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt
-Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data
default is NLT_specimens.txt
-z use z component differenences for pTRM calculation
INPUT
a thellier_redo file is Specimen_name Tmin Tmax (where Tmin and Tmax are in Centigrade)
"""
dir_path = "."
critout = ""
version_num = pmag.get_version()
field, first_save = -1, 1
spec, recnum, start, end = 0, 0, 0, 0
crfrac = 0
NltRecs, PmagSpecs, AniSpecRecs, NltSpecRecs, CRSpecs = [], [], [], [], []
meas_file, pmag_file, mk_file = "magic_measurements.txt", "thellier_specimens.txt", "thellier_redo"
anis_file = "rmag_anisotropy.txt"
anisout, nltout = "AC_specimens.txt", "NLT_specimens.txt"
crout = "CR_specimens.txt"
nlt_file = ""
samp_file = ""
comment, user = "", "unknown"
anis, nltrm = 0, 0
jackknife = 0 # maybe in future can do jackknife
args = sys.argv
Zdiff = 0
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = sys.argv[ind + 1]
if "-leg" in args:
comment = "Recalculated from original measurements; supercedes published results. "
cool = 0
if "-CR" in args:
cool = 1
ind = args.index("-CR")
crfrac = 0.01 * float(sys.argv[ind + 1])
crtype = "DA-CR-" + sys.argv[ind + 2]
if "-Fcr" in args:
ind = args.index("-Fcr")
crout = sys.argv[ind + 1]
if "-f" in args:
ind = args.index("-f")
meas_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
pmag_file = sys.argv[ind + 1]
if "-fre" in args:
ind = args.index("-fre")
mk_file = args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + "/" + args[ind + 1]
Samps, file_type = pmag.magic_read(samp_file)
SampCRs = pmag.get_dictitem(Samps, "cooling_rate_corr", "", "F") # get samples cooling rate corrections
cool = 1
if file_type != "er_samples":
print "not a valid er_samples.txt file"
sys.exit()
#
#
if "-ANI" in args:
anis = 1
ind = args.index("-ANI")
if "-Fac" in args:
ind = args.index("-Fac")
anisout = args[ind + 1]
if "-fan" in args:
ind = args.index("-fan")
anis_file = args[ind + 1]
#
if "-NLT" in args:
if "-Fnl" in args:
ind = args.index("-Fnl")
nltout = args[ind + 1]
if "-fnl" in args:
ind = args.index("-fnl")
nlt_file = args[ind + 1]
if "-z" in args:
Zdiff = 1
if "-fcr" in sys.argv:
ind = args.index("-fcr")
critout = sys.argv[ind + 1]
#
# start reading in data:
#
meas_file = dir_path + "/" + meas_file
mk_file = dir_path + "/" + mk_file
accept = pmag.default_criteria(1)[0] # set criteria to none
if critout != "":
critout = dir_path + "/" + critout
crit_data, file_type = pmag.magic_read(critout)
if file_type != "pmag_criteria":
print "bad pmag_criteria file, using no acceptance criteria"
print "Acceptance criteria read in from ", critout
for critrec in crit_data:
if "sample_int_sigma_uT" in critrec.keys(): # accommodate Shaar's new criterion
critrec["sample_int_sigma"] = "%10.3e" % (eval(critrec["sample_int_sigma_uT"]) * 1e-6)
for key in critrec.keys():
if key not in accept.keys() and critrec[key] != "":
accept[key] = critrec[key]
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != "magic_measurements":
print file_type
print file_type, "This is not a valid magic_measurements file "
sys.exit()
try:
mk_f = open(mk_file, "rU")
except:
print "Bad redo file"
sys.exit()
mkspec = []
speclist = []
for line in mk_f.readlines():
tmp = line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if anis == 1:
anis_file = dir_path + "/" + anis_file
anis_data, file_type = pmag.magic_read(anis_file)
if file_type != "rmag_anisotropy":
print file_type
print file_type, "This is not a valid rmag_anisotropy file "
sys.exit()
if nlt_file == "":
nlt_data = pmag.get_dictitem(
meas_data, "magic_method_codes", "LP-TRM", "has"
) # look for trm acquisition data in the meas_data file
else:
nlt_file = dir_path + "/" + nlt_file
nlt_data, file_type = pmag.magic_read(nlt_file)
if len(nlt_data) > 0:
nltrm = 1
#
# sort the specimen names and step through one by one
#
sids = pmag.get_specs(meas_data)
#
print "Processing ", len(speclist), " specimens - please wait "
while spec < len(speclist):
s = speclist[spec]
recnum = 0
datablock = []
PmagSpecRec = {}
PmagSpecRec["er_analyst_mail_names"] = user
PmagSpecRec["er_citation_names"] = "This study"
PmagSpecRec["magic_software_packages"] = version_num
methcodes, inst_code = [], ""
#
# find the data from the meas_data file for this specimen
#
datablock = pmag.get_dictitem(meas_data, "er_specimen_name", s, "T")
datablock = pmag.get_dictitem(
datablock, "magic_method_codes", "LP-PI-TRM", "has"
) # pick out the thellier experiment data
if len(datablock) > 0:
for rec in datablock:
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"] = "unknown"
#
# collect info for the PmagSpecRec dictionary
#
rec = datablock[0]
PmagSpecRec["er_specimen_name"] = s
PmagSpecRec["er_sample_name"] = rec["er_sample_name"]
PmagSpecRec["er_site_name"] = rec["er_site_name"]
PmagSpecRec["er_location_name"] = rec["er_location_name"]
PmagSpecRec["measurement_step_unit"] = "K"
PmagSpecRec["specimen_correction"] = "u"
if "er_expedition_name" in rec.keys():
PmagSpecRec["er_expedition_name"] = rec["er_expedition_name"]
if "magic_instrument_codes" not in rec.keys():
PmagSpecRec["magic_instrument_codes"] = "unknown"
else:
PmagSpecRec["magic_instrument_codes"] = rec["magic_instrument_codes"]
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"] = ""
else:
PmagSpecRec["magic_experiment_names"] = rec["magic_experiment_name"]
meths = rec["magic_experiment_name"].split(":")
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:
methcodes.append(meth.strip())
#
# sort out the data into first_Z, first_I, ptrm_check, ptrm_tail
#
araiblock, field = pmag.sortarai(datablock, s, Zdiff)
first_Z = araiblock[0]
first_I = araiblock[1]
ptrm_check = araiblock[2]
ptrm_tail = araiblock[3]
if len(first_I) < 3 or len(first_Z) < 4:
spec += 1
print "skipping specimen ", s
else:
#
# get start, end
#
for redospec in mkspec:
if redospec[0] == s:
b, e = float(redospec[1]), float(redospec[2])
break
if e > float(first_Z[-1][0]):
e = float(first_Z[-1][0])
for recnum in range(len(first_Z)):
if first_Z[recnum][0] == b:
start = recnum
if first_Z[recnum][0] == e:
end = recnum
nsteps = end - start
if nsteps > 2:
zijdblock, units = pmag.find_dmag_rec(s, meas_data)
pars, errcode = pmag.PintPars(datablock, araiblock, zijdblock, start, end, accept)
if "specimen_scat" in pars.keys():
PmagSpecRec["specimen_scat"] = pars["specimen_scat"]
if "specimen_frac" in pars.keys():
PmagSpecRec["specimen_frac"] = "%5.3f" % (pars["specimen_frac"])
if "specimen_gmax" in pars.keys():
PmagSpecRec["specimen_gmax"] = "%5.3f" % (pars["specimen_gmax"])
pars["measurement_step_unit"] = units
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars["specimen_b"]
PmagSpecRec["measurement_step_min"] = "%8.3e" % (pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"] = "%8.3e" % (pars["measurement_step_max"])
PmagSpecRec["specimen_int_n"] = "%i" % (pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"] = "%8.3e" % (pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"] = "%9.4e " % (pars["specimen_int"])
PmagSpecRec["specimen_b"] = "%5.3f " % (pars["specimen_b"])
PmagSpecRec["specimen_q"] = "%5.1f " % (pars["specimen_q"])
PmagSpecRec["specimen_f"] = "%5.3f " % (pars["specimen_f"])
PmagSpecRec["specimen_fvds"] = "%5.3f" % (pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"] = "%5.3f" % (pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"] = "%7.1f" % (pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"] = "%7.1f" % (pars["specimen_Z"])
PmagSpecRec["specimen_gamma"] = "%7.1f" % (pars["specimen_gamma"])
if pars["method_codes"] != "" and pars["method_codes"] not in methcodes:
methcodes.append(pars["method_codes"])
PmagSpecRec["specimen_dec"] = "%7.1f" % (pars["specimen_dec"])
PmagSpecRec["specimen_inc"] = "%7.1f" % (pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"] = "-1"
PmagSpecRec["specimen_direction_type"] = "l"
PmagSpecRec["direction_type"] = "l" # this is redudant, but helpful - won't be imported
PmagSpecRec["specimen_dang"] = "%7.1f " % (pars["specimen_dang"])
PmagSpecRec["specimen_drats"] = "%7.1f " % (pars["specimen_drats"])
PmagSpecRec["specimen_drat"] = "%7.1f " % (pars["specimen_drat"])
PmagSpecRec["specimen_int_ptrm_n"] = "%i " % (pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"] = "%6.4f " % (pars["specimen_rsc"])
PmagSpecRec["specimen_md"] = "%i " % (int(pars["specimen_md"]))
if PmagSpecRec["specimen_md"] == "-1":
PmagSpecRec["specimen_md"] = ""
PmagSpecRec["specimen_b_sigma"] = "%5.3f " % (pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:
methcodes.append("IE-TT")
methods = ""
for meth in methcodes:
methods = methods + meth + ":"
PmagSpecRec["magic_method_codes"] = methods.strip(":")
PmagSpecRec["magic_software_packages"] = version_num
PmagSpecRec["specimen_description"] = comment
if critout != "":
kill = pmag.grade(PmagSpecRec, accept, "specimen_int")
if len(kill) > 0:
Grade = "F" # fails
else:
Grade = "A" # passes
PmagSpecRec["specimen_grade"] = Grade
else:
PmagSpecRec["specimen_grade"] = "" # not graded
if nltrm == 0 and anis == 0 and cool != 0: # apply cooling rate correction
SCR = pmag.get_dictitem(
SampCRs, "er_sample_name", PmagSpecRec["er_sample_name"], "T"
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(PmagSpecRec, SCR, crfrac, crtype)
if CrSpecRec["er_specimen_name"] != "none":
CrSpecs.append(CrSpecRec)
PmagSpecs.append(PmagSpecRec)
NltSpecRec = ""
#
# check on non-linear TRM correction
#
if nltrm == 1:
#
# find the data from the nlt_data list for this specimen
#
TRMs, Bs = [], []
NltSpecRec = ""
NltRecs = pmag.get_dictitem(
nlt_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "has"
) # fish out all the NLT data for this specimen
if len(NltRecs) > 2:
for NltRec in NltRecs:
Bs.append(float(NltRec["treatment_dc_field"]))
TRMs.append(float(NltRec["measurement_magn_moment"]))
NLTpars = nlt.NLtrm(
Bs,
TRMs,
float(PmagSpecRec["specimen_int"]),
float(PmagSpecRec["specimen_lab_field_dc"]),
0,
)
if NLTpars["banc"] > 0:
NltSpecRec = {}
for key in PmagSpecRec.keys():
NltSpecRec[key] = PmagSpecRec[key]
NltSpecRec["specimen_int"] = "%9.4e" % (NLTpars["banc"])
NltSpecRec["magic_method_codes"] = PmagSpecRec["magic_method_codes"] + ":DA-NL"
NltSpecRec["specimen_correction"] = "c"
NltSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
NltSpecRec["magic_software_packages"] = version_num
print NltSpecRec["er_specimen_name"], " Banc= ", float(NLTpars["banc"]) * 1e6
if anis == 0 and cool != 0:
SCR = pmag.get_dictitem(
SampCRs, "er_sample_name", NltSpecRec["er_sample_name"], "T"
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(NltSpecRec, SCR, crfrac, crtype)
if CrSpecRec["er_specimen_name"] != "none":
CrSpecs.append(CrSpecRec)
NltSpecRecs.append(NltSpecRec)
#
# check on anisotropy correction
if anis == 1:
if NltSpecRec != "":
Spc = NltSpecRec
else: # find uncorrected data
Spc = PmagSpecRec
AniSpecs = pmag.get_dictitem(
anis_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "T"
)
if len(AniSpecs) > 0:
AniSpec = AniSpecs[0]
AniSpecRec = pmag.doaniscorr(Spc, AniSpec)
AniSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
AniSpecRec["magic_instrument_codes"] = PmagSpecRec["magic_instrument_codes"]
AniSpecRec["specimen_correction"] = "c"
AniSpecRec["magic_software_packages"] = version_num
if cool != 0:
SCR = pmag.get_dictitem(
SampCRs, "er_sample_name", AniSpecRec["er_sample_name"], "T"
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(AniSpecRec, SCR, crfrac, crtype)
if CrSpecRec["er_specimen_name"] != "none":
CrSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
elif anis == 1:
AniSpecs = pmag.get_dictitem(
anis_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "T"
)
if len(AniSpecs) > 0:
AniSpec = AniSpecs[0]
AniSpecRec = pmag.doaniscorr(PmagSpecRec, AniSpec)
AniSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
AniSpecRec["magic_instrument_codes"] = PmagSpecRec["magic_instrument_codes"]
AniSpecRec["specimen_correction"] = "c"
AniSpecRec["magic_software_packages"] = version_num
if crfrac != 0:
CrSpecRec = {}
for key in AniSpecRec.keys():
CrSpecRec[key] = AniSpecRec[key]
inten = frac * float(CrSpecRec["specimen_int"])
CrSpecRec["specimen_int"] = "%9.4e " % (
inten
) # adjust specimen intensity by cooling rate correction
CrSpecRec["magic_method_codes"] = CrSpecRec["magic_method_codes"] + ":DA-CR-" + crtype
CRSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
spec += 1
else:
print "skipping ", s
spec += 1
pmag_file = dir_path + "/" + pmag_file
pmag.magic_write(pmag_file, PmagSpecs, "pmag_specimens")
print "uncorrected thellier data saved in: ", pmag_file
if anis == 1 and len(AniSpecRecs) > 0:
anisout = dir_path + "/" + anisout
pmag.magic_write(anisout, AniSpecRecs, "pmag_specimens")
print "anisotropy corrected data saved in: ", anisout
if nltrm == 1 and len(NltSpecRecs) > 0:
nltout = dir_path + "/" + nltout
pmag.magic_write(nltout, NltSpecRecs, "pmag_specimens")
print "non-linear TRM corrected data saved in: ", nltout
if crfrac != 0:
crout = dir_path + "/" + crout
pmag.magic_write(crout, CRSpecs, "pmag_specimens")
print "cooling rate corrected data saved in: ", crout
def main():
"""
NAME
combine_magic.py
DESCRIPTION
Combines magic format files of the same type together.
SYNTAX
combine_magic.py [-h] [-i] -out filename -in file1 file2 ....
OPTIONS
-h prints help message
-i allows interactive entry of input and output filenames
-F specify output file name [must come BEFORE input file names]
-f specify input file names [ must come last]
"""
#
# set up magic meta data type requirements
#
filenames=[]
datasets=[]
dir_path='.'
#
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-F" in sys.argv:
ind=sys.argv.index("-F")
output=dir_path+'/'+sys.argv[ind+1]
if "-f" in sys.argv:
ind=sys.argv.index("-f")
for k in range(ind+1,len(sys.argv)):
filenames.append(dir_path+'/'+sys.argv[k])
for infile in filenames:
dataset,file_type=pmag.magic_read(infile)
print "File ",infile," read in with ",len(dataset), " records"
for rec in dataset:
datasets.append(rec)
if '-i' in sys.argv:
quit,dataset,datasets=0,[],[]
while quit==0:
infile=raw_input('\n\n Enter magic files for combining, <return> when done: ')
if infile=='':
quit = 1
break
dataset,file_type=pmag.magic_read(infile)
print "File ",infile," read in with ",len(dataset), " records"
for rec in dataset:
datasets.append(rec)
#
# collect all the keys from all the files
#
Recs,keys=pmag.fillkeys(datasets)
#
# write out the datasets into a combined file
#
pmag.magic_write(output,Recs,file_type)
print "All records stored in ",output
def main():
"""
NAME
thellier_magic_redo.py
DESCRIPTION
Calculates paleointensity parameters for thellier-thellier type data using bounds
stored in the "redo" file
SYNTAX
thellier_magic_redo [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-fcr CRIT, set criteria for grading
-f IN: specify input file, default is magic_measurements.txt
-fre REDO: specify redo file, default is "thellier_redo"
-F OUT: specify output file, default is thellier_specimens.txt
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
-CR PERC TYPE: apply a cooling rate correction.
PERC should be a percentage of original (say reduce to 90%)
TYPE should be one of the following:
EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs)
-Fcr CRout: specify pmag_specimen format file for cooling rate corrected data
-ANI: there are anisotropy data to correct thellier results
-fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt
-Fac ACout: specify pmag_specimen format file for anisotropy corrected data
default is AC_specimens.txt
-NLT: there are non-linear trm data in the measurements file to correct thellier results
-fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt
-Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data
default is NLT_specimens.txt
-z use z component differenences for pTRM calculation
"""
dir_path='.'
critout=""
version_num=pmag.get_version()
field,first_save=-1,1
spec,recnum,start,end=0,0,0,0
frac=0
NltRecs,PmagSpecs,AniSpecRecs,NltSpecRecs,CRSpecs=[],[],[],[],[]
meas_file,pmag_file,mk_file="magic_measurements.txt","thellier_specimens.txt","thellier_redo"
anis_file="rmag_anisotropy.txt"
anisout,nltout="AC_specimens.txt","NLT_specimens.txt"
crout="CR_specimens.txt"
nlt_file=""
comment,user="","unknown"
anis,nltrm=0,0
jackknife=0 # maybe in future can do jackknife
args=sys.argv
Zdiff=0
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
if "-CR" in args:
ind=args.index("-CR")
frac=.01*float(sys.argv[ind+1])
crtype=sys.argv[ind+2]
if "-Fcr" in args:
ind=args.index("-Fcr")
crout=sys.argv[ind+1]
if "-f" in args:
ind=args.index("-f")
meas_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
pmag_file=sys.argv[ind+1]
if "-fre" in args:
ind=args.index("-fre")
mk_file=args[ind+1]
#
#
if "-ANI" in args:
anis=1
ind=args.index("-ANI")
if "-Fac" in args:
ind=args.index("-Fac")
anisout=args[ind+1]
if "-fan" in args:
ind=args.index("-fan")
anis_file=args[ind+1]
#
if "-NLT" in args:
nltrm=1
if "-Fnl" in args:
ind=args.index("-Fnl")
nltout=args[ind+1]
if "-fnl" in args:
ind=args.index("-fnl")
nlt_file=args[ind+1]
if "-z" in args: Zdiff=1
if '-fcr' in sys.argv:
ind=args.index("-fcr")
critout=sys.argv[ind+1]
#
# start reading in data:
#
meas_file=dir_path+"/"+meas_file
mk_file=dir_path+"/"+mk_file
critout=dir_path+"/"+critout
try:
open(critout,'rU')
accept_keys=['specimen_int_ptrm_n','specimen_md','specimen_fvds','specimen_b_beta','specimen_dang','specimen_drats','specimen_Z']
crit_data,file_type=pmag.magic_read(critout)
print "Acceptance criteria read in from ", critout
accept={}
accept['specimen_int_ptrm_n']=2.0
for critrec in crit_data:
if critrec["pmag_criteria_code"]=="IE-SPEC":
for key in accept_keys:
if key not in critrec.keys():
accept[key]=-1
else:
accept[key]=float(critrec[key])
except:
critout="" # no acceptance criteria specified
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
try:
mk_f=open(mk_file,'rU')
except:
print "Bad redo file"
sys.exit()
mkspec=[]
speclist=[]
for line in mk_f.readlines():
tmp=line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if anis==1:
anis_file=dir_path+"/"+anis_file
anis_data,file_type=pmag.magic_read(anis_file)
if file_type != 'rmag_anisotropy':
print file_type
print file_type,"This is not a valid rmag_anisotropy file "
sys.exit()
if nlt_file=="":
nlt_data=meas_data # look for trm acquisition data in the meas_data file
else:
nlt_file=dir_path+"/"+nlt_file
nlt_data,file_type=pmag.magic_read(nlt_file)
#
# sort the specimen names and step through one by one
#
sids=pmag.get_specs(meas_data)
#
print 'Processing ',len(speclist),' specimens - please wait '
while spec < len(speclist):
s=speclist[spec]
recnum=0
datablock=[]
PmagSpecRec={}
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["er_citation_names"]="This study"
PmagSpecRec["magic_software_packages"]=version_num
methcodes,inst_code=[],""
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"].lower()==s.lower():
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"]="unknown"
meths=rec["magic_method_codes"]
for meth in meths:meth.strip() # get rid of annoying spaces in method codes
if "LP-PI-TRM" in meths: datablock.append(rec)
#
# collect info for the PmagSpecRec dictionary
#
if len(datablock)>0:
rec=datablock[0]
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
PmagSpecRec["measurement_step_unit"]="K"
PmagSpecRec["specimen_correction"]='u'
if "magic_instrument_codes" not in rec.keys():
PmagSpecRec["magic_instrument_codes"]="unknown"
else:
PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
meths=rec["magic_experiment_name"].split(":")
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip())
#
# sort out the data into first_Z, first_I, ptrm_check, ptrm_tail
#
araiblock,field=pmag.sortarai(datablock,s,Zdiff)
first_Z=araiblock[0]
first_I=araiblock[1]
ptrm_check=araiblock[2]
ptrm_tail=araiblock[3]
if len(first_I)<3 or len(first_Z)<4:
spec+=1
print 'skipping specimen ', s
else:
#
# get start, end
#
for redospec in mkspec:
if redospec[0]==s:
b,e=float(redospec[1]),float(redospec[2])
break
if e > float(first_Z[-1][0]):e=float(first_Z[-1][0])
for recnum in range(len(first_Z)):
if first_Z[recnum][0]==b:start=recnum
if first_Z[recnum][0]==e:end=recnum
nsteps=end-start
if nsteps>2:
zijdblock,units=pmag.find_dmag_rec(s,meas_data)
pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end)
pars['measurement_step_unit']=units
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"])
PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"])
PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"])
PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"])
PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"])
PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"])
PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"])
if pars["method_codes"]!="" and pars["method_codes"] not in methcodes: methcodes.append(pars["method_codes"])
PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"]='-1'
PmagSpecRec["specimen_direction_type"]='l'
PmagSpecRec["direction_type"]='l' # this is redudant, but helpful - won't be imported
PmagSpecRec["specimen_dang"]='%7.1f '%(pars["specimen_dang"])
PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"])
PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"])
PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"]))
if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]=""
PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:methcodes.append("IE-TT")
methods=""
for meth in methcodes:
methods=methods+meth+":"
PmagSpecRec["magic_method_codes"]=methods[:-1]
PmagSpecRec["magic_software_packages"]=version_num
PmagSpecRec["specimen_description"]=comment
if critout!="":
score,kill=pmag.grade(PmagSpecRec,accept)
Grade=""
if score==len(accept.keys()):Grade='A'
if score==len(accept.keys())-1:Grade='B'
if score==len(accept.keys())-2:Grade='C'
if score==len(accept.keys())-3:Grade='D'
if score<=len(accept.keys())-4:Grade='F'
PmagSpecRec["specimen_grade"]=Grade
else:
PmagSpecRec["specimen_grade"]=""
if nltrm==0 and anis==0 and frac!=0: # apply cooling rate correction
CrSpecRec={}
for key in PmagSpecRec.keys():CrSpecRec[key]=PmagSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CrSpecRec["specimen_correction"]='c'
CRSpecs.append(CrSpecRec)
PmagSpecs.append(PmagSpecRec)
NltSpecRec=""
#
# check on non-linear TRM correction
#
if nltrm==1:
#
# find the data from the nlt_data list for this specimen
#
TRMs,Bs=[],[]
NltSpecRec=""
NltRecs=[]
for NltRec in nlt_data:
if NltRec['er_specimen_name']==PmagSpecRec["er_specimen_name"]:
meths=NltRec["magic_method_codes"].split(":")
for meth in meths:meth.strip()
if "LP-TRM" in meths: NltRecs.append(NltRec)
if len(NltRecs) > 2:
for NltRec in NltRecs:
Bs.append(float(NltRec['treatment_dc_field']))
TRMs.append(float(NltRec['measurement_magn_moment']))
NLTpars=nlt.NLtrm(Bs,TRMs,float(PmagSpecRec['specimen_int']),float(PmagSpecRec['specimen_lab_field_dc']),0)
if NLTpars['banc']>0:
NltSpecRec={}
for key in PmagSpecRec.keys():
NltSpecRec[key]=PmagSpecRec[key]
NltSpecRec['specimen_int']='%9.4e'%(NLTpars['banc'])
NltSpecRec['magic_method_codes']=PmagSpecRec["magic_method_codes"]+":DA-NL"
NltSpecRec["specimen_correction"]='c'
NltSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
NltSpecRec["magic_software_packages"]=version_num
print NltSpecRec['er_specimen_name'], ' Banc= ',float(NLTpars['banc'])*1e6
if anis==0 and frac!=0:
CrSpecRec={}
for key in NltSpecRec.keys():CrSpecRec[key]=NltSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CRSpecs.append(CrSpecRec)
NltSpecRecs.append(NltSpecRec)
#
# check on anisotropy correction
if anis==1:
if NltSpecRec!="":
Spc=NltSpecRec
else: # find uncorrected data
Spc=PmagSpecRec
for AniSpec in anis_data:
if AniSpec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
AniSpecRec=pmag.thellier_anis_corr(Spc,AniSpec)
AniSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
inst_codes=Spc["magic_instrument_codes"]
if "magic_instrument_codes" in AniSpec.keys():
if inst_codes=="unknown":
inst_codes=AniSpec["magic_instrument_codes"]
else:
inst_codes=inst_codes+":"+AniSpec["magic_instrument_codes"]
AniSpecRec["magic_instrument_codes"]=inst_codes
AniSpecRec["specimen_correction"]='c'
AniSpecRec["magic_software_packages"]=version_num
if frac!=0:
CrSpecRec={}
for key in AniSpecRec.keys():CrSpecRec[key]=AniSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CRSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
break
elif anis==1:
for AniSpec in anis_data:
if AniSpec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
AniSpecRec=pmag.thellier_anis_corr(PmagSpecRec,AniSpec)
AniSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
inst_codes=PmagSpecRec["magic_instrument_codes"]
if "magic_instrument_codes" in AniSpec.keys():
if inst_codes=="unknown":
inst_codes=AniSpec["magic_instrument_codes"]
else:
inst_codes=inst_codes+":"+AniSpec["magic_instrument_codes"]
AniSpecRec["magic_instrument_codes"]=inst_codes
AniSpecRec["specimen_correction"]='c'
AniSpecRec["magic_software_packages"]=version_num
if frac!=0:
CrSpecRec={}
for key in AniSpecRec.keys():CrSpecRec[key]=AniSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CRSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
break
spec +=1
else:
print "skipping ",s
spec+=1
pmag_file=dir_path+'/'+pmag_file
pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
if anis==1:
anisout=dir_path+'/'+anisout
pmag.magic_write(anisout,AniSpecRecs,'pmag_specimens')
if nltrm==1:
nltout=dir_path+'/'+nltout
pmag.magic_write(nltout,NltSpecRecs,'pmag_specimens')
if frac!=0:
crout=dir_path+'/'+crout
pmag.magic_write(crout,CRSpecs,'pmag_specimens')
def main():
"""
NAME
sort_specimens.py
DESCRIPTION
Reads in a pmag_specimen formatted file and separates it into different components (A,B...etc.)
SYNTAX
sort_specimens.py [-h] [command line options]
INPUT
takes pmag_specimens.txt formatted input file
OPTIONS
-h: prints help message and quits
-f FILE: specify input file, default is 'pmag_specimens.txt'
OUTPUT
makes pmag_specimen formatted files with input filename plus _X_Y
where X is the component name and Y is s,g,t for coordinate system
"""
dir_path='.'
inspec="pmag_specimens.txt"
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
inspec=sys.argv[ind+1]
basename=inspec.split('.')[:-1]
inspec=dir_path+"/"+inspec
ofile_base=dir_path+"/"+basename[0]
#
# read in data
#
prior_spec_data,file_type=pmag.magic_read(inspec)
if file_type != 'pmag_specimens':
print file_type, " this is not a valid pmag_specimens file"
sys.exit()
# get list of specimens in file, components, coordinate systems available
specs,comps,coords=[],[],[]
for spec in prior_spec_data:
if spec['er_specimen_name'] not in specs:specs.append(spec['er_specimen_name'])
if 'specimen_comp_name' not in spec.keys():spec['specimen_comp_name']='A'
if 'specimen_tilt_correction' not in spec.keys():spec['tilt_correction']='-1' # assume specimen coordinates
if spec['specimen_comp_name'] not in comps:comps.append(spec['specimen_comp_name'])
if spec['specimen_tilt_correction'] not in coords:coords.append(spec['specimen_tilt_correction'])
# work on separating out components, coordinate systems by specimen
for coord in coords:
print coord
for comp in comps:
print comp
speclist=[]
for spec in prior_spec_data:
if spec['specimen_tilt_correction']==coord and spec['specimen_comp_name']==comp:speclist.append(spec)
ofile=ofile_base+'_'+coord+'_'+comp+'.txt'
pmag.magic_write(ofile,speclist,'pmag_specimens')
print 'coordinate system: ',coord,' component name: ',comp,' saved in ',ofile
def main():
"""
NAME
core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth or age. plots data flagged as 'FS-SS-C' as discrete samples.
SYNTAX
core_depthplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic_measurments format file from magi
-fsum FILE: specify input LIMS database (IODP) core summary csv file
-fwig FILE: specify input depth,wiggle to plot, in magic format with sample_core_depth key for depth
-fsa FILE: specify input er_samples format file from magic for depth
-fa FILE: specify input er_ages format file from magic for age
NB: must have either -fsa OR -fa (not both)
-fsp FILE sym size: specify input zeq_specimen format file from magic, sym and size
NB: PCAs will have specified color, while fisher means will be white with specified color as the edgecolor
-fres FILE specify input pmag_results file from magic, sym and size
-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot
-S do not plot blanket treatment data (if this is set, you don't need the -LP)
-sym SYM SIZE, symbol, size for continuous points (e.g., ro 5, bs 10, g^ 10 for red dot, blue square, green triangle), default is blue dot at 5 pt
-D do not plot declination
-M do not plot magnetization
-log plot magnetization on a log scale
-L do not connect dots with a line
-I do not plot inclination
-d min max [in m] depth range to plot
-n normalize by weight in er_specimen table
-Iex: plot the expected inc at lat - only available for results with lat info in file
-ts TS amin amax: plot the GPTS for the time interval between amin and amax (numbers in Ma)
TS: [ck95, gts04, gts12]
-ds [mbsf,mcd] specify depth scale, mbsf default
-fmt [svg, eps, pdf, png] specify output format for plot (default: svg)
-sav save plot silently
DEFAULTS:
Measurements file: magic_measurements.txt
Samples file: er_samples.txt
NRM step
Summary file: none
"""
meas_file='magic_measurements.txt'
intlist=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
samp_file='er_samples.txt'
depth_scale='sample_core_depth'
wt_file=''
verbose=pmagplotlib.verbose
width=10
sym,size='bo',5
Ssym,Ssize='cs',5
method,fmt="LT-NO",'.svg'
step=0
pcol=3
pel=3
pltD,pltI,pltM,pltL,pltS=1,1,1,1,1
logit=0
maxInt=-1000
minInt=1e10
maxSuc=-1000
minSuc=10000
plotexp,pTS=0,0
dir_path="."
sum_file=""
suc_file=""
age_file=""
spc_file=""
res_file=""
ngr_file=""
wig_file=""
title,location="",""
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
norm=0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-L' in sys.argv:
pltL=0
if '-S' in sys.argv: pltS=0 # don't plot the bulk measurements at all
if '-D' in sys.argv:
pltD=0
pcol-=1
pel-=1
width-=2
if '-I' in sys.argv:
pltI=0
pcol-=1
pel-=1
width-=2
if '-M' in sys.argv:
pltM=0
pcol-=1
pel-=1
width-=2
if '-log' in sys.argv:logit=1
if '-ds' in sys.argv and 'mcd' in sys.argv:depth_scale='sample_composite_depth'
if '-sym' in sys.argv:
ind=sys.argv.index('-sym')
sym=sys.argv[ind+1]
size=float(sys.argv[ind+2])
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index('-fsa')
samp_file=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=sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
spc_file=dir_path+'/'+sys.argv[ind+1]
spc_sym=sys.argv[ind+2]
spc_size=float(sys.argv[ind+3])
if '-fres' in sys.argv:
ind=sys.argv.index('-fres')
res_file=dir_path+'/'+sys.argv[ind+1]
res_sym=sys.argv[ind+2]
res_size=float(sys.argv[ind+3])
if '-fwig' in sys.argv:
ind=sys.argv.index('-fwig')
wig_file=dir_path+'/'+sys.argv[ind+1]
pcol+=1
width+=2
if '-fsum' in sys.argv:
ind=sys.argv.index('-fsum')
sum_file=dir_path+'/'+sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-sav' in sys.argv:
plots=1
verbose=0
if '-LP' in sys.argv:
ind=sys.argv.index('-LP')
meth=sys.argv[ind+1]
if meth=="AF":
step=round(float(sys.argv[ind+2])*1e-3,6)
method='LT-AF-Z'
elif meth== 'T':
step=round(float(sys.argv[ind+2])+273,6)
method='LT-T-Z'
elif meth== 'ARM':
method='LT-AF-I'
step=round(float(sys.argv[ind+2])*1e-3,6)
elif meth== 'IRM':
method='LT-IRM'
step=round(float(sys.argv[ind+2])*1e-3,6)
elif meth== 'X':
method='LP-X'
pcol+=1
if sys.argv[ind+2]=='mass':
suc_key='measurement_chi_mass'
elif sys.argv[ind+2]=='vol':
suc_key='measurement_chi_volume'
else:
print('error in susceptibility units')
sys.exit()
else:
print('method not supported')
sys.exit()
if '-n' in sys.argv:
ind=sys.argv.index('-n')
wt_file=dir_path+'/'+sys.argv[ind+1]
norm=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 '-ts' in sys.argv:
ind=sys.argv.index('-ts')
ts=sys.argv[ind+1]
amin=float(sys.argv[ind+2])
amax=float(sys.argv[ind+3])
pTS=1
pcol+=1
width+=2
#
#
# get data read in
meas_file=dir_path+'/'+meas_file
if age_file=="":
samp_file=dir_path+'/'+samp_file
Samps,file_type=pmag.magic_read(samp_file)
else:
depth_scale='age'
age_file=dir_path+'/'+age_file
Samps,file_type=pmag.magic_read(age_file)
age_unit=""
if spc_file!="":Specs,file_type=pmag.magic_read(spc_file)
if res_file!="":Results,file_type=pmag.magic_read(res_file)
if norm==1:
ErSpecs,file_type=pmag.magic_read(wt_file)
print(len(ErSpecs), ' specimens read in from ',wt_file)
Cores=[]
core_depth_key="Top depth cored CSF (m)"
if sum_file!="":
input=open(sum_file,'r').readlines()
if "Core Summary" in input[0]:
headline=1
else:
headline=0
keys=input[headline].replace('\n','').split(',')
if "Core Top (m)" in keys:core_depth_key="Core Top (m)"
if "Core Label" in keys:core_label_key="Core Label"
if "Core label" in keys:core_label_key="Core label"
for line in input[2:]:
if 'TOTALS' not in line:
CoreRec={}
for k in range(len(keys)):CoreRec[keys[k]]=line.split(',')[k]
Cores.append(CoreRec)
if len(Cores)==0:
print('no Core depth information available: import core summary file')
sum_file=""
Data=[]
if depth_scale=='sample_core_depth':
ylab="Depth (mbsf)"
elif depth_scale=='age':
ylab="Age"
else:
ylab="Depth (mcd)"
# collect the data for plotting declination
Depths,Decs,Incs,Ints=[],[],[],[]
SDepths,SDecs,SIncs,SInts=[],[],[],[]
SSucs=[]
samples=[]
methods,steps,m2=[],[],[]
if pltS: # plot the bulk measurement data
Meas,file_type=pmag.magic_read(meas_file)
meas_key='measurement_magn_moment'
print(len(Meas), ' measurements read in from ',meas_file)
for m in intlist: # find the intensity key with data
meas_data=pmag.get_dictitem(Meas,m,'','F') # get all non-blank data for this specimen
if len(meas_data)>0:
meas_key=m
break
m1=pmag.get_dictitem(Meas,'magic_method_codes',method,'has') # fish out the desired method code
if method=='LT-T-Z':
m2=pmag.get_dictitem(m1,'treatment_temp',str(step),'eval') # fish out the desired step
elif 'LT-AF' in method:
m2=pmag.get_dictitem(m1,'treatment_ac_field',str(step),'eval')
elif 'LT-IRM' in method:
m2=pmag.get_dictitem(m1,'treatment_dc_field',str(step),'eval')
elif 'LT-X' in method:
m2=pmag.get_dictitem(m1,suc_key,'','F')
if len(m2)>0:
for rec in m2: # fish out depths and weights
D=pmag.get_dictitem(Samps,'er_sample_name',rec['er_sample_name'],'T')
if not D: # if using an age_file, you may need to sort by site
D=pmag.get_dictitem(Samps,'er_site_name',rec['er_site_name'],'T')
depth=pmag.get_dictitem(D,depth_scale,'','F')
if len(depth)>0:
if ylab=='Age': ylab=ylab+' ('+depth[0]['age_unit']+')' # get units of ages - assume they are all the same!
rec['core_depth'] = float(depth[0][depth_scale])
rec['magic_method_codes'] = rec['magic_method_codes']+':'+depth[0]['magic_method_codes']
if norm==1:
specrecs=pmag.get_dictitem(ErSpecs,'er_specimen_name',rec['er_specimen_name'],'T')
specwts=pmag.get_dictitem(specrecs,'specimen_weight',"",'F')
if len(specwts)>0:
rec['specimen_weight'] = specwts[0]['specimen_weight']
Data.append(rec) # fish out data with core_depth and (if needed) weights
else:
Data.append(rec) # fish out data with core_depth and (if needed) weights
if title=="":
pieces=rec['er_sample_name'].split('-')
location=rec['er_location_name']
title=location
SData=pmag.sort_diclist(Data,'core_depth')
for rec in SData: # fish out bulk measurement data from desired depths
if dmax==-1 or float(rec['core_depth'])<dmax and float(rec['core_depth'])>dmin:
Depths.append((rec['core_depth']))
if method=="LP-X":
SSucs.append(float(rec[suc_key]))
else:
if pltD==1:Decs.append(float(rec['measurement_dec']))
if pltI==1:Incs.append(float(rec['measurement_inc']))
if norm==0 and pltM==1:Ints.append(float(rec[meas_key]))
if norm==1 and pltM==1:Ints.append(old_div(float(rec[meas_key]),float(rec['specimen_weight'])))
if len(SSucs)>0:
maxSuc=max(SSucs)
minSuc=min(SSucs)
if len(Ints)>1:
maxInt=max(Ints)
minInt=min(Ints)
if len(Depths)==0:
print('no bulk measurement data matched your request')
SpecDepths,SpecDecs,SpecIncs=[],[],[]
FDepths,FDecs,FIncs=[],[],[]
if spc_file!="": # add depths to spec data
print('spec file found')
BFLs=pmag.get_dictitem(Specs,'magic_method_codes','DE-BFL','has') # get all the discrete data with best fit lines
for spec in BFLs:
if location=="":
location=spec['er_location_name']
samp=pmag.get_dictitem(Samps,'er_sample_name',spec['er_sample_name'],'T')
if len(samp)>0 and depth_scale in list(samp[0].keys()) and samp[0][depth_scale]!="":
if ylab=='Age': ylab=ylab+' ('+samp[0]['age_unit']+')' # get units of ages - assume they are all the same!
if dmax==-1 or float(samp[0][depth_scale])<dmax and float(samp[0][depth_scale])>dmin: # filter for depth
SpecDepths.append(float(samp[0][depth_scale])) # fish out data with core_depth
SpecDecs.append(float(spec['specimen_dec'])) # fish out data with core_depth
SpecIncs.append(float(spec['specimen_inc'])) # fish out data with core_depth
else:
print('no core_depth found for: ',spec['er_specimen_name'])
FMs=pmag.get_dictitem(Specs,'magic_method_codes','DE-FM','has') # get all the discrete data with best fit lines
for spec in FMs:
if location=="":
location=spec['er_location_name']
samp=pmag.get_dictitem(Samps,'er_sample_name',spec['er_sample_name'],'T')
if len(samp)>0 and depth_scale in list(samp[0].keys()) and samp[0][depth_scale]!="":
if ylab=='Age': ylab=ylab+' ('+samp[0]['age_unit']+')' # get units of ages - assume they are all the same!
if dmax==-1 or float(samp[0][depth_scale])<dmax and float(samp[0][depth_scale])>dmin: # filter for depth
FDepths.append(float(samp[0][depth_scale]))# fish out data with core_depth
FDecs.append(float(spec['specimen_dec'])) # fish out data with core_depth
FIncs.append(float(spec['specimen_inc'])) # fish out data with core_depth
else:
print('no core_depth found for: ',spec['er_specimen_name'])
ResDepths,ResDecs,ResIncs=[],[],[]
if 'age' in depth_scale: # set y-key
res_scale='average_age'
else:
res_scale='average_height'
if res_file!="": #creates lists of Result Data
for res in Results:
meths=res['magic_method_codes'].split(":")
if 'DE-FM' in meths:
if dmax==-1 or float(res[res_scale])<dmax and float(res[res_scale])>dmin: # filter for depth
ResDepths.append(float(res[res_scale])) # fish out data with core_depth
ResDecs.append(float(res['average_dec'])) # fish out data with core_depth
ResIncs.append(float(res['average_inc'])) # fish out data with core_depth
Susc,Sus_depths=[],[]
if dmin==-1:
if len(Depths)>0: dmin,dmax=Depths[0],Depths[-1]
if len(FDepths)>0: dmin,dmax=Depths[0],Depths[-1]
if pltS==1 and len(SDepths)>0:
if SDepths[0]<dmin:dmin=SDepths[0]
if SDepths[-1]>dmax:dmax=SDepths[-1]
if len(SpecDepths)>0:
if min(SpecDepths)<dmin:dmin=min(SpecDepths)
if max(SpecDepths)>dmax:dmax=max(SpecDepths)
if len(ResDepths)>0:
if min(ResDepths)<dmin:dmin=min(ResDepths)
if max(ResDepths)>dmax:dmax=max(ResDepths)
if suc_file!="":
sucdat=open(suc_file,'r').readlines()
keys=sucdat[0].replace('\n','').split(',') # splits on underscores
for line in sucdat[1:]:
SucRec={}
for k in range(len(keys)):SucRec[keys[k]]=line.split(',')[k]
if float(SucRec['Top Depth (m)'])<dmax and float(SucRec['Top Depth (m)'])>dmin and SucRec['Magnetic Susceptibility (80 mm)']!="":
Susc.append(float(SucRec['Magnetic Susceptibility (80 mm)']))
if Susc[-1]>maxSuc:maxSuc=Susc[-1]
if Susc[-1]<minSuc:minSuc=Susc[-1]
Sus_depths.append(float(SucRec['Top Depth (m)']))
WIG,WIG_depths=[],[]
if wig_file!="":
wigdat,file_type=pmag.magic_read(wig_file)
swigdat=pmag.sort_diclist(wigdat,depth_scale)
keys=list(wigdat[0].keys())
for key in keys:
if key!=depth_scale:
plt_key=key
break
for wig in swigdat:
if float(wig[depth_scale])<dmax and float(wig[depth_scale])>dmin:
WIG.append(float(wig[plt_key]))
WIG_depths.append(float(wig[depth_scale]))
tint=4.5
plt=1
if len(Decs)>0 and len(Depths)>0 or (len(SpecDecs)>0 and len(SpecDepths)>0) or (len(ResDecs)>0 and len(ResDepths)>0) or (len(SDecs)>0 and len(SDepths)>0) or (len(SInts)>0 and len(SDepths)>0) or (len(SIncs)>0 and len(SDepths)>0):
pylab.figure(1,figsize=(width,8))
version_num=pmag.get_version()
pylab.figtext(.02,.01,version_num)
if pltD==1:
ax=pylab.subplot(1,pcol,plt)
if pltL==1:
pylab.plot(Decs,Depths,'k')
if len(Decs)>0:
pylab.plot(Decs,Depths,sym,markersize=size)
if len(Decs)==0 and pltL==1 and len(SDecs)>0:
pylab.plot(SDecs,SDepths,'k')
if len(SDecs)>0:
pylab.plot(SDecs,SDepths,Ssym,markersize=Ssize)
if spc_file!="":
pylab.plot(SpecDecs,SpecDepths,spc_sym,markersize=spc_size)
if spc_file!="" and len(FDepths)>0:
pylab.scatter(FDecs,FDepths,marker=spc_sym[-1],edgecolor=spc_sym[0],facecolor='white',s=spc_size**2)
if res_file!="":
pylab.plot(ResDecs,ResDepths,res_sym,markersize=res_size)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
if depth>dmin and depth<dmax:
pylab.plot([0,360.],[depth,depth],'b--')
if pel==plt:pylab.text(360,depth+tint,core[core_label_key])
if pel==plt:
pylab.axis([0,400,dmax,dmin])
else:
pylab.axis([0,360.,dmax,dmin])
pylab.xlabel('Declination')
pylab.ylabel(ylab)
plt+=1
pmagplotlib.delticks(ax) # dec xticks are too crowded otherwise
if pltI==1:
pylab.subplot(1,pcol,plt)
if pltL==1:pylab.plot(Incs,Depths,'k')
if len(Incs)>0:pylab.plot(Incs,Depths,sym,markersize=size)
if len(Incs)==0 and pltL==1 and len(SIncs)>0:pylab.plot(SIncs,SDepths,'k')
if len(SIncs)>0:pylab.plot(SIncs,SDepths,Ssym,markersize=Ssize)
if spc_file!="" and len(SpecDepths)>0:pylab.plot(SpecIncs,SpecDepths,spc_sym,markersize=spc_size)
if spc_file!="" and len(FDepths)>0:
pylab.scatter(FIncs,FDepths,marker=spc_sym[-1],edgecolor=spc_sym[0],facecolor='white',s=spc_size**2)
if res_file!="":pylab.plot(ResIncs,ResDepths,res_sym,markersize=res_size)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
if depth>dmin and depth<dmax:
if pel==plt:pylab.text(90,depth+tint,core[core_label_key])
pylab.plot([-90,90],[depth,depth],'b--')
pylab.plot([0,0],[dmax,dmin],'k-')
if pel==plt:
pylab.axis([-90,110,dmax,dmin])
else:
pylab.axis([-90,90,dmax,dmin])
pylab.xlabel('Inclination')
pylab.ylabel('')
plt+=1
if pltM==1 and len(Ints)>0 or len(SInts)>0:
pylab.subplot(1,pcol,plt)
for pow in range(-10,10):
if maxInt*10**pow>1:break
if logit==0:
for k in range(len(Ints)):
Ints[k]=Ints[k]*10**pow
for k in range(len(SInts)):
SInts[k]=SInts[k]*10**pow
if pltL==1 and len(Ints)>0: pylab.plot(Ints,Depths,'k')
if len(Ints)>0:pylab.plot(Ints,Depths,sym,markersize=size)
if len(Ints)==0 and pltL==1 and len(SInts)>0:pylab.plot(SInts,SDepths,'k-')
if len(SInts)>0:pylab.plot(SInts,SDepths,Ssym,markersize=Ssize)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
pylab.plot([0,maxInt*10**pow+.1],[depth,depth],'b--')
if depth>dmin and depth<dmax:pylab.text(maxInt*10**pow-.2*maxInt*10**pow,depth+tint,core[core_label_key])
pylab.axis([0,maxInt*10**pow+.1,dmax,dmin])
if norm==0:
pylab.xlabel('%s %i %s'%('Intensity (10^-',pow,' Am^2)'))
else:
pylab.xlabel('%s %i %s'%('Intensity (10^-',pow,' Am^2/kg)'))
else:
if pltL==1: pylab.semilogx(Ints,Depths,'k')
if len(Ints)>0:pylab.semilogx(Ints,Depths,sym,markersize=size)
if len(Ints)==0 and pltL==1 and len(SInts)>0:pylab.semilogx(SInts,SDepths,'k')
if len(Ints)==0 and pltL==1 and len(SInts)>0:pylab.semilogx(SInts,SDepths,'k')
if len(SInts)>0:pylab.semilogx(SInts,SDepths,Ssym,markersize=Ssize)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
pylab.semilogx([minInt,maxInt],[depth,depth],'b--')
if depth>dmin and depth<dmax:pylab.text(maxInt-.2*maxInt,depth+tint,core[core_label_key])
pylab.axis([0,maxInt,dmax,dmin])
if norm==0:
pylab.xlabel('Intensity (Am^2)')
else:
pylab.xlabel('Intensity (Am^2/kg)')
plt+=1
if suc_file!="" or len(SSucs)>0:
pylab.subplot(1,pcol,plt)
if len(Susc)>0:
if pltL==1:pylab.plot(Susc,Sus_depths,'k')
if logit==0:pylab.plot(Susc,Sus_depths,sym,markersize=size)
if logit==1:pylab.semilogx(Susc,Sus_depths,sym,markersize=size)
if len(SSucs)>0:
if logit==0:pylab.plot(SSucs,SDepths,sym,markersize=size)
if logit==1:pylab.semilogx(SSucs,SDepths,sym,markersize=size)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
if logit==0:pylab.plot([minSuc,maxSuc],[depth,depth],'b--')
if logit==1:pylab.semilogx([minSuc,maxSuc],[depth,depth],'b--')
pylab.axis([minSuc,maxSuc,dmax,dmin])
pylab.xlabel('Susceptibility')
plt+=1
if wig_file!="":
pylab.subplot(1,pcol,plt)
pylab.plot(WIG,WIG_depths,'k')
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
pylab.plot([WIG[0],WIG[-1]],[depth,depth],'b--')
pylab.axis([min(WIG),max(WIG),dmax,dmin])
pylab.xlabel(plt_key)
plt+=1
if pTS==1:
ax1=pylab.subplot(1,pcol,plt)
ax1.axis([-.25,1.5,amax,amin])
plt+=1
TS,Chrons=pmag.get_ts(ts)
X,Y,Y2=[0,1],[],[]
cnt=0
if amin<TS[1]: # in the Brunhes
Y=[amin,amin] # minimum age
Y1=[TS[1],TS[1]] # age of the B/M boundary
ax1.fill_between(X,Y,Y1,facecolor='black') # color in Brunhes, black
for d in TS[1:]:
pol=cnt%2
cnt+=1
if d<=amax and d>=amin:
ind=TS.index(d)
Y=[TS[ind],TS[ind]]
Y1=[TS[ind+1],TS[ind+1]]
if pol: ax1.fill_between(X,Y,Y1,facecolor='black') # fill in every other time
ax1.plot([0,1,1,0,0],[amin,amin,amax,amax,amin],'k-')
ax2=ax1.twinx()
pylab.ylabel("Age (Ma): "+ts)
for k in range(len(Chrons)-1):
c=Chrons[k]
cnext=Chrons[k+1]
d=cnext[1]-old_div((cnext[1]-c[1]),3.)
if d>=amin and d<amax:
ax2.plot([1,1.5],[c[1],c[1]],'k-') # make the Chron boundary tick
ax2.text(1.05,d,c[0]) #
ax2.axis([-.25,1.5,amax,amin])
figname=location+'_m:_'+method+'_core-depthplot'+fmt
pylab.title(location)
if verbose:
pylab.draw()
ans=input("S[a]ve plot? ")
if ans=='a':
pylab.savefig(figname)
print('Plot saved as ',figname)
elif plots:
pylab.savefig(figname)
print('Plot saved as ',figname)
sys.exit()
def main():
"""
NAME
biplot_magic.py
DESCRIPTION
makes a biplot of specified variables from magic_measurements.txt format file
SYNTAX
biplot_magic.py [-h] [-i] [command line options]
INPUT
takes magic formated magic_measurments file
OPTIONS
-h prints help message and quits
-i interactively set filename and axes for plotting
-f FILE: specifies file name, default: magic_measurements.txt
-fmt [svg,png,jpg], format for images - default is svg
-x XMETH:key:step, specify method code for X axis (optional key and treatment values)
-y YMETH:key:step, specify method code for X axis
-obj OBJ: specify object [loc, sit, sam, spc] for plot, default is whole file
-n [V,M] plot volume or mass normalized data only
NOTES
if nothing is specified for x and y, the user will be presented with options
key = ['treatment_ac_field','treatment_dc_field',treatment_temp']
step in mT for fields, K for temperatures
"""
#
file='magic_measurements.txt'
methx,methy,fmt="","",'.svg'
plot_key=''
norm_by=""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-n' in sys.argv:
ind=sys.argv.index('-n')
norm_by=sys.argv[ind+1]
xtreat_key,ytreat_key,xstep,ystep="","","",""
if '-x' in sys.argv:
ind=sys.argv.index('-x')
meths=sys.argv[ind+1].split(':')
methx=meths[0]
if len(meths)>1:
xtreat_key=meths[1]
xstep=float(meths[2])
if '-y' in sys.argv:
ind=sys.argv.index('-y')
meths=sys.argv[ind+1].split(':')
methy=meths[0]
if len(meths)>1:
ytreat_key=meths[1]
ystep=float(meths[2])
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
if plot_by=='loc':plot_key='er_location_name'
if plot_by=='sit':plot_key='er_site_name'
if plot_by=='sam':plot_key='er_sample_name'
if plot_by=='spc':plot_key='er_specimen_name'
if '-i' in sys.argv:
#
# get name of file from command line
#
file=raw_input("Input magic_measurments file name? [magic_measurements.txt] ")
if file=="":file="magic_measurements.txt"
#
#
FIG={'fig':1}
pmagplotlib.plot_init(FIG['fig'],5,5)
data,file_type=pmag.magic_read(file)
if file_type!="magic_measurements":
print file_type,' not correct format for magic_measurments file'
sys.exit()
#
# collect method codes
methods,plotlist=[],[]
for rec in data:
if plot_key!="":
if rec[plot_key] not in plotlist:plotlist.append(rec[plot_key])
elif len(plotlist)==0:
plotlist.append('All')
meths=rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip() not in methods and meth.strip()!="LP-":
methods.append(meth.strip())
#
if '-i' in sys.argv:
print methods
elif methx =="" or methy=="":
print methods
sys.exit()
GoOn=1
while GoOn==1:
if '-i' in sys.argv:methx=raw_input('Select method for x axis: ')
if methx not in methods:
if '-i' in sys.argv:
print 'try again! method not available'
else:
print main.__doc__
print '\n must specify X axis method\n'
sys.exit()
else:
if pmagplotlib.verbose: print methx, ' selected for X axis'
GoOn=0
GoOn=1
while GoOn==1:
if '-i' in sys.argv:methy=raw_input('Select method for y axis: ')
if methy not in methods:
if '-i' in sys.argv:
print 'try again! method not available'
else:
print main.__doc__
print '\n must specify Y axis method\n'
sys.exit()
else:
if pmagplotlib.verbose: print methy, ' selected for Y axis'
GoOn=0
if norm_by=="":
measkeys=['measurement_magn_mass','measurement_magn_volume','measurement_magn_moment','measurement_magnitude','measurement_chi_volume','measurement_chi_mass','measurement_chi']
elif norm_by=="V":
measkeys=['measurement_magn_volume','measurement_chi_volume']
elif norm_by=="M":
measkeys=['measurement_magn_mass','measurement_chi_mass']
xmeaskey,ymeaskey="",""
plotlist.sort()
for plot in plotlist: # go through objects
if pmagplotlib.verbose: print plot
X,Y=[],[]
x,y='',''
for rec in data:
if plot_key!="" and rec[plot_key]!=plot:
pass
else:
meths=rec['magic_method_codes'].split(':')
for meth in meths:
if meth.strip()==methx:
if xmeaskey=="":
for key in measkeys:
if key in rec.keys() and rec[key]!="":
xmeaskey=key
if pmagplotlib.verbose: print xmeaskey,' being used for plotting X.'
break
if meth.strip()==methy:
if ymeaskey=="":
for key in measkeys:
if key in rec.keys() and rec[key]!="":
ymeaskey=key
if pmagplotlib.verbose: print ymeaskey,' being used for plotting Y'
break
if ymeaskey!="" and xmeaskey!="":
for rec in data:
x,y='',''
spec=rec['er_specimen_name'] # get the ydata for this specimen
if rec[ymeaskey]!="" and methy in rec['magic_method_codes'].split(':'):
if ytreat_key=="" or (ytreat_key in rec.keys() and float(rec[ytreat_key])==ystep):
y=float(rec[ymeaskey])
for rec in data: # now find the xdata
if rec['er_specimen_name']==spec and rec[xmeaskey]!="" and methx in rec['magic_method_codes'].split(':'):
if xtreat_key=="" or (xtreat_key in rec.keys() and float(rec[xtreat_key])==xstep):
x=float(rec[xmeaskey])
if x != '' and y!= '':
X.append(x)
Y.append(y)
if len(X)>0:
pmagplotlib.clearFIG(FIG['fig'])
pmagplotlib.plotXY(FIG['fig'],X,Y,'ro',methx,methy,plot+':Biplot')
if not pmagplotlib.isServer:
ans=raw_input('S[a]ve plots, [q]uit, Return for next plot ' )
if ans=='a':
files={}
for key in FIG.keys(): files[key]=plot+'_'+key+fmt
pmagplotlib.saveP(FIG,files)
if ans=='q':
print "Good-bye\n"
sys.exit()
else:
files={}
for key in FIG.keys(): files[key]=plot+'_'+key+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['fig']='X Y Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
print 'nothing to plot for ',plot
def main():
"""
NAME
lnp_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimen formatted file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
SYNTAX
lnp_magic [command line options]
INPUT
takes magic formatted pmag_specimens file
OUPUT
prints site_name n_lines n_planes K alpha95 dec inc R
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is 'pmag_specimens.txt'
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is specimen
-fmt [svg,png,jpg] format for plots, default is svg
-P: do not plot
-F FILE, specify output file of dec, inc, alpha95 data for plotting with plotdi_a and plotdi_e
-exc use criteria in pmag_criteria.txt
"""
dir_path='.'
FIG={} # plot dictionary
FIG['eqarea']=1 # eqarea is figure 1
in_file,plot_key,coord='pmag_specimens.txt','er_site_name',"-1"
out_file=""
fmt,plot='svg',1
Crits=""
M,N=180.,1
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-exc' in sys.argv:
Crits,file_type=pmag.magic_read(dir_path+'/pmag_criteria.txt')
for crit in Crits:
if crit['pmag_criteria_code']=='DE-SPEC':
M=float(crit['specimen_mad'])
N=float(crit['specimen_n'])
if '-F' in sys.argv:
ind=sys.argv.index("-F")
out_file=sys.argv[ind+1]
out=open(dir_path+'/'+out_file,'w')
if '-crd' in sys.argv:
ind=sys.argv.index("-crd")
crd=sys.argv[ind+1]
if crd=='s':coord="-1"
if crd=='g':coord="0"
if crd=='t':coord="100"
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-P' in sys.argv:plot=0
#
in_file=dir_path+'/'+in_file
Specs,file_type=pmag.magic_read(in_file)
sitelist=[]
for rec in Specs:
if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name'])
sitelist.sort()
if plot==1:
import pmagplotlib
EQ={}
EQ['eqarea']=1
pmagplotlib.plot_init(EQ['eqarea'],4,4)
for site in sitelist:
print site
data=[]
for spec in Specs:
if 'specimen_tilt_correction' not in spec.keys():spec['specimen_tilt_correction']='-1' # assume unoriented
if spec['er_site_name']==site:
if 'specimen_mad' not in spec.keys() or spec['specimen_mad']=="":
if 'specimen_alpha95' in spec.keys() and spec['specimen_alpha95']!="":
spec['specimen_mad']=spec['specimen_alpha95']
else:
spec['specimen_mad']='180'
if spec['specimen_tilt_correction']==coord and float(spec['specimen_mad'])<=M and float(spec['specimen_n'])>=N:
rec={}
for key in spec.keys():rec[key]=spec[key]
rec["dec"]=float(spec['specimen_dec'])
rec["inc"]=float(spec['specimen_inc'])
rec["tilt_correction"]=spec['specimen_tilt_correction']
data.append(rec)
if len(data)>2:
fpars=pmag.dolnp(data,'specimen_direction_type')
print "Site lines planes kappa a95 dec inc"
print site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"]
if out_file!="":
if float(fpars["alpha95"])<=acutoff and float(fpars["K"])>=kcutoff:
out.write('%s %s %s\n'%(fpars["dec"],fpars['inc'],fpars['alpha95']))
print '% tilt correction: ',coord
if plot==1:
pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type')
ans=raw_input("s[a]ve plot, [q]uit, <return> to continue:\n ")
if ans=="a":
files={}
files['eqarea']=site+'_'+crd+'_'+'eqarea'+'.'+fmt
pmagplotlib.saveP(EQ,files)
if ans=="q": sys.exit()
else:
print 'skipping site - not enough data with specified coordinate system'
def main():
"""
NAME
MsT_magic.py
DESCRIPTION
converts MsT data (T,M) to magic_measurements format files
SYNTAX
MsT_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify T,M format input file, required
-fsa SFILE: name with sample, site, location information
-F FILE: specify output file, default is MsT_measurements.txt
-dc H: specify applied field during measurement, default is 0.5 T
-syn : This is a synthetic specimen and has no sample/site/location information
-spn SPEC: specimen name
-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
-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.
INPUT files:
T M: T is in Centigrade and M is uncalibrated magnitude
"""
# initialize some stuff
samp_con,Z="1","0"
dir_path='.'
citation='This study'
args=sys.argv
specnum,measnum=0,1
#
# get command line arguments
#
user=""
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
meas_file=dir_path+"/MsT_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
labfield='0.5'
if "-dc" in args:
ind=args.index("-dc")
labfield=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]
Samps,file_type=pmag.magic_read(samp_file)
if '-f' in args:
ind=args.index("-f")
infile=dir_path+'/'+args[ind+1]
try:
input=open(infile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print main.__doc__
print "-f is required option"
sys.exit()
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
er_location_name,syn,specimen_name='unknown',0,'unknown'
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-spn" in args:
ind=args.index("-spn")
specimen_name=args[ind+1]
else:
print main.__doc__
print "-spn is required option"
sys.exit()
if "-syn" in args: syn=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"
samp_con=sys.argv[ind+1]
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"
MagRecs,specs=[],[]
version_num=pmag.get_version()
data=input.readlines()
T0=float(data[0].split()[0])
for line in data:
instcode=""
if len(line)>1:
MagRec={}
if syn==0: MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_dc_field"]=labfield
rec=line.split()
T=float(rec[0])
MagRec["measurment_temp"]='%8.3e' % (float(rec[0])+273.) # temp in kelvin
if T>T0:
MagRec["magic_method_codes"]='LP-MW-I'
elif T<T0:
MagRec["magic_method_codes"]='LP-MC-I'
T0=T
else:
print 'skipping repeated temperature step'
MagRec["magic_method_codes"]=''
T0=T
MagRec["measurement_magnitude"]='%10.3e'% (float(rec[1])) # uncalibrated magnitude
if syn==0:
MagRec["er_specimen_name"]=specimen_name
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=specimen_name[:specnum]
else:
MagRec["er_sample_name"]=specimen_name
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
else:
MagRec["er_synthetic_name"]=specimen_name
MagRec["er_location_name"]=""
MagRec["er_sample_name"]=""
MagRec["er_site_name"]=""
MagRec["er_specimen_name"]=""
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["measurement_flag"]='g'
MagRec["measurement_number"]=str(measnum)
measnum+=1
MagRecs.append(MagRec)
for rec in MagRecs: # sort out the measurements by experiment type
rec['magic_experiment_name']=specimen_name
if rec['magic_method_codes']=='LP-MW-I':
rec["magic_experiment_name"]=specimen_name+':LP-MW-I:Curie'
elif rec['magic_method_codes']=='LP-MC-I':
rec["magic_experiment_name"]=specimen_name+':LP-MC-I'
pmag.magic_write(meas_file,MagRecs,'magic_measurements')
print "results put in ",meas_file
def main():
"""
NAME
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a pmag_results table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE pmag_results format file, [default is pmag_results.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
DEFAULTS
FILE: pmag_results.txt
res: c
prj: mercator
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
dir_path='.'
res,ages='c',0
proj='npstere'
results_file='pmag_results.txt'
ell,flip=0,0
lat_0,lon_0=90.,0.
fmt='pdf'
sym,size='ro',8
rsym,rsize='g^',8
anti=0
coord=""
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-S' in sys.argv:anti=1
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
if '-rev' in sys.argv:
flip=1
ind = sys.argv.index('-rev')
rsym=(sys.argv[ind+1])
rsize=int(sys.argv[ind+2])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym=(sys.argv[ind+1])
size=int(sys.argv[ind+2])
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0=float(sys.argv[ind+1])
lon_0=float(sys.argv[ind+2])
if '-ell' in sys.argv: ell=1
if '-age' in sys.argv: ages=1
if '-f' in sys.argv:
ind = sys.argv.index('-f')
results_file=sys.argv[ind+1]
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd=sys.argv[ind+1]
if crd=='g':coord='0'
if crd=='t':coord='100'
results_file=dir_path+'/'+results_file
data,file_type=pmag.magic_read(results_file)
if file_type!='pmag_results':
print "bad results file"
sys.exit()
FIG={'map':1}
pmagplotlib.plot_init(FIG['map'],6,6)
# read in er_sites file
lats,lons,dp,dm,a95=[],[],[],[],[]
Pars=[]
dates,rlats,rlons=[],[],[]
Results=[]
for rec in data:
if 'pmag_result_name' in rec.keys():
name=rec['pmag_result_name'].split()
if 'Site' in name:
if coord=="" or rec['tilt_correction']==coord:Results.append(rec)
elif coord=="" or rec['tilt_correction']==coord:Results.append(rec)
for rec in Results:
if 'vgp_lat' in rec.keys() and rec['vgp_lat']!="" and 'vgp_lon' in rec.keys() and rec['vgp_lon']!="":
if 'average_age' in rec.keys() and rec['average_age']!="" and ages==1:
dates.append(rec['average_age'])
lat=float(rec['vgp_lat'])
lon=float(rec['vgp_lon'])
if flip==0:
lats.append(lat)
lons.append(lon)
elif flip==1:
if lat<0:
rlats.append(-lat)
lon=lon+180.
if lon>360:lon=lon-360.
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
elif anti==1:
lats.append(-lat)
lon=lon+180.
if lon>360:lon=lon-360.
lons.append(lon)
ppars=[]
ppars.append(lon)
ppars.append(lat)
ell1,ell2="",""
if 'vgp_dm' in rec.keys() and rec['vgp_dm']!="":ell1=float(rec['vgp_dm'])
if 'vgp_dp' in rec.keys() and rec['vgp_dp']!="":ell2=float(rec['vgp_dp'])
if 'vgp_alpha95' in rec.keys() and rec['vgp_alpha95']!="":ell1,ell2=float(rec['vgp_alpha95']),float(rec['vgp_alpha95'])
if ell1!="" and ell2!="":
ppars=[]
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign=abs(lats[-1])/lats[-1]
ppars.append(lats[-1]-isign*90.)
ppars.append(ell2)
ppars.append(lons[-1]+90.)
ppars.append(0.)
Pars.append(ppars)
Opts={'latmin':-90,'latmax':90,'lonmin':0.,'lonmax':360.,'lat_0':lat_0,'lon_0':lon_0,'proj':proj,'sym':'bs','symsize':3,'pltgrid':0,'res':res,'boundinglat':0.}
Opts['details']={'coasts':1,'rivers':0, 'states':0, 'countries':0,'ocean':1}
pmagplotlib.plotMAP(FIG['map'],[90.],[0.],Opts) # make the base map with a blue triangle at the pole`
Opts['details']={'coasts':0,'rivers':0, 'states':0, 'countries':0,'ocean':0}
Opts['pltgrid']=-1
Opts['sym']=sym
Opts['symsize']=size
if len(dates)>0:Opts['names']=dates
if len(lats)>0:pmagplotlib.plotMAP(FIG['map'],lats,lons,Opts) # add the lats and lons of the poles
Opts['names']=[]
if len(rlats)>0:
Opts['sym']=rsym
Opts['symsize']=rsize
pmagplotlib.plotMAP(FIG['map'],rlats,rlons,Opts) # add the lats and lons of the poles
pmagplotlib.drawFIGS(FIG)
if ell==1: # add ellipses if desired.
Opts['details']={'coasts':0,'rivers':0, 'states':0, 'countries':0,'ocean':0}
Opts['pltgrid']=-1 # turn off meridian replotting
Opts['symsize']=2
Opts['sym']='g-'
for ppars in Pars:
if ppars[2]!=0:
PTS=pmagplotlib.plotELL(FIG['map'],ppars,'g.',0,0)
elats,elons=[],[]
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
pmagplotlib.plotMAP(FIG['map'],elats,elons,Opts) # make the base map with a blue triangle at the pole`
pmagplotlib.drawFIGS(FIG)
files={}
for key in FIG.keys():
files[key]='VGP_map'+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='VGP Map'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
ans=raw_input(" S[a]ve to save plot, Return to quit: ")
if ans=="a":
pmagplotlib.saveP(FIG,files)
else:
print "Good bye"
sys.exit()
def main():
"""
NAME
plotxy_magic.py
DESCRIPTION
Makes simple X,Y plots
INPUT FORMAT
Any MagIC formatted file
SYNTAX
plotxy_magic.py [command line options]
OPTIONS
-h prints this help message
-f FILE to set file name on command rec
-c col1 col2 specify columns names to plot
-sym SYM SIZE specify symbol and size to plot: default is red dots
-S don't plot symbols
-xlab XLAB
-ylab YLAB
-l connect symbols with lines
-b xmin xmax ymin ymax, sets bounds
# -b [key:max:min,key:max:min,etc.] leave or min blank for no cutoff
"""
col1, col2 = 0, 1
sym, size = "ro", 20
xlab, ylab = "", ""
lines = 0
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-f" in sys.argv:
ind = sys.argv.index("-f")
file = sys.argv[ind + 1]
else:
"-f option is a required field"
print main.__doc__
sys.exit()
if "-c" in sys.argv:
ind = sys.argv.index("-c")
col1 = sys.argv[ind + 1]
col2 = sys.argv[ind + 2]
else:
"Column headers a required field"
print main.__doc__
sys.exit()
if "-xlab" in sys.argv:
ind = sys.argv.index("-xlab")
xlab = sys.argv[ind + 1]
if "-ylab" in sys.argv:
ind = sys.argv.index("-ylab")
ylab = sys.argv[ind + 1]
# if '-b' in sys.argv:
# ind=sys.argv.index('-b')
# bounds=sys.argv[ind+1].split(',')
if "-b" in sys.argv:
ind = sys.argv.index("-b")
xmin = float(sys.argv[ind + 1])
xmax = float(sys.argv[ind + 2])
ymin = float(sys.argv[ind + 3])
ymax = float(sys.argv[ind + 4])
if "-sym" in sys.argv:
ind = sys.argv.index("-sym")
sym = sys.argv[ind + 1]
size = int(sys.argv[ind + 2])
if "-l" in sys.argv:
lines = 1
if "-S" in sys.argv:
sym = ""
X, Y = [], []
data, file_type = pmag.magic_read(file)
print file_type
for rec in data:
if col1 not in rec.keys() or col2 not in rec.keys():
print col1, " and/or ", col2, " not in file headers"
print "try again"
sys.exit()
if rec[col1] != "" and rec[col2] != "":
skip = 0
if "-crit" in sys.argv:
for crit in bounds:
crits = crit.split(":")
crit_key = crits[0]
crit_min = crits[1]
crit_max = crits[2]
if rec[crit_key] == "":
skip = 1
else:
if crit_min != "" and float(rec[crit_key]) < float(crit_min):
skip = 1
if crit_max != "" and float(rec[crit_key]) > float(crit_min):
skip = 1
if skip == 0:
X.append(float(rec[col1]))
Y.append(float(rec[col2]))
if len(X) == 0:
print col1, " and/or ", col2, " have no data "
print "try again"
sys.exit()
else:
print len(X), " data points"
if sym != "":
pylab.scatter(X, Y, c=sym[0], marker=sym[1], s=size)
if xlab != "":
pylab.xlabel(xlab)
if ylab != "":
pylab.ylabel(ylab)
if lines == 1:
pylab.plot(X, Y, "k-")
if "-b" in sys.argv:
pylab.axis([xmin, xmax, ymin, ymax])
pylab.draw()
ans = raw_input("Press return to quit ")
sys.exit()
