def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available plots.
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
# reset log files
for fname in ['log.txt', 'errors.txt']:
f = os.path.join(os.getcwd(), fname)
if os.path.exists(f):
os.remove(f)
dirlist = ['./']
dir_path = os.getcwd()
#
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
else:
fmt = 'png'
if '-f' in sys.argv:
ind = sys.argv.index("-f")
filelist = [sys.argv[ind + 1]]
else:
filelist = os.listdir(dir_path)
## initialize some variables
samp_file = 'samples.txt'
azimuth_key = 'azimuth'
meas_file = 'measurements.txt'
loc_key = 'location'
loc_file = 'locations.txt'
method_key = 'method_codes'
dec_key = 'dir_dec'
inc_key = 'dir_inc'
tilt_corr_key = "dir_tilt_correction"
aniso_tilt_corr_key = "aniso_tilt_correction"
hyst_bcr_key = "hyst_bcr"
hyst_mr_key = "hyst_mr_moment"
hyst_ms_key = "hyst_ms_moment"
hyst_bc_key = "hyst_bc"
Mkeys = ['magnitude', 'magn_moment', 'magn_volume', 'magn_mass']
results_file = 'sites.txt'
hyst_file = 'specimens.txt'
aniso_file = 'specimens.txt'
# create contribution and propagate data throughout
con = cb.Contribution()
con.propagate_location_to_measurements()
con.propagate_location_to_specimens()
con.propagate_location_to_samples()
if not con.tables:
print('-E- No MagIC tables could be found in this directory')
error_log("No MagIC tables found")
return
# check to see if propagation worked, otherwise you can't plot by location
lowest_table = None
for table in con.ancestry:
if table in con.tables:
lowest_table = table
break
do_full_directory = False
# check that locations propagated down to the lowest table in the contribution
if 'location' in con.tables[lowest_table].df.columns:
# are there any locations in the lowest table?
if not all(con.tables[lowest_table].df['location'].isnull()):
locs = con.tables['locations'].df.index.unique()
lowest_locs = con.tables[lowest_table].df['location'].unique()
incorrect_locs = set(lowest_locs).difference(set(locs))
# are they actual locations?
if not incorrect_locs:
info_log(
'location names propagated to {}'.format(lowest_table))
else:
do_full_directory = True
error_log('location names did not propagate fully to {} table'.
format(lowest_table))
else:
do_full_directory = True
error_log(
'could not propagate location names down to {} table'.format(
lowest_table))
else:
do_full_directory = True
error_log('could not propagate location names down to {} table'.format(
lowest_table))
all_data = {}
all_data['measurements'] = con.tables.get('measurements', None)
all_data['specimens'] = con.tables.get('specimens', None)
all_data['samples'] = con.tables.get('samples', None)
all_data['sites'] = con.tables.get('sites', None)
all_data['locations'] = con.tables.get('locations', None)
locations = con.tables['locations'].df.index.unique()
dirlist = [loc for loc in locations if cb.not_null(loc) and loc != 'nan']
if not dirlist:
dirlist = ["./"]
if do_full_directory:
dirlist = ["./"]
# plot the whole contribution as one location
if dirlist == ["./"]:
error_log('plotting the entire contribution as one location')
for fname in os.listdir("."):
if fname.endswith(".txt"):
shutil.copy(fname, "tmp_" + fname)
# if possible, go through all data by location
# use tmp_*.txt files to separate out by location
for loc in dirlist:
print('\nworking on: ', loc)
def get_data(dtype, loc_name):
"""
Extract data of type dtype for location loc_name.
Write tmp_dtype.txt files if possible.
"""
if cb.not_null(all_data[dtype]):
data_container = all_data[dtype]
data_df = data_container.df[data_container.df['location'] ==
loc_name]
data = data_container.convert_to_pmag_data_list(df=data_df)
res = data_container.write_magic_file(
'tmp_{}.txt'.format(dtype), df=data_df)
if not res:
return []
return data
meas_data = get_data('measurements', loc)
spec_data = get_data('specimens', loc)
samp_data = get_data('samples', loc)
site_data = get_data('sites', loc)
location_data = get_data('locations', loc)
if loc == "./": # if you can't sort by location, do everything together
try:
meas_data = con.tables[
'measurements'].convert_to_pmag_data_list()
except KeyError:
meas_data = None
try:
spec_data = con.tables['specimens'].convert_to_pmag_data_list()
except KeyError:
spec_data = None
try:
samp_data = con.tables['samples'].convert_to_pmag_data_list()
except KeyError:
samp_data = None
try:
site_data = con.tables['sites'].convert_to_pmag_data_list()
except KeyError:
site_data = None
crd = 's'
if samp_file in filelist: # find coordinate systems
samps = samp_data
file_type = "samples"
# get all non blank sample orientations
Srecs = pmag.get_dictitem(samps, azimuth_key, '', 'F')
if len(Srecs) > 0:
crd = 'g'
print('using geographic coordinates')
else:
print('using specimen coordinates')
else:
if VERBOSE:
print('-I- No sample data found')
if meas_file in filelist: # start with measurement data
print('working on measurements data')
data = meas_data
file_type = 'measurements'
# looking for zeq_magic possibilities
# get all non blank method codes
AFZrecs = pmag.get_dictitem(data, method_key, 'LT-AF-Z', 'has')
# get all non blank method codes
TZrecs = pmag.get_dictitem(data, method_key, 'LT-T-Z', 'has')
# get all non blank method codes
MZrecs = pmag.get_dictitem(data, method_key, 'LT-M-Z', 'has')
# get all dec measurements
Drecs = pmag.get_dictitem(data, dec_key, '', 'F')
# get all inc measurements
Irecs = pmag.get_dictitem(data, inc_key, '', 'F')
for key in Mkeys:
Mrecs = pmag.get_dictitem(data, key, '',
'F') # get intensity data
if len(Mrecs) > 0:
break
# potential for stepwise demag curves
if len(AFZrecs) > 0 or len(TZrecs) > 0 or len(MZrecs) > 0 and len(
Drecs) > 0 and len(Irecs) > 0 and len(Mrecs) > 0:
CMD = 'zeq_magic.py -f tmp_measurements.txt -fsp tmp_specimens.txt -fsa tmp_samples.txt -fsi tmp_sites.txt -sav -fmt ' + fmt + ' -crd ' + crd
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# looking for thellier_magic possibilities
if len(pmag.get_dictitem(data, method_key, 'LP-PI-TRM',
'has')) > 0:
CMD = 'thellier_magic.py -f tmp_measurements.txt -fsp tmp_specimens.txt -sav -fmt ' + fmt
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# looking for hysteresis possibilities
if len(pmag.get_dictitem(data, method_key, 'LP-HYS',
'has')) > 0: # find hyst experiments
# check for reqd columns
missing = check_for_reqd_cols(data, ['treat_temp'])
if missing:
error_log(
'LP-HYS method code present, but required column(s) [{}] missing'
.format(", ".join(missing)), loc, "quick_hyst.py")
else:
CMD = 'quick_hyst.py -f tmp_measurements.txt -sav -fmt ' + fmt
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# equal area plots of directional data
# at measurment level (by specimen)
if data:
missing = check_for_reqd_cols(data, ['dir_dec', 'dir_inc'])
if not missing:
CMD = "eqarea_magic.py -f tmp_measurements.txt -obj spc -sav -no-tilt -fmt " + fmt
print(CMD)
os.system(CMD)
info_log(CMD, loc, "eqarea_magic.py")
else:
if VERBOSE:
print('-I- No measurement data found')
# site data
if results_file in filelist:
print('-I- result file found', results_file)
data = site_data
file_type = 'sites'
print('-I- working on site directions')
print('number of datapoints: ', len(data), loc)
dec_key = 'dir_dec'
inc_key = 'dir_inc'
int_key = 'int_abs'
SiteDIs = pmag.get_dictitem(data, dec_key, "", 'F') # find decs
SiteDIs = pmag.get_dictitem(SiteDIs, inc_key, "",
'F') # find decs and incs
dir_data_found = len(SiteDIs)
print('{} Dec/inc pairs found'.format(dir_data_found))
# only individual results - not poles
# get only individual results (if result_type col is available)
if SiteDIs:
if 'result_type' in SiteDIs[0]:
SiteDIs = pmag.get_dictitem(SiteDIs, 'result_type', 'i',
'has')
# then convert tilt_corr_key to correct format
old_SiteDIs = SiteDIs
SiteDIs = []
for rec in old_SiteDIs:
if tilt_corr_key not in rec:
error_log(
"Directional data found, but missing {}, can't plot directions"
.format(tilt_corr_key), loc, "eqarea_magic.py")
break
if cb.is_null(
rec[tilt_corr_key]) and rec[tilt_corr_key] != 0:
rec[tilt_corr_key] = ""
else:
try:
rec[tilt_corr_key] = str(
int(float(rec[tilt_corr_key])))
except ValueError:
rec[tilt_corr_key] = ""
SiteDIs.append(rec)
print('number of individual directions: ', len(SiteDIs))
# tilt corrected coordinates
SiteDIs_t = pmag.get_dictitem(SiteDIs,
tilt_corr_key,
'100',
'T',
float_to_int=True)
print('number of tilt corrected directions: ', len(SiteDIs_t))
SiteDIs_g = pmag.get_dictitem(
SiteDIs, tilt_corr_key, '0', 'T',
float_to_int=True) # geographic coordinates
print('number of geographic directions: ', len(SiteDIs_g))
SiteDIs_s = pmag.get_dictitem(
SiteDIs, tilt_corr_key, '-1', 'T',
float_to_int=True) # sample coordinates
print('number of sample directions: ', len(SiteDIs_s))
SiteDIs_x = pmag.get_dictitem(SiteDIs, tilt_corr_key, '',
'T') # no coordinates
print('number of no coordinates directions: ', len(SiteDIs_x))
if len(SiteDIs_t) > 0 or len(SiteDIs_g) > 0 or len(
SiteDIs_s) > 0 or len(SiteDIs_x) > 0:
CRD = ""
if len(SiteDIs_t) > 0:
CRD = ' -crd t'
elif len(SiteDIs_g) > 0:
CRD = ' -crd g'
elif len(SiteDIs_s) > 0:
CRD = ' -crd s'
CMD = 'eqarea_magic.py -f tmp_sites.txt -fsp tmp_specimens.txt -fsa tmp_samples.txt -flo tmp_locations.txt -sav -fmt ' + fmt + CRD
print(CMD)
info_log(CMD, loc)
os.system(CMD)
else:
if dir_data_found:
error_log(
'{} dec/inc pairs found, but no equal area plots were made'
.format(dir_data_found), loc, "equarea_magic.py")
#
print('-I- working on VGP map')
VGPs = pmag.get_dictitem(SiteDIs, 'vgp_lat', "",
'F') # are there any VGPs?
if len(VGPs) > 0: # YES!
CMD = 'vgpmap_magic.py -f tmp_sites.txt -prj moll -res c -sym ro 5 -sav -fmt png'
print(CMD)
info_log(CMD, loc, 'vgpmap_magic.py')
os.system(CMD)
else:
print('-I- No vgps found')
print('-I- Look for intensities')
# is there any intensity data?
if site_data:
if int_key in site_data[0].keys():
# old way, wasn't working right:
#CMD = 'magic_select.py -key ' + int_key + ' 0. has -F tmp1.txt -f tmp_sites.txt'
Selection = pmag.get_dictkey(site_data, int_key, dtype="f")
with open('intensities.txt', 'w') as out:
for rec in Selection:
if rec != 0:
out.write(str(rec * 1e6) + "\n")
histfile = 'LO:_' + loc + \
'_TY:_intensities_histogram:_.' + fmt
# maybe run histplot.main here instead, so you can return an error message
CMD = "histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f intensities.txt -F " + histfile
os.system(CMD)
info_log(CMD, loc)
print(CMD)
else:
print('-I- No intensities found')
else:
print('-I- No intensities found')
##
if hyst_file in filelist:
print('working on hysteresis', hyst_file)
data = spec_data
file_type = 'specimens'
hdata = pmag.get_dictitem(data, hyst_bcr_key, '', 'F')
hdata = pmag.get_dictitem(hdata, hyst_mr_key, '', 'F')
hdata = pmag.get_dictitem(hdata, hyst_ms_key, '', 'F')
# there are data for a dayplot
hdata = pmag.get_dictitem(hdata, hyst_bc_key, '', 'F')
if len(hdata) > 0:
CMD = 'dayplot_magic.py -f tmp_specimens.txt -sav -fmt ' + fmt
info_log(CMD, loc)
print(CMD)
else:
print('no hysteresis data found')
if aniso_file in filelist: # do anisotropy plots if possible
print('working on anisotropy', aniso_file)
data = spec_data
file_type = 'specimens'
# make sure there is some anisotropy data
if not data:
print('No anisotropy data found')
elif 'aniso_s' not in data[0]:
print('No anisotropy data found')
else:
# get specimen coordinates
if aniso_tilt_corr_key not in data[0]:
sdata = data
else:
sdata = pmag.get_dictitem(data,
aniso_tilt_corr_key,
'-1',
'T',
float_to_int=True)
# get specimen coordinates
gdata = pmag.get_dictitem(data,
aniso_tilt_corr_key,
'0',
'T',
float_to_int=True)
# get specimen coordinates
tdata = pmag.get_dictitem(data,
aniso_tilt_corr_key,
'100',
'T',
float_to_int=True)
CRD = ""
CMD = 'aniso_magic.py -x -B -sav -fmt ' + fmt
if len(sdata) > 3:
CMD = CMD + ' -crd s'
print(CMD)
info_log(CMD, loc)
os.system(CMD)
if len(gdata) > 3:
CMD = CMD + ' -crd g'
print(CMD)
info_log(CMD, loc)
os.system(CMD)
if len(tdata) > 3:
CMD = CMD + ' -crd t'
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# remove temporary files
for fname in glob.glob('tmp*.txt'):
os.remove(fname)
try:
os.remove('intensities.txt')
except FileNotFoundError:
pass
if loc_file in filelist:
data, file_type = pmag.magic_read(loc_file) # read in location data
print('-I- working on pole map')
poles = pmag.get_dictitem(data, 'pole_lat', "",
'F') # are there any poles?
poles = pmag.get_dictitem(poles, 'pole_lon', "",
'F') # are there any poles?
if len(poles) > 0: # YES!
CMD = 'polemap_magic.py -sav -fmt png'
print(CMD)
info_log(CMD, "all locations", "polemap_magic.py")
os.system(CMD)
else:
print('-I- No poles found')
def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available plots.
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
"""
dirlist=['./']
dir_path=os.getcwd()
names=os.listdir(dir_path)
for n in names:
if 'Location' in n:
dirlist.append(n)
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
else: fmt='png'
if '-f' in sys.argv:
ind=sys.argv.index("-f")
filelist=[sys.argv[ind+1]]
else:
filelist=os.listdir(dir_path)
if '-h' in sys.argv:
print main.__doc__
sys.exit()
for loc in dirlist:
print 'working on: ',loc
os.chdir(loc) # change working directories to each location
crd='s'
if 'er_samples.txt' in filelist: # find coordinate systems
samps,file_type=pmag.magic_read('er_samples.txt') # read in data
Srecs=pmag.get_dictitem(samps,'sample_azimuth','','F')# get all none blank sample orientations
if len(Srecs)>0:
crd='g'
if 'magic_measurements.txt' in filelist: # start with measurement data
print 'working on measurements data'
data,file_type=pmag.magic_read('magic_measurements.txt') # read in data
if loc == './': data=pmag.get_dictitem(data,'er_location_name','','T') # get all the blank location names from data file
# looking for zeq_magic possibilities
AFZrecs=pmag.get_dictitem(data,'magic_method_codes','LT-AF-Z','has')# get all none blank method codes
TZrecs=pmag.get_dictitem(data,'magic_method_codes','LT-T-Z','has')# get all none blank method codes
MZrecs=pmag.get_dictitem(data,'magic_method_codes','LT-M-Z','has')# get all none blank method codes
Drecs=pmag.get_dictitem(data,'measurement_dec','','F') # get all dec measurements
Irecs=pmag.get_dictitem(data,'measurement_inc','','F') # get all dec measurements
Mkeys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
for key in Mkeys:
Mrecs=pmag.get_dictitem(data,key,'','F') # get intensity data
if len(Mrecs)>0:break
if len(AFZrecs)>0 or len(TZrecs)>0 or len(MZrecs)>0 and len(Drecs)>0 and len(Irecs)>0 and len(Mrecs)>0: # potential for stepwise demag curves
print 'zeq_magic.py -fsp pmag_specimens.txt -sav -fmt '+fmt+' -crd '+crd
os.system('zeq_magic.py -sav -fmt '+fmt+' -crd '+crd )
# looking for thellier_magic possibilities
if len(pmag.get_dictitem(data,'magic_method_codes','LP-PI-TRM','has'))>0:
print 'thellier_magic.py -fsp pmag_specimens.txt -sav -fmt '+fmt
os.system('thellier_magic.py -sav -fmt '+fmt)
# looking for hysteresis possibilities
if len(pmag.get_dictitem(data,'magic_method_codes','LP-HYS','has'))>0: # find hyst experiments
print 'quick_hyst.py -sav -fmt '+fmt
os.system('quick_hyst.py -sav -fmt '+fmt)
if 'pmag_results.txt' in filelist: # start with measurement data
data,file_type=pmag.magic_read('pmag_results.txt') # read in data
print 'number of datapoints: ',len(data)
if loc == './': data=pmag.get_dictitem(data,'er_location_names',':','has') # get all the concatenated location names from data file
print 'number of datapoints: ',len(data) ,loc
print 'working on pmag_results directions'
SiteDIs=pmag.get_dictitem(data,'average_dec',"",'F') # find decs
print 'number of directions: ',len(SiteDIs)
SiteDIs=pmag.get_dictitem(SiteDIs,'average_inc',"",'F') # find decs and incs
print 'number of directions: ',len(SiteDIs)
SiteDIs=pmag.get_dictitem(SiteDIs,'data_type','i','has') # only individual results - not poles
print 'number of directions: ',len(SiteDIs)
SiteDIs_t=pmag.get_dictitem(SiteDIs,'tilt_correction','100','T')# tilt corrected coordinates
print 'number of directions: ',len(SiteDIs)
if len(SiteDIs_t)>0:
print 'eqarea_magic.py -sav -crd t -fmt '+fmt
os.system('eqarea_magic.py -sav -crd t -fmt '+fmt)
elif len(SiteDIs)>0 and 'tilt_correction' not in SiteDIs[0].keys():
print 'eqarea_magic.py -sav -fmt '+fmt
os.system('eqarea_magic.py -sav -fmt '+fmt)
else:
SiteDIs_g=pmag.get_dictitem(SiteDIs,'tilt_correction','0','T')# geographic coordinates
if len(SiteDIs_g)>0:
print 'eqarea_magic.py -sav -crd g -fmt '+fmt
os.system('eqarea_magic.py -sav -crd g -fmt '+fmt)
else:
SiteDIs_s=pmag.get_dictitem(SiteDIs,'tilt_correction','-1','T')# sample coordinates
if len(SiteDIs_s)>0:
print 'eqarea_magic.py -sav -crd s -fmt '+fmt
os.system('eqarea_magic.py -sav -crd s -fmt '+fmt)
else:
SiteDIs_x=pmag.get_dictitem(SiteDIs,'tilt_correction','','T')# no coordinates
if len(SiteDIs_x)>0:
print 'eqarea_magic.py -sav -fmt '+fmt
os.system('eqarea_magic.py -sav -fmt '+fmt)
print 'working on pmag_results VGP map'
VGPs=pmag.get_dictitem(SiteDIs,'vgp_lat',"",'F') # are there any VGPs?
if len(VGPs)>0: # YES!
os.system('vgpmap_magic.py -prj moll -res c -sym ro 5 -sav -fmt png')
print 'working on pmag_results intensities'
os.system('magic_select.py -f pmag_results.txt -key data_type i T -F tmp.txt')
os.system('magic_select.py -f tmp.txt -key average_int 0. has -F tmp1.txt')
os.system("grab_magic_key.py -f tmp1.txt -key average_int | awk '{print $1*1e6}' >tmp2.txt")
data,file_type=pmag.magic_read('tmp1.txt') # read in data
locations=pmag.get_dictkey(data,'er_location_names',"")
histfile='LO:_'+locations[0]+'_intensities_histogram:_.'+fmt
os.system("histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F " +histfile)
print "histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F " +histfile
os.system('rm tmp*.txt')
if 'rmag_hysteresis.txt' in filelist: # start with measurement data
print 'working on rmag_hysteresis'
data,file_type=pmag.magic_read('rmag_hysteresis.txt') # read in data
if loc == './': data=pmag.get_dictitem(data,'er_location_name','','T') # get all the blank location names from data file
hdata=pmag.get_dictitem(data,'hysteresis_bcr','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_mr_moment','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_ms_moment','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_bc','','F') # there are data for a dayplot
if len(hdata)>0:
print 'dayplot_magic.py -sav -fmt '+fmt
os.system('dayplot_magic.py -sav -fmt '+fmt)
#if 'er_sites.txt' in filelist: # start with measurement data
# print 'working on er_sites'
#os.system('basemap_magic.py -sav -fmt '+fmt)
if 'rmag_anisotropy.txt' in filelist: # do anisotropy plots if possible
print 'working on rmag_anisotropy'
data,file_type=pmag.magic_read('rmag_anisotropy.txt') # read in data
if loc == './': data=pmag.get_dictitem(data,'er_location_name','','T') # get all the blank location names from data file
sdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','-1','T') # get specimen coordinates
gdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','0','T') # get specimen coordinates
tdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','100','T') # get specimen coordinates
if len(sdata)>3:
print 'aniso_magic.py -x -B -crd s -sav -fmt '+fmt
os.system('aniso_magic.py -x -B -crd s -sav -fmt '+fmt)
if len(gdata)>3:
os.system('aniso_magic.py -x -B -crd g -sav -fmt '+fmt)
if len(tdata)>3:
os.system('aniso_magic.py -x -B -crd t -sav -fmt '+fmt)
if loc!='./':os.chdir('..') # change working directories to each location
def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available plots.
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
"""
dirlist = ['./']
dir_path = os.getcwd()
names = os.listdir(dir_path)
for n in names:
if 'Location' in n:
dirlist.append(n)
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
else:
fmt = 'png'
if '-f' in sys.argv:
ind = sys.argv.index("-f")
filelist = [sys.argv[ind + 1]]
else:
filelist = os.listdir(dir_path)
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
for loc in dirlist:
print('working on: ', loc)
os.chdir(loc) # change working directories to each location
crd = 's'
if 'er_samples.txt' in filelist: # find coordinate systems
samps, file_type = pmag.magic_read(
'er_samples.txt') # read in data
Srecs = pmag.get_dictitem(
samps, 'sample_azimuth', '',
'F') # get all none blank sample orientations
if len(Srecs) > 0:
crd = 'g'
if 'magic_measurements.txt' in filelist: # start with measurement data
print('working on measurements data')
data, file_type = pmag.magic_read(
'magic_measurements.txt') # read in data
if loc == './':
data = pmag.get_dictitem(
data, 'er_location_name', '',
'T') # get all the blank location names from data file
# looking for zeq_magic possibilities
AFZrecs = pmag.get_dictitem(
data, 'magic_method_codes', 'LT-AF-Z',
'has') # get all none blank method codes
TZrecs = pmag.get_dictitem(
data, 'magic_method_codes', 'LT-T-Z',
'has') # get all none blank method codes
MZrecs = pmag.get_dictitem(
data, 'magic_method_codes', 'LT-M-Z',
'has') # get all none blank method codes
Drecs = pmag.get_dictitem(data, 'measurement_dec', '',
'F') # get all dec measurements
Irecs = pmag.get_dictitem(data, 'measurement_inc', '',
'F') # get all dec measurements
Mkeys = [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass'
]
for key in Mkeys:
Mrecs = pmag.get_dictitem(data, key, '',
'F') # get intensity data
if len(Mrecs) > 0: break
if len(AFZrecs) > 0 or len(TZrecs) > 0 or len(MZrecs) > 0 and len(
Drecs) > 0 and len(Irecs) > 0 and len(
Mrecs) > 0: # potential for stepwise demag curves
print('zeq_magic.py -fsp pmag_specimens.txt -sav -fmt ' + fmt +
' -crd ' + crd)
os.system('zeq_magic.py -sav -fmt ' + fmt + ' -crd ' + crd)
# looking for thellier_magic possibilities
if len(
pmag.get_dictitem(data, 'magic_method_codes', 'LP-PI-TRM',
'has')) > 0:
print('thellier_magic.py -fsp pmag_specimens.txt -sav -fmt ' +
fmt)
os.system('thellier_magic.py -sav -fmt ' + fmt)
# looking for hysteresis possibilities
if len(
pmag.get_dictitem(data, 'magic_method_codes', 'LP-HYS',
'has')) > 0: # find hyst experiments
print('quick_hyst.py -sav -fmt ' + fmt)
os.system('quick_hyst.py -sav -fmt ' + fmt)
if 'pmag_results.txt' in filelist: # start with measurement data
data, file_type = pmag.magic_read(
'pmag_results.txt') # read in data
print('number of datapoints: ', len(data))
if loc == './':
data = pmag.get_dictitem(
data, 'er_location_names', ':', 'has'
) # get all the concatenated location names from data file
print('number of datapoints: ', len(data), loc)
print('working on pmag_results directions')
SiteDIs = pmag.get_dictitem(data, 'average_dec', "",
'F') # find decs
print('number of directions: ', len(SiteDIs))
SiteDIs = pmag.get_dictitem(SiteDIs, 'average_inc', "",
'F') # find decs and incs
print('number of directions: ', len(SiteDIs))
SiteDIs = pmag.get_dictitem(
SiteDIs, 'data_type', 'i',
'has') # only individual results - not poles
print('number of directions: ', len(SiteDIs))
SiteDIs_t = pmag.get_dictitem(SiteDIs, 'tilt_correction', '100',
'T') # tilt corrected coordinates
print('number of directions: ', len(SiteDIs))
if len(SiteDIs_t) > 0:
print('eqarea_magic.py -sav -crd t -fmt ' + fmt)
os.system('eqarea_magic.py -sav -crd t -fmt ' + fmt)
elif len(SiteDIs) > 0 and 'tilt_correction' not in SiteDIs[0].keys(
):
print('eqarea_magic.py -sav -fmt ' + fmt)
os.system('eqarea_magic.py -sav -fmt ' + fmt)
else:
SiteDIs_g = pmag.get_dictitem(SiteDIs, 'tilt_correction', '0',
'T') # geographic coordinates
if len(SiteDIs_g) > 0:
print('eqarea_magic.py -sav -crd g -fmt ' + fmt)
os.system('eqarea_magic.py -sav -crd g -fmt ' + fmt)
else:
SiteDIs_s = pmag.get_dictitem(SiteDIs, 'tilt_correction',
'-1',
'T') # sample coordinates
if len(SiteDIs_s) > 0:
print('eqarea_magic.py -sav -crd s -fmt ' + fmt)
os.system('eqarea_magic.py -sav -crd s -fmt ' + fmt)
else:
SiteDIs_x = pmag.get_dictitem(SiteDIs,
'tilt_correction', '',
'T') # no coordinates
if len(SiteDIs_x) > 0:
print('eqarea_magic.py -sav -fmt ' + fmt)
os.system('eqarea_magic.py -sav -fmt ' + fmt)
print('working on pmag_results VGP map')
VGPs = pmag.get_dictitem(SiteDIs, 'vgp_lat', "",
'F') # are there any VGPs?
if len(VGPs) > 0: # YES!
os.system(
'vgpmap_magic.py -prj moll -res c -sym ro 5 -sav -fmt png')
print('working on pmag_results intensities')
os.system(
'magic_select.py -f pmag_results.txt -key data_type i T -F tmp.txt'
)
os.system(
'magic_select.py -f tmp.txt -key average_int 0. has -F tmp1.txt'
)
os.system(
"grab_magic_key.py -f tmp1.txt -key average_int | awk '{print $1*1e6}' >tmp2.txt"
)
data, file_type = pmag.magic_read('tmp1.txt') # read in data
locations = pmag.get_dictkey(data, 'er_location_names', "")
histfile = 'LO:_' + locations[0] + '_intensities_histogram:_.' + fmt
os.system(
"histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F "
+ histfile)
print(
"histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F "
+ histfile)
os.system('rm tmp*.txt')
if 'rmag_hysteresis.txt' in filelist: # start with measurement data
print('working on rmag_hysteresis')
data, file_type = pmag.magic_read(
'rmag_hysteresis.txt') # read in data
if loc == './':
data = pmag.get_dictitem(
data, 'er_location_name', '',
'T') # get all the blank location names from data file
hdata = pmag.get_dictitem(data, 'hysteresis_bcr', '', 'F')
hdata = pmag.get_dictitem(hdata, 'hysteresis_mr_moment', '', 'F')
hdata = pmag.get_dictitem(hdata, 'hysteresis_ms_moment', '', 'F')
hdata = pmag.get_dictitem(hdata, 'hysteresis_bc', '',
'F') # there are data for a dayplot
if len(hdata) > 0:
print('dayplot_magic.py -sav -fmt ' + fmt)
os.system('dayplot_magic.py -sav -fmt ' + fmt)
#if 'er_sites.txt' in filelist: # start with measurement data
# print 'working on er_sites'
#os.system('basemap_magic.py -sav -fmt '+fmt)
if 'rmag_anisotropy.txt' in filelist: # do anisotropy plots if possible
print('working on rmag_anisotropy')
data, file_type = pmag.magic_read(
'rmag_anisotropy.txt') # read in data
if loc == './':
data = pmag.get_dictitem(
data, 'er_location_name', '',
'T') # get all the blank location names from data file
sdata = pmag.get_dictitem(data, 'anisotropy_tilt_correction', '-1',
'T') # get specimen coordinates
gdata = pmag.get_dictitem(data, 'anisotropy_tilt_correction', '0',
'T') # get specimen coordinates
tdata = pmag.get_dictitem(data, 'anisotropy_tilt_correction',
'100', 'T') # get specimen coordinates
if len(sdata) > 3:
print('aniso_magic.py -x -B -crd s -sav -fmt ' + fmt)
os.system('aniso_magic.py -x -B -crd s -sav -fmt ' + fmt)
if len(gdata) > 3:
os.system('aniso_magic.py -x -B -crd g -sav -fmt ' + fmt)
if len(tdata) > 3:
os.system('aniso_magic.py -x -B -crd t -sav -fmt ' + fmt)
if loc != './':
os.chdir('..') # change working directories to each location
def main():
"""
NAME
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav save plots and quit
"""
fmt, plot = "svg", 0
FIG = {} # plot dictionary
FIG["lowrie"] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG["lowrie"], 6, 6)
norm = 1 # default is to normalize by maximum axis
if len(sys.argv) > 1:
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-N" in sys.argv:
norm = 0 # don't normalize
if "-sav" in sys.argv:
plot = 1 # don't normalize
if "-fmt" in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if "-f" in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print main.__doc__
print "you must supply a file name"
sys.exit()
else:
print main.__doc__
print "you must supply a file name"
sys.exit()
data = open(in_file).readlines() # open the SIO format file
PmagRecs = [] # set up a list for the results
keys = ["specimen", "treatment", "csd", "M", "dec", "inc"]
for line in data:
PmagRec = {}
rec = line.replace("\n", "").split()
for k in range(len(keys)):
PmagRec[keys[k]] = rec[k]
PmagRecs.append(PmagRec)
specs = pmag.get_dictkey(PmagRecs, "specimen", "")
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print spc
specdata = pmag.get_dictitem(PmagRecs, "specimen", spc, "T") # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([float(dat["dec"]), float(dat["inc"]), float(dat["M"]) * 1e-3])
Temps.append(float(dat["treatment"]))
carts = pmag.dir2cart(DIMs).transpose()
# if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm == 1: # want to normalize
nrm = DIMs[0][2] # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1.0 # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[0]) / nrm, sym="r-")
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[0]) / nrm, sym="ro") # X direction
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[1]) / nrm, sym="c-")
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[1]) / nrm, sym="cs") # Y direction
pmagplotlib.plotXY(FIG["lowrie"], Temps, abs(carts[2]) / nrm, sym="k-")
pmagplotlib.plotXY(
FIG["lowrie"], Temps, abs(carts[2]) / nrm, sym="k^", title=spc, xlab=xlab, ylab=ylab
) # Z direction
files = {"lowrie": "lowrie:_" + spc + "_." + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = raw_input("S[a]ve figure? [q]uit, <return> to continue ")
if ans == "a":
pmagplotlib.saveP(FIG, files)
elif ans == "q":
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG["lowrie"])
def main():
"""
NAME
sites_locations.py
DESCRIPTION
reads in er_sites.txt file and finds all locations and bounds of locations
outputs er_locations.txt file
SYNTAX
sites_locations.py [command line options]
OPTIONS
-h prints help message and quits
-f: specimen input er_sites format file, default is "er_sites.txt"
-F: locations table: default is "er_locations.txt"
"""
# set defaults
site_file = "er_sites.txt"
loc_file = "er_locations.txt"
Names, user = [], "unknown"
Done = []
version_num = pmag.get_version()
args = sys.argv
dir_path = '.'
# get command line stuff
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")
site_file = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
loc_file = args[ind + 1]
#
site_file = dir_path + '/' + site_file
loc_file = dir_path + '/' + loc_file
Sites, file_type = pmag.magic_read(site_file)
if file_type != 'er_sites':
print(file_type)
print(file_type, "This is not a valid er_sites file ")
sys.exit()
# read in site data
#
LocNames, Locations = [], []
for site in Sites:
if site['er_location_name'] not in LocNames: # new location name
LocNames.append(site['er_location_name'])
sites_locs = pmag.get_dictitem(Sites, 'er_location_name',
site['er_location_name'],
'T') # get all sites for this loc
lats = pmag.get_dictkey(sites_locs, 'site_lat',
'f') # get all the latitudes as floats
lons = pmag.get_dictkey(sites_locs, 'site_lon',
'f') # get all the longitudes as floats
LocRec = {
'er_citation_names': 'This study',
'er_location_name': site['er_location_name'],
'location_type': ''
}
LocRec['location_begin_lat'] = str(min(lats))
LocRec['location_end_lat'] = str(max(lats))
LocRec['location_begin_lon'] = str(min(lons))
LocRec['location_end_lon'] = str(max(lons))
Locations.append(LocRec)
if len(Locations) > 0:
pmag.magic_write(loc_file, Locations, "er_locations")
print("Locations written to: ", loc_file)
def main():
"""
NAME
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav save plots and quit
"""
fmt, plot = 'svg', 0
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv:
norm = 0 # don't normalize
if '-sav' in sys.argv:
plot = 1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
data = pmag.open_file(in_file)
PmagRecs = [] # set up a list for the results
keys = ['specimen', 'treatment', 'csd', 'M', 'dec', 'inc']
for line in data:
PmagRec = {}
rec = line.replace('\n', '').split()
for k in range(len(keys)):
PmagRec[keys[k]] = rec[k]
PmagRecs.append(PmagRec)
specs = pmag.get_dictkey(PmagRecs, 'specimen', '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(PmagRecs, 'specimen', spc,
'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append(
[float(dat['dec']),
float(dat['inc']),
float(dat['M']) * 1e-3])
Temps.append(float(dat['treatment']))
carts = pmag.dir2cart(DIMs).transpose()
# if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k^',
title=spc,
xlab=xlab,
ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.saveP(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available data and makes plots
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
# reset log files
for fname in ['log.txt', 'errors.txt']:
f = os.path.join(os.getcwd(), fname)
if os.path.exists(f):
os.remove(f)
image_recs = []
dirlist = ['./']
dir_path = os.getcwd()
#
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
else:
fmt = 'png'
if '-f' in sys.argv:
ind = sys.argv.index("-f")
filelist = [sys.argv[ind + 1]]
else:
filelist = os.listdir(dir_path)
## initialize some variables
samp_file = 'samples.txt'
meas_file = 'measurements.txt'
#loc_key = 'location'
loc_file = 'locations.txt'
method_key = 'method_codes'
dec_key = 'dir_dec'
inc_key = 'dir_inc'
tilt_corr_key = "dir_tilt_correction"
aniso_tilt_corr_key = "aniso_tilt_correction"
hyst_bcr_key = "hyst_bcr"
hyst_mr_key = "hyst_mr_moment"
hyst_ms_key = "hyst_ms_moment"
hyst_bc_key = "hyst_bc"
Mkeys = ['magnitude', 'magn_moment', 'magn_volume', 'magn_mass']
results_file = 'sites.txt'
hyst_file = 'specimens.txt'
aniso_file = 'specimens.txt'
# create contribution and propagate data throughout
full_con = cb.Contribution()
full_con.propagate_location_to_measurements()
full_con.propagate_location_to_specimens()
full_con.propagate_location_to_samples()
if not full_con.tables:
print('-E- No MagIC tables could be found in this directory')
error_log("No MagIC tables found")
return
# try to get the contribution id for error logging
con_id = ""
if 'contribution' in full_con.tables:
if 'id' in full_con.tables['contribution'].df.columns:
con_id = full_con.tables['contribution'].df.iloc[0]['id']
# check to see if propagation worked, otherwise you can't plot by location
lowest_table = None
for table in full_con.ancestry:
if table in full_con.tables:
lowest_table = table
break
do_full_directory = False
# check that locations propagated down to the lowest table in the contribution
if 'location' in full_con.tables[lowest_table].df.columns:
if 'locations' not in full_con.tables:
info_log(
'location names propagated to {}, but could not be validated'.
format(lowest_table))
# are there any locations in the lowest table?
elif not all(full_con.tables[lowest_table].df['location'].isnull()):
locs = full_con.tables['locations'].df.index.unique()
lowest_locs = full_con.tables[lowest_table].df['location'].unique()
incorrect_locs = set(lowest_locs).difference(set(locs))
# are they actual locations?
if not incorrect_locs:
info_log(
'location names propagated to {}'.format(lowest_table))
else:
do_full_directory = True
error_log(
'location names did not propagate fully to {} table (looks like there are some naming inconsistencies between tables)'
.format(lowest_table),
con_id=con_id)
else:
do_full_directory = True
error_log(
'could not propagate location names down to {} table'.format(
lowest_table),
con_id=con_id)
else:
do_full_directory = True
error_log('could not propagate location names down to {} table'.format(
lowest_table),
con_id=con_id)
all_data = {}
all_data['measurements'] = full_con.tables.get('measurements', None)
all_data['specimens'] = full_con.tables.get('specimens', None)
all_data['samples'] = full_con.tables.get('samples', None)
all_data['sites'] = full_con.tables.get('sites', None)
all_data['locations'] = full_con.tables.get('locations', None)
if 'locations' in full_con.tables:
locations = full_con.tables['locations'].df.index.unique()
else:
locations = ['']
dirlist = [
loc for loc in locations if cb.not_null(loc, False) and loc != 'nan'
]
if not dirlist:
dirlist = ["./"]
if do_full_directory:
dirlist = ["./"]
# plot the whole contribution as one location
if dirlist == ["./"]:
error_log('plotting the entire contribution as one location',
con_id=con_id)
for fname in os.listdir("."):
if fname.endswith(".txt"):
shutil.copy(fname, "tmp_" + fname)
# if possible, go through all data by location
# use tmp_*.txt files to separate out by location
for loc in dirlist:
print('\nworking on: ', loc)
def get_data(dtype, loc_name):
"""
Extract data of type dtype for location loc_name.
Write tmp_dtype.txt files if possible.
"""
if cb.not_null(all_data[dtype], False):
data_container = all_data[dtype]
if loc_name == "./":
data_df = data_container.df
else:
# awkward workaround for chars like "(" and "?" that break in regex
try:
data_df = data_container.df[data_container.df[
'location'].astype(str).str.contains(loc_name,
na=False)]
except: #sre_constants.error:
data_df = data_container.df[
data_container.df['location'] == loc_name]
data = data_container.convert_to_pmag_data_list(df=data_df)
res = data_container.write_magic_file(
'tmp_{}.txt'.format(dtype), df=data_df)
if not res:
return [], []
return data, data_df
return [], []
meas_data, meas_df = get_data('measurements', loc)
spec_data, spec_df = get_data('specimens', loc)
samp_data, samp_df = get_data('samples', loc)
site_data, site_df = get_data('sites', loc)
loc_data, loc_df = get_data('locations', loc)
con = cb.Contribution(read_tables=[])
con.tables['measurements'] = cb.MagicDataFrame(df=meas_df,
dtype="measurements")
con.tables['specimens'] = cb.MagicDataFrame(df=spec_df,
dtype="specimens")
con.tables['samples'] = cb.MagicDataFrame(df=samp_df, dtype="samples")
con.tables['sites'] = cb.MagicDataFrame(df=site_df, dtype="sites")
con.tables['locations'] = cb.MagicDataFrame(df=loc_df,
dtype="locations")
if loc == "./": # if you can't sort by location, do everything together
con = full_con
try:
meas_data = con.tables[
'measurements'].convert_to_pmag_data_list()
except KeyError:
meas_data = None
try:
spec_data = con.tables['specimens'].convert_to_pmag_data_list()
except KeyError:
spec_data = None
try:
samp_data = con.tables['samples'].convert_to_pmag_data_list()
except KeyError:
samp_data = None
try:
site_data = con.tables['sites'].convert_to_pmag_data_list()
except KeyError:
site_data = None
crd = 's'
if 'samples' in con.tables:
if 'azimuth' in con.tables['samples'].df.columns:
if any(con.tables['samples'].df['azimuth'].dropna()):
crd = 'g'
if crd == 's':
print('using specimen coordinates')
else:
print('using geographic coordinates')
if meas_file in filelist and meas_data: # start with measurement data
print('working on plotting measurements data')
data = meas_data
file_type = 'measurements'
# looking for zeq_magic possibilities
# get all non blank method codes
AFZrecs = pmag.get_dictitem(data, method_key, 'LT-AF-Z', 'has')
# get all non blank method codes
TZrecs = pmag.get_dictitem(data, method_key, 'LT-T-Z', 'has')
# get all non blank method codes
MZrecs = pmag.get_dictitem(data, method_key, 'LT-M-Z', 'has')
# get all dec measurements
Drecs = pmag.get_dictitem(data, dec_key, '', 'F')
# get all inc measurements
Irecs = pmag.get_dictitem(data, inc_key, '', 'F')
for key in Mkeys:
Mrecs = pmag.get_dictitem(data, key, '',
'F') # get intensity data
if len(Mrecs) > 0:
break
# potential for stepwise demag curves
if len(AFZrecs) > 0 or len(TZrecs) > 0 or len(MZrecs) > 0 and len(
Drecs) > 0 and len(Irecs) > 0 and len(Mrecs) > 0:
#CMD = 'zeq_magic.py -f tmp_measurements.txt -fsp tmp_specimens.txt -fsa tmp_samples.txt -fsi tmp_sites.txt -sav -fmt ' + fmt + ' -crd ' + crd + " -new"
CMD = "ipmag.zeq_magic(crd={}, n_plots='all', contribution={}, image_records=True)".format(
crd, con)
print(CMD)
info_log(CMD, loc)
res, outfiles, zeq_images = ipmag.zeq_magic(crd=crd,
n_plots='all',
contribution=con,
image_records=True)
image_recs.extend(zeq_images)
# looking for thellier_magic possibilities
if len(pmag.get_dictitem(data, method_key, 'LP-PI-TRM',
'has')) > 0:
#CMD = 'thellier_magic.py -f tmp_measurements.txt -fsp tmp_specimens.txt -sav -fmt ' + fmt
CMD = "ipmag.thellier_magic(n_specs='all', fmt='png', contribution={}, image_records=True)".format(
con)
print(CMD)
info_log(CMD, loc)
res, outfiles, thellier_images = ipmag.thellier_magic(
n_specs='all',
fmt="png",
contribution=con,
image_records=True)
image_recs.extend(thellier_images)
# looking for hysteresis possibilities
if len(pmag.get_dictitem(data, method_key, 'LP-HYS',
'has')) > 0: # find hyst experiments
# check for reqd columns
missing = check_for_reqd_cols(data, ['treat_temp'])
if missing:
error_log(
'LP-HYS method code present, but required column(s) [{}] missing'
.format(", ".join(missing)),
loc,
"quick_hyst.py",
con_id=con_id)
else:
#CMD = 'quick_hyst.py -f tmp_measurements.txt -sav -fmt ' + fmt
CMD = "ipmag.quick_hyst(fmt='png', n_plots='all', contribution={}, image_records=True)".format(
con)
print(CMD)
info_log(CMD, loc)
res, outfiles, quick_hyst_recs = ipmag.quick_hyst(
fmt="png",
n_plots='all',
contribution=con,
image_records=True)
image_recs.extend(quick_hyst_recs)
# equal area plots of directional data
# at measurement level (by specimen)
if data:
missing = check_for_reqd_cols(data, ['dir_dec', 'dir_inc'])
if not missing:
#CMD = "eqarea_magic.py -f tmp_measurements.txt -obj spc -sav -no-tilt -fmt " + fmt
CMD = "ipmag.eqarea_magic(fmt='png', n_plots='all', ignore_tilt=True, plot_by='spc', contribution={}, source_table='measurements', image_records=True)".format(
con)
print(CMD)
info_log(CMD, loc, "eqarea_magic.py")
res, outfiles, eqarea_spc_images = ipmag.eqarea_magic(
fmt="png",
n_plots='all',
ignore_tilt=True,
plot_by="spc",
contribution=con,
source_table="measurements",
image_records=True)
image_recs.extend(eqarea_spc_images)
else:
if VERBOSE:
print('-I- No measurement data found')
# site data
if results_file in filelist and site_data:
print('-I- result file found', results_file)
data = site_data
file_type = 'sites'
print('-I- working on site directions')
print('number of datapoints: ', len(data), loc)
dec_key = 'dir_dec'
inc_key = 'dir_inc'
int_key = 'int_abs'
SiteDIs = pmag.get_dictitem(data, dec_key, "", 'F') # find decs
SiteDIs = pmag.get_dictitem(SiteDIs, inc_key, "",
'F') # find decs and incs
dir_data_found = len(SiteDIs)
print('{} Dec/inc pairs found'.format(dir_data_found))
if SiteDIs:
# then convert tilt_corr_key to correct format
old_SiteDIs = SiteDIs
SiteDIs = []
for rec in old_SiteDIs:
if tilt_corr_key not in rec:
rec[tilt_corr_key] = "0"
# make sure tilt_corr_key is a correct format
try:
rec[tilt_corr_key] = str(int(float(
rec[tilt_corr_key])))
except ValueError:
rec[tilt_corr_key] = "0"
SiteDIs.append(rec)
print('number of individual directions: ', len(SiteDIs))
# tilt corrected coordinates
SiteDIs_t = pmag.get_dictitem(SiteDIs,
tilt_corr_key,
'100',
'T',
float_to_int=True)
print('number of tilt corrected directions: ', len(SiteDIs_t))
SiteDIs_g = pmag.get_dictitem(
SiteDIs, tilt_corr_key, '0', 'T',
float_to_int=True) # geographic coordinates
print('number of geographic directions: ', len(SiteDIs_g))
SiteDIs_s = pmag.get_dictitem(
SiteDIs, tilt_corr_key, '-1', 'T',
float_to_int=True) # sample coordinates
print('number of sample directions: ', len(SiteDIs_s))
SiteDIs_x = pmag.get_dictitem(SiteDIs, tilt_corr_key, '',
'T') # no coordinates
print('number of no coordinates directions: ', len(SiteDIs_x))
if len(SiteDIs_t) > 0 or len(SiteDIs_g) > 0 or len(
SiteDIs_s) > 0 or len(SiteDIs_x) > 0:
CRD = ""
if len(SiteDIs_t) > 0:
CRD = ' -crd t'
crd = "t"
elif len(SiteDIs_g) > 0:
CRD = ' -crd g'
crd = "g"
elif len(SiteDIs_s) > 0:
CRD = ' -crd s'
crd = "s"
#CMD = 'eqarea_magic.py -f tmp_sites.txt -fsp tmp_specimens.txt -fsa tmp_samples.txt -flo tmp_locations.txt -sav -fmt ' + fmt + CRD
CMD = "ipmag.eqarea_magic(crd={}, fmt='png', n_plots='all', contribution={}, source_table='sites')".format(
crd, con)
print(CMD)
info_log(CMD, loc)
res, outfiles, eqarea_site_recs = ipmag.eqarea_magic(
crd=crd,
fmt="png",
n_plots='all',
contribution=con,
source_table="sites",
image_records=True)
image_recs.extend(eqarea_site_recs)
else:
if dir_data_found:
error_log(
'{} dec/inc pairs found, but no equal area plots were made'
.format(dir_data_found),
loc,
"equarea_magic.py",
con_id=con_id)
#
print('-I- working on VGP map')
VGPs = pmag.get_dictitem(SiteDIs, 'vgp_lat', "",
'F') # are there any VGPs?
if len(VGPs) > 0: # YES!
#CMD = 'vgpmap_magic.py -f tmp_sites.txt -prj moll -res c -sym ro 5 -sav -fmt png'
CMD = "ipmag.vgpmap_magic(proj='moll', sym='ro', size=5, fmt='png', contribution={})".format(
con)
print(CMD)
info_log(CMD, loc, 'vgpmap_magic.py')
res, outfiles, vgpmap_recs = ipmag.vgpmap_magic(
proj='moll',
sym='ro',
size=5,
fmt="png",
contribution=con,
image_records=True)
image_recs.extend(vgpmap_recs)
else:
print('-I- No vgps found')
print('-I- Look for intensities')
# is there any intensity data?
if site_data:
if int_key in site_data[0].keys():
# old way, wasn't working right:
#CMD = 'magic_select.py -key ' + int_key + ' 0. has -F tmp1.txt -f tmp_sites.txt'
Selection = pmag.get_dictkey(site_data, int_key, dtype="f")
selection = [i * 1e6 for i in Selection if i != 0]
loc = loc.replace(" ", "_")
if loc == "./":
loc_name = ""
else:
loc_name = loc
histfile = 'LO:_' + loc_name + \
'_TY:_intensities_histogram:_.' + fmt
CMD = "histplot.py -twin -b 1 -xlab 'Intensity (uT)' -sav -f intensities.txt -F " + histfile
CMD = "ipmag.histplot(data=selection, outfile=histfile, xlab='Intensity (uT)', binsize=1, norm=-1, save_plots=True)".format(
histfile)
info_log(CMD, loc)
print(CMD)
ipmag.histplot(data=selection,
outfile=histfile,
xlab="Intensity (uT)",
binsize=1,
norm=-1,
save_plots=True)
histplot_rec = {
'file': histfile,
'type': 'Other',
'title': 'Intensity histogram',
'software_packages': version.version,
'keywords': "",
'timestamp': datetime.date.today().isoformat()
}
image_recs.append(histplot_rec)
else:
print('-I- No intensities found')
else:
print('-I- No intensities found')
##
if hyst_file in filelist and spec_data:
print('working on hysteresis', hyst_file)
data = spec_data
file_type = 'specimens'
hdata = pmag.get_dictitem(data, hyst_bcr_key, '', 'F')
hdata = pmag.get_dictitem(hdata, hyst_mr_key, '', 'F')
hdata = pmag.get_dictitem(hdata, hyst_ms_key, '', 'F')
# there are data for a dayplot
hdata = pmag.get_dictitem(hdata, hyst_bc_key, '', 'F')
if len(hdata) > 0:
CMD = "ipmag.dayplot_magic(save=True, fmt='png', contribution={}, image_records=True)".format(
con)
info_log(CMD, loc)
print(CMD)
res, outfiles, dayplot_recs = ipmag.dayplot_magic(
save=True, fmt='png', contribution=con, image_records=True)
image_recs.extend(dayplot_recs)
else:
print('no hysteresis data found')
if aniso_file in filelist and spec_data: # do anisotropy plots if possible
print('working on anisotropy', aniso_file)
data = spec_data
file_type = 'specimens'
# make sure there is some anisotropy data
if not data:
print('No anisotropy data found')
elif 'aniso_s' not in data[0]:
print('No anisotropy data found')
else:
# get specimen coordinates
if aniso_tilt_corr_key not in data[0]:
sdata = data
else:
sdata = pmag.get_dictitem(data,
aniso_tilt_corr_key,
'-1',
'T',
float_to_int=True)
# get specimen coordinates
gdata = pmag.get_dictitem(data,
aniso_tilt_corr_key,
'0',
'T',
float_to_int=True)
# get specimen coordinates
tdata = pmag.get_dictitem(data,
aniso_tilt_corr_key,
'100',
'T',
float_to_int=True)
if len(sdata) > 3:
CMD = "ipmag.aniso_magic(iboot=0, ihext=1, crd='s', fmt='png', contribution={})".format(
con)
print(CMD)
info_log(CMD, loc)
res, files, aniso_recs = ipmag.aniso_magic(
iboot=0,
ihext=1,
crd="s",
fmt="png",
contribution=con,
image_records=True)
image_recs.extend(aniso_recs)
if len(gdata) > 3:
CMD = "ipmag.aniso_magic(iboot=0, ihext=1, crd='g', fmt='png', contribution={})".format(
con)
print(CMD)
info_log(CMD, loc)
res, files, aniso_recs = ipmag.aniso_magic(
iboot=0,
ihext=1,
crd="g",
fmt="png",
contribution=con,
image_records=True)
image_recs.extend(aniso_recs)
if len(tdata) > 3:
CMD = "ipmag.aniso_magic(iboot=0, ihext=1, crd='g', fmt='png', contribution={})".format(
con)
print(CMD)
info_log(CMD, loc)
res, files, aniso_recs = ipmag.aniso_magic(
iboot=0,
ihext=1,
crd="t",
fmt="png",
contribution=con,
image_records=True)
image_recs.extend(aniso_recs)
# remove temporary files
for fname in glob.glob('tmp*.txt'):
os.remove(fname)
# now we need full contribution data
if loc_file in filelist and loc_data:
#data, file_type = pmag.magic_read(loc_file) # read in location data
data = loc_data
print('-I- working on pole map')
poles = pmag.get_dictitem(data, 'pole_lat', "",
'F') # are there any poles?
poles = pmag.get_dictitem(poles, 'pole_lon', "",
'F') # are there any poles?
if len(poles) > 0: # YES!
CMD = 'polemap_magic.py -sav -fmt png -rev gv 40'
CMD = 'ipmag.polemap_magic(flip=True, rsym="gv", rsymsize=40, fmt="png", contribution={})'.format(
full_con)
print(CMD)
info_log(CMD, "all locations", "polemap_magic.py")
res, outfiles, polemap_recs = ipmag.polemap_magic(
flip=True,
rsym="gv",
rsymsize=40,
fmt="png",
contribution=full_con,
image_records=True)
image_recs.extend(polemap_recs)
else:
print('-I- No poles found')
if image_recs:
new_image_file = os.path.join(dir_path, 'new_images.txt')
old_image_file = os.path.join(dir_path, 'images.txt')
pmag.magic_write(new_image_file, image_recs, 'images')
if os.path.exists(old_image_file):
ipmag.combine_magic([old_image_file, new_image_file],
outfile=old_image_file,
magic_table="images",
dir_path=dir_path)
else:
os.rename(new_image_file, old_image_file)
if set_env.isServer:
thumbnails.make_thumbnails(dir_path)
def main():
"""
NAME
sites_locations.py
DESCRIPTION
reads in er_sites.txt file and finds all locations and bounds of locations
outputs er_locations.txt file
SYNTAX
sites_locations.py [command line options]
OPTIONS
-h prints help message and quits
-f: specimen input er_sites format file, default is "er_sites.txt"
-F: locations table: default is "er_locations.txt"
"""
# set defaults
site_file="er_sites.txt"
loc_file="er_locations.txt"
Names,user=[],"unknown"
Done=[]
version_num=pmag.get_version()
args=sys.argv
dir_path='.'
# get command line stuff
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")
site_file=args[ind+1]
if '-F' in args:
ind=args.index("-F")
loc_file=args[ind+1]
#
site_file=dir_path+'/'+site_file
loc_file=dir_path+'/'+loc_file
Sites,file_type=pmag.magic_read(site_file)
if file_type != 'er_sites':
print(file_type)
print(file_type,"This is not a valid er_sites file ")
sys.exit()
# read in site data
#
LocNames,Locations=[],[]
for site in Sites:
if site['er_location_name'] not in LocNames: # new location name
LocNames.append(site['er_location_name'])
sites_locs=pmag.get_dictitem(Sites,'er_location_name',site['er_location_name'],'T') # get all sites for this loc
lats=pmag.get_dictkey(sites_locs,'site_lat','f') # get all the latitudes as floats
lons=pmag.get_dictkey(sites_locs,'site_lon','f') # get all the longitudes as floats
LocRec={'er_citation_names':'This study','er_location_name':site['er_location_name'],'location_type':''}
LocRec['location_begin_lat']=str(min(lats))
LocRec['location_end_lat']=str(max(lats))
LocRec['location_begin_lon']=str(min(lons))
LocRec['location_end_lon']=str(max(lons))
Locations.append(LocRec)
if len(Locations)>0:
pmag.magic_write(loc_file,Locations,"er_locations")
print("Locations written to: ",loc_file)
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes magic_measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
"""
fmt,plot='svg',0
FIG={} # plot dictionary
FIG['lowrie']=1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'],6,6)
norm=1 # default is to normalize by maximum axis
in_file,dir_path='magic_measurements.txt','.'
if len(sys.argv)>1:
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 '-N' in sys.argv: norm=0 # don't normalize
if '-sav' in sys.argv: plot=1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-f' in sys.argv: # sets input filename
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
else:
print main.__doc__
print 'you must supply a file name'
sys.exit()
in_file=dir_path+'/'+in_file
print in_file
PmagRecs,file_type=pmag.magic_read(in_file)
if file_type!="magic_measurements":
print 'bad input file'
sys.exit()
PmagRecs=pmag.get_dictitem(PmagRecs,'magic_method_codes','LP-IRM-3D','has') # get all 3D IRM records
if len(PmagRecs)==0:
print 'no records found'
sys.exit()
specs=pmag.get_dictkey(PmagRecs,'er_specimen_name','')
sids=[]
for spec in specs:
if spec not in sids:sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print spc
specdata=pmag.get_dictitem(PmagRecs,'er_specimen_name',spc,'T') # get all this one's data
DIMs,Temps=[],[]
for dat in specdata: # step through the data
DIMs.append([float(dat['measurement_dec']),float(dat['measurement_inc']),float(dat['measurement_magn_moment'])])
Temps.append(float(dat['treatment_temp'])-273.)
carts=pmag.dir2cart(DIMs).transpose()
if norm==1: # want to normalize
nrm=(DIMs[0][2]) # normalize by NRM
ylab="M/M_o"
else:
nrm=1. # don't normalize
ylab="Magnetic moment (Am^2)"
xlab="Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[0])/nrm,sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[1])/nrm,sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],Temps,abs(carts[2])/nrm,sym='k^',title=spc,xlab=xlab,ylab=ylab) # Z direction
files={'lowrie':'lowrie:_'+spc+'_.'+fmt}
if plot==0:
pmagplotlib.drawFIGS(FIG)
ans=raw_input('S[a]ve figure? [q]uit, <return> to continue ')
if ans=='a':
pmagplotlib.saveP(FIG,files)
elif ans=='q':
sys.exit()
else:
pmagplotlib.saveP(FIG,files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available plots.
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
-DM [2,3] define data model
"""
dirlist = ['./']
dir_path = os.getcwd()
names = os.listdir(dir_path)
for n in names:
if 'Location' in n:
dirlist.append(n)
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
else:
fmt = 'png'
if '-f' in sys.argv:
ind = sys.argv.index("-f")
filelist = [sys.argv[ind + 1]]
else:
filelist = os.listdir(dir_path)
new_model = 0
if '-DM' in sys.argv:
ind = sys.argv.index("-DM")
data_model = sys.argv[ind + 1]
if data_model == '3': new_model = 1
if new_model:
samp_file = 'samples.txt'
azimuth_key = 'azimuth'
meas_file = 'measurements.txt'
loc_key = 'location'
method_key = 'method_codes'
dec_key = 'dir_dec'
inc_key = 'dir_inc'
Mkeys = ['magnitude', 'magn_moment', 'magn_volume', 'magn_mass']
results_file = 'sites.txt'
tilt_key = 'direction_tilt_correction'
hyst_file = 'specimens.txt'
aniso_file = 'specimens.txt'
else:
new_model = 0
samp_file = 'er_samples.txt'
azimuth_key = 'sample_azimuth'
meas_file = 'magic_measurements.txt'
loc_key = 'er_location_name'
method_key = 'magic_method_codes'
dec_key = 'measurement_dec'
inc_key = 'measurement_inc'
Mkeys = [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass'
]
results_file = 'pmag_results.txt'
tilt_key = 'tilt_correction'
hyst_file = 'rmag_hysteresis'
aniso_file = 'rmag_anisotropy'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
for loc in dirlist:
print 'working on: ', loc
os.chdir(loc) # change working directories to each location
crd = 's'
print samp_file
if samp_file in filelist: # find coordinate systems
print 'found sample file'
samps, file_type = pmag.magic_read(samp_file) # read in data
Srecs = pmag.get_dictitem(
samps, azimuth_key, '',
'F') # get all none blank sample orientations
if len(Srecs) > 0:
crd = 'g'
if meas_file in filelist: # start with measurement data
print 'working on measurements data'
data, file_type = pmag.magic_read(meas_file) # read in data
if loc == './':
data = pmag.get_dictitem(
data, loc_key, '',
'T') # get all the blank location names from data file
# looking for zeq_magic possibilities
AFZrecs = pmag.get_dictitem(
data, method_key, 'LT-AF-Z',
'has') # get all none blank method codes
TZrecs = pmag.get_dictitem(
data, method_key, 'LT-T-Z',
'has') # get all none blank method codes
MZrecs = pmag.get_dictitem(
data, method_key, 'LT-M-Z',
'has') # get all none blank method codes
Drecs = pmag.get_dictitem(data, dec_key, '',
'F') # get all dec measurements
Irecs = pmag.get_dictitem(data, inc_key, '',
'F') # get all inc measurements
for key in Mkeys:
Mrecs = pmag.get_dictitem(data, key, '',
'F') # get intensity data
if len(Mrecs) > 0: break
if len(AFZrecs) > 0 or len(TZrecs) > 0 or len(MZrecs) > 0 and len(
Drecs) > 0 and len(Irecs) > 0 and len(
Mrecs) > 0: # potential for stepwise demag curves
if new_model:
CMD = 'zeq_magic3.0.py -fsp specimens.txt -sav -fmt ' + fmt + ' -crd ' + crd
else:
CMD = 'zeq_magic.py -fsp pmag_specimens.txt -sav -fmt ' + fmt + ' -crd ' + crd
print CMD
os.system(CMD)
# looking for thellier_magic possibilities
if len(pmag.get_dictitem(data, method_key, 'LP-PI-TRM',
'has')) > 0:
if new_model:
CMD = 'thellier_magic3.0.py -fsp specimens.txt -sav -fmt ' + fmt
else:
CMD = 'thellier_magic.py -fsp pmag_specimens.txt -sav -fmt ' + fmt
print CMD
os.system(CMD)
# looking for hysteresis possibilities
if len(pmag.get_dictitem(data, method_key, 'LP-HYS',
'has')) > 0: # find hyst experiments
if new_model:
CMD = 'quick_hyst3.0.py -sav -fmt ' + fmt
else:
CMD = 'quick_hyst.py -sav -fmt ' + fmt
print CMD
os.system(CMD)
if results_file in filelist: # start with measurement data
data, file_type = pmag.magic_read(results_file) # read in data
print 'number of datapoints: ', len(data)
if loc == './':
data = pmag.get_dictitem(
data, loc_key, ':', 'has'
) # get all the concatenated location names from data file
print 'number of datapoints: ', len(data), loc
if new_model:
print 'working on site directions'
dec_key = 'dir_dec'
inc_key = 'dir_inc'
int_key = 'int_abs'
else:
print 'working on results directions'
dec_key = 'average_dec'
inc_key = 'average_inc'
int_key = 'average_int'
SiteDIs = pmag.get_dictitem(data, dec_key, "", 'F') # find decs
SiteDIs = pmag.get_dictitem(SiteDIs, inc_key, "",
'F') # find decs and incs
SiteDIs = pmag.get_dictitem(
SiteDIs, 'data_type', 'i',
'has') # only individual results - not poles
print 'number of directions: ', len(SiteDIs)
SiteDIs_t = pmag.get_dictitem(SiteDIs, tilt_key, '100',
'T') # tilt corrected coordinates
print 'number of tilt corrected directions: ', len(SiteDIs)
SiteDIs_g = pmag.get_dictitem(SiteDIs, tilt_key, '0',
'T') # geographic coordinates
SiteDIs_s = pmag.get_dictitem(SiteDIs, 'tilt_correction', '-1',
'T') # sample coordinates
SiteDIs_x = pmag.get_dictitem(SiteDIs, 'tilt_correction', '',
'T') # no coordinates
if len(SiteDIs_t) > 0 or len(SiteDIs_g) > 0 or len(
SiteDIs_s) > 0 or len(SiteDIs_x) > 0:
CRD = ""
if len(SiteDIs_t) > 0:
CRD = ' -crd t'
elif len(SiteDIs_g) > 0:
CRD = ' -crd g'
elif len(SiteDIs_s) > 0:
CRD = ' -crd s'
if new_model:
CMD = 'eqarea_magic3.0.py -sav -crd t -fmt ' + fmt + CRD
else:
CMD = 'eqarea_magic.py -sav -crd t -fmt ' + fmt + CRD
print CMD
os.system(CMD)
print 'working on VGP map'
VGPs = pmag.get_dictitem(SiteDIs, 'vgp_lat', "",
'F') # are there any VGPs?
if len(VGPs) > 0: # YES!
os.system(
'vgpmap_magic.py -prj moll -res c -sym ro 5 -sav -fmt png')
print 'working on intensities'
if not new_model:
CMD = 'magic_select.py -f ' + results_file + ' -key data_type i T -F tmp.txt'
os.system(CMD)
infile = ' tmp.txt'
else:
infile = results_file
print int_key
CMD = 'magic_select.py -key ' + int_key + ' 0. has -F tmp1.txt -f ' + infile
os.system(CMD)
CMD = "grab_magic_key.py -f tmp1.txt -key " + int_key + " | awk '{print $1*1e6}' >tmp2.txt"
os.system(CMD)
data, file_type = pmag.magic_read('tmp1.txt') # read in data
if new_model:
locations = pmag.get_dictkey(data, loc_key, "")
else:
locations = pmag.get_dictkey(data, loc_key + 's', "")
histfile = 'LO:_' + locations[0] + '_intensities_histogram:_.' + fmt
os.system(
"histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F "
+ histfile)
print "histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F " + histfile
os.system('rm tmp*.txt')
if hyst_file in filelist: # start with measurement data
print 'working on hysteresis'
data, file_type = pmag.magic_read(hyst_file) # read in data
if loc == './':
data = pmag.get_dictitem(
data, loc_key, '',
'T') # get all the blank location names from data file
hdata = pmag.get_dictitem(data, 'hysteresis_bcr', '', 'F')
hdata = pmag.get_dictitem(hdata, 'hysteresis_mr_moment', '', 'F')
hdata = pmag.get_dictitem(hdata, 'hysteresis_ms_moment', '', 'F')
hdata = pmag.get_dictitem(hdata, 'hysteresis_bc', '',
'F') # there are data for a dayplot
if len(hdata) > 0:
print 'dayplot_magic.py -sav -fmt ' + fmt
os.system('dayplot_magic.py -sav -fmt ' + fmt)
if aniso_file in filelist: # do anisotropy plots if possible
print 'working on anisotropy'
data, file_type = pmag.magic_read(aniso_file) # read in data
if loc == './':
data = pmag.get_dictitem(
data, loc_key, '',
'T') # get all the blank location names from data file
sdata = pmag.get_dictitem(data, 'anisotropy_tilt_correction', '-1',
'T') # get specimen coordinates
gdata = pmag.get_dictitem(data, 'anisotropy_tilt_correction', '0',
'T') # get specimen coordinates
tdata = pmag.get_dictitem(data, 'anisotropy_tilt_correction',
'100', 'T') # get specimen coordinates
CRD = ""
if new_model:
CMD = 'aniso_magic3.0.py -x -B -sav -fmt ' + fmt
else:
CMD = 'aniso_magic.py -x -B -sav -fmt ' + fmt
if len(sdata) > 3:
CMD = CMD + ' -crd s'
print CMD
os.system(CMD)
if len(gdata) > 3:
CMD = CMD + ' -crd g'
print CMD
os.system(CMD)
if len(tdata) > 3:
CMD = CMD + ' -crd t'
print CMD
os.system(CMD)
if loc != './':
os.chdir('..') # change working directories to each location
def main():
"""
NAME
lowrie.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie -h [command line options]
INPUT
takes SIO formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav save plots and quit
"""
fmt, plot = 'svg', 0
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
if len(sys.argv) > 1:
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-N' in sys.argv:
norm = 0 # don't normalize
if '-sav' in sys.argv:
plot = 1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
data = pmag.open_file(in_file)
PmagRecs = [] # set up a list for the results
keys = ['specimen', 'treatment', 'csd', 'M', 'dec', 'inc']
for line in data:
PmagRec = {}
rec = line.replace('\n', '').split()
for k in range(len(keys)):
PmagRec[keys[k]] = rec[k]
PmagRecs.append(PmagRec)
specs = pmag.get_dictkey(PmagRecs, 'specimen', '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(
PmagRecs, 'specimen', spc, 'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([float(dat['dec']), float(
dat['inc']), float(dat['M']) * 1e-3])
Temps.append(float(dat['treatment']))
carts = pmag.dir2cart(DIMs).transpose()
# if norm==1: # want to normalize
# nrm=max(max(abs(carts[0])),max(abs(carts[1])),max(abs(carts[2]))) # by maximum of x,y,z values
# ylab="M/M_max"
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[0]), nrm), sym='r-')
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[0]), nrm), sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[1]), nrm), sym='c-')
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[1]), nrm), sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[2]), nrm), sym='k-')
pmagplotlib.plotXY(FIG['lowrie'], Temps, old_div(
abs(carts[2]), nrm), sym='k^', title=spc, xlab=xlab, ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.saveP(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available data and makes plots
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
# reset log files
for fname in ['log.txt', 'errors.txt']:
f = os.path.join(os.getcwd(), fname)
if os.path.exists(f):
os.remove(f)
dirlist = ['./']
dir_path = os.getcwd()
#
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
else:
fmt = 'png'
if '-f' in sys.argv:
ind = sys.argv.index("-f")
filelist = [sys.argv[ind + 1]]
else:
filelist = os.listdir(dir_path)
## initialize some variables
samp_file = 'samples.txt'
azimuth_key = 'azimuth'
meas_file = 'measurements.txt'
loc_key = 'location'
loc_file = 'locations.txt'
method_key = 'method_codes'
dec_key = 'dir_dec'
inc_key = 'dir_inc'
tilt_corr_key = "dir_tilt_correction"
aniso_tilt_corr_key = "aniso_tilt_correction"
hyst_bcr_key = "hyst_bcr"
hyst_mr_key = "hyst_mr_moment"
hyst_ms_key = "hyst_ms_moment"
hyst_bc_key = "hyst_bc"
Mkeys = ['magnitude', 'magn_moment', 'magn_volume', 'magn_mass']
results_file = 'sites.txt'
hyst_file = 'specimens.txt'
aniso_file = 'specimens.txt'
# create contribution and propagate data throughout
con = cb.Contribution()
con.propagate_location_to_measurements()
con.propagate_location_to_specimens()
con.propagate_location_to_samples()
if not con.tables:
print('-E- No MagIC tables could be found in this directory')
error_log("No MagIC tables found")
return
# try to get the contribution id for error logging
con_id = ""
if 'contribution' in con.tables:
if 'id' in con.tables['contribution'].df.columns:
con_id = con.tables['contribution'].df.iloc[0]['id']
# check to see if propagation worked, otherwise you can't plot by location
lowest_table = None
for table in con.ancestry:
if table in con.tables:
lowest_table = table
break
do_full_directory = False
# check that locations propagated down to the lowest table in the contribution
if 'location' in con.tables[lowest_table].df.columns:
if 'locations' not in con.tables:
info_log('location names propagated to {}, but could not be validated'.format(lowest_table))
# are there any locations in the lowest table?
elif not all(con.tables[lowest_table].df['location'].isnull()):
locs = con.tables['locations'].df.index.unique()
lowest_locs = con.tables[lowest_table].df['location'].unique()
incorrect_locs = set(lowest_locs).difference(set(locs))
# are they actual locations?
if not incorrect_locs:
info_log('location names propagated to {}'.format(lowest_table))
else:
do_full_directory = True
error_log('location names did not propagate fully to {} table (looks like there are some naming inconsistencies between tables)'.format(lowest_table), con_id=con_id)
else:
do_full_directory = True
error_log('could not propagate location names down to {} table'.format(lowest_table), con_id=con_id)
else:
do_full_directory = True
error_log('could not propagate location names down to {} table'.format(lowest_table), con_id=con_id)
all_data = {}
all_data['measurements'] = con.tables.get('measurements', None)
all_data['specimens'] = con.tables.get('specimens', None)
all_data['samples'] = con.tables.get('samples', None)
all_data['sites'] = con.tables.get('sites', None)
all_data['locations'] = con.tables.get('locations', None)
if 'locations' in con.tables:
locations = con.tables['locations'].df.index.unique()
else:
locations = ['']
dirlist = [loc for loc in locations if cb.not_null(loc, False) and loc != 'nan']
if not dirlist:
dirlist = ["./"]
if do_full_directory:
dirlist = ["./"]
# plot the whole contribution as one location
if dirlist == ["./"]:
error_log('plotting the entire contribution as one location', con_id=con_id)
for fname in os.listdir("."):
if fname.endswith(".txt"):
shutil.copy(fname, "tmp_" + fname)
# if possible, go through all data by location
# use tmp_*.txt files to separate out by location
for loc in dirlist:
print('\nworking on: ', loc)
def get_data(dtype, loc_name):
"""
Extract data of type dtype for location loc_name.
Write tmp_dtype.txt files if possible.
"""
if cb.not_null(all_data[dtype], False):
data_container = all_data[dtype]
if loc_name == "./":
data_df = data_container.df
else:
# awkward workaround for chars like "(" and "?" that break in regex
try:
data_df = data_container.df[data_container.df['location'].astype(str).str.contains(loc_name, na=False)]
except: #sre_constants.error:
data_df = data_container.df[data_container.df['location'] == loc_name]
data = data_container.convert_to_pmag_data_list(df=data_df)
res = data_container.write_magic_file('tmp_{}.txt'.format(dtype), df=data_df)
if not res:
return []
return data
meas_data = get_data('measurements', loc)
spec_data = get_data('specimens', loc)
samp_data = get_data('samples', loc)
site_data = get_data('sites', loc)
loc_data = get_data('locations', loc)
if loc == "./": # if you can't sort by location, do everything together
try:
meas_data = con.tables['measurements'].convert_to_pmag_data_list()
except KeyError:
meas_data = None
try:
spec_data = con.tables['specimens'].convert_to_pmag_data_list()
except KeyError:
spec_data = None
try:
samp_data = con.tables['samples'].convert_to_pmag_data_list()
except KeyError:
samp_data = None
try:
site_data = con.tables['sites'].convert_to_pmag_data_list()
except KeyError:
site_data = None
crd = 's'
if samp_file in filelist and samp_data: # find coordinate systems
samps = samp_data
file_type = "samples"
# get all non blank sample orientations
Srecs = pmag.get_dictitem(samps, azimuth_key, '', 'F')
if len(Srecs) > 0:
crd = 'g'
print('using geographic coordinates')
else:
print('using specimen coordinates')
else:
if VERBOSE:
print('-I- No sample data found')
if meas_file in filelist and meas_data: # start with measurement data
print('working on measurements data')
data = meas_data
file_type = 'measurements'
# looking for zeq_magic possibilities
# get all non blank method codes
AFZrecs = pmag.get_dictitem(data, method_key, 'LT-AF-Z', 'has')
# get all non blank method codes
TZrecs = pmag.get_dictitem(data, method_key, 'LT-T-Z', 'has')
# get all non blank method codes
MZrecs = pmag.get_dictitem(data, method_key, 'LT-M-Z', 'has')
# get all dec measurements
Drecs = pmag.get_dictitem(data, dec_key, '', 'F')
# get all inc measurements
Irecs = pmag.get_dictitem(data, inc_key, '', 'F')
for key in Mkeys:
Mrecs = pmag.get_dictitem(
data, key, '', 'F') # get intensity data
if len(Mrecs) > 0:
break
# potential for stepwise demag curves
if len(AFZrecs) > 0 or len(TZrecs) > 0 or len(MZrecs) > 0 and len(Drecs) > 0 and len(Irecs) > 0 and len(Mrecs) > 0:
CMD = 'zeq_magic.py -f tmp_measurements.txt -fsp tmp_specimens.txt -fsa tmp_samples.txt -fsi tmp_sites.txt -sav -fmt ' + fmt + ' -crd ' + crd + " -new"
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# looking for thellier_magic possibilities
if len(pmag.get_dictitem(data, method_key, 'LP-PI-TRM', 'has')) > 0:
CMD = 'thellier_magic.py -f tmp_measurements.txt -fsp tmp_specimens.txt -sav -fmt ' + fmt
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# looking for hysteresis possibilities
if len(pmag.get_dictitem(data, method_key, 'LP-HYS', 'has')) > 0: # find hyst experiments
# check for reqd columns
missing = check_for_reqd_cols(data, ['treat_temp'])
if missing:
error_log('LP-HYS method code present, but required column(s) [{}] missing'.format(", ".join(missing)), loc, "quick_hyst.py", con_id=con_id)
else:
CMD = 'quick_hyst.py -f tmp_measurements.txt -sav -fmt ' + fmt
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# equal area plots of directional data
# at measurment level (by specimen)
if data:
missing = check_for_reqd_cols(data, ['dir_dec', 'dir_inc'])
if not missing:
CMD = "eqarea_magic.py -f tmp_measurements.txt -obj spc -sav -no-tilt -fmt " + fmt
print(CMD)
os.system(CMD)
info_log(CMD, loc, "eqarea_magic.py")
else:
if VERBOSE:
print('-I- No measurement data found')
# site data
if results_file in filelist and site_data:
print('-I- result file found', results_file)
data = site_data
file_type = 'sites'
print('-I- working on site directions')
print('number of datapoints: ', len(data), loc)
dec_key = 'dir_dec'
inc_key = 'dir_inc'
int_key = 'int_abs'
SiteDIs = pmag.get_dictitem(data, dec_key, "", 'F') # find decs
SiteDIs = pmag.get_dictitem(
SiteDIs, inc_key, "", 'F') # find decs and incs
dir_data_found = len(SiteDIs)
print('{} Dec/inc pairs found'.format(dir_data_found))
if SiteDIs:
# then convert tilt_corr_key to correct format
old_SiteDIs = SiteDIs
SiteDIs = []
for rec in old_SiteDIs:
if tilt_corr_key not in rec:
rec[tilt_corr_key] = "0"
# make sure tilt_corr_key is a correct format
try:
rec[tilt_corr_key] = str(int(float(rec[tilt_corr_key])))
except ValueError:
rec[tilt_corr_key] = "0"
SiteDIs.append(rec)
print('number of individual directions: ', len(SiteDIs))
# tilt corrected coordinates
SiteDIs_t = pmag.get_dictitem(SiteDIs, tilt_corr_key, '100',
'T', float_to_int=True)
print('number of tilt corrected directions: ', len(SiteDIs_t))
SiteDIs_g = pmag.get_dictitem(
SiteDIs, tilt_corr_key, '0', 'T', float_to_int=True) # geographic coordinates
print('number of geographic directions: ', len(SiteDIs_g))
SiteDIs_s = pmag.get_dictitem(
SiteDIs, tilt_corr_key, '-1', 'T', float_to_int=True) # sample coordinates
print('number of sample directions: ', len(SiteDIs_s))
SiteDIs_x = pmag.get_dictitem(
SiteDIs, tilt_corr_key, '', 'T') # no coordinates
print('number of no coordinates directions: ', len(SiteDIs_x))
if len(SiteDIs_t) > 0 or len(SiteDIs_g) > 0 or len(SiteDIs_s) > 0 or len(SiteDIs_x) > 0:
CRD = ""
if len(SiteDIs_t) > 0:
CRD = ' -crd t'
elif len(SiteDIs_g) > 0:
CRD = ' -crd g'
elif len(SiteDIs_s) > 0:
CRD = ' -crd s'
CMD = 'eqarea_magic.py -f tmp_sites.txt -fsp tmp_specimens.txt -fsa tmp_samples.txt -flo tmp_locations.txt -sav -fmt ' + fmt + CRD
print(CMD)
info_log(CMD, loc)
os.system(CMD)
else:
if dir_data_found:
error_log('{} dec/inc pairs found, but no equal area plots were made'.format(dir_data_found), loc, "equarea_magic.py", con_id=con_id)
#
print('-I- working on VGP map')
VGPs = pmag.get_dictitem(
SiteDIs, 'vgp_lat', "", 'F') # are there any VGPs?
if len(VGPs) > 0: # YES!
CMD = 'vgpmap_magic.py -f tmp_sites.txt -prj moll -res c -sym ro 5 -sav -fmt png'
print(CMD)
info_log(CMD, loc, 'vgpmap_magic.py')
os.system(CMD)
else:
print('-I- No vgps found')
print('-I- Look for intensities')
# is there any intensity data?
if site_data:
if int_key in site_data[0].keys():
# old way, wasn't working right:
#CMD = 'magic_select.py -key ' + int_key + ' 0. has -F tmp1.txt -f tmp_sites.txt'
Selection = pmag.get_dictkey(site_data, int_key, dtype="f")
with open('intensities.txt', 'w') as out:
for rec in Selection:
if rec != 0:
out.write(str(rec * 1e6) + "\n")
loc = loc.replace(" ", "_")
if loc == "./":
loc_name = ""
else:
loc_name = loc
histfile = 'LO:_' + loc_name + \
'_TY:_intensities_histogram:_.' + fmt
# maybe run histplot.main here instead, so you can return an error message
CMD = "histplot.py -twin -b 1 -xlab 'Intensity (uT)' -sav -f intensities.txt -F " + histfile
os.system(CMD)
info_log(CMD, loc)
print(CMD)
else:
print('-I- No intensities found')
else:
print('-I- No intensities found')
##
if hyst_file in filelist and spec_data:
print('working on hysteresis', hyst_file)
data = spec_data
file_type = 'specimens'
hdata = pmag.get_dictitem(data, hyst_bcr_key, '', 'F')
hdata = pmag.get_dictitem(hdata, hyst_mr_key, '', 'F')
hdata = pmag.get_dictitem(hdata, hyst_ms_key, '', 'F')
# there are data for a dayplot
hdata = pmag.get_dictitem(hdata, hyst_bc_key, '', 'F')
if len(hdata) > 0:
CMD = 'dayplot_magic.py -f tmp_specimens.txt -sav -fmt ' + fmt
info_log(CMD, loc)
print(CMD)
else:
print('no hysteresis data found')
if aniso_file in filelist and spec_data: # do anisotropy plots if possible
print('working on anisotropy', aniso_file)
data = spec_data
file_type = 'specimens'
# make sure there is some anisotropy data
if not data:
print('No anisotropy data found')
elif 'aniso_s' not in data[0]:
print('No anisotropy data found')
else:
# get specimen coordinates
if aniso_tilt_corr_key not in data[0]:
sdata = data
else:
sdata = pmag.get_dictitem(
data, aniso_tilt_corr_key, '-1', 'T', float_to_int=True)
# get specimen coordinates
gdata = pmag.get_dictitem(
data, aniso_tilt_corr_key, '0', 'T', float_to_int=True)
# get specimen coordinates
tdata = pmag.get_dictitem(
data, aniso_tilt_corr_key, '100', 'T', float_to_int=True)
CRD = ""
CMD = 'aniso_magic.py -x -B -sav -fmt ' + fmt + " -new"
if len(sdata) > 3:
CMD = CMD + ' -crd s'
print(CMD)
info_log(CMD, loc)
os.system(CMD)
if len(gdata) > 3:
CMD = CMD + ' -crd g'
print(CMD)
info_log(CMD, loc)
os.system(CMD)
if len(tdata) > 3:
CMD = CMD + ' -crd t'
print(CMD)
info_log(CMD, loc)
os.system(CMD)
# remove temporary files
for fname in glob.glob('tmp*.txt'):
os.remove(fname)
try:
os.remove('intensities.txt')
except FileNotFoundError:
pass
if loc_file in filelist and loc_data:
#data, file_type = pmag.magic_read(loc_file) # read in location data
data = loc_data
print('-I- working on pole map')
poles = pmag.get_dictitem(
data, 'pole_lat', "", 'F') # are there any poles?
poles = pmag.get_dictitem(
poles, 'pole_lon', "", 'F') # are there any poles?
if len(poles) > 0: # YES!
CMD = 'polemap_magic.py -sav -fmt png -rev gv 40'
print(CMD)
info_log(CMD, "all locations", "polemap_magic.py")
os.system(CMD)
else:
print('-I- No poles found')
thumbnails.make_thumbnails(dir_path)
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
-DM [2, 3] MagIC data model number
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if len(sys.argv) <= 1:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
in_file = pmag.get_named_arg("-f", "measurements.txt")
dir_path = pmag.get_named_arg("-WD", ".")
in_file = pmag.resolve_file_name(in_file, dir_path)
data_model = pmag.get_named_arg("-DM", 3)
data_model = int(float(data_model))
fmt = pmag.get_named_arg("-fmt", "svg")
if '-N' in sys.argv:
norm = 0 # don't normalize
if '-sav' in sys.argv:
plot = 1 # silently save and quit
else:
plot = 0 # generate plots
print(in_file)
# read in data
PmagRecs, file_type = pmag.magic_read(in_file)
if data_model == 2 and file_type != "magic_measurements":
print('bad input file', file_type)
sys.exit()
if data_model == 3 and file_type != "measurements":
print('bad input file', file_type)
sys.exit()
if data_model == 2:
meth_code_col = 'magic_method_codes'
spec_col = 'er_specimen_name'
dec_col = "measurement_dec"
inc_col = 'measurement_inc'
moment_col = 'measurement_magn_moment'
temp_col = 'treatment_temp'
else:
meth_code_col = 'method_codes'
spec_col = 'specimen'
dec_col = 'dir_dec'
inc_col = 'dir_inc'
moment_col = 'magn_moment'
temp_col = "treat_temp"
PmagRecs = pmag.get_dictitem(
PmagRecs, meth_code_col, 'LP-IRM-3D', 'has') # get all 3D IRM records
if len(PmagRecs) == 0:
print('no records found with the method code LP-IRM-3D')
sys.exit()
specs = pmag.get_dictkey(PmagRecs, spec_col, '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(
PmagRecs, spec_col, spc, 'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([float(dat[dec_col]), float(
dat[inc_col]), float(dat[moment_col])])
Temps.append(float(dat[temp_col])-273.)
carts = pmag.dir2cart(DIMs).transpose()
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[0]) / nrm, sym='r-')
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[0]) / nrm, sym='ro') # X direction
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[1]) / nrm, sym='c-')
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[1]) / nrm, sym='cs') # Y direction
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[2]) / nrm, sym='k-')
pmagplotlib.plot_xy(FIG['lowrie'], Temps, abs(carts[2]) / nrm, sym='k^', title=spc, xlab=xlab, ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_'+spc+'_.'+fmt}
if plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.save_plots(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.save_plots(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes magic_measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
"""
fmt, plot = 'svg', 0
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
in_file, dir_path = 'magic_measurements.txt', '.'
if len(sys.argv) > 1:
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 '-N' in sys.argv: norm = 0 # don't normalize
if '-sav' in sys.argv: plot = 1 # don't normalize
if '-fmt' in sys.argv: # sets input filename
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-f' in sys.argv: # sets input filename
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
else:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
in_file = dir_path + '/' + in_file
print(in_file)
PmagRecs, file_type = pmag.magic_read(in_file)
if file_type != "magic_measurements":
print('bad input file')
sys.exit()
PmagRecs = pmag.get_dictitem(PmagRecs, 'magic_method_codes', 'LP-IRM-3D',
'has') # get all 3D IRM records
if len(PmagRecs) == 0:
print('no records found')
sys.exit()
specs = pmag.get_dictkey(PmagRecs, 'er_specimen_name', '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(PmagRecs, 'er_specimen_name', spc,
'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([
float(dat['measurement_dec']),
float(dat['measurement_inc']),
float(dat['measurement_magn_moment'])
])
Temps.append(float(dat['treatment_temp']) - 273.)
carts = pmag.dir2cart(DIMs).transpose()
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='r-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[0]), nrm),
sym='ro') # X direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='c-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[1]), nrm),
sym='cs') # Y direction
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k-')
pmagplotlib.plotXY(FIG['lowrie'],
Temps,
old_div(abs(carts[2]), nrm),
sym='k^',
title=spc,
xlab=xlab,
ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.drawFIGS(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.saveP(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.saveP(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
def main():
"""
NAME
plot_map_pts.py
DESCRIPTION
plots points on map
SYNTAX
plot_map_pts.py [command line options]
OPTIONS
-h prints help and quits
-sym [ro, bs, g^, r., b-, etc.] [1,5,10] symbol and size for points
colors are r=red,b=blue,g=green, etc.
symbols are '.' for points, ^, for triangle, s for square, etc.
-, for lines, -- for dotted lines, see matplotlib online documentation for plot()
-eye ELAT ELON [specify eyeball location]
-etp put on topography
-f FILE, specify input file
-o color ocean blue/land green (default is not)
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-fmt [pdf,eps, png] specify output format (default is pdf)
-R don't plot details of rivers
-B don't plot national/state boundaries, etc.
-pad [LAT LON] pad bounding box by LAT/LON (default is not)
-grd SPACE specify grid spacing
-sav save plot and quit
-prj PROJ, specify one of the supported projections: (see basemap.py online documentation)
aeqd = Azimuthal Equidistant
poly = Polyconic
gnom = Gnomonic
moll = Mollweide
tmerc = Transverse Mercator
nplaea = North-Polar Lambert Azimuthal
mill = Miller Cylindrical
merc = Mercator
stere = Stereographic
npstere = North-Polar Stereographic
geos = Geostationary
laea = Lambert Azimuthal Equal Area
sinu = Sinusoidal
spstere = South-Polar Stereographic
lcc = Lambert Conformal
npaeqd = North-Polar Azimuthal Equidistant
eqdc = Equidistant Conic
cyl = Cylindrical Equidistant
omerc = Oblique Mercator
aea = Albers Equal Area
spaeqd = South-Polar Azimuthal Equidistant
ortho = Orthographic
cass= Cassini-Soldner
splaea = South-Polar Lambert Azimuthal
robin = Robinson
Special codes for MagIC formatted input files:
-n
-l
INPUTS
space or tab delimited LON LAT data
OR:
standard MagIC formatted er_sites or pmag_results table
DEFAULTS
res: c
prj: mollweide; lcc for MagIC format files
ELAT,ELON = 0,0
pad LAT,LON=0,0
NB: high resolution or lines can be very slow
"""
dir_path='.'
plot=0
ocean=0
res='c'
proj='moll'
Lats,Lons=[],[]
fmt='pdf'
sym='ro'
symsize=5
fancy=0
rivers,boundaries,ocean=1,1,0
latmin,latmax,lonmin,lonmax,lat_0,lon_0=-90,90,0.,360.,0.,0.
padlat,padlon,gridspace=0,0,30
lat_0,lon_0="",""
prn_name,prn_loc,names,locs=0,0,[],[]
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 '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if res!= 'c' and res!='l':
print('this resolution will take a while - be patient')
if '-etp' in sys.argv: fancy=1
if '-sav' in sys.argv: plot=1
if '-R' in sys.argv:rivers=0
if '-B' in sys.argv:boundaries=0
if '-o' in sys.argv:ocean=1
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace=float(sys.argv[ind+1])
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 '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym=sys.argv[ind+1]
symsize=int(sys.argv[ind+2])
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat=float(sys.argv[ind+1])
padlon=float(sys.argv[ind+2])
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file=dir_path+'/'+sys.argv[ind+1]
header=open(file,'r').readlines()[0].split('\t')
if 'tab' in header[0]:
if '-n' in sys.argv:prn_name=1
if '-l' in sys.argv:prn_loc=1
proj='lcc'
if 'results' in header[1]:
latkey='average_lat'
lonkey='average_lon'
namekey='pmag_result_name'
lockey='er_location_names'
elif 'sites' in header[1]:
latkey='site_lat'
lonkey='site_lon'
namekey='er_site_name'
lockey='er_location_name'
else:
print('file type not supported')
print(main.__doc__)
sys.exit()
Sites,file_type=pmag.magic_read(file)
Lats=pmag.get_dictkey(Sites,latkey,'f')
Lons=pmag.get_dictkey(Sites,lonkey,'f')
if prn_name==1:names=pmag.get_dictkey(Sites,namekey,'')
if prn_loc==1:names=pmag.get_dictkey(Sites,lockey,'')
else:
ptdata=numpy.loadtxt(file)
Lons=ptdata.transpose()[0]
Lats=ptdata.transpose()[1]
latmin=numpy.min(Lats)-padlat
lonmin=numpy.min(Lons)-padlon
latmax=numpy.max(Lats)+padlat
lonmax=numpy.max(Lons)+padlon
if lon_0=="":
lon_0=0.5*(lonmin+lonmax)
lat_0=0.5*(latmin+latmax)
else:
print("input file must be specified")
sys.exit()
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
FIG={'map':1}
pmagplotlib.plot_init(FIG['map'],6,6)
if res=='c':skip=8
if res=='l':skip=5
if res=='i':skip=2
if res=='h':skip=1
cnt=0
Opts={'latmin':latmin,'latmax':latmax,'lonmin':lonmin,'lonmax':lonmax,'lat_0':lat_0,'lon_0':lon_0,'proj':proj,'sym':sym,'symsize':3,'pltgrid':1,'res':res,'boundinglat':0.,'padlon':padlon,'padlat':padlat,'gridspace':gridspace}
Opts['details']={}
Opts['details']['coasts']=1
Opts['details']['rivers']=rivers
Opts['details']['states']=boundaries
Opts['details']['countries']=boundaries
Opts['details']['ocean']=ocean
Opts['details']['fancy']=fancy
if len(names)>0:Opts['names']=names
if len(locs)>0:Opts['loc_name']=locs
if proj=='merc':
Opts['latmin']=-70
Opts['latmax']=70
Opts['lonmin']=-180
Opts['lonmax']=180
print('please wait to draw points')
Opts['sym']=sym
Opts['symsize']=symsize
pmagplotlib.plotMAP(FIG['map'],Lats,Lons,Opts)
files={}
titles={}
titles['map']='PT Map'
for key in list(FIG.keys()):
files[key]='Map_PTS'+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
if plot==1:
pmagplotlib.saveP(FIG,files)
else:
pmagplotlib.drawFIGS(FIG)
ans=input(" S[a]ve to save plot, Return to quit: ")
if ans=="a": pmagplotlib.saveP(FIG,files)
def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available plots.
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt [png,eps,svg,jpg,pdf] specify format, default is png
-DM [2,3] define data model
"""
dirlist=['./']
dir_path=os.getcwd()
names=os.listdir(dir_path)
for n in names:
if 'Location' in n:
dirlist.append(n)
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
else: fmt='png'
if '-f' in sys.argv:
ind=sys.argv.index("-f")
filelist=[sys.argv[ind+1]]
else:
filelist=os.listdir(dir_path)
new_model=0
if '-DM' in sys.argv:
ind=sys.argv.index("-DM")
data_model=sys.argv[ind+1]
if data_model=='3': new_model=1
if new_model:
samp_file='samples.txt'
azimuth_key='azimuth'
meas_file='measurements.txt'
loc_key='location'
method_key='method_codes'
dec_key='dir_dec'
inc_key='dir_inc'
Mkeys=['magnitude','magn_moment','magn_volume','magn_mass']
results_file='sites.txt'
tilt_key='direction_tilt_correction'
hyst_file='specimens.txt'
aniso_file='specimens.txt'
else:
new_model=0
samp_file='er_samples.txt'
azimuth_key='sample_azimuth'
meas_file='magic_measurements.txt'
loc_key='er_location_name'
method_key='magic_method_codes'
dec_key='measurement_dec'
inc_key='measurement_inc'
Mkeys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
results_file='pmag_results.txt'
tilt_key='tilt_correction'
hyst_file='rmag_hysteresis'
aniso_file='rmag_anisotropy'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
for loc in dirlist:
print('working on: ',loc)
os.chdir(loc) # change working directories to each location
crd='s'
print(samp_file)
if samp_file in filelist: # find coordinate systems
print('found sample file')
samps,file_type=pmag.magic_read(samp_file) # read in data
Srecs=pmag.get_dictitem(samps,azimuth_key,'','F')# get all none blank sample orientations
if len(Srecs)>0:
crd='g'
if meas_file in filelist: # start with measurement data
print('working on measurements data')
data,file_type=pmag.magic_read(meas_file) # read in data
if loc == './': data=pmag.get_dictitem(data,loc_key,'','T') # get all the blank location names from data file
# looking for zeq_magic possibilities
AFZrecs=pmag.get_dictitem(data,method_key,'LT-AF-Z','has')# get all none blank method codes
TZrecs=pmag.get_dictitem(data,method_key,'LT-T-Z','has')# get all none blank method codes
MZrecs=pmag.get_dictitem(data,method_key,'LT-M-Z','has')# get all none blank method codes
Drecs=pmag.get_dictitem(data,dec_key,'','F') # get all dec measurements
Irecs=pmag.get_dictitem(data,inc_key,'','F') # get all inc measurements
for key in Mkeys:
Mrecs=pmag.get_dictitem(data,key,'','F') # get intensity data
if len(Mrecs)>0:break
if len(AFZrecs)>0 or len(TZrecs)>0 or len(MZrecs)>0 and len(Drecs)>0 and len(Irecs)>0 and len(Mrecs)>0: # potential for stepwise demag curves
if new_model:
CMD = 'zeq_magic3.py -fsp specimens.txt -sav -fmt '+fmt+' -crd '+crd
else:
CMD='zeq_magic.py -fsp pmag_specimens.txt -sav -fmt '+fmt+' -crd '+crd
print(CMD)
os.system(CMD)
# looking for thellier_magic possibilities
if len(pmag.get_dictitem(data,method_key,'LP-PI-TRM','has'))>0:
if new_model:
CMD= 'thellier_magic3.py -fsp specimens.txt -sav -fmt '+fmt
else:
CMD= 'thellier_magic.py -fsp pmag_specimens.txt -sav -fmt '+fmt
print(CMD)
os.system(CMD)
# looking for hysteresis possibilities
if len(pmag.get_dictitem(data,method_key,'LP-HYS','has'))>0: # find hyst experiments
if new_model:
CMD= 'quick_hyst3.py -sav -fmt '+fmt
else:
CMD= 'quick_hyst.py -sav -fmt '+fmt
print(CMD)
os.system(CMD)
if results_file in filelist: # start with measurement data
data,file_type=pmag.magic_read(results_file) # read in data
print('number of datapoints: ',len(data))
if loc == './': data=pmag.get_dictitem(data,loc_key,':','has') # get all the concatenated location names from data file
print('number of datapoints: ',len(data) ,loc)
if new_model:
print('working on site directions')
dec_key='dir_dec'
inc_key='dir_inc'
int_key='int_abs'
else:
print('working on results directions')
dec_key='average_dec'
inc_key='average_inc'
int_key='average_int'
SiteDIs=pmag.get_dictitem(data,dec_key,"",'F') # find decs
SiteDIs=pmag.get_dictitem(SiteDIs,inc_key,"",'F') # find decs and incs
SiteDIs=pmag.get_dictitem(SiteDIs,'data_type','i','has') # only individual results - not poles
print('number of directions: ',len(SiteDIs))
SiteDIs_t=pmag.get_dictitem(SiteDIs,tilt_key,'100','T')# tilt corrected coordinates
print('number of tilt corrected directions: ',len(SiteDIs))
SiteDIs_g=pmag.get_dictitem(SiteDIs,tilt_key,'0','T')# geographic coordinates
SiteDIs_s=pmag.get_dictitem(SiteDIs,'tilt_correction','-1','T')# sample coordinates
SiteDIs_x=pmag.get_dictitem(SiteDIs,'tilt_correction','','T')# no coordinates
if len(SiteDIs_t)>0 or len(SiteDIs_g) >0 or len(SiteDIs_s)>0 or len(SiteDIs_x)>0:
CRD=""
if len(SiteDIs_t)>0:
CRD=' -crd t'
elif len(SiteDIs_g )>0:
CRD=' -crd g'
elif len(SiteDIs_s )>0:
CRD=' -crd s'
if new_model:
CMD= 'eqarea_magic3.py -sav -crd t -fmt '+fmt +CRD
else:
CMD= 'eqarea_magic.py -sav -crd t -fmt '+fmt +CRD
print(CMD)
os.system(CMD)
print('working on VGP map')
VGPs=pmag.get_dictitem(SiteDIs,'vgp_lat',"",'F') # are there any VGPs?
if len(VGPs)>0: # YES!
os.system('vgpmap_magic.py -prj moll -res c -sym ro 5 -sav -fmt png')
print('working on intensities')
if not new_model:
CMD='magic_select.py -f '+results_file+' -key data_type i T -F tmp.txt'
os.system(CMD)
infile=' tmp.txt'
else: infile=results_file
print(int_key)
CMD='magic_select.py -key '+int_key +' 0. has -F tmp1.txt -f '+infile
os.system(CMD)
CMD="grab_magic_key.py -f tmp1.txt -key "+int_key+ " | awk '{print $1*1e6}' >tmp2.txt"
os.system(CMD)
data,file_type=pmag.magic_read('tmp1.txt') # read in data
if new_model:
locations=pmag.get_dictkey(data,loc_key,"")
else:
locations=pmag.get_dictkey(data,loc_key+'s',"")
histfile='LO:_'+locations[0]+'_intensities_histogram:_.'+fmt
os.system("histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F " +histfile)
print("histplot.py -b 1 -xlab 'Intensity (uT)' -sav -f tmp2.txt -F " +histfile)
os.system('rm tmp*.txt')
if hyst_file in filelist: # start with measurement data
print('working on hysteresis')
data,file_type=pmag.magic_read(hyst_file) # read in data
if loc == './': data=pmag.get_dictitem(data,loc_key,'','T') # get all the blank location names from data file
hdata=pmag.get_dictitem(data,'hysteresis_bcr','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_mr_moment','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_ms_moment','','F')
hdata=pmag.get_dictitem(hdata,'hysteresis_bc','','F') # there are data for a dayplot
if len(hdata)>0:
print('dayplot_magic.py -sav -fmt '+fmt)
os.system('dayplot_magic.py -sav -fmt '+fmt)
if aniso_file in filelist: # do anisotropy plots if possible
print('working on anisotropy')
data,file_type=pmag.magic_read(aniso_file) # read in data
if loc == './': data=pmag.get_dictitem(data,loc_key,'','T') # get all the blank location names from data file
sdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','-1','T') # get specimen coordinates
gdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','0','T') # get specimen coordinates
tdata=pmag.get_dictitem(data,'anisotropy_tilt_correction','100','T') # get specimen coordinates
CRD=""
if new_model:
CMD= 'aniso_magic3.py -x -B -sav -fmt '+fmt
else:
CMD= 'aniso_magic.py -x -B -sav -fmt '+fmt
if len(sdata)>3:
CMD=CMD+' -crd s'
print(CMD)
os.system(CMD)
if len(gdata)>3:
CMD=CMD+' -crd g'
print(CMD)
os.system(CMD)
if len(tdata)>3:
CMD=CMD+' -crd t'
print(CMD)
os.system(CMD)
if loc!='./':os.chdir('..') # change working directories to each location
def main():
"""
NAME
lowrie_magic.py
DESCRIPTION
plots intensity decay curves for Lowrie experiments
SYNTAX
lowrie_magic.py -h [command line options]
INPUT
takes measurements formatted input files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is magic_measurements.txt
-N do not normalize by maximum magnetization
-fmt [svg, pdf, eps, png] specify fmt, default is svg
-sav saves plots and quits
-DM [2, 3] MagIC data model number
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if len(sys.argv) <= 1:
print(main.__doc__)
print('you must supply a file name')
sys.exit()
FIG = {} # plot dictionary
FIG['lowrie'] = 1 # demag is figure 1
pmagplotlib.plot_init(FIG['lowrie'], 6, 6)
norm = 1 # default is to normalize by maximum axis
in_file = pmag.get_named_arg("-f", "measurements.txt")
dir_path = pmag.get_named_arg("-WD", ".")
in_file = pmag.resolve_file_name(in_file, dir_path)
data_model = pmag.get_named_arg("-DM", 3)
data_model = int(float(data_model))
fmt = pmag.get_named_arg("-fmt", "svg")
if '-N' in sys.argv:
norm = 0 # don't normalize
if '-sav' in sys.argv:
plot = 1 # silently save and quit
else:
plot = 0 # generate plots
print(in_file)
# read in data
PmagRecs, file_type = pmag.magic_read(in_file)
if data_model == 2 and file_type != "magic_measurements":
print('bad input file', file_type)
sys.exit()
if data_model == 3 and file_type != "measurements":
print('bad input file', file_type)
sys.exit()
if data_model == 2:
meth_code_col = 'magic_method_codes'
spec_col = 'er_specimen_name'
dec_col = "measurement_dec"
inc_col = 'measurement_inc'
moment_col = 'measurement_magn_moment'
temp_col = 'treatment_temp'
else:
meth_code_col = 'method_codes'
spec_col = 'specimen'
dec_col = 'dir_dec'
inc_col = 'dir_inc'
moment_col = 'magn_moment'
temp_col = "treat_temp"
PmagRecs = pmag.get_dictitem(PmagRecs, meth_code_col, 'LP-IRM-3D',
'has') # get all 3D IRM records
if len(PmagRecs) == 0:
print('no records found with the method code LP-IRM-3D')
sys.exit()
specs = pmag.get_dictkey(PmagRecs, spec_col, '')
sids = []
for spec in specs:
if spec not in sids:
sids.append(spec) # get list of unique specimen names
for spc in sids: # step through the specimen names
print(spc)
specdata = pmag.get_dictitem(PmagRecs, spec_col, spc,
'T') # get all this one's data
DIMs, Temps = [], []
for dat in specdata: # step through the data
DIMs.append([
float(dat[dec_col]),
float(dat[inc_col]),
float(dat[moment_col])
])
Temps.append(float(dat[temp_col]) - 273.)
carts = pmag.dir2cart(DIMs).transpose()
if norm == 1: # want to normalize
nrm = (DIMs[0][2]) # normalize by NRM
ylab = "M/M_o"
else:
nrm = 1. # don't normalize
ylab = "Magnetic moment (Am^2)"
xlab = "Temperature (C)"
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[0]) / nrm,
sym='r-')
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[0]) / nrm,
sym='ro') # X direction
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[1]) / nrm,
sym='c-')
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[1]) / nrm,
sym='cs') # Y direction
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[2]) / nrm,
sym='k-')
pmagplotlib.plot_xy(FIG['lowrie'],
Temps,
abs(carts[2]) / nrm,
sym='k^',
title=spc,
xlab=xlab,
ylab=ylab) # Z direction
files = {'lowrie': 'lowrie:_' + spc + '_.' + fmt}
if plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input('S[a]ve figure? [q]uit, <return> to continue ')
if ans == 'a':
pmagplotlib.save_plots(FIG, files)
elif ans == 'q':
sys.exit()
else:
pmagplotlib.save_plots(FIG, files)
pmagplotlib.clearFIG(FIG['lowrie'])
