def main():
"""
NAME
combine_magic.py
DESCRIPTION
Combines magic format files of the same type together.
SYNTAX
combine_magic.py [-h] [-i] -out filename -in file1 file2 ....
OPTIONS
-h prints help message
-i allows interactive entry of input and output filenames
-F specify output file name [must come BEFORE input file names]
-f specify input file names [ must come last]
"""
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-i" in sys.argv: # interactive
dataset,datasets=[],[]
while True:
infile=raw_input('\n\n Enter magic files for combining, <return> when done: ')
if infile=='':
break
if os.path.isfile(infile):
filenames.append(infile)
else:
print "-W- You have not provided a valid filename.\nIf the file is not in your current working directory, you will need to provide the full path to the file"
outfile=raw_input('\n\n Enter name for new combined file')
if not outfile:
return False
else: # non-interactive
dataframe = extractor.command_line_dataframe([["F", True, '']])
args = extractor.extract_and_check_args(sys.argv, dataframe)
dir_path, outfile, filenames = extractor.get_vars(["WD", "F", "f"], args)
#dir_path = pmag.get_named_arg_from_sys("-WD", ".")
#outfile = pmag.get_named_arg_from_sys("-F", reqd=True)
#if "-f" in sys.argv:
# ind=sys.argv.index("-f")
# for k in range(ind+1,len(sys.argv)):
# filenames.append(os.path.join(dir_path, sys.argv[k]))
#else:
# raise pmag.MissingCommandLineArgException("-f")
files=[]
for f in filenames.split():
files.append(os.path.join(dir_path,f))
outfile=(os.path.join(dir_path,outfile))
ipmag.combine_magic(files, outfile)
def test_with_remove_rows(self):
flist = ['extra_specimens.txt', 'specimens.txt']
flist = [os.path.join(self.input_dir, fname) for fname in flist]
#flist = [os.path.join(self.input_dir, fname) for fname in flist]
res = ipmag.combine_magic(flist, 'custom.out', data_model=3)
with open(os.path.join(WD, 'custom.out')) as f:
n = len(f.readlines()) - 2
self.assertEqual(n, 2747)
def test_with_remove_rows(self):
flist = ['extra_specimens.txt', 'specimens.txt']
flist = [os.path.join(self.input_dir, fname) for fname in flist]
#flist = [os.path.join(self.input_dir, fname) for fname in flist]
res = ipmag.combine_magic(flist, 'custom.out', data_model=3)
with open(os.path.join(WD, 'custom.out')) as f:
n = len(f.readlines()) - 2
self.assertEqual(n, 2747)
def test_measurement_sequence(self):
df = cb.MagicDataFrame(os.path.join(self.input_dir, "measurements.txt"))
df.df['specimen'] = df.df['specimen'].apply(lambda x: x + "_new")
df.write_magic_file("new_measurements.txt", dir_path=self.input_dir)
res = ipmag.combine_magic(['measurements.txt', 'new_measurements.txt'], 'custom.out',
input_dir_path=self.input_dir)
self.assertTrue(res)
df = cb.MagicDataFrame('custom.out', dtype="measurements")
self.assertEqual(df.df.sequence[-1], len(df.df))
def test_with_custom_name(self):
outfile = os.path.join(self.input_dir, 'custom_outfile.txt')
if os.path.exists(outfile):
os.remove(outfile)
flist = ['locations.txt', 'new_locations.txt']
flist = [os.path.join(self.input_dir, fname) for fname in flist]
#res = ipmag.combine_magic(flist, 'custom_outfile.txt', 3, 'locations')
res = ipmag.combine_magic(flist, outfile, 3, 'locations')
self.assertTrue(res)
self.assertEqual(res, outfile)
self.assertTrue(os.path.exists(outfile))
def test_with_custom_name(self):
outfile = os.path.join(self.input_dir, 'custom_outfile.txt')
if os.path.exists(outfile):
os.remove(outfile)
flist = ['locations.txt', 'new_locations.txt']
flist = [os.path.join(self.input_dir, fname) for fname in flist]
#res = ipmag.combine_magic(flist, 'custom_outfile.txt', 3, 'locations')
res = ipmag.combine_magic(flist, outfile, 3, 'locations')
self.assertTrue(res)
self.assertEqual(res, outfile)
self.assertTrue(os.path.exists(outfile))
def combine(filenames, outfile, dir_path='.', data_model=2.5):
files = []
for f in filenames.split():
files.append(os.path.join(dir_path, f))
outfile = (os.path.join(dir_path, outfile))
ipmag.combine_magic(files, outfile, data_model=data_model)
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 combine_magic_files(self, WD, magic_files, data_model=3.0): # 2.5
if type(magic_files) != dict:
return
if data_model == 3.0:
# try:
if 'measurements' in magic_files.keys():
for dot_magic in magic_files['measurements']:
if not os.path.isfile(dot_magic):
magic_files['measurements'].remove(dot_magic)
print('-W- No data for {}'.format(dot_magic))
combine_magic(magic_files['measurements'],
os.path.join(WD, "measurements.txt"))
if 'specimens' in magic_files.keys():
combine_magic(magic_files['specimens'],
os.path.join(WD, "specimens.txt"))
if 'samples' in magic_files.keys():
combine_magic(magic_files['samples'],
os.path.join(WD, "samples.txt"))
if 'sites' in magic_files.keys():
combine_magic(magic_files['sites'],
os.path.join(WD, "sites.txt"))
if 'locations' in magic_files.keys():
combine_magic(magic_files['locations'],
os.path.join(WD, "locations.txt"))
# except FileNotFoundError:
# pass
else:
if 'measurements' in magic_files.keys():
combine_magic(magic_files['measurements'],
os.path.join(WD, "magic_measurements.txt"))
if 'specimens' in magic_files.keys():
combine_magic(magic_files['specimens'],
os.path.join(WD, "er_specimens.txt"))
if 'samples' in magic_files.keys():
combine_magic(magic_files['samples'],
os.path.join(WD, "er_samples.txt"))
if 'sites' in magic_files.keys():
combine_magic(magic_files['sites'],
os.path.join(WD, "er_sites.txt"))
def on_okButton(self, event):
outfiles = []
for i in range(self.max_files):
# read directiory path
dir_path = self.dir_paths[i].GetValue()
if not os.path.exists(dir_path):
continue
# get experiment
experiment = self.protocol_infos[i].GetValue()
# get location/user name
user_name = self.file_info_users[i].GetValue()
location_name = self.file_locations[i].GetValue()
# get Blab direction
lab_dec = self.file_info_Blab_dec[i].GetValue()
lab_inc = self.file_info_Blab_inc[i].GetValue()
# get Moment units
moment_units = self.moment_units[i].GetValue()
# get sample volume
volume = self.volumes[i].GetValue()
# get sample-specimen naming convention
samp_name_con = str(self.sample_naming[i].GetValue())
samp_name_chars = str(
self.sample_naming_char[i].GetValue())
# get site-sample naming convention
site_name_con = str(self.site_naming[i].GetValue())
site_name_chars = str(
self.site_naming_char[i].GetValue())
# create temporary outfile name
meas_file = os.path.join(self.WD, 'measurements_{}.txt'.format(i))
spec_file = os.path.join(self.WD, 'specimens_{}.txt'.format(i))
samp_file = os.path.join(self.WD, 'samples_{}.txt'.format(i))
site_file = os.path.join(self.WD, 'sites_{}.txt'.format(i))
loc_file = os.path.join(self.WD, 'locations_{}.txt'.format(i))
if dir_path:
res, fname = convert_2_magic.tdt(dir_path, experiment, meas_file,
spec_file, samp_file,
site_file, loc_file,
user_name, location_name, lab_dec, lab_inc, moment_units,
samp_name_con, samp_name_chars,
site_name_con, site_name_chars, volume,
output_dir_path=self.WD)
outfiles.append(fname)
# combine measurement files
ipmag.combine_magic(outfiles, self.output_file_path.GetValue(), magic_table="measurements")
for fname in outfiles:
os.remove(os.path.join(self.WD, fname))
# combine other types of files
fnames = os.listdir(self.WD)
for dtype in ['specimens', 'samples', 'sites', 'locations']:
outfile = os.path.join(self.WD, dtype + ".txt")
files = [f for f in fnames if dtype + "_" in f]
ipmag.combine_magic(files, outfile, magic_table=dtype)
for fname in files:
os.remove(os.path.join(self.WD, fname))
if res:
dlg1 = wx.MessageDialog(None, caption="Message:", message="file converted to {}\n you can try running thellier gui...\n".format(
self.output_file_path.GetValue()), style=wx.OK | wx.ICON_INFORMATION)
else:
dlg1 = wx.MessageDialog(
None, caption="Warning:", message="No file was created. Make sure you have selected folders that contain .tdt format files")
dlg1.ShowModal()
dlg1.Destroy()
self.Destroy()
def on_okButton(self, event):
outfiles = []
for i in range(self.max_files):
# read directiory path
dir_path = self.dir_paths[i].GetValue()
if not os.path.exists(dir_path):
continue
# get experiment
experiment = self.protocol_infos[i].GetValue()
# get location/user name
user_name = self.file_info_users[i].GetValue()
location_name = self.file_locations[i].GetValue()
# get Blab direction
lab_dec = self.file_info_Blab_dec[i].GetValue()
lab_inc = self.file_info_Blab_inc[i].GetValue()
# get Moment units
moment_units = self.moment_units[i].GetValue()
# get sample volume
volume = self.volumes[i].GetValue()
# get sample-specimen naming convention
samp_name_con = str(self.sample_naming[i].GetValue())
samp_name_chars = str(self.sample_naming_char[i].GetValue())
# get site-sample naming convention
site_name_con = str(self.site_naming[i].GetValue())
site_name_chars = str(self.site_naming_char[i].GetValue())
# create temporary outfile name
meas_file = os.path.join(self.WD, 'measurements_{}.txt'.format(i))
spec_file = os.path.join(self.WD, 'specimens_{}.txt'.format(i))
samp_file = os.path.join(self.WD, 'samples_{}.txt'.format(i))
site_file = os.path.join(self.WD, 'sites_{}.txt'.format(i))
loc_file = os.path.join(self.WD, 'locations_{}.txt'.format(i))
if dir_path:
res, fname = convert_2_magic.tdt(dir_path,
experiment,
meas_file,
spec_file,
samp_file,
site_file,
loc_file,
user_name,
location_name,
lab_dec,
lab_inc,
moment_units,
samp_name_con,
samp_name_chars,
site_name_con,
site_name_chars,
volume,
output_dir_path=self.WD)
outfiles.append(fname)
# combine measurement files
ipmag.combine_magic(outfiles,
self.output_file_path.GetValue(),
magic_table="measurements")
for fname in outfiles:
os.remove(os.path.join(self.WD, fname))
# combine other types of files
fnames = os.listdir(self.WD)
for dtype in ['specimens', 'samples', 'sites', 'locations']:
outfile = os.path.join(self.WD, dtype + ".txt")
files = [f for f in fnames if dtype + "_" in f]
ipmag.combine_magic(files, outfile, magic_table=dtype)
for fname in files:
os.remove(os.path.join(self.WD, fname))
if res:
dlg1 = wx.MessageDialog(
None,
caption="Message:",
message=
"file converted to {}\n you can try running thellier gui...\n".
format(self.output_file_path.GetValue()),
style=wx.OK | wx.ICON_INFORMATION)
else:
dlg1 = wx.MessageDialog(
None,
caption="Warning:",
message=
"No file was created. Make sure you have selected folders that contain .tdt format files"
)
dlg1.ShowModal()
dlg1.Destroy()
self.Destroy()
def test_with_input_output_dir(self):
flist = ['specimens.txt', 'extra_specimens.txt']
res = ipmag.combine_magic(flist, 'custom.out', data_model=3,
input_dir_path=self.input_dir)
self.assertTrue(res)
self.assertTrue(os.path.exists("custom.out"))
def on_okButton(self, event):
meas_files = []
spec_files = []
samp_files = []
site_files = []
loc_files = []
for i in range(self.max_files):
# read directory path
dirpath = self.dir_paths[i].GetValue()
if dirpath != "":
dir_name = os.path.realpath(dirpath)
#dir_name = str(dirpath.split("/")[-1])
else:
continue
# get location
location_name = self.file_locations[i].GetValue()
# get sample-specimen naming convention
samp_con = str(self.naming_con_boxes[i].GetValue())
samp_chars = str(self.naming_con_char[i].GetValue())
samp_chars = samp_chars.strip('"').strip("'")
if samp_con == "character delimited" and not samp_chars:
pw.simple_warning("To delimit samples by character, you must provide the delimiter, (eg. \"-\" or \"_\")!")
return
# get site-sample naming convention
site_con = str(self.site_name_conventions[i].GetValue())
site_chars = str(self.site_name_chars[i].GetValue())
site_chars = site_chars.strip('"').strip("'")
if site_con == "character delimited" and not site_chars:
pw.simple_warning("To delimit sites by character, you must provide the delimiter, (eg. \"-\" or \"_\")!")
return
# name output files
if self.data_model_num == 2:
meas_out = "magic_measurements_{}.txt".format(i)
spec_out = "er_specimens_{}.txt".format(i)
samp_out = "er_samples_{}.txt".format(i)
site_out = "er_sites_{}.txt".format(i)
loc_out = "er_locations_{}.txt".format(i)
else:
meas_out = "measurements_{}.txt".format(i)
spec_out = "specimens_{}.txt".format(i)
samp_out = "samples_{}.txt".format(i)
site_out = "sites_{}.txt".format(i)
loc_out = "locations_{}.txt".format(i)
# do conversion
convert.livdb(dir_name, self.WD, meas_out, spec_out,
samp_out, site_out, loc_out,
samp_con, samp_chars, site_con,
site_chars, location_name)
meas_files.append(meas_out)
spec_files.append(spec_out)
samp_files.append(samp_out)
site_files.append(site_out)
loc_files.append(loc_out)
if self.data_model_num == 2:
res = ipmag.combine_magic(meas_files, "magic_measurements.txt", 2)
ipmag.combine_magic(spec_files, "er_specimens.txt", 2)
else:
res = ipmag.combine_magic(meas_files, "measurements.txt", 3)
ipmag.combine_magic(spec_files, "specimens.txt", 3)
ipmag.combine_magic(samp_files, "samples.txt", 3)
ipmag.combine_magic(site_files, "sites.txt", 3)
ipmag.combine_magic(loc_files, "locations.txt", 3)
pmag.remove_files(meas_files)
pmag.remove_files(spec_files)
pmag.remove_files(samp_files)
pmag.remove_files(site_files)
pmag.remove_files(loc_files)
if res:
self.after_convert_dia()
else:
pw.simple_warning("Something when wrong with one or more of your files.\nSee Terminal/Command Prompt output for more details")
def combine(filenames,outfile,dir_path='.',data_model=2.5):
files=[]
for f in filenames.split():
files.append(os.path.join(dir_path,f))
outfile=(os.path.join(dir_path,outfile))
ipmag.combine_magic(files, outfile, data_model=data_model)
def on_okButton(self, event):
meas_files = []
spec_files = []
samp_files = []
site_files = []
loc_files = []
for i in range(self.max_files):
# read directory path
dirpath = self.dir_paths[i].GetValue()
if dirpath != "":
dir_name = os.path.realpath(dirpath)
#dir_name = str(dirpath.split("/")[-1])
else:
continue
# get location
location_name = self.file_locations[i].GetValue()
# get sample-specimen naming convention
samp_con = str(self.naming_con_boxes[i].GetValue())
samp_chars = str(self.naming_con_char[i].GetValue())
samp_chars = samp_chars.strip('"').strip("'")
if samp_con == "character delimited" and not samp_chars:
pw.simple_warning(
"To delimit samples by character, you must provide the delimiter, (eg. \"-\" or \"_\")!"
)
return
# get site-sample naming convention
site_con = str(self.site_name_conventions[i].GetValue())
site_chars = str(self.site_name_chars[i].GetValue())
site_chars = site_chars.strip('"').strip("'")
if site_con == "character delimited" and not site_chars:
pw.simple_warning(
"To delimit sites by character, you must provide the delimiter, (eg. \"-\" or \"_\")!"
)
return
# name output files
if self.data_model_num == 2:
meas_out = "magic_measurements_{}.txt".format(i)
spec_out = "er_specimens_{}.txt".format(i)
samp_out = "er_samples_{}.txt".format(i)
site_out = "er_sites_{}.txt".format(i)
loc_out = "er_locations_{}.txt".format(i)
else:
meas_out = "measurements_{}.txt".format(i)
spec_out = "specimens_{}.txt".format(i)
samp_out = "samples_{}.txt".format(i)
site_out = "sites_{}.txt".format(i)
loc_out = "locations_{}.txt".format(i)
# do conversion
convert.livdb(dir_name, self.WD, meas_out, spec_out, samp_out,
site_out, loc_out, samp_con, samp_chars, site_con,
site_chars, location_name)
meas_files.append(meas_out)
spec_files.append(spec_out)
samp_files.append(samp_out)
site_files.append(site_out)
loc_files.append(loc_out)
if self.data_model_num == 2:
res = ipmag.combine_magic(meas_files, "magic_measurements.txt", 2)
ipmag.combine_magic(spec_files, "er_specimens.txt", 2)
else:
res = ipmag.combine_magic(meas_files, "measurements.txt", 3)
ipmag.combine_magic(spec_files, "specimens.txt", 3)
ipmag.combine_magic(samp_files, "samples.txt", 3)
ipmag.combine_magic(site_files, "sites.txt", 3)
ipmag.combine_magic(loc_files, "locations.txt", 3)
pmag.remove_files(meas_files)
pmag.remove_files(spec_files)
pmag.remove_files(samp_files)
pmag.remove_files(site_files)
pmag.remove_files(loc_files)
if res:
self.after_convert_dia()
else:
pw.simple_warning(
"Something when wrong with one or more of your files.\nSee Terminal/Command Prompt output for more details"
)
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={})".format(crd, con)
print(CMD)
info_log(CMD, loc)
#os.system(CMD)
res, outfiles, zeq_images = ipmag.zeq_magic(crd=crd, n_plots="all", contribution=con)
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={}".format(con)
print(CMD)
info_log(CMD, loc)
#os.system(CMD)
ipmag.thellier_magic(n_specs='all', fmt="png", contribution=con)
# 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={}".format(con)
print(CMD)
info_log(CMD, loc)
#os.system(CMD)
ipmag.quick_hyst(fmt="png", n_plots='all', contribution=con)
# 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')".format(con)
print(CMD)
info_log(CMD, loc, "eqarea_magic.py")
ipmag.eqarea_magic(fmt="png", n_plots='all', ignore_tilt=True, plot_by="spc",
contribution=con, source_table="measurements")
#os.system(CMD)
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)
ipmag.eqarea_magic(crd=crd, fmt="png", n_plots='all', contribution=con, source_table="sites")
#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'
CMD = "ipmag.vgpmap_magic(proj='moll', sym='ro', size=5, fmt='png', contribution={})".format(con)
print(CMD)
info_log(CMD, loc, 'vgpmap_magic.py')
ipmag.vgpmap_magic(proj='moll', sym='ro', size=5, fmt="png", contribution=con)
#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
CMD = "histplot.py -twin -b 1 -xlab 'Intensity (uT)' -sav -f intensities.txt -F " + histfile
CMD = "ipmag.histplot('intensities.txt', outfile=histfile, xlab='Intensity (uT)', binsize=1, norm=-1, save_plots=True)".format(histfile)
info_log(CMD, loc)
print(CMD)
ipmag.histplot("intensities.txt", outfile=histfile, xlab="Intensity (uT)",
binsize=1, norm=-1, save_plots=True)
#os.system(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
if len(sdata) > 3:
CMD = CMD + ' -crd s'
CMD = "ipmag.aniso_magic(iboot=0, ihext=1, crd='s', fmt='png', contribution={})".format(con)
print(CMD)
info_log(CMD, loc)
#iboot, ihext = 0, 1
ipmag.aniso_magic(iboot=0, ihext=1, crd="s", fmt="png", contribution=con)
#os.system(CMD)
if len(gdata) > 3:
CMD = CMD + ' -crd g'
CMD = "ipmag.aniso_magic(iboot=0, ihext=1, crd='g', fmt='png', contribution={})".format(con)
print(CMD)
info_log(CMD, loc)
ipmag.aniso_magic(iboot=0, ihext=1, crd="g", fmt="png", contribution=con)
#os.system(CMD)
if len(tdata) > 3:
CMD = CMD + ' -crd t'
CMD = "ipmag.aniso_magic(iboot=0, ihext=1, crd='g', fmt='png', contribution={})".format(con)
print(CMD)
info_log(CMD, loc)
ipmag.aniso_magic(iboot=0, ihext=1, crd="t", fmt="png", contribution=con)
#os.system(CMD)
# remove temporary files
for fname in glob.glob('tmp*.txt'):
os.remove(fname)
try:
os.remove('intensities.txt')
except FileNotFoundError:
pass
# 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")
ipmag.polemap_magic(flip=True, rsym="gv", rsymsize=40, fmt="png", contribution=full_con)
#os.system(CMD)
else:
print('-I- No poles found')
if image_recs:
new_image_file = os.path.join('new_images.txt', dir_path)
old_image_file = os.path.join('images.txt', dir_path)
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],
magic_table="images", dir_path=dir_path)
else:
os.rename(new_image_file, old_image_file)
thumbnails.make_thumbnails(dir_path)
