def main():
"""
NAME
chi_magic.py
DESCRIPTION
plots magnetic susceptibility as a function of frequency and temperature and AC field
SYNTAX
chi_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, specify measurements format file, default "measurements.txt"
-T IND, specify temperature step to plot -- NOT IMPLEMENTED
-e EXP, specify experiment name to plot
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
-sav save figure and quit
"""
if "-h" in sys.argv:
print(main.__doc__)
return
infile = pmag.get_named_arg("-f", "measurements.txt")
dir_path = pmag.get_named_arg("-WD", ".")
infile = pmag.resolve_file_name(infile, dir_path)
fmt = pmag.get_named_arg("-fmt", "svg")
save_plots = False
interactive = True
if "-sav" in sys.argv:
interactive = False
save_plots = True
experiments = pmag.get_named_arg("-e", "")
ipmag.chi_magic(infile, dir_path, experiments, fmt, save_plots,
interactive)
def main():
"""
NAME
pmag_results_extract.py
DESCRIPTION
make a tab delimited output file from pmag_results table
SYNTAX
pmag_results_extract.py [command line options]
OPTIONS
-h prints help message and quits
-f RFILE, specify pmag_results table; default is pmag_results.txt
-fa AFILE, specify er_ages table; default is NONE
-fsp SFILE, specify pmag_specimens table, default is NONE
-fcr CFILE, specify pmag_criteria table, default is NONE
-g include specimen_grade in table - only works for PmagPy generated pmag_specimen formatted files.
-tex, output in LaTeX format
"""
do_help = pmag.get_flag_arg_from_sys('-h')
if do_help:
print(main.__doc__)
return False
res_file = pmag.get_named_arg('-f', 'pmag_results.txt')
crit_file = pmag.get_named_arg('-fcr', '')
spec_file = pmag.get_named_arg('-fsp', '')
age_file = pmag.get_named_arg('-fa', '')
grade = pmag.get_flag_arg_from_sys('-g')
latex = pmag.get_flag_arg_from_sys('-tex')
WD = pmag.get_named_arg('-WD', os.getcwd())
ipmag.pmag_results_extract(res_file, crit_file, spec_file, age_file, latex, grade, WD)
def main():
"""
NAME
chi_magic.py
DESCRIPTION
plots magnetic susceptibility as a function of frequency and temperature and AC field
SYNTAX
chi_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, specify measurements format file, default "measurements.txt"
-T IND, specify temperature step to plot -- NOT IMPLEMENTED
-e EXP, specify experiment name to plot
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
-sav save figure and quit
"""
if "-h" in sys.argv:
print(main.__doc__)
return
infile = pmag.get_named_arg("-f", "measurements.txt")
dir_path = pmag.get_named_arg("-WD", ".")
infile = pmag.resolve_file_name(infile, dir_path)
fmt = pmag.get_named_arg("-fmt", "svg")
save_plots = False
interactive = True
if "-sav" in sys.argv:
interactive = False
save_plots = True
experiments = pmag.get_named_arg("-e", "")
ipmag.chi_magic(infile, dir_path, experiments, fmt, save_plots, interactive)
def main():
"""
NAME
dayplot_magic.py
DESCRIPTION
makes 'day plots' (Day et al. 1977) and squareness/coercivity,
plots 'linear mixing' curve from Dunlop and Carter-Stiglitz (2006).
squareness coercivity of remanence (Neel, 1955) plots after
Tauxe et al. (2002)
SYNTAX
dayplot_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input hysteresis file, default is specimens.txt
-fmt [svg,png,jpg] format for output plots, default svg
-sav saves plots and quits quietly
"""
args = sys.argv
if "-h" in args:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg('-WD', '.')
fmt = pmag.get_named_arg('-fmt', 'svg')
save_plots = False
interactive = True
if '-sav' in sys.argv:
save_plots = True
interactive = False
infile = pmag.get_named_arg("-f", "specimens.txt")
ipmag.dayplot_magic(dir_path, infile, save=save_plots,
fmt=fmt, interactive=interactive)
def main():
"""
NAME
zeq_magic.py
DESCRIPTION
reads in a MagIC measurements formatted file, makes plots of remanence decay
during demagnetization experiments. Reads in prior interpretations saved in
a specimens formatted file interpretations in a specimens file.
interpretations are saved in the coordinate system used.
SYNTAX
zeq_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEASFILE: sets measurements format input file, default: measurements.txt
-fsp SPECFILE: sets specimens format file with prior interpreations, default: specimens.txt
-fsa SAMPFILE: sets samples format file sample=>site information, default: samples.txt
-fsi SITEFILE: sets sites format file with site=>location informationprior interpreations, default: samples.txt
-Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve)
-crd [s,g,t]: sets coordinate system, g=geographic, t=tilt adjusted, default: specimen coordinate system
-spc SPEC plots single specimen SPEC, saves plot with specified format
with optional -dir settings and quits
-dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none
beg: starting step for PCA calculation
end: ending step for PCA calculation
[L,P,F]: calculation type for line, plane or fisher mean
must be used with -spc option
-fmt FMT: set format of saved plot [png,svg,jpg]
-A: suppresses averaging of replicate measurements, default is to average
-sav: saves all plots without review
"""
if '-h' in sys.argv:
print(main.__doc__)
return
dir_path = pmag.get_named_arg("-WD", default_val=os.getcwd())
meas_file = pmag.get_named_arg("-f", default_val="measurements.txt")
spec_file = pmag.get_named_arg("-fsp", default_val="specimens.txt")
specimen = pmag.get_named_arg("-spc", default_val="")
samp_file = pmag.get_named_arg("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg("-fsi", default_val="sites.txt")
plot_file = pmag.get_named_arg("-Fp", default_val="")
crd = pmag.get_named_arg("-crd", default_val="s")
fmt = pmag.get_named_arg("-fmt", "svg")
specimen = pmag.get_named_arg("-spc", default_val="")
interactive = True
save_plots = False
if "-sav" in sys.argv:
interactive = False
save_plots = True
ipmag.zeq_magic(meas_file,
spec_file,
crd,
dir_path,
n_plots="all",
save_plots=save_plots,
fmt=fmt,
interactive=interactive,
specimen=specimen)
def main():
"""
NAME
histplot.py
DESCRIPTION
makes histograms for data
OPTIONS
-h prints help message and quits
-f input file name
-b binsize
-fmt [svg,png,pdf,eps,jpg] specify format for image, default is svg
-sav save figure and quit
-F output file name, default is hist.fmt
-N don't normalize
-twin plot both normalized and un-normalized y axes
-xlab Label of X axis
-ylab Label of Y axis
INPUT FORMAT
single variable
SYNTAX
histplot.py [command line options] [<file]
"""
interactive = True
save_plots = False
if '-sav' in sys.argv:
save_plots = True
interactive = False
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
fmt = pmag.get_named_arg('-fmt', 'svg')
fname = pmag.get_named_arg('-f', '')
outfile = pmag.get_named_arg("-F", "")
norm = 1
if '-N' in sys.argv:
norm = 0
if '-twin' in sys.argv:
norm = -1
binsize = pmag.get_named_arg('-b', 0)
if '-xlab' in sys.argv:
ind = sys.argv.index('-xlab')
xlab = sys.argv[ind + 1]
else:
xlab = 'x'
data = []
if not fname:
print('-I- Trying to read from stdin... <ctrl>-c to quit')
data = np.loadtxt(sys.stdin, dtype=np.float)
ipmag.histplot(fname, data, outfile, xlab, binsize, norm, fmt, save_plots,
interactive)
def main():
"""
NAME
histplot.py
DESCRIPTION
makes histograms for data
OPTIONS
-h prints help message and quits
-f input file name
-b binsize
-fmt [svg,png,pdf,eps,jpg] specify format for image, default is svg
-sav save figure and quit
-F output file name, default is hist.fmt
-N don't normalize
-twin plot both normalized and un-normalized y axes
-xlab Label of X axis
-ylab Label of Y axis
INPUT FORMAT
single variable
SYNTAX
histplot.py [command line options] [<file]
"""
interactive = True
save_plots = False
if '-sav' in sys.argv:
save_plots = True
interactive = False
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
fmt = pmag.get_named_arg('-fmt', 'svg')
fname = pmag.get_named_arg('-f', '')
outfile = pmag.get_named_arg("-F", "")
norm = 1
if '-N' in sys.argv:
norm = 0
if '-twin' in sys.argv:
norm = - 1
binsize = pmag.get_named_arg('-b', 0)
if '-xlab' in sys.argv:
ind = sys.argv.index('-xlab')
xlab = sys.argv[ind+1]
else:
xlab = 'x'
data = []
if not fname:
print('-I- Trying to read from stdin... <ctrl>-c to quit')
data = np.loadtxt(sys.stdin, dtype=np.float)
ipmag.histplot(fname, data, outfile, xlab, binsize, norm,
fmt, save_plots, interactive)
def main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or a file
downloaded from the MagIC database (http://earthref.org/MagIC)
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
-sep write location data to separate subdirectories (Location_*), (default False)
-O do not overwrite duplicate Location_* directories while downloading
-DM data model (2 or 3, default 3)
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
# interactive entry
if '-i' in sys.argv:
infile = input("Magic txt file for unpacking? ")
dir_path = '.'
input_dir_path = '.'
# non-interactive
else:
infile = pmag.get_named_arg("-f", reqd=True)
# if -O flag is present, overwrite is False
overwrite = pmag.get_flag_arg_from_sys("-O", true=False, false=True)
# if -sep flag is present, sep is True
sep = pmag.get_flag_arg_from_sys("-sep", true=True, false=False)
data_model = pmag.get_named_arg("-DM", default_val=3, reqd=False)
dir_path = pmag.get_named_arg("-WD", default_val=".", reqd=False)
input_dir_path = pmag.get_named_arg("-ID", default_val=".", reqd=False)
#if '-ID' not in sys.argv and '-WD' in sys.argv:
# input_dir_path = dir_path
if "-WD" not in sys.argv and "-ID" not in sys.argv:
input_dir_path = os.path.split(infile)[0]
if not input_dir_path:
input_dir_path = "."
ipmag.download_magic(infile, dir_path, input_dir_path, overwrite, True,
data_model, sep)
def main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or a file
downloaded from the MagIC database (http://earthref.org/MagIC)
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
-sep write location data to separate subdirectories (Location_*), (default False)
-O do not overwrite duplicate Location_* directories while downloading
-DM data model (2 or 3, default 3)
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
# interactive entry
if '-i' in sys.argv:
infile=input("Magic txt file for unpacking? ")
dir_path = '.'
input_dir_path = '.'
# non-interactive
else:
infile = pmag.get_named_arg("-f", reqd=True)
# if -O flag is present, overwrite is False
overwrite = pmag.get_flag_arg_from_sys("-O", true=False, false=True)
# if -sep flag is present, sep is True
sep = pmag.get_flag_arg_from_sys("-sep", true=True, false=False)
data_model = pmag.get_named_arg("-DM", default_val=3, reqd=False)
dir_path = pmag.get_named_arg("-WD", default_val=".", reqd=False)
input_dir_path = pmag.get_named_arg("-ID", default_val=".", reqd=False)
#if '-ID' not in sys.argv and '-WD' in sys.argv:
# input_dir_path = dir_path
if "-WD" not in sys.argv and "-ID" not in sys.argv:
input_dir_path = os.path.split(infile)[0]
if not input_dir_path:
input_dir_path = "."
ipmag.download_magic(infile, dir_path, input_dir_path, overwrite, True, data_model, sep)
def main():
"""
NAME
zeq_magic.py
DESCRIPTION
reads in a MagIC measurements formatted file, makes plots of remanence decay
during demagnetization experiments. Reads in prior interpretations saved in
a specimens formatted file interpretations in a specimens file.
interpretations are saved in the coordinate system used.
SYNTAX
zeq_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEASFILE: sets measurements format input file, default: measurements.txt
-fsp SPECFILE: sets specimens format file with prior interpreations, default: specimens.txt
-fsa SAMPFILE: sets samples format file sample=>site information, default: samples.txt
-fsi SITEFILE: sets sites format file with site=>location informationprior interpreations, default: samples.txt
-Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve)
-crd [s,g,t]: sets coordinate system, g=geographic, t=tilt adjusted, default: specimen coordinate system
-spc SPEC plots single specimen SPEC, saves plot with specified format
with optional -dir settings and quits
-dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none
beg: starting step for PCA calculation
end: ending step for PCA calculation
[L,P,F]: calculation type for line, plane or fisher mean
must be used with -spc option
-fmt FMT: set format of saved plot [png,svg,jpg]
-A: suppresses averaging of replicate measurements, default is to average
-sav: saves all plots without review
"""
if '-h' in sys.argv:
print(main.__doc__)
return
dir_path = pmag.get_named_arg("-WD", default_val=os.getcwd())
meas_file = pmag.get_named_arg(
"-f", default_val="measurements.txt")
spec_file = pmag.get_named_arg(
"-fsp", default_val="specimens.txt")
specimen = pmag.get_named_arg(
"-spc", default_val="")
samp_file = pmag.get_named_arg("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg("-fsi", default_val="sites.txt")
plot_file = pmag.get_named_arg("-Fp", default_val="")
crd = pmag.get_named_arg("-crd", default_val="s")
fmt = pmag.get_named_arg("-fmt", "svg")
specimen = pmag.get_named_arg("-spc", default_val="")
interactive = True
save_plots = False
if "-sav" in sys.argv:
interactive = False
save_plots = True
ipmag.zeq_magic(meas_file, spec_file, crd, dir_path, n_plots="all",
save_plots=save_plots, fmt=fmt, interactive=interactive, specimen=specimen)
def main():
kwargs = {}
# get command line arguments
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
kwargs['dir_path'] = sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
kwargs['input_dir_path'] = sys.argv[ind+1]
if "-h" in sys.argv:
help(__name__)
sys.exit()
if '-F' in sys.argv:
ind = sys.argv.index("-F")
kwargs['meas_file'] = sys.argv[ind+1]
if '-Fsp' in sys.argv:
ind = sys.argv.index("-Fsp")
kwargs['spec_file'] = sys.argv[ind+1]
if '-f' in sys.argv:
ind = sys.argv.index("-f")
kwargs['jr6_file'] = sys.argv[ind+1]
if "-A" in sys.argv:
kwargs['noave'] = True
if "-lat" in sys.argv:
ind = sys.argv.index("-lat")
kwargs['lat'] = sys.argv[ind+1]
if "-lon" in sys.argv:
ind = sys.argv.index("-lon")
kwargs['lon'] = sys.argv[ind+1]
if "-v" in sys.argv:
ind = sys.argv.index("-v")
kwargs['volume'] = sys.argv[ind+1]
kwargs['dc_field'] = pmag.get_named_arg('-dc', default_val=50e-6)
# do conversion
convert.iodp_jr6_lore(**kwargs)
def main():
if '-h' in sys.argv:
print(
"Some mapping utilities use the Etopo package for topography and these data sets do not come standard with the Python installation of Basemap. To install these additional files, use: 'install_etopo.py'."
)
print(
"However, if you are using cartopy for plotting (recommended), you do not need to run install_etopo.py."
)
return
try:
from mpl_toolkits.basemap import basemap_datadir
except:
print(
"-I- Some mapping utilities use the Etopo package for topography and these data sets do not come standard with the Python installation of Basemap. However, if you are using cartopy for plotting (recommended), you do not need to run install_etopo.py."
)
print(
"-E- Basemap does not appear to be installed, aborting program...")
else:
# allow user to specify what directory to find the data_files in
custom_dir = pmag.get_named_arg('-source-dir', default_val="")
if os.path.isdir(custom_dir):
data_dir = custom_dir
# if user didn't specify a directory, find the etopo20 directory
else:
# if installed by pip, etopo20 is in sys.prefix
pip_data_dir = os.path.join(sys.prefix, 'data_files', 'etopo20')
if os.path.isdir(pip_data_dir):
data_dir = pip_data_dir
else:
# if not installed by pip, etopo20 is in the local PmagPy directory
from pmagpy import find_pmag_dir
pmag_dir = find_pmag_dir.get_pmag_dir()
data_dir = os.path.join(pmag_dir, 'data_files', 'etopo20')
# if none of those options worked, warn the user:
if not os.path.isdir(data_dir):
print(
"-W- Could not find data_files to copy in {}".format(data_dir))
print(
"-I- You can run this program with the command line flag -source-dir to specify the location of the etopo20 directory."
)
print(
"-I- For example: 'install_etopo.py -source-dir ~/Python/PmagPy/data_files/etopo20'"
)
return
print("installing etopo20 files from ",
path.join(data_dir, 'etopo20*'))
print("to the basemap data directory: ", basemap_datadir)
if sys.platform in ['win32', 'win64']:
command = 'copy ' + path.join(data_dir,
'etopo20*') + " " + basemap_datadir
else:
command = 'cp ' + path.join(data_dir,
'etopo20*') + " " + basemap_datadir
os.system(command)
def param_argvs(inputs=None):
docm = '''
NAME
forc_diagram.py
DESCRIPTION
This is for FORC diagrams, including conventional and irregualar FORCs.
OPTIONS
-h prints help message and quits
-f input file name
-sf smooth factor
-fmt [svg,png,pdf,eps,jpg] specify format for image, default is svg
-sav save figure and quit
INPUT FILE:
the measured FORC data file must contain the line " Field Moment "
before the measured data.
SYNTAX
forc_diagram.py -f path_to_file/file.txt [command line options]
'''
fileAdres, SF = None, None
if '-h' in inputs:
print(docm)
sys.exit(0)
save = False
if '-sav' in inputs:
save = True
fmt = pmag.get_named_arg('-fmt', "svg")
fileAdres = pmag.get_named_arg('-f', reqd=True)
if not os.path.isfile(fileAdres):
print('-f file not exist')
return
SF = pmag.get_named_arg('-sf', reqd=True)
try:
SF = int(inputs[4])
except:
print('-sf has to be int')
return
return fileAdres, SF, save, fmt
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
if "-h" in args:
print(main.__doc__)
sys.exit()
pltspec = ""
verbose = pmagplotlib.verbose
dir_path = pmag.get_named_arg('-WD', '.')
dir_path = os.path.realpath(dir_path)
meas_file = pmag.get_named_arg('-f', 'measurements.txt')
fmt = pmag.get_named_arg('-fmt', 'png')
save_plots = False
interactive = True
if '-sav' in args:
verbose = False
save_plots = True
interactive = False
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind+1]
verbose = False
save_plots = True
ipmag.quick_hyst(dir_path, meas_file, save_plots,
interactive, fmt, pltspec, verbose)
def main():
"""
NAME
quick_hyst.py
DESCRIPTION
makes plots of hysteresis data
SYNTAX
quick_hyst.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is measurements.txt
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
if "-h" in args:
print(main.__doc__)
sys.exit()
pltspec = ""
verbose = pmagplotlib.verbose
dir_path = pmag.get_named_arg('-WD', '.')
dir_path = os.path.realpath(dir_path)
meas_file = pmag.get_named_arg('-f', 'measurements.txt')
fmt = pmag.get_named_arg('-fmt', 'png')
save_plots = False
interactive = True
if '-sav' in args:
verbose = False
save_plots = True
interactive = False
if '-spc' in args:
ind = args.index("-spc")
pltspec = args[ind + 1]
verbose = False
save_plots = True
ipmag.quick_hyst(dir_path, meas_file, save_plots, interactive, fmt,
pltspec, verbose)
def main():
"""
Take out dos problem characters from any file
"""
filename = pmag.get_named_arg('-f')
if not filename:
return
with open(filename, 'rb+') as f:
content = f.read()
f.seek(0)
f.write(content.replace(b'\r', b''))
f.truncate()
def main():
if '-h' in sys.argv:
print(" Help for move_data_files.py:")
print(
" Choose the folder where you want the PmagPy data files to be."
)
print(
" Navigate to that folder, and use the command: 'move_data_files.py'"
)
print(
" Alternatively, you may use the full path to the directory of your choice from anywhere in the file system, using the '-d' flag: 'move_data_files.py -d /Users/***/Desktop' where *** is your username"
)
print(
" **IMPORTANT** If you have a developer install, move_data_files.py won't work. Simply navigate to your PmagPy directory. You can find the data_files directory and all PmagPy notebooks there."
)
sys.exit()
# create PmagPy-data directory
dest = pmag.get_named_arg('-d', '.', False)
dest = path.realpath(dest)
dest = path.join(dest, 'PmagPy-data')
if not path.exists(dest):
try:
os.mkdir(dest)
except FileNotFoundError:
pass
# get source of data_files
source = pmag.get_named_arg('-s', sys.prefix, False)
source = path.realpath(source)
if source.endswith('data_files') or source.endswith('data_files/'):
source = path.split(source)[0]
# copy data_files to PmagPy-data directory
data_files = path.join(source, 'data_files')
copy_directory(data_files, dest)
# now try to get notebooks
pmagpy_dir = find_pmag_dir.get_pmag_dir()
# needs all the notebooks
for notebook_location in glob.glob(
path.join(source, "data_files", "PmagPy*.ipynb")):
notebook_name = os.path.split(notebook_location)[1]
shutil.copy(notebook_location, path.join(dest, notebook_name))
def main():
if '-h' in sys.argv:
print("Choose the folder where you want the PmagPy data files to be.")
print(
"Navigate to that folder, and use the command: 'move_data_files.py'"
)
print(
"Alternatively, you may use the full path to the directory of your choice from anywhere in the file system, using the '-d' flag: 'move_data_files.py -d /Users/***/Desktop' where *** is your username"
)
sys.exit()
# create PmagPy-data directory
dest = pmag.get_named_arg('-d', '.', False)
dest = path.realpath(dest)
dest = path.join(dest, 'PmagPy-data')
if not path.exists(dest):
try:
os.mkdir(dest)
except FileNotFoundError:
pass
# get source of data_files
source = pmag.get_named_arg('-s', sys.prefix, False)
source = path.realpath(source)
if source.endswith('data_files') or source.endswith('data_files/'):
source = path.split(source)[0]
# copy data_files to PmagPy-data directory
data_files = path.join(source, 'data_files')
copy_directory(data_files, dest)
# now try to get notebooks
pmagpy_dir = find_pmag_dir.get_pmag_dir()
for notebook in ['PmagPy.ipynb', 'PmagPy-cli.ipynb']:
# for pip install
notebook_location = path.join(dest, 'data_files', notebook)
if path.exists(notebook_location):
shutil.copy(path.join(dest, 'data_files', notebook),
path.join(dest, notebook))
# for developer install
elif pmagpy_dir:
if path.exists(path.join(pmagpy_dir, notebook)):
shutil.copy(path.join(pmagpy_dir, notebook),
path.join(dest, notebook))
def main():
if '-h' in sys.argv:
help_msg = """
Runs Pmag GUI for uploading, downloading, analyzing and visualizing
data.
SYNTAX
pmag_gui.py [command line options]
# or, for Anaconda users:
pmag_gui_anaconda [command line options]
OPTIONS
-DM NUM: MagIC data model number, default 3
-WD DIR: working directory, default current directory
EXAMPLE
pmag_gui.py -DM 2 -WD projects/my_old_project
INFORMATION
See https://earthref.org/PmagPy/cookbook/#pmag_gui.py for a complete tutorial
"""
print(help_msg)
sys.exit()
print('-I- Starting Pmag GUI - please be patient')
# if redirect is true, wxpython makes its own output window for stdout/stderr
if 'darwin' in sys.platform and (not set_env.IS_FROZEN):
app = wx.App(redirect=False)
else:
app = wx.App(redirect=True)
dir_path = pmag.get_named_arg("-WD", None)
data_model = pmag.get_named_arg('-DM', None)
app.frame = MagMainFrame(DM=data_model, WD=dir_path)
app.frame.Show()
app.frame.Center()
## use for debugging:
#if '-i' in sys.argv:
# import wx.lib.inspection
# wx.lib.inspection.InspectionTool().Show()
app.MainLoop()
def main():
kwargs = {}
if '-h' in sys.argv:
help(__name__)
sys.exit()
# if "-WD" in sys.argv:
# ind=sys.argv.index("-WD")
# kwargs['wd']=sys.argv[ind+1]
wd = pmag.get_named_arg('-WD', '.')
kwargs['wd'] = wd
if "-A" in sys.argv:
kwargs['noave'] = True
#convert_tdt_files_to_MagIC(wd, **kwargs)
convert(**kwargs)
def main():
kwargs = {}
if '-h' in sys.argv:
help(__name__)
sys.exit()
# if "-WD" in sys.argv:
# ind=sys.argv.index("-WD")
# kwargs['wd']=sys.argv[ind+1]
wd = pmag.get_named_arg('-WD', '.')
kwargs['wd'] = wd
if "-A" in sys.argv:
kwargs['noave'] = True
#convert_tdt_files_to_MagIC(wd, **kwargs)
convert(**kwargs)
def main():
if '-h' in sys.argv:
print(" Help for move_data_files.py:")
print(" Choose the folder where you want the PmagPy data files to be.")
print(" Navigate to that folder, and use the command: 'move_data_files.py'")
print(" Alternatively, you may use the full path to the directory of your choice from anywhere in the file system, using the '-d' flag: 'move_data_files.py -d /Users/***/Desktop' where *** is your username")
print(" **IMPORTANT** If you have a developer install, this won\'t work. Simply navigate to your PmagPy directory. You can find data_files, PmagPy.ipynb and PmagPy-cli.ipynb there.")
sys.exit()
# create PmagPy-data directory
dest = pmag.get_named_arg('-d', '.', False)
dest = path.realpath(dest)
dest = path.join(dest, 'PmagPy-data')
if not path.exists(dest):
try:
os.mkdir(dest)
except FileNotFoundError:
pass
# get source of data_files
source = pmag.get_named_arg('-s', sys.prefix, False)
source = path.realpath(source)
if source.endswith('data_files') or source.endswith('data_files/'):
source = path.split(source)[0]
# copy data_files to PmagPy-data directory
data_files = path.join(source, 'data_files')
copy_directory(data_files, dest)
# now try to get notebooks
pmagpy_dir = find_pmag_dir.get_pmag_dir()
for notebook in ['PmagPy.ipynb', 'PmagPy-cli.ipynb']:
# for pip install
notebook_location = path.join(dest, 'data_files', notebook)
if path.exists(notebook_location):
shutil.copy(path.join(dest, 'data_files', notebook), path.join(dest, notebook))
# for developer install
elif pmagpy_dir:
if path.exists(path.join(pmagpy_dir, notebook)):
shutil.copy(path.join(pmagpy_dir, notebook), path.join(dest, notebook))
def __init__(self, WD):
wx.Frame.__init__(self, None, wx.ID_ANY, self.title)
self.panel = wx.Panel(self)
self.max_files = 10
self.WD = WD
self.create_menu()
self.InitUI()
self.data_model_num = int(pmag.get_named_arg("-DM", 3))
if "-WD" in sys.argv:
ind = sys.argv.index('-WD')
self.WD = sys.argv[ind + 1]
else:
self.WD = "."
self.WD = os.path.realpath(self.WD)
os.chdir(self.WD)
def __init__(self, WD):
wx.Frame.__init__(self, None, wx.ID_ANY, self.title)
self.panel = wx.Panel(self)
self.max_files = 10
self.WD = WD
self.create_menu()
self.InitUI()
self.data_model_num = int(pmag.get_named_arg("-DM", 3))
if "-WD" in sys.argv:
ind = sys.argv.index('-WD')
self.WD = sys.argv[ind+1]
else:
self.WD = "."
self.WD = os.path.realpath(self.WD)
os.chdir(self.WD)
def main():
if '-h' in sys.argv:
help_msg = """
MagIC GUI is for creating and uploading contributions to the MagIC database.
Note: if you are starting with a measurement file, it is better to use
Pmag GUI instead.
MagIC GUI is mainly meant for contributions with specimen-level data and higher.
SYNTAX
magic_gui.py [command line options]
# or, for Anaconda users:
magic_gui_anaconda [command line options]
OPTIONS
-WD DIR: working directory, default current directory
EXAMPLE
magic_gui.py -WD projects/my_project
INFORMATION
See https://earthref.org/PmagPy/cookbook/#magic_gui.py for a complete tutorial
"""
print(help_msg)
sys.exit()
print('-I- Starting MagIC GUI - please be patient')
# if redirect is true, wxpython makes its own output window for stdout/stderr
if 'darwin' in sys.platform and (not set_env.IS_FROZEN):
app = wx.App(redirect=False)
else:
app = wx.App(redirect=True)
working_dir = pmag.get_named_arg('-WD', '')
app.frame = MainFrame(working_dir)
app.frame.Show()
app.frame.Center()
## use for debugging:
#if '-i' in sys.argv:
# import wx.lib.inspection
# wx.lib.inspection.InspectionTool().Show()
app.MainLoop()
def main():
kwargs = {}
if "-h" in sys.argv:
help(__name__)
sys.exit()
if '-WD' in sys.argv:
ind = sys.argv.index("-WD")
kwargs['dir_path'] = sys.argv[ind + 1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
kwargs['input_dir_path'] = sys.argv[ind + 1]
if "-A" in sys.argv:
kwargs['noave'] = 1
if '-f' in sys.argv:
ind = sys.argv.index("-f")
kwargs['srm_file'] = sys.argv[ind + 1]
if '-F' in sys.argv:
ind = sys.argv.index("-F")
kwargs['meas_file'] = sys.argv[ind + 1]
if '-Fsp' in sys.argv:
ind = sys.argv.index("-Fsp")
kwargs['spec_file'] = sys.argv[ind + 1]
if '-Fsi' in sys.argv:
ind = sys.argv.index("-Fsi")
kwargs['site_file'] = sys.argv[ind + 1]
if '-Fsa' in sys.argv:
ind = sys.argv.index("-Fsa")
kwargs['samp_file'] = sys.argv[ind + 1]
if '-Flo' in sys.argv:
ind = sys.argv.index("-Flo")
kwargs['loc_file'] = sys.argv[ind + 1]
if "-lat" in sys.argv:
ind = sys.argv.index("-lat")
kwargs['lat'] = sys.argv[ind + 1]
if "-lon" in sys.argv:
ind = sys.argv.index("-lon")
kwargs['lon'] = sys.argv[ind + 1]
kwargs['comp_depth_key'] = pmag.get_named_arg("-key", 'Depth CSF-B (m)')
# do conversion
convert.iodp_srm_lore(**kwargs)
def main():
if '-h' in sys.argv:
print("Some mapping utilities use the Etopo package for topography and these data sets do not come standard with the Python installation of Basemap. To install these additional files, use: 'install_etopo.py'.")
print("However, if you are using cartopy for plotting (recommended), you do not need to run install_etopo.py.")
return
try:
from mpl_toolkits.basemap import basemap_datadir
except:
print("-I- Some mapping utilities use the Etopo package for topography and these data sets do not come standard with the Python installation of Basemap. However, if you are using cartopy for plotting (recommended), you do not need to run install_etopo.py.")
print("-E- Basemap does not appear to be installed, aborting program...")
else:
# allow user to specify what directory to find the data_files in
custom_dir = pmag.get_named_arg('-source-dir', default_val="")
if os.path.isdir(custom_dir):
data_dir = custom_dir
# if user didn't specify a directory, find the etopo20 directory
else:
# if installed by pip, etopo20 is in sys.prefix
pip_data_dir = os.path.join(sys.prefix, 'data_files', 'etopo20')
if os.path.isdir(pip_data_dir):
data_dir = pip_data_dir
else:
# if not installed by pip, etopo20 is in the local PmagPy directory
from pmagpy import find_pmag_dir
pmag_dir = find_pmag_dir.get_pmag_dir()
data_dir = os.path.join(pmag_dir, 'data_files', 'etopo20')
# if none of those options worked, warn the user:
if not os.path.isdir(data_dir):
print("-W- Could not find data_files to copy in {}".format(data_dir))
print("-I- You can run this program with the command line flag -source-dir to specify the location of the etopo20 directory.")
print("-I- For example: 'install_etopo.py -source-dir ~/Python/PmagPy/data_files/etopo20'")
return
print("installing etopo20 files from ", path.join(data_dir, 'etopo20*'))
print("to the basemap data directory: ",basemap_datadir)
if sys.platform in ['win32', 'win64']:
command = 'copy ' + path.join(data_dir, 'etopo20*') + " "+ basemap_datadir
else:
command = 'cp ' + path.join(data_dir, 'etopo20*') + " "+ basemap_datadir
os.system(command)
def main():
if '-h' in sys.argv:
help_msg = """
Runs Pmag GUI for uploading, downloading, analyzing and visualizing
data.
SYNTAX
pmag_gui.py [command line options]
# or, for Anaconda users:
pmag_gui_anaconda [command line options]
OPTIONS
-DM NUM: MagIC data model number, default 3
-WD DIR: working directory, default current directory
EXAMPLE
pmag_gui.py -DM 2 -WD projects/my_old_project
INFORMATION
See https://earthref.org/PmagPy/cookbook/#pmag_gui.py for a complete tutorial
"""
print(help_msg)
sys.exit()
print('-I- Starting Pmag GUI - please be patient')
# if redirect is true, wxpython makes its own output window for stdout/stderr
if 'darwin' in sys.platform:
app = wx.App(redirect=False)
else:
app = wx.App(redirect=True)
app.frame = MagMainFrame()
working_dir = pmag.get_named_arg('-WD', '.')
app.frame.Show()
app.frame.Center()
## use for debugging:
#if '-i' in sys.argv:
# import wx.lib.inspection
# wx.lib.inspection.InspectionTool().Show()
app.MainLoop()
def main():
if '-h' in sys.argv:
print("See https://earthref.org/PmagPy/cookbook/#magic_gui.py for a complete tutorial")
sys.exit()
print('-I- Starting MagIC GUI - please be patient')
# if redirect is true, wxpython makes its own output window for stdout/stderr
app = wx.App(redirect=True)
working_dir = pmag.get_named_arg('-WD', '.')
app.frame = MainFrame(working_dir)
## this causes an error with Canopy Python
## (it works with brew Python)
## need to use these lines for Py2app
if working_dir == '.':
app.frame.on_change_dir_button(None)
app.frame.Show()
app.frame.Center()
## use for debugging:
#if '-i' in sys.argv:
# import wx.lib.inspection
# wx.lib.inspection.InspectionTool().Show()
app.MainLoop()
def main():
"""
NAME
upload_magic.py
DESCRIPTION
This program will prepare your MagIC text files for uploading to the MagIC database
it will check for all the MagIC text files and skip the missing ones
SYNTAX
upload_magic.py
INPUT
MagIC txt files
OPTIONS
-h prints help message and quits
-all include all the measurement data, default is only those used in interpretations
-DM specify which MagIC data model number to use (2 or 3). Default is 3.
OUTPUT
upload file: file for uploading to MagIC database
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
else:
data_model_num = pmag.get_named_arg("-DM", 3)
dataframe = extractor.command_line_dataframe([['cat', False, 0], ['F', False, ''], ['f', False, '']])
checked_args = extractor.extract_and_check_args(sys.argv, dataframe)
dir_path, concat = extractor.get_vars(['WD', 'cat'], checked_args)
data_model_num = int(float(data_model_num))
if data_model_num == 2:
ipmag.upload_magic2(concat, dir_path)
else:
ipmag.upload_magic(concat, dir_path)
def main():
"""
NAME
hysteresis_magic.py
DESCRIPTION
calculates hystereis parameters and saves them in 3.0 specimen format file
makes plots if option selected
SYNTAX
hysteresis_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f: specify input file, default is agm_measurements.txt
-F: specify specimens.txt output file
-WD: directory to output files to (default : current directory)
Note: if using Windows, all figures will output to current directory
-ID: directory to read files from (default : same as -WD)
-P: do not make the plots
-spc SPEC: specify specimen name to plot and quit
-sav save all plots and quit
-fmt [png,svg,eps,jpg]
"""
args = sys.argv
fmt = pmag.get_named_arg('-fmt', 'svg')
output_dir_path = pmag.get_named_arg('-WD', '.')
input_dir_path = pmag.get_named_arg('-ID', "")
if "-h" in args:
print(main.__doc__)
sys.exit()
meas_file = pmag.get_named_arg('-f', 'measurements.txt')
spec_file = pmag.get_named_arg('-F', 'specimens.txt')
make_plots = True
save_plots = False
if '-P' in args:
make_plots = False
if '-sav' in args:
save_plots = True
pltspec = pmag.get_named_arg('-spc', 0)
ipmag.hysteresis_magic(output_dir_path, input_dir_path, spec_file, meas_file,
fmt, save_plots, make_plots, pltspec)
def main():
"""
NAME
mk_redo.py
DESCRIPTION
Makes thellier_redo and zeq_redo files from existing pmag_specimens format file
SYNTAX
mk_redo.py [-h] [command line options]
INPUT
takes specimens.txt formatted input file
OPTIONS
-h: prints help message and quits
-f FILE: specify input file, default is 'specimens.txt'
-F REDO: specify output file suffix, default is redo so that
output filenames are 'thellier_redo' for thellier data and 'zeq_redo' for direction only data
OUTPUT
makes a thellier_redo or a zeq_redo format file
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
zfile, tfile = 'zeq_redo', 'thellier_redo'
zredo, tredo = "", ""
dir_path = pmag.get_named_arg('-WD', '.')
inspec = pmag.get_named_arg('-f', 'specimens.txt')
if '-F' in sys.argv:
ind = sys.argv.index('-F')
redo = sys.argv[ind + 1]
tfile = redo
zfile = redo
inspec = pmag.resolve_file_name(inspec, dir_path)
zfile = pmag.resolve_file_name(zfile, dir_path)
tfile = pmag.resolve_file_name(tfile, dir_path)
#
# read in data
#
specs = []
prior_spec_data, file_type = pmag.magic_read(inspec)
if file_type != 'specimens':
print(file_type, " this is not a valid pmag_specimens file")
sys.exit()
outstrings = []
for spec in prior_spec_data:
tmp = spec["method_codes"].split(":")
meths = []
for meth in tmp:
methods = meth.strip().split('-')
for m in methods:
if m not in meths:
meths.append(m)
if 'DIR' in meths: # DE-BFL, DE-BFP or DE-FM
specs.append(spec['specimen'])
if 'dir_comp' in list(spec.keys()) and spec['dir_comp'] != "" and spec['dir_comp'] != " ":
comp_name = spec['dir_comp']
else:
comp_name = string.ascii_uppercase[specs.count(
spec['specimen']) - 1]
calculation_type = "DE-BFL" # assume default calculation type is best-fit line
if "BFP" in meths:
calculation_type = 'DE-BFP'
elif "FM" in meths:
calculation_type = 'DE-FM'
if zredo == "":
zredo = open(zfile, "w")
outstring = '%s %s %s %s %s \n' % (
spec["specimen"], calculation_type, spec["meas_step_min"], spec["meas_step_max"], comp_name)
if outstring not in outstrings:
zredo.write(outstring)
outstrings.append(outstring) # only writes unique interpretions
elif "PI" in meths and "TRM" in meths: # thellier record
if tredo == "":
tredo = open(tfile, "w")
outstring = '%s %i %i \n' % (spec["specimen"], float(
spec["meas_step_min"]), float(spec["meas_step_max"]))
if outstring not in outstrings:
tredo.write(outstring)
outstrings.append(outstring) # only writes unique interpretions
print('Redo files saved to: ', zfile, tfile)
def main():
"""
NAME
s_magic.py
DESCRIPTION
converts .s format data to measurements format.
SYNTAX
s_magic.py [command line options]
OPTIONS
-h prints help message and quits
-DM DATA_MODEL_NUM data model number (default is 3)
-f SFILE specifies the .s file name
-sig last column has sigma
-typ Anisotropy type: AMS,AARM,ATRM (default is AMS)
-F FILE specifies the specimens formatted file name
-usr USER specify username
-loc location specify location/study name
-spc NUM : specify number of characters to
designate a specimen, default = 0
-spn SPECNAME, this specimen has the name SPECNAME
-n first column has specimen name
-crd [s,g,t], specify coordinate system of data
s=specimen,g=geographic,t=tilt adjusted, default is 's'
-ncn NCON: naming convention
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] sample, site, location info in er_samples.txt -- NOT CURRENTLY SUPPORTED
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
DEFAULT
FILE: specimens.txt
INPUT
X11,X22,X33,X12,X23,X13 (.s format file)
X11,X22,X33,X12,X23,X13,sigma (.s format file with -sig option)
SID, X11,X22,X33,X12,X23,X13 (.s format file with -n option)
OUTPUT
specimens.txt format file
NOTE
because .s files do not have specimen names or location information, the output MagIC files
will have to be changed prior to importing to data base.
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
data_model_num = pmag.get_named_arg("-DM", 3)
data_model_num = int(float(data_model_num))
sfile = pmag.get_named_arg("-f", reqd=True)
if data_model_num == 2:
anisfile = pmag.get_named_arg("-F", "rmag_anisotropy.txt")
else:
anisfile = pmag.get_named_arg("-F", "specimens.txt")
location = pmag.get_named_arg("-loc", "unknown")
user = pmag.get_named_arg("-usr", "")
sitename = pmag.get_named_arg("unknown", "")
specnum = pmag.get_named_arg("-spc", 0)
specnum = -int(specnum)
dir_path = pmag.get_named_arg("-WD", ".")
name = pmag.get_flag_arg_from_sys("-n")
sigma = pmag.get_flag_arg_from_sys("-sig")
spec = pmag.get_named_arg("-spn", "unknown")
atype = pmag.get_named_arg("-typ", 'AMS')
samp_con = pmag.get_named_arg("-ncn", "1")
#if '-sig' in sys.argv:
# sigma = 1
#if "-n" in sys.argv:
# name = 1
coord_type = pmag.get_named_arg("-crd", 's')
convert.s_magic(sfile, anisfile, dir_path, atype,
coord_type, sigma, samp_con, specnum,
location, spec, sitename, user, data_model_num, name)
def main():
"""
NAME
strip_magic.py
DESCRIPTION
plots various parameters versus depth or age
SYNTAX
strip_magic.py [command line optins]
OPTIONS
-h prints help message and quits
-DM NUM: specify data model num, options 2 (legacy) or 3 (default)
-f FILE: specify input magic format file from magic,default='pmag_results.txt'
supported types=[pmag_specimens, pmag_samples, pmag_sites, pmag_results, magic_web]
-obj [sit,sam,all]: specify object to site,sample,all for pmag_result table, default is all
-fmt [svg,png,jpg], format for images - default is svg
-x [age,pos]: specify whether age or stratigraphic position
-y [dec,inc,int,chi,lat,lon,vdm,vadm]
(lat and lon are VGP lat and lon)
-Iex: plot the expected inc at lat - only available for results with lat info in file
-ts TS amin amax: plot the GPTS for the time interval between amin and amax (numbers in Ma)
TS: [ck95, gts04]
-mcd method_code, specify method code, default is first one encountered
-sav save plot and quit
NOTES
when x and/or y are not specified, a list of possibilities will be presented to the user for choosing
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
xaxis, xplotind, yplotind = "", 0, 0 # (0 for strat pos)
yaxis, Xinc = "", ""
plot = 0
obj = 'all'
data_model_num = int(pmag.get_named_arg("-DM", 3))
# 2.5 keys
if data_model_num == 2:
supported = [
'pmag_specimens', 'pmag_samples', 'pmag_sites', 'pmag_results',
'magic_web'
] # available file types
Depth_keys = [
'specimen_core_depth', 'specimen_height', 'specimen_elevation',
'specimen_composite_depth', 'sample_core_depth', 'sample_height',
'sample_elevation', 'sample_composite_depth', 'site_core_depth',
'site_height', 'site_elevation', 'site_composite_depth',
'average_height'
]
Age_keys = [
'specimen_inferred_age', 'sample_inferred_age',
'site_inferred_age', 'average_age'
]
Unit_keys = {
'specimen_inferred_age': 'specimen_inferred_age_unit',
'sample_inferred_age': 'sample_inferred_age_unit',
'site_inferred_age': 'site_inferred_age_unit',
'average_age': 'average_age_unit'
}
Dec_keys = [
'measurement_dec', 'specimen_dec', 'sample_dec', 'site_dec',
'average_dec'
]
Inc_keys = [
'measurement_inc', 'specimen_inc', 'sample_inc', 'site_inc',
'average_inc'
]
Int_keys = [
'measurement_magnitude', 'measurement_magn_moment',
'measurement_magn_volume', 'measurement_magn_mass', 'specimen_int',
'specimen_int_rel', 'sample_int', 'sample_int_rel', 'site_int',
'site_int_rel', 'average_int', 'average_int_rel'
]
Chi_keys = ['measurement_chi_volume', 'measurement_chi_mass']
Lat_keys = ['sample_lat', 'site_lat', 'average_lat']
VLat_keys = ['vgp_lat']
VLon_keys = ['vgp_lon']
Vdm_keys = ['vdm']
Vadm_keys = ['vadm']
method_col_name = "magic_method_codes"
else:
# 3.0 keys
supported = ["specimens", "samples", "sites",
"locations"] # available file types
Depth_keys = ["height", "core_depth", "elevation", "composite_depth"]
Age_keys = ["age"]
Unit_keys = {"age": "age"}
Chi_keys = ["susc_chi_volume", "susc_chi_mass"]
Int_keys = [
"magn_moment", "magn_volume", "magn_mass", "int_abs", "int_rel"
]
Inc_keys = ["dir_inc"]
Dec_keys = ["dir_dec"]
Lat_Keys = ["lat"]
VLat_keys = ["vgp_lat", "pole_lat"]
VLon_keys = ["vgp_lon", "pole_lon"]
Vdm_keys = ["vdm", "pdm"]
Vadm_keys = ["vadm", "padm"]
method_col_name = "method_codes"
#
X_keys = [Age_keys, Depth_keys]
Y_keys = [
Dec_keys, Inc_keys, Int_keys, Chi_keys, VLat_keys, VLon_keys, Vdm_keys,
Vadm_keys
]
method, fmt = "", 'svg'
FIG = {'strat': 1}
plotexp, pTS = 0, 0
dir_path = pmag.get_named_arg("-WD", ".")
# default files
if data_model_num == 3:
res_file = pmag.get_named_arg("-f", "sites.txt")
else:
res_file = pmag.get_named_arg("-f", "pmag_results.txt")
res_file = pmag.resolve_file_name(res_file, dir_path)
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-obj' in sys.argv:
ind = sys.argv.index('-obj')
obj = sys.argv[ind + 1]
if '-x' in sys.argv:
ind = sys.argv.index('-x')
xaxis = sys.argv[ind + 1]
if '-y' in sys.argv:
ind = sys.argv.index('-y')
yaxis = sys.argv[ind + 1]
if yaxis == 'dec':
ykeys = Dec_keys
if yaxis == 'inc':
ykeys = Inc_keys
if yaxis == 'int':
ykeys = Int_keys
if yaxis == 'chi':
ykeys = Chi_keys
if yaxis == 'lat':
ykeys = VLat_keys
if yaxis == 'lon':
ykeys = VLon_keys
if yaxis == 'vdm':
ykeys = Vdm_keys
if yaxis == 'vadm':
ykeys = Vadm_keys
if '-mcd' in sys.argv:
ind = sys.argv.index('-mcd')
method = sys.argv[ind + 1]
if '-ts' in sys.argv:
ind = sys.argv.index('-ts')
ts = sys.argv[ind + 1]
amin = float(sys.argv[ind + 2])
amax = float(sys.argv[ind + 3])
pTS = 1
if '-Iex' in sys.argv:
plotexp = 1
if '-sav' in sys.argv:
plot = 1
#
#
# get data read in
Results, file_type = pmag.magic_read(res_file)
if file_type not in supported:
print("Unsupported file type ({}), try again".format(file_type))
sys.exit()
PltObjs = ['all']
if data_model_num == 2:
if file_type == 'pmag_results': # find out what to plot
for rec in Results:
resname = rec['pmag_result_name'].split()
if 'Sample' in resname and 'sam' not in PltObjs:
PltObjs.append('sam')
if 'Site' in resname and 'sit' not in PltObjs:
PltObjs.append('sit')
methcodes = []
# need to know all the measurement types from method_codes
if "magic_method_codes" in list(Results[0].keys()):
for rec in Results:
meths = rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in methcodes and 'LP' in meth:
# look for the lab treatments
methcodes.append(meth.strip())
#
# initialize some variables
X_unit = "" # Unit for age or depth plotting (meters if depth)
Xplots, Yplots = [], []
Xunits = []
yplotind, xplotind = 0, 0
#
# step through possible plottable keys
#
if xaxis == "" or yaxis == "":
for key in list(Results[0].keys()):
for keys in X_keys:
for xkeys in keys:
if key in xkeys:
for ResRec in Results:
if ResRec[key] != "":
# only plot something if there is something to plot!
Xplots.append(key)
break
for keys in Y_keys:
for pkeys in keys:
if key in pkeys:
for ResRec in Results:
if ResRec[key] != "":
Yplots.append(key)
break
X, Y = [], []
for plt in Xplots:
if plt in Age_keys and 'age' not in X:
X.append('age')
if plt in Depth_keys and 'pos' not in X:
X.append('pos')
for plt in Yplots:
if plt in Dec_keys and 'dec' not in Y:
Y.append('dec')
if plt in Inc_keys and 'inc' not in Y:
Y.append('inc')
if plt in Int_keys and 'int' not in Y:
Y.append('int')
if plt in Chi_keys and 'chi' not in Y:
Y.append('chi')
if plt in VLat_keys and 'lat' not in Y:
Y.append('lat')
if plt in VLon_keys and 'lon' not in Y:
Y.append('lon')
if plt in Vadm_keys and 'vadm' not in Y:
Y.append('vadm')
if plt in Vdm_keys and 'vdm' not in Y:
Y.append('vdm')
if file_type == 'pmag_results':
print('available objects for plotting: ', PltObjs)
print('available X plots: ', X)
print('available Y plots: ', Y)
print('available method codes: ', methcodes)
f = open(dir_path + '/.striprc', 'w')
for x in X:
f.write('x:' + x + '\n')
for y in Y:
f.write('y:' + y + '\n')
for m in methcodes:
f.write('m:' + m + '\n')
for obj in PltObjs:
f.write('obj:' + obj + '\n')
sys.exit()
if plotexp == 1:
for lkey in Lat_keys:
for key in list(Results[0].keys()):
if key == lkey:
lat = float(Results[0][lkey])
Xinc = [pmag.pinc(lat), -pmag.pinc(lat)]
break
if Xinc == "":
print('can not plot expected inc for site - lat unknown')
if method != "" and method not in methcodes:
print('your method not available, but these are: ')
print(methcodes)
print('use ', methcodes[0], '? ^D to quit')
if xaxis == 'age':
for akey in Age_keys:
for key in list(Results[0].keys()):
if key == akey:
Xplots.append(key)
Xunits.append(Unit_keys[key])
if xaxis == 'pos':
for dkey in Depth_keys:
for key in list(Results[0].keys()):
if key == dkey:
Xplots.append(key)
if len(Xplots) == 0:
print('desired X axis information not found')
sys.exit()
if xaxis == 'age':
age_unit = Results[0][Xunits[0]]
if len(Xplots) > 1:
print('multiple X axis keys found, using: ', Xplots[xplotind])
for ykey in ykeys:
for key in list(Results[0].keys()):
if key == ykey:
Yplots.append(key)
if len(Yplots) == 0:
print('desired Y axis information not found')
sys.exit()
if len(Yplots) > 1:
print('multiple Y axis keys found, using: ', Yplots[yplotind])
# check if age or depth info
if len(Xplots) == 0:
print("Must have either age or height info to plot ")
sys.exit()
#
# check for variable to plot
#
#
# determine X axis (age or depth)
#
if xaxis == "age":
plotind = "1"
if method == "":
try:
method = methcodes[0]
except IndexError:
method = ""
if xaxis == 'pos':
xlab = "Stratigraphic Height (meters)"
else:
xlab = "Age (" + age_unit + ")"
Xkey = Xplots[xplotind]
Ykey = Yplots[yplotind]
ylab = Ykey
#
# collect the data for plotting
XY = []
isign = 1.
# if float(Results[0][Xkey])/float(Results[-1][Xkey])>0 and float(Results[0][Xkey])<0:
# isign=-1. # x axis all same sign and negative, take positive (e.g.,for depth in core)
# xlab="Stratigraphic Position (meters)"
# else:
# isign=1.
for rec in Results:
if "magic_method_codes" in list(rec.keys()):
meths = rec["magic_method_codes"].split(":")
if method in meths: # make sure it is desired lab treatment step
if obj == 'all' and rec[Xkey].strip() != "":
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
elif rec[Xkey].strip() != "":
name = rec['pmag_result_name'].split()
if obj == 'sit' and "Site" in name:
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
if obj == 'sam' and "Sample" in name:
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
elif method == "":
if obj == 'all' and rec[Xkey].strip() != "":
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
elif rec[Xkey].strip() != "":
name = rec['pmag_result_name'].split()
if obj == 'sit' and "Site" in name:
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
if obj == 'sam' and "Sample" in name:
XY.append([isign * float(rec[Xkey]), float(rec[Ykey])])
else:
print("Something wrong with your plotting choices")
break
XY.sort()
title = ""
if "er_locations_names" in list(Results[0].keys()):
title = Results[0]["er_location_names"]
if "er_locations_name" in list(Results[0].keys()):
title = Results[0]["er_location_name"]
labels = [xlab, ylab, title]
pmagplotlib.plot_init(FIG['strat'], 10, 5)
pmagplotlib.plot_strat(FIG['strat'], XY, labels) # plot them
if plotexp == 1:
pmagplotlib.plot_hs(FIG['strat'], Xinc, 'b', '--')
if yaxis == 'inc' or yaxis == 'lat':
pmagplotlib.plot_hs(FIG['strat'], [0], 'b', '-')
pmagplotlib.plot_hs(FIG['strat'], [-90, 90], 'g', '-')
if pTS == 1:
FIG['ts'] = 2
pmagplotlib.plot_init(FIG['ts'], 10, 5)
pmagplotlib.plot_ts(FIG['ts'], [amin, amax], ts)
files = {}
for key in list(FIG.keys()):
files[key] = key + '.' + fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
files = {}
files['strat'] = xaxis + '_' + yaxis + '_.' + fmt
files['ts'] = 'ts.' + fmt
titles = {}
titles['strat'] = 'Depth/Time Series Plot'
titles['ts'] = 'Time Series Plot'
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif plot == 1:
pmagplotlib.save_plots(FIG, files)
else:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, [q]uit without saving: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
def main():
"""
NAME
agm_magic.py
DESCRIPTION
converts Micromag agm files to magic format
SYNTAX
agm_magic.py [-h] [command line options]
OPTIONS
-usr USER: identify user, default is "" - put in quotation marks!
-bak: this is a IRM backfield curve
-f FILE, specify input file, required
-fsa SAMPFILE, specify er_samples.txt file relating samples, site and locations names,default is none
-F MFILE, specify magic measurements formatted output file, default is agm_measurements.txt
-spn SPEC, specimen name, default is base of input file name, e.g. SPECNAME.agm
-spc NUM, specify number of characters to designate a specimen, default = 0
-Fsp SPECFILE : name of er_specimens.txt file for appending data to
[default: er_specimens.txt]
-ncn NCON,: specify naming convention: default is #1 below
-syn SYN, synthetic specimen name
-loc LOCNAME : specify location/study name,
should have either LOCNAME or SAMPFILE (unless synthetic)
-ins INST : specify which instrument was used (e.g, SIO-Maud), default is ""
-u units: [cgs,SI], default is cgs
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
[8] specimen is a synthetic - it has no sample, site, location information
NB: all others you will have to customize your self
or e-mail [email protected] for help.
OUTPUT
MagIC format files: magic_measurements, er_specimens, er_sample, er_site
"""
citation = 'This study'
MeasRecs = []
units = 'cgs'
meth = "LP-HYS"
version_num = pmag.get_version()
args = sys.argv
fmt = 'old'
er_sample_name, er_site_name, er_location_name = "", "", ""
inst = ""
er_location_name = "unknown"
er_synthetic_name = ""
user = ""
er_site_name = ""
dir_path = '.'
dm = 3
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-ID" in args:
ind = args.index("-ID")
input_dir_path = args[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
specfile = output_dir_path + '/er_specimens.txt'
output = output_dir_path + "/agm_measurements.txt"
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-bak" in args:
meth = "LP-IRM-DCD"
output = output_dir_path + "/irm_measurements.txt"
if "-new" in args: fmt = 'new'
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
output = output_dir_path + '/' + args[ind + 1]
if '-f' in args:
ind = args.index("-f")
agm_file = input_dir_path + '/' + args[ind + 1]
er_specimen_name = args[ind + 1].split('.')[0]
else:
print("agm_file field is required option")
print(main.__doc__)
sys.exit()
if '-Fsp' in args:
ind = args.index("-Fsp")
specfile = output_dir_path + '/' + args[ind + 1]
specnum, samp_con, Z = 0, '1', 1
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0: specnum = -specnum
if "-spn" in args:
ind = args.index("-spn")
er_specimen_name = args[ind + 1]
#elif "-syn" not in args:
# print "you must specify a specimen name"
# sys.exit()
if "-syn" in args:
ind = args.index("-syn")
er_synthetic_name = args[ind + 1]
er_specimen_name = ""
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
sampfile = input_dir_path + '/' + args[ind + 1]
Samps, file_type = pmag.magic_read(sampfile)
print('sample_file successfully read in')
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if "-ins" in args:
ind = args.index("-ins")
inst = args[ind + 1]
if "-u" in args:
ind = args.index("-u")
units = args[ind + 1]
dm = pmag.get_named_arg("-DM", 2)
ErSpecRecs, filetype = pmag.magic_read(specfile)
ErSpecRec, MeasRec = {}, {}
ErSpecRec['er_citation_names'] = "This study"
ErSpecRec['er_specimen_name'] = er_specimen_name
ErSpecRec['er_synthetic_name'] = er_synthetic_name
if specnum != 0:
ErSpecRec["er_sample_name"] = er_specimen_name[:specnum]
else:
ErSpecRec["er_sample_name"] = er_specimen_name
if "-fsa" in args and er_synthetic_name == "":
for samp in Samps:
if samp["er_sample_name"] == ErSpecRec["er_sample_name"]:
ErSpecRec["er_location_name"] = samp["er_location_name"]
ErSpecRec["er_site_name"] = samp["er_site_name"]
break
elif int(samp_con) != 6 and int(samp_con) != 8:
site = pmag.parse_site(ErSpecRec['er_sample_name'], samp_con, Z)
ErSpecRec["er_site_name"] = site
ErSpecRec["er_location_name"] = er_location_name
ErSpecRec['er_scientist_mail_names'] = user.strip()
insert = 1
for rec in ErSpecRecs:
if rec['er_specimen_name'] == er_specimen_name:
insert = 0
break
if insert == 1:
ErSpecRecs.append(ErSpecRec)
ErSpecRecs, keylist = pmag.fillkeys(ErSpecRecs)
pmag.magic_write(specfile, ErSpecRecs, 'er_specimens')
print("specimen name put in ", specfile)
f = open(agm_file, 'r')
Data = f.readlines()
if "ASCII" not in Data[0]: fmt = 'new'
measnum, start = 1, ""
if fmt == 'new': # new Micromag formatted file
end = 2
for skip in range(len(Data)):
line = Data[skip]
rec = line.split()
if 'Units' in line: units = rec[-1]
if "Raw" in rec:
start = skip + 2
if "Field" in rec and "Moment" in rec and start == "":
start = skip + 2
break
else:
start = 2
end = 1
for i in range(start, len(Data) - end): # skip header stuff
MeasRec = {}
for key in list(ErSpecRec.keys()):
MeasRec[key] = ErSpecRec[key]
MeasRec['magic_instrument_codes'] = inst
MeasRec['magic_method_codes'] = meth
if 'er_synthetic_name' in list(
MeasRec.keys()) and MeasRec['er_synthetic_name'] != "":
MeasRec['magic_experiment_name'] = er_synthetic_name + ':' + meth
else:
MeasRec['magic_experiment_name'] = er_specimen_name + ':' + meth
line = Data[i]
rec = line.split(',') # data comma delimited
if rec[0] != '\n':
if units == 'cgs':
field = float(rec[0]) * 1e-4 # convert from oe to tesla
else:
field = float(rec[0]) # field in tesla
if meth == "LP-HYS":
MeasRec['measurement_lab_field_dc'] = '%10.3e' % (field)
MeasRec['treatment_dc_field'] = ''
else:
MeasRec['measurement_lab_field_dc'] = ''
MeasRec['treatment_dc_field'] = '%10.3e' % (field)
if units == 'cgs':
MeasRec['measurement_magn_moment'] = '%10.3e' % (
float(rec[1]) * 1e-3) # convert from emu to Am^2
else:
MeasRec['measurement_magn_moment'] = '%10.3e' % (float(rec[1])
) # Am^2
MeasRec['treatment_temp'] = '273' # temp in kelvin
MeasRec['measurement_temp'] = '273' # temp in kelvin
MeasRec['measurement_flag'] = 'g'
MeasRec['measurement_standard'] = 'u'
MeasRec['measurement_number'] = '%i' % (measnum)
measnum += 1
MeasRec['magic_software_packages'] = version_num
MeasRecs.append(MeasRec)
# now we have to relabel LP-HYS method codes. initial loop is LP-IMT, minor loops are LP-M - do this in measurements_methods function
if meth == 'LP-HYS':
recnum = 0
while float(MeasRecs[recnum]['measurement_lab_field_dc']) < float(
MeasRecs[recnum + 1]['measurement_lab_field_dc']
) and recnum + 1 < len(MeasRecs): # this is LP-IMAG
MeasRecs[recnum]['magic_method_codes'] = 'LP-IMAG'
MeasRecs[recnum]['magic_experiment_name'] = MeasRecs[recnum][
'er_specimen_name'] + ":" + 'LP-IMAG'
recnum += 1
#
if int(dm) == 2:
pmag.magic_write(output, MeasRecs, 'magic_measurements')
else:
print('MagIC 3 is not supported yet')
sys.exit()
pmag.magic_write(output, MeasRecs, 'measurements')
print("results put in ", output)
def main():
"""
NAME
mk_redo.py
DESCRIPTION
Makes thellier_redo and zeq_redo files from existing pmag_specimens format file
SYNTAX
mk_redo.py [-h] [command line options]
INPUT
takes specimens.txt formatted input file
OPTIONS
-h: prints help message and quits
-f FILE: specify input file, default is 'specimens.txt'
-F REDO: specify output file suffix, default is redo so that
output filenames are 'thellier_redo' for thellier data and 'zeq_redo' for direction only data
OUTPUT
makes a thellier_redo or a zeq_redo format file
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
zfile, tfile = 'zeq_redo', 'thellier_redo'
zredo, tredo = "", ""
dir_path = pmag.get_named_arg('-WD', '.')
inspec = pmag.get_named_arg('-f', 'specimens.txt')
if '-F' in sys.argv:
ind = sys.argv.index('-F')
redo = sys.argv[ind + 1]
tfile = redo
zfile = redo
inspec = pmag.resolve_file_name(inspec, dir_path)
zfile = pmag.resolve_file_name(zfile, dir_path)
tfile = pmag.resolve_file_name(tfile, dir_path)
#
# read in data
#
specs = []
prior_spec_data, file_type = pmag.magic_read(inspec)
if file_type != 'specimens':
print(file_type, " this is not a valid pmag_specimens file")
sys.exit()
outstrings = []
for spec in prior_spec_data:
tmp = spec["method_codes"].split(":")
meths = []
for meth in tmp:
methods = meth.strip().split('-')
for m in methods:
if m not in meths:
meths.append(m)
if 'DIR' in meths: # DE-BFL, DE-BFP or DE-FM
specs.append(spec['specimen'])
if 'dir_comp' in list(spec.keys(
)) and spec['dir_comp'] != "" and spec['dir_comp'] != " ":
comp_name = spec['dir_comp']
else:
comp_name = string.ascii_uppercase[
specs.count(spec['specimen']) - 1]
calculation_type = "DE-BFL" # assume default calculation type is best-fit line
if "BFP" in meths:
calculation_type = 'DE-BFP'
elif "FM" in meths:
calculation_type = 'DE-FM'
if zredo == "":
zredo = open(zfile, "w")
outstring = '%s %s %s %s %s \n' % (
spec["specimen"], calculation_type, spec["meas_step_min"],
spec["meas_step_max"], comp_name)
if outstring not in outstrings:
zredo.write(outstring)
outstrings.append(outstring) # only writes unique interpretions
elif "PI" in meths and "TRM" in meths: # thellier record
if tredo == "":
tredo = open(tfile, "w")
outstring = '%s %i %i \n' % (spec["specimen"],
float(spec["meas_step_min"]),
float(spec["meas_step_max"]))
if outstring not in outstrings:
tredo.write(outstring)
outstrings.append(outstring) # only writes unique interpretions
print('Redo files saved to: ', zfile, tfile)
def main():
"""
NAME
chi_magic.py
DESCRIPTION
plots magnetic susceptibility as a function of frequency and temperature and AC field
SYNTAX
chi_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, specify measurements format file, default "measurements.txt"
-T IND, specify temperature step to plot
-e EXP, specify experiment name to plot
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
-sav save figure and quit
"""
if "-h" in sys.argv:
print(main.__doc__)
return
infile = pmag.get_named_arg("-f", "measurements.txt")
dir_path = pmag.get_named_arg("-WD", ".")
infile = pmag.resolve_file_name(infile, dir_path)
fmt = pmag.get_named_arg("-fmt", "svg")
show_plots = True
if "-sav" in sys.argv:
show_plots = False
experiments = pmag.get_named_arg("-e", "")
# read in data from data model 3 example file
chi_data_all = pd.read_csv(infile, sep='\t', header=1)
if not experiments:
try:
experiments = chi_data_all.experiment.unique()
except Exception as ex:
print(ex)
experiments = ["all"]
else:
experiments = [experiments]
plotnum = 0
figs = {}
fnames = {}
for exp in experiments:
if exp == "all":
chi_data = chi_data_all
chi_data = chi_data_all[chi_data_all.experiment == exp]
if len(chi_data) <= 1:
print('Not enough data to plot {}'.format(exp))
continue
plotnum += 1
pmagplotlib.plot_init(plotnum, 5, 5) # set up plot
figs[str(plotnum)] = plotnum
fnames[str(plotnum)] = exp + '_temperature.{}'.format(fmt)
# get arrays of available temps, frequencies and fields
Ts = np.sort(chi_data.meas_temp.unique())
Fs = np.sort(chi_data.meas_freq.unique())
Bs = np.sort(chi_data.meas_field_ac.unique())
# plot chi versus temperature at constant field
b = Bs.max()
for num, f in enumerate(Fs):
this_f = chi_data[chi_data.meas_freq == f]
this_f = this_f[this_f.meas_field_ac == b]
plt.plot(this_f.meas_temp, 1e6*this_f.susc_chi_volume,
label='%i' % (f)+' Hz')
plt.legend()
plt.xlabel('Temperature (K)')
plt.ylabel('$\chi$ ($\mu$SI)')
plt.title('B = '+'%7.2e' % (b) + ' T')
plotnum += 1
figs[str(plotnum)] = plotnum
fnames[str(plotnum)] = exp + '_frequency.{}'.format(fmt)
pmagplotlib.plot_init(plotnum, 5, 5) # set up plot
## plot chi versus frequency at constant B
b = Bs.max()
t = Ts.min()
this_t = chi_data[chi_data.meas_temp == t]
this_t = this_t[this_t.meas_field_ac == b]
plt.semilogx(this_t.meas_freq, 1e6 *
this_t.susc_chi_volume, label='%i' % (t)+' K')
plt.legend()
plt.xlabel('Frequency (Hz)')
plt.ylabel('$\chi$ ($\mu$SI)')
plt.title('B = '+'%7.2e' % (b) + ' T')
if show_plots:
pmagplotlib.draw_figs(figs)
ans = input(
"enter s[a]ve to save files, [return] to quit ")
if ans == 'a':
pmagplotlib.save_plots(figs, fnames)
sys.exit()
else:
sys.exit()
else:
pmagplotlib.save_plots(figs, fnames)
def main():
"""
NAME
dmag_magic.py
DESCRIPTION
plots intensity decay curves for demagnetization experiments
SYNTAX
dmag_magic -h [command line options]
INPUT
takes magic formatted measurements.txt files
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is: measurements.txt
-obj OBJ: specify object [loc, sit, sam, spc] for plot,
default is by location
-LT [AF,T,M]: specify lab treatment type, default AF
-XLP [PI]: exclude specific lab protocols,
(for example, method codes like LP-PI)
-N do not normalize by NRM magnetization
-sav save plots silently and quit
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
NOTE
loc: location (study); sit: site; sam: sample; spc: specimen
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
# initialize variables from command line + defaults
dir_path = pmag.get_named_arg("-WD", default_val=".")
input_dir_path = pmag.get_named_arg('-ID', '')
if not input_dir_path:
input_dir_path = dir_path
in_file = pmag.get_named_arg("-f", default_val="measurements.txt")
in_file = pmag.resolve_file_name(in_file, input_dir_path)
if "-ID" not in sys.argv:
input_dir_path = os.path.split(in_file)[0]
plot_by = pmag.get_named_arg("-obj", default_val="loc")
LT = pmag.get_named_arg("-LT", "AF")
no_norm = pmag.get_flag_arg_from_sys("-N")
norm = False if no_norm else True
save_plots = pmag.get_flag_arg_from_sys("-sav")
fmt = pmag.get_named_arg("-fmt", "svg")
XLP = pmag.get_named_arg("-XLP", "")
spec_file = pmag.get_named_arg("-fsp", default_val="specimens.txt")
samp_file = pmag.get_named_arg("-fsa", default_val="samples.txt")
site_file = pmag.get_named_arg("-fsi", default_val="sites.txt")
loc_file = pmag.get_named_arg("-flo", default_val="locations.txt")
plot(in_file, dir_path, input_dir_path, spec_file, samp_file,
site_file, loc_file, plot_by, LT, norm, XLP,
save_plots, fmt)
def __init__(self, WD=None, DM=None, dmodel=None):
"""
Input working directory, data model number (2.5 or 3),
and data model (optional).
"""
wx.Frame.__init__(self,
None,
wx.ID_ANY,
self.title,
name='pmag_gui mainframe')
#set icon
self.icon = wx.Icon()
icon_path = os.path.join(PMAGPY_DIRECTORY, 'programs', 'images',
'PmagPy.ico')
if os.path.isfile(icon_path):
self.icon.CopyFromBitmap(wx.Bitmap(icon_path, wx.BITMAP_TYPE_ANY))
self.SetIcon(self.icon)
else:
print("-I- PmagPy icon file not found -- skipping")
# if DM was provided:
if DM:
self.data_model_num = int(float(DM))
# try to get DM from command line args
if not DM:
self.data_model_num = int(float(pmag.get_named_arg("-DM", 0)))
DM = self.data_model_num
# if WD was provided:
if WD:
self.WD = WD
else:
WD = pmag.get_named_arg("-WD", '')
self.WD = WD
self.WD = os.path.realpath(self.WD)
self.data_model = dmodel
self.FIRST_RUN = True
self.panel = wx.Panel(self, name='pmag_gui main panel')
self.InitUI()
if WD and DM:
self.set_dm(self.data_model_num)
if WD:
self.dir_path.SetValue(self.WD)
# for use as module:
self.resource_dir = os.getcwd()
# set some things
self.HtmlIsOpen = False
self.Bind(wx.EVT_CLOSE, self.on_menu_exit)
# if not specified on the command line,
# make the user choose data model num (2 or 3)
# and working directory
wx.CallAfter(self.get_dm_and_wd, DM, WD)
# if specified directory doesn't exist, try to make it
try:
if not os.path.exists(self.WD):
os.mkdir(self.WD)
pw.simple_warning("New directory: {}\nwill be created".format(
self.WD))
except FileNotFoundError:
pw.simple_warning(
"You have provided a directory that does not exist and cannot be created.\n Please pick a different directory."
)
print(
"-W- You have provided a directory that does not exist and cannot be created.\n Please pick a different directory."
)
def main():
"""
NAME
trmaq_magic.py
DESCTIPTION
does non-linear trm acquisisiton correction
SYNTAX
trmaq_magic.py [-h][-i][command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-f MFILE, sets magic_measurements input file
-ft TSPEC, sets thellier_specimens input file
-F OUT, sets output for non-linear TRM acquisition corrected data
-sav save figures and quit
-fmt [png, svg, pdf]
-DM [2, 3] MagIC data model, default 3
DEFAULTS
MFILE: trmaq_measurements.txt
TSPEC: thellier_specimens.txt
OUT: NLT_specimens.txt
"""
meas_file = 'trmaq_measurements.txt'
tspec = "thellier_specimens.txt"
output = 'NLT_specimens.txt'
data_model_num = int(float(pmag.get_named_arg("-DM", 3)))
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-i' in sys.argv:
meas_file = input(
"Input magic_measurements file name? [trmaq_measurements.txt] ")
if meas_file == "":
meas_file = "trmaq_measurements.txt"
tspec = input(
" thellier_specimens file name? [thellier_specimens.txt] ")
if tspec == "":
tspec = "thellier_specimens.txt"
output = input(
"File for non-linear TRM adjusted specimen data: [NLTspecimens.txt] ")
if output == "":
output = "NLT_specimens.txt"
if '-f' in sys.argv:
ind = sys.argv.index('-f')
meas_file = sys.argv[ind+1]
if '-ft' in sys.argv:
ind = sys.argv.index('-ft')
tspec = sys.argv[ind+1]
if '-F' in sys.argv:
ind = sys.argv.index('-F')
output = sys.argv[ind+1]
if '-sav' in sys.argv:
save_plots = True
else:
save_plots = False
fmt = pmag.get_named_arg("-fmt", "svg")
#
PLT = {'aq': 1}
if not save_plots:
pmagplotlib.plot_init(PLT['aq'], 5, 5)
#
# get name of file from command line
#
comment = ""
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if 'measurements' not in file_type:
print(file_type, "This is not a valid measurements file ")
sys.exit()
if data_model_num == 2:
spec_col = "er_specimen_name"
lab_field_dc_col = "specimen_lab_field_dc"
int_col = "specimen_int"
meth_col = "magic_method_codes"
treat_dc_col = "treatment_dc_field"
magn_moment_col = "measurement_magn_moment"
experiment_col = "magic_experiment_name"
outfile_type = "pmag_specimens"
else:
spec_col = "specimen"
lab_field_dc_col = "int_treat_dc_field"
int_col = "int_abs"
meth_col = "method_codes"
treat_dc_col = "treat_dc_field"
magn_moment_col = "magn_moment"
experiment_col = "experiment"
outfile_type = "specimens"
sids = pmag.get_specs(meas_data)
specimen = 0
#
# read in thellier_specimen data
#
nrm, file_type = pmag.magic_read(tspec)
PmagSpecRecs= []
while specimen < len(sids):
#
# find corresoponding paleointensity data for this specimen
#
s = sids[specimen]
blab, best = "", ""
for nrec in nrm: # pick out the Banc data for this spec
if nrec[spec_col] == s:
try:
blab = float(nrec[lab_field_dc_col])
except ValueError:
continue
best = float(nrec[int_col])
TrmRec = nrec
break
if blab == "":
print("skipping ", s, " : no best ")
specimen += 1
else:
print(sids[specimen], specimen+1, 'of ',
len(sids), 'Best = ', best*1e6)
MeasRecs = []
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec[spec_col] == s:
meths = rec[meth_col].split(":")
methcodes = []
for meth in meths:
methcodes.append(meth.strip())
if "LP-TRM" in methcodes:
MeasRecs.append(rec)
if len(MeasRecs) < 2:
specimen += 1
print('skipping specimen - no trm acquisition data ', s)
#
# collect info for the PmagSpecRec dictionary
#
else:
TRMs, Bs = [], []
for rec in MeasRecs:
Bs.append(float(rec[treat_dc_col]))
TRMs.append(float(rec[magn_moment_col]))
# calculate best fit parameters through TRM acquisition data, and get new banc
NLpars = nlt.NLtrm(Bs, TRMs, best, blab, 0)
#
Mp, Bp = [], []
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
# predicted NRM for this field
npred = nlt.TRM(Bp[-1], NLpars['xopt']
[0], NLpars['xopt'][1])
Mp.append(npred)
pmagplotlib.plot_trm(
PLT['aq'], Bs, TRMs, Bp, Mp, NLpars, rec[experiment_col])
if not save_plots:
pmagplotlib.draw_figs(PLT)
print('Banc= ', float(NLpars['banc'])*1e6)
trmTC = {}
for key in list(TrmRec.keys()):
# copy of info from thellier_specimens record
trmTC[key] = TrmRec[key]
trmTC[int_col] = '%8.3e' % (NLpars['banc'])
trmTC[meth_col] = TrmRec[meth_col]+":DA-NL"
PmagSpecRecs.append(trmTC)
if not save_plots:
ans = input("Return for next specimen, s[a]ve plot ")
if ans == 'a':
Name = {'aq': rec[spec_col]+'_TRM.{}'.format(fmt)}
pmagplotlib.save_plots(PLT, Name)
else:
Name = {'aq': rec[spec_col]+'_TRM.{}'.format(fmt)}
pmagplotlib.save_plots(PLT, Name)
specimen += 1
pmag.magic_write(output, PmagSpecRecs, outfile_type)
def main():
"""
NAME
foldtest_magic.py
DESCRIPTION
does a fold test (Tauxe, 2010) on data
INPUT FORMAT
pmag_specimens format file, er_samples.txt format file (for bedding)
SYNTAX
foldtest_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f sites formatted file [default for 3.0 is sites.txt, for 2.5, pmag_sites.txt]
-fsa samples formatted file
-fsi sites formatted file
-exc use criteria to set acceptance criteria (supported only for data model 3)
-n NB, set number of bootstraps, default is 1000
-b MIN, MAX, set bounds for untilting, default is -10, 150
-fmt FMT, specify format - default is svg
-sav saves plots and quits
-DM NUM MagIC data model number (2 or 3, default 3)
OUTPUT
Geographic: is an equal area projection of the input data in
original coordinates
Stratigraphic: is an equal area projection of the input data in
tilt adjusted coordinates
% Untilting: The dashed (red) curves are representative plots of
maximum eigenvalue (tau_1) as a function of untilting
The solid line is the cumulative distribution of the
% Untilting required to maximize tau for all the
bootstrapped data sets. The dashed vertical lines
are 95% confidence bounds on the % untilting that yields
the most clustered result (maximum tau_1).
Command line: prints out the bootstrapped iterations and
finally the confidence bounds on optimum untilting.
If the 95% conf bounds include 0, then a pre-tilt magnetization is indicated
If the 95% conf bounds include 100, then a post-tilt magnetization is indicated
If the 95% conf bounds exclude both 0 and 100, syn-tilt magnetization is
possible as is vertical axis rotation or other pathologies
"""
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
kappa = 0
dir_path = pmag.get_named_arg("-WD", ".")
nboot = int(float(pmag.get_named_arg("-n", 1000))) # number of bootstraps
fmt = pmag.get_named_arg("-fmt", "svg")
data_model_num = int(float(pmag.get_named_arg("-DM", 3)))
if data_model_num == 3:
infile = pmag.get_named_arg("-f", 'sites.txt')
orfile = 'samples.txt'
site_col = 'site'
dec_col = 'dir_dec'
inc_col = 'dir_inc'
tilt_col = 'dir_tilt_correction'
dipkey, azkey = 'bed_dip', 'bed_dip_direction'
crit_col = 'criterion'
critfile = 'criteria.txt'
else:
infile = pmag.get_named_arg("-f", 'pmag_sites.txt')
orfile = 'er_samples.txt'
site_col = 'er_site_name'
dec_col = 'site_dec'
inc_col = 'site_inc'
tilt_col = 'site_tilt_correction'
dipkey, azkey = 'sample_bed_dip', 'sample_bed_dip_direction'
crit_col = 'pmag_criteria_code'
critfile = 'pmag_criteria.txt'
if '-sav' in sys.argv:
plot = 1
else:
plot = 0
if '-b' in sys.argv:
ind = sys.argv.index('-b')
untilt_min = int(sys.argv[ind+1])
untilt_max = int(sys.argv[ind+2])
else:
untilt_min, untilt_max = -10, 150
if '-fsa' in sys.argv:
orfile = pmag.get_named_arg("-fsa", "")
elif '-fsi' in sys.argv:
orfile = pmag.get_named_arg("-fsi", "")
if data_model_num == 3:
dipkey, azkey = 'bed_dip', 'bed_dip_direction'
else:
dipkey, azkey = 'site_bed_dip', 'site_bed_dip_direction'
else:
if data_model_num == 3:
orfile = 'sites.txt'
else:
orfile = 'pmag_sites.txt'
orfile = pmag.resolve_file_name(orfile, dir_path)
infile = pmag.resolve_file_name(infile, dir_path)
critfile = pmag.resolve_file_name(critfile, dir_path)
df = pd.read_csv(infile, sep='\t', header=1)
# keep only records with tilt_col
data = df.copy()
data = data[data[tilt_col].notnull()]
data = data.where(data.notnull(), "")
# turn into pmag data list
data = list(data.T.apply(dict))
# get orientation data
if data_model_num == 3:
# often orientation will be in infile (sites table)
if os.path.split(orfile)[1] == os.path.split(infile)[1]:
ordata = df[df[azkey].notnull()]
ordata = ordata[ordata[dipkey].notnull()]
ordata = list(ordata.T.apply(dict))
# sometimes orientation might be in a sample file instead
else:
ordata = pd.read_csv(orfile, sep='\t', header=1)
ordata = list(ordata.T.apply(dict))
else:
ordata, file_type = pmag.magic_read(orfile)
if '-exc' in sys.argv:
crits, file_type = pmag.magic_read(critfile)
SiteCrits = []
for crit in crits:
if crit[crit_col] == "DE-SITE":
SiteCrits.append(crit)
#break
# get to work
#
PLTS = {'geo': 1, 'strat': 2, 'taus': 3} # make plot dictionary
if not set_env.IS_WIN:
pmagplotlib.plot_init(PLTS['geo'], 5, 5)
pmagplotlib.plot_init(PLTS['strat'], 5, 5)
pmagplotlib.plot_init(PLTS['taus'], 5, 5)
if data_model_num == 2:
GEOrecs = pmag.get_dictitem(data, tilt_col, '0', 'T')
else:
GEOrecs = data
if len(GEOrecs) > 0: # have some geographic data
num_dropped = 0
DIDDs = [] # set up list for dec inc dip_direction, dip
for rec in GEOrecs: # parse data
dip, dip_dir = 0, -1
Dec = float(rec[dec_col])
Inc = float(rec[inc_col])
orecs = pmag.get_dictitem(
ordata, site_col, rec[site_col], 'T')
if len(orecs) > 0:
if orecs[0][azkey] != "":
dip_dir = float(orecs[0][azkey])
if orecs[0][dipkey] != "":
dip = float(orecs[0][dipkey])
if dip != 0 and dip_dir != -1:
if '-exc' in sys.argv:
keep = 1
for site_crit in SiteCrits:
crit_name = site_crit['table_column'].split('.')[1]
if crit_name and crit_name in rec.keys() and rec[crit_name]:
# get the correct operation (<, >=, =, etc.)
op = OPS[site_crit['criterion_operation']]
# then make sure the site record passes
if op(float(rec[crit_name]), float(site_crit['criterion_value'])):
keep = 0
if keep == 1:
DIDDs.append([Dec, Inc, dip_dir, dip])
else:
num_dropped += 1
else:
DIDDs.append([Dec, Inc, dip_dir, dip])
if num_dropped:
print("-W- Dropped {} records because each failed one or more criteria".format(num_dropped))
else:
print('no geographic directional data found')
sys.exit()
pmagplotlib.plot_eq(PLTS['geo'], DIDDs, 'Geographic')
data = np.array(DIDDs)
D, I = pmag.dotilt_V(data)
TCs = np.array([D, I]).transpose()
pmagplotlib.plot_eq(PLTS['strat'], TCs, 'Stratigraphic')
if plot == 0:
pmagplotlib.draw_figs(PLTS)
Percs = list(range(untilt_min, untilt_max))
Cdf, Untilt = [], []
plt.figure(num=PLTS['taus'])
print('doing ', nboot, ' iterations...please be patient.....')
for n in range(nboot): # do bootstrap data sets - plot first 25 as dashed red line
if n % 50 == 0:
print(n)
Taus = [] # set up lists for taus
PDs = pmag.pseudo(DIDDs)
if kappa != 0:
for k in range(len(PDs)):
d, i = pmag.fshdev(kappa)
dipdir, dip = pmag.dodirot(d, i, PDs[k][2], PDs[k][3])
PDs[k][2] = dipdir
PDs[k][3] = dip
for perc in Percs:
tilt = np.array([1., 1., 1., 0.01*perc])
D, I = pmag.dotilt_V(PDs*tilt)
TCs = np.array([D, I]).transpose()
ppars = pmag.doprinc(TCs) # get principal directions
Taus.append(ppars['tau1'])
if n < 25:
plt.plot(Percs, Taus, 'r--')
# tilt that gives maximum tau
Untilt.append(Percs[Taus.index(np.max(Taus))])
Cdf.append(float(n) / float(nboot))
plt.plot(Percs, Taus, 'k')
plt.xlabel('% Untilting')
plt.ylabel('tau_1 (red), CDF (green)')
Untilt.sort() # now for CDF of tilt of maximum tau
plt.plot(Untilt, Cdf, 'g')
lower = int(.025*nboot)
upper = int(.975*nboot)
plt.axvline(x=Untilt[lower], ymin=0, ymax=1, linewidth=1, linestyle='--')
plt.axvline(x=Untilt[upper], ymin=0, ymax=1, linewidth=1, linestyle='--')
tit = '%i - %i %s' % (Untilt[lower], Untilt[upper], 'Percent Unfolding')
print(tit)
plt.title(tit)
if plot == 0:
pmagplotlib.draw_figs(PLTS)
ans = input('S[a]ve all figures, <Return> to quit \n ')
if ans != 'a':
print("Good bye")
sys.exit()
files = {}
for key in list(PLTS.keys()):
files[key] = ('foldtest_'+'%s' % (key.strip()[:2])+'.'+fmt)
pmagplotlib.save_plots(PLTS, files)
def main():
"""
NAME
foldtest_magic.py
DESCRIPTION
does a fold test (Tauxe, 2010) on data
INPUT FORMAT
pmag_specimens format file, er_samples.txt format file (for bedding)
SYNTAX
foldtest_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f sites formatted file [default for 3.0 is sites.txt, for 2.5, pmag_sites.txt]
-fsa samples formatted file
-fsi sites formatted file
-exc use criteria to set acceptance criteria (supported only for data model 3)
-n NB, set number of bootstraps, default is 1000
-b MIN, MAX, set bounds for untilting, default is -10, 150
-fmt FMT, specify format - default is svg
-sav saves plots and quits
-DM NUM MagIC data model number (2 or 3, default 3)
OUTPUT
Geographic: is an equal area projection of the input data in
original coordinates
Stratigraphic: is an equal area projection of the input data in
tilt adjusted coordinates
% Untilting: The dashed (red) curves are representative plots of
maximum eigenvalue (tau_1) as a function of untilting
The solid line is the cumulative distribution of the
% Untilting required to maximize tau for all the
bootstrapped data sets. The dashed vertical lines
are 95% confidence bounds on the % untilting that yields
the most clustered result (maximum tau_1).
Command line: prints out the bootstrapped iterations and
finally the confidence bounds on optimum untilting.
If the 95% conf bounds include 0, then a pre-tilt magnetization is indicated
If the 95% conf bounds include 100, then a post-tilt magnetization is indicated
If the 95% conf bounds exclude both 0 and 100, syn-tilt magnetization is
possible as is vertical axis rotation or other pathologies
"""
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
kappa = 0
dir_path = pmag.get_named_arg("-WD", ".")
nboot = int(float(pmag.get_named_arg("-n", 1000))) # number of bootstraps
fmt = pmag.get_named_arg("-fmt", "svg")
data_model_num = int(float(pmag.get_named_arg("-DM", 3)))
if data_model_num == 3:
infile = pmag.get_named_arg("-f", 'sites.txt')
orfile = 'samples.txt'
site_col = 'site'
dec_col = 'dir_dec'
inc_col = 'dir_inc'
tilt_col = 'dir_tilt_correction'
dipkey, azkey = 'bed_dip', 'bed_dip_direction'
crit_col = 'criterion'
critfile = 'criteria.txt'
else:
infile = pmag.get_named_arg("-f", 'pmag_sites.txt')
orfile = 'er_samples.txt'
site_col = 'er_site_name'
dec_col = 'site_dec'
inc_col = 'site_inc'
tilt_col = 'site_tilt_correction'
dipkey, azkey = 'sample_bed_dip', 'sample_bed_dip_direction'
crit_col = 'pmag_criteria_code'
critfile = 'pmag_criteria.txt'
if '-sav' in sys.argv:
plot = 1
else:
plot = 0
if '-b' in sys.argv:
ind = sys.argv.index('-b')
untilt_min = int(sys.argv[ind + 1])
untilt_max = int(sys.argv[ind + 2])
else:
untilt_min, untilt_max = -10, 150
if '-fsa' in sys.argv:
orfile = pmag.get_named_arg("-fsa", "")
elif '-fsi' in sys.argv:
orfile = pmag.get_named_arg("-fsi", "")
if data_model_num == 3:
dipkey, azkey = 'bed_dip', 'bed_dip_direction'
else:
dipkey, azkey = 'site_bed_dip', 'site_bed_dip_direction'
else:
if data_model_num == 3:
orfile = 'sites.txt'
else:
orfile = 'pmag_sites.txt'
orfile = pmag.resolve_file_name(orfile, dir_path)
infile = pmag.resolve_file_name(infile, dir_path)
critfile = pmag.resolve_file_name(critfile, dir_path)
df = pd.read_csv(infile, sep='\t', header=1)
# keep only records with tilt_col
data = df.copy()
data = data[data[tilt_col].notnull()]
data = data.where(data.notnull(), "")
# turn into pmag data list
data = list(data.T.apply(dict))
# get orientation data
if data_model_num == 3:
# often orientation will be in infile (sites table)
if os.path.split(orfile)[1] == os.path.split(infile)[1]:
ordata = df[df[azkey].notnull()]
ordata = ordata[ordata[dipkey].notnull()]
ordata = list(ordata.T.apply(dict))
# sometimes orientation might be in a sample file instead
else:
ordata = pd.read_csv(orfile, sep='\t', header=1)
ordata = list(ordata.T.apply(dict))
else:
ordata, file_type = pmag.magic_read(orfile)
if '-exc' in sys.argv:
crits, file_type = pmag.magic_read(critfile)
SiteCrits = []
for crit in crits:
if crit[crit_col] == "DE-SITE":
SiteCrits.append(crit)
#break
# get to work
#
PLTS = {'geo': 1, 'strat': 2, 'taus': 3} # make plot dictionary
if not set_env.IS_WIN:
pmagplotlib.plot_init(PLTS['geo'], 5, 5)
pmagplotlib.plot_init(PLTS['strat'], 5, 5)
pmagplotlib.plot_init(PLTS['taus'], 5, 5)
if data_model_num == 2:
GEOrecs = pmag.get_dictitem(data, tilt_col, '0', 'T')
else:
GEOrecs = data
if len(GEOrecs) > 0: # have some geographic data
num_dropped = 0
DIDDs = [] # set up list for dec inc dip_direction, dip
for rec in GEOrecs: # parse data
dip, dip_dir = 0, -1
Dec = float(rec[dec_col])
Inc = float(rec[inc_col])
orecs = pmag.get_dictitem(ordata, site_col, rec[site_col], 'T')
if len(orecs) > 0:
if orecs[0][azkey] != "":
dip_dir = float(orecs[0][azkey])
if orecs[0][dipkey] != "":
dip = float(orecs[0][dipkey])
if dip != 0 and dip_dir != -1:
if '-exc' in sys.argv:
keep = 1
for site_crit in SiteCrits:
crit_name = site_crit['table_column'].split('.')[1]
if crit_name and crit_name in rec.keys(
) and rec[crit_name]:
# get the correct operation (<, >=, =, etc.)
op = OPS[site_crit['criterion_operation']]
# then make sure the site record passes
if op(float(rec[crit_name]),
float(site_crit['criterion_value'])):
keep = 0
if keep == 1:
DIDDs.append([Dec, Inc, dip_dir, dip])
else:
num_dropped += 1
else:
DIDDs.append([Dec, Inc, dip_dir, dip])
if num_dropped:
print(
"-W- Dropped {} records because each failed one or more criteria"
.format(num_dropped))
else:
print('no geographic directional data found')
sys.exit()
pmagplotlib.plot_eq(PLTS['geo'], DIDDs, 'Geographic')
data = np.array(DIDDs)
D, I = pmag.dotilt_V(data)
TCs = np.array([D, I]).transpose()
pmagplotlib.plot_eq(PLTS['strat'], TCs, 'Stratigraphic')
if plot == 0:
pmagplotlib.draw_figs(PLTS)
Percs = list(range(untilt_min, untilt_max))
Cdf, Untilt = [], []
plt.figure(num=PLTS['taus'])
print('doing ', nboot, ' iterations...please be patient.....')
for n in range(
nboot
): # do bootstrap data sets - plot first 25 as dashed red line
if n % 50 == 0:
print(n)
Taus = [] # set up lists for taus
PDs = pmag.pseudo(DIDDs)
if kappa != 0:
for k in range(len(PDs)):
d, i = pmag.fshdev(kappa)
dipdir, dip = pmag.dodirot(d, i, PDs[k][2], PDs[k][3])
PDs[k][2] = dipdir
PDs[k][3] = dip
for perc in Percs:
tilt = np.array([1., 1., 1., 0.01 * perc])
D, I = pmag.dotilt_V(PDs * tilt)
TCs = np.array([D, I]).transpose()
ppars = pmag.doprinc(TCs) # get principal directions
Taus.append(ppars['tau1'])
if n < 25:
plt.plot(Percs, Taus, 'r--')
# tilt that gives maximum tau
Untilt.append(Percs[Taus.index(np.max(Taus))])
Cdf.append(float(n) / float(nboot))
plt.plot(Percs, Taus, 'k')
plt.xlabel('% Untilting')
plt.ylabel('tau_1 (red), CDF (green)')
Untilt.sort() # now for CDF of tilt of maximum tau
plt.plot(Untilt, Cdf, 'g')
lower = int(.025 * nboot)
upper = int(.975 * nboot)
plt.axvline(x=Untilt[lower], ymin=0, ymax=1, linewidth=1, linestyle='--')
plt.axvline(x=Untilt[upper], ymin=0, ymax=1, linewidth=1, linestyle='--')
tit = '%i - %i %s' % (Untilt[lower], Untilt[upper], 'Percent Unfolding')
print(tit)
plt.title(tit)
if plot == 0:
pmagplotlib.draw_figs(PLTS)
ans = input('S[a]ve all figures, <Return> to quit \n ')
if ans != 'a':
print("Good bye")
sys.exit()
files = {}
for key in list(PLTS.keys()):
files[key] = ('foldtest_' + '%s' % (key.strip()[:2]) + '.' + fmt)
pmagplotlib.save_plots(PLTS, files)
def main():
"""
NAME
revtest_magic.py
DESCRIPTION
calculates bootstrap statistics to test for antipodality
INPUT FORMAT
takes dec/inc data from sites table
SYNTAX
revtest_magic.py [command line options]
OPTION
-h prints help message and quits
-f FILE, sets pmag_sites filename on command line
-crd [s,g,t], set coordinate system, default is geographic
-exc use criteria file to set acceptance criteria (only available for data model 3)
-fmt [svg,png,jpg], sets format for image output
-sav saves plot and quits
-DM [2, 3] MagIC data model num, default is 3
"""
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
dir_path = pmag.get_named_arg("-WD", ".")
coord = pmag.get_named_arg("-crd",
"0") # default to geographic coordinates
if coord == 's':
coord = '-1'
elif coord == 'g':
coord = '0'
elif coord == 't':
coord = '100'
fmt = pmag.get_named_arg("-fmt", "svg")
if '-sav' in sys.argv:
plot = 1
data_model = int(float(pmag.get_named_arg("-DM")))
if data_model == 2:
infile = pmag.get_named_arg("-f", "pmag_sites.txt")
critfile = "pmag_criteria.txt"
tilt_corr_col = 'site_tilt_correction'
dec_col = "site_dec"
inc_col = "site_inc"
crit_code_col = "pmag_criteria_code"
else:
infile = pmag.get_named_arg("-f", "sites.txt")
critfile = "criteria.txt"
tilt_corr_col = "dir_tilt_correction"
dec_col = "dir_dec"
inc_col = "dir_inc"
crit_code_col = "criterion"
D = []
#
infile = pmag.resolve_file_name(infile, dir_path)
dir_path = os.path.split(infile)[0]
critfile = pmag.resolve_file_name(critfile, dir_path)
#
if data_model == 2:
Accept = ['site_k', 'site_alpha95', 'site_n', 'site_n_lines']
else:
Accept = [
'dir_k', 'dir_alpha95', 'dir_n_samples', 'dir_n_specimens_line'
]
data, file_type = pmag.magic_read(infile)
if 'sites' not in file_type:
print("Error opening file", file_type)
sys.exit()
# ordata,file_type=pmag.magic_read(orfile)
SiteCrits = []
if '-exc' in sys.argv and data_model != 2:
crits, file_type = pmag.magic_read(critfile)
for crit in crits:
if crit[crit_code_col] == "DE-SITE":
SiteCrit = crit
SiteCrits.append(SiteCrit)
elif '-exc' in sys.argv and data_model == 2:
print(
'-W- You have selected the -exc option, which is not available with MagIC data model 2.'
)
for rec in data:
if rec[tilt_corr_col] == coord:
Dec = float(rec[dec_col])
Inc = float(rec[inc_col])
if '-exc' in sys.argv and data_model != 2:
fail = False
for SiteCrit in SiteCrits:
for key in Accept:
if key not in SiteCrit['table_column']:
continue
if key not in rec:
continue
if SiteCrit['criterion_value'] != "":
op = OPS[SiteCrit['criterion_operation']]
if not op(float(rec[key]),
float(SiteCrit['criterion_value'])):
fail = True
if not fail:
D.append([Dec, Inc, 1.])
else:
D.append([Dec, Inc, 1.])
# set up plots
CDF = {'X': 1, 'Y': 2, 'Z': 3}
pmagplotlib.plot_init(CDF['X'], 5, 5)
pmagplotlib.plot_init(CDF['Y'], 5, 5)
pmagplotlib.plot_init(CDF['Z'], 5, 5)
#
# flip reverse mode
#
D1, D2 = pmag.flip(D)
counter, NumSims = 0, 500
#
# get bootstrapped means for each data set
#
if len(D1) < 5 or len(D2) < 5:
print('not enough data in two different modes for reversals test')
sys.exit()
print('doing first mode, be patient')
BDI1 = pmag.di_boot(D1)
print('doing second mode, be patient')
BDI2 = pmag.di_boot(D2)
pmagplotlib.plot_com(CDF, BDI1, BDI2, [""])
files = {}
for key in list(CDF.keys()):
files[key] = 'REV' + '_' + key + '.' + fmt
if plot == 0:
pmagplotlib.draw_figs(CDF)
ans = input("s[a]ve plots, [q]uit: ")
if ans == 'a':
pmagplotlib.save_plots(CDF, files)
else:
pmagplotlib.save_plots(CDF, files)
sys.exit()
def main():
if "-h" in sys.argv:
help(__name__)
sys.exit()
mag_file = pmag.get_named_arg('-f', reqd=True)
dir_path = pmag.get_named_arg('-WD', '.')
input_dir_path = pmag.get_named_arg('-ID', '')
meas_file = pmag.get_named_arg('-F', 'measurements.txt')
spec_file = pmag.get_named_arg('-Fsp', 'specimens.txt')
samp_file = pmag.get_named_arg('-Fsa', 'samples.txt')
site_file = pmag.get_named_arg('-Fsi', 'sites.txt')
loc_file = pmag.get_named_arg('-Flo', 'locations.txt')
lat = pmag.get_named_arg('-lat', '')
lon = pmag.get_named_arg('-lon', '')
specnum = pmag.get_named_arg('-spc', 0)
samp_con = pmag.get_named_arg('-ncn', '1')
location = pmag.get_named_arg('-loc', 'unknown')
noave = 0
if "-A" in sys.argv:
noave = 1
meth_code = pmag.get_named_arg('-mcd', "LP-NO")
convert.pmd(mag_file, dir_path, input_dir_path, meas_file,
spec_file, samp_file, site_file, loc_file,
lat, lon, specnum, samp_con, location, noave,
meth_code)
def main():
"""
NAME
mst_magic.py
DESCRIPTION
converts MsT data (T,M) to measurements format files
SYNTAX
mst_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify T,M format input file, required
-spn SPEC: specimen name, required
-fsa SFILE: name with sample, site, location information
-F FILE: specify output file, default is measurements.txt
-dc H: specify applied field during measurement, default is 0.5 T
-DM NUM: output to MagIC data model 2.5 or 3, default 3
-syn : This is a synthetic specimen and has no sample/site/location information
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT files:
T M: T is in Centigrade and M is uncalibrated magnitude
"""
#
# get command line arguments
#
args = sys.argv
if "-h" in args:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg("-WD", ".")
user = pmag.get_named_arg("-usr", "")
labfield = pmag.get_named_arg("-dc", '0.5')
meas_file = pmag.get_named_arg("-F", "measurements.txt")
samp_file = pmag.get_named_arg("-fsa", "samples.txt")
try:
infile = pmag.get_named_arg("-f", reqd=True)
except pmag.MissingCommandLineArgException:
print(main.__doc__)
print("-f is required option")
sys.exit()
specnum = int(pmag.get_named_arg("-spc", 0))
location = pmag.get_named_arg("-loc", "")
specimen_name = pmag.get_named_arg("-spn", reqd=True)
syn = 0
if "-syn" in args:
syn = 1
samp_con = pmag.get_named_arg("-ncn", "1")
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind+1]
data_model_num = int(pmag.get_named_arg("-DM", 3))
convert.mst(infile, specimen_name, dir_path, "", meas_file, samp_file,
user, specnum, samp_con, labfield, location, syn, data_model_num)
# bottom = height * .81
# with new aniso_magic
elif "ty:_aniso_data" in lower_infile or "ty:_aniso_conf" in lower_infile:
left = 0 + width * .215
top = 0 + height * .115
right = width * .86
bottom = height * .875
elif "ty:_aniso_tcdf" in lower_infile:
left = 0 + width * .124
top = 0 + height * .155
right = width * .902
bottom = height * .86
else:
error_log("Could not crop {}".format(infile))
im.save(infile[:-4] + ".thumb.{}".format(fmt), fmt, dpi=(300, 300))
continue
cropped = im.crop((left, top, right, bottom))
#cropped_example.show()
cropped.thumbnail((300, 300), Image.ANTIALIAS)
cropped.save(infile[:-4] + ".thumb.{}".format(fmt), fmt, dpi=(300, 300))
# Pixels ÷ DPI = Inches
if __name__ == "__main__":
if "-h" in sys.argv:
print('Make thumbnails for every png in current directory, or use: thumbnails.py -WD <directory>')
print('Specify input/output format with: -fmt <format>. Tested formats include [jpg, png]')
print('Output files will follow the naming convention: "original_filename.thumb.fmt"')
else:
make_thumbnails(pmag.get_named_arg("-WD", "."), pmag.get_named_arg("-fmt", "png"))
def main():
"""
NAME
plotXY.py
DESCRIPTION
Makes simple X,Y plots
INPUT FORMAT
X,Y data in columns
SYNTAX
plotxy.py [command line options]
OPTIONS
-h prints this help message
-f FILE to set file name on command line
-c col1 col2 specify columns to plot
-xsig col3 specify xsigma if desired
-ysig col4 specify xsigma if desired
-b xmin xmax ymin ymax, sets bounds
-sym SYM SIZE specify symbol to plot: default is red dots, 10 pt
-S don't plot the symbols
-xlab XLAB
-ylab YLAB
-l connect symbols with lines
-fmt [svg,png,pdf,eps] specify output format, default is svg
-sav saves plot and quits
-poly X plot a degree X polynomial through the data
-skip n Number of lines to skip before reading in data
"""
fmt,plot='svg',0
col1,col2=0,1
sym,size = 'ro',50
xlab,ylab='',''
lines=0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:plot=1
if '-c' in sys.argv:
ind=sys.argv.index('-c')
col1=int(sys.argv[ind+1])-1
col2=int(sys.argv[ind+2])-1
if '-xsig' in sys.argv:
ind=sys.argv.index('-xsig')
col3=int(sys.argv[ind+1])-1
if '-ysig' in sys.argv:
ind=sys.argv.index('-ysig')
col4=int(sys.argv[ind+1])-1
if '-xlab' in sys.argv:
ind=sys.argv.index('-xlab')
xlab=sys.argv[ind+1]
if '-ylab' in sys.argv:
ind=sys.argv.index('-ylab')
ylab=sys.argv[ind+1]
if '-b' in sys.argv:
ind=sys.argv.index('-b')
xmin=float(sys.argv[ind+1])
xmax=float(sys.argv[ind+2])
ymin=float(sys.argv[ind+3])
ymax=float(sys.argv[ind+4])
if '-poly' in sys.argv:
ind=sys.argv.index('-poly')
degr=sys.argv[ind+1]
if '-sym' in sys.argv:
ind=sys.argv.index('-sym')
sym=sys.argv[ind+1]
size=int(sys.argv[ind+2])
if '-l' in sys.argv: lines=1
if '-S' in sys.argv: sym=''
skip = int(pmag.get_named_arg('-skip', default_val=0))
X,Y=[],[]
Xerrs,Yerrs=[],[]
f=open(file,'r')
for num in range(skip):
f.readline()
data=f.readlines()
for line in data:
line.replace('\n','')
line.replace('\t',' ')
rec=line.split()
X.append(float(rec[col1]))
Y.append(float(rec[col2]))
if '-xsig' in sys.argv:Xerrs.append(float(rec[col3]))
if '-ysig' in sys.argv:Yerrs.append(float(rec[col4]))
if '-poly' in sys.argv:
pylab.plot(xs,ys)
coeffs=numpy.polyfit(X,Y,degr)
correl=numpy.corrcoef(X,Y)**2
polynomial=numpy.poly1d(coeffs)
xs=numpy.linspace(numpy.min(X),numpy.max(X),10)
ys=polynomial(xs)
pylab.plot(xs,ys)
print(polynomial)
if degr=='1': print('R-square value =', '%5.4f'%(correl[0,1]))
if sym!='':
pylab.scatter(X,Y,marker=sym[1],c=sym[0],s=size)
else:
pylab.plot(X,Y)
if '-xsig' in sys.argv and '-ysig' in sys.argv:
pylab.errorbar(X,Y,xerr=Xerrs,yerr=Yerrs,fmt=None)
if '-xsig' in sys.argv and '-ysig' not in sys.argv:
pylab.errorbar(X,Y,xerr=Xerrs,fmt=None)
if '-xsig' not in sys.argv and '-ysig' in sys.argv:
pylab.errorbar(X,Y,yerr=Yerrs,fmt=None)
if xlab!='':pylab.xlabel(xlab)
if ylab!='':pylab.ylabel(ylab)
if lines==1:pylab.plot(X,Y,'k-')
if '-b' in sys.argv:pylab.axis([xmin,xmax,ymin,ymax])
if plot==0:
pylab.show()
else:
pylab.savefig('plotXY.'+fmt)
print('Figure saved as ','plotXY.'+fmt)
sys.exit()
def main():
"""
NAME
lnp_magic.py
DESCRIPTION
makes equal area projections site by site
from specimen formatted file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
SYNTAX
lnp_magic [command line options]
INPUT
takes magic formatted specimens file
OUPUT
prints site_name n_lines n_planes K alpha95 dec inc R
OPTIONS
-h prints help message and quits
-f FILE: specify input file, default is 'specimens.txt', ('pmag_specimens.txt' for legacy data model 2)
-fsa FILE: specify samples file, required to plot by site for data model 3 (otherwise will plot by sample)
default is 'samples.txt'
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is specimen
-fmt [svg,png,jpg] format for plots, default is svg
-sav save plots and quit
-P: do not plot
-F FILE, specify output file of dec, inc, alpha95 data for plotting with plotdi_a and plotdi_e
-exc use criteria in criteria table # NOT IMPLEMENTED
-DM NUMBER MagIC data model (2 or 3, default 3)
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg("-WD", ".")
data_model = int(float(pmag.get_named_arg("-DM", 3)))
fmt = pmag.get_named_arg("-fmt", 'svg')
if data_model == 2:
in_file = pmag.get_named_arg('-f', 'pmag_specimens.txt')
crit_file = "pmag_criteria.txt"
else:
in_file = pmag.get_named_arg('-f', 'specimens.txt')
samp_file = pmag.get_named_arg('-fsa', 'samples.txt')
crit_file = "criteria.txt"
in_file = pmag.resolve_file_name(in_file, dir_path)
dir_path = os.path.split(in_file)[0]
if data_model == 3:
samp_file = pmag.resolve_file_name(samp_file, dir_path)
if '-crd' in sys.argv:
ind = sys.argv.index("-crd")
crd = sys.argv[ind+1]
if crd == 's':
coord = "-1"
if crd == 'g':
coord = "0"
if crd == 't':
coord = "100"
else:
coord = "-1"
out_file = pmag.get_named_arg('-F', '')
if out_file:
out = open(dir_path+'/'+out_file, 'w')
if '-P' in sys.argv:
make_plots = 0 # do not plot
else:
make_plots = 1 # do plot
if '-sav' in sys.argv:
plot = 1 # save plots and quit
else:
plot = 0 # show plots intereactively (if make_plots)
#
if data_model == 2:
Specs, file_type = pmag.magic_read(in_file)
if 'specimens' not in file_type:
print('Error opening ', in_file, file_type)
sys.exit()
else:
fnames = {'specimens': in_file, 'samples': samp_file}
con = cb.Contribution(dir_path, read_tables=['samples', 'specimens'],
custom_filenames=fnames)
con.propagate_name_down('site', 'specimens')
if 'site' in con.tables['specimens'].df.columns:
site_col = 'site'
else:
site_col = 'sample'
tilt_corr_col = "dir_tilt_correction"
mad_col = "dir_mad_free"
alpha95_col = "dir_alpha95"
site_alpha95_col = "dir_alpha95"
dec_col = "dir_dec"
inc_col = "dir_inc"
num_meas_col = "dir_n_measurements"
k_col = "dir_k"
cols = [site_col, tilt_corr_col, mad_col, alpha95_col, dec_col, inc_col]
con.tables['specimens'].front_and_backfill(cols)
con.tables['specimens'].df = con.tables['specimens'].df.where(con.tables['specimens'].df.notnull(), "")
Specs = con.tables['specimens'].convert_to_pmag_data_list()
## using criteria file was never fully implemented
#if '-exc' in sys.argv:
# Crits, file_type = pmag.magic_read(pmag.resolve_file_name(crit_file, dir_path))
# for crit in Crits:
# if mad_col in crit:
# M = float(crit['specimen_mad'])
# if num_meas_col in crit:
# N = float(crit['specimen_n'])
# if site_alpha95_col in crit and 'site' in crit:
# acutoff = float(crit['site_alpha95'])
# if k_col in crit:
# kcutoff = float(crit['site_k'])
#else:
# Crits = ""
sitelist = []
# initialize some variables
FIG = {} # plot dictionary
FIG['eqarea'] = 1 # eqarea is figure 1
M, N, acutoff, kcutoff = 180., 1, 180., 0.
if data_model == 2:
site_col = 'er_site_name'
tilt_corr_col = "specimen_tilt_correction"
mad_col = "specimen_mad"
alpha95_col = 'specimen_alpha95'
dec_col = "specimen_dec"
inc_col = "specimen_inc"
num_meas_col = "specimen_n"
site_alpha95_col = "site_alpha95"
else: # data model 3
pass
for rec in Specs:
if rec[site_col] not in sitelist:
sitelist.append(rec[site_col])
sitelist.sort()
if make_plots == 1:
EQ = {}
EQ['eqarea'] = 1
for site in sitelist:
pmagplotlib.plot_init(EQ['eqarea'], 4, 4)
print(site)
data = []
for spec in Specs:
if tilt_corr_col not in list(spec.keys()):
spec[tilt_corr_col] = '-1' # assume unoriented
if spec[site_col] == site:
if mad_col not in list(spec.keys()) or spec[mad_col] == "":
if alpha95_col in list(spec.keys()) and spec[alpha95_col] != "":
spec[mad_col] = spec[alpha95_col]
else:
spec[mad_col] = '180'
if not spec[num_meas_col]:
continue
if (float(spec[tilt_corr_col]) == float(coord)) and (float(spec[mad_col]) <= M) and (float(spec[num_meas_col]) >= N):
rec = {}
for key in list(spec.keys()):
rec[key] = spec[key]
rec["dec"] = float(spec[dec_col])
rec["inc"] = float(spec[inc_col])
rec["tilt_correction"] = spec[tilt_corr_col]
data.append(rec)
if len(data) > 2:
fpars = pmag.dolnp(data, 'specimen_direction_type')
print("Site lines planes kappa a95 dec inc")
print(site, fpars["n_lines"], fpars["n_planes"], fpars["K"],
fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"])
if out_file != "":
if float(fpars["alpha95"]) <= acutoff and float(fpars["K"]) >= kcutoff:
out.write('%s %s %s\n' %
(fpars["dec"], fpars['inc'], fpars['alpha95']))
print('% tilt correction: ', coord)
if make_plots == 1:
files = {}
files['eqarea'] = site+'_'+crd+'_'+'eqarea'+'.'+fmt
pmagplotlib.plot_lnp(EQ['eqarea'], site,
data, fpars, 'specimen_direction_type')
if plot == 0:
pmagplotlib.draw_figs(EQ)
ans = input(
"s[a]ve plot, [q]uit, <return> to continue:\n ")
if ans == "a":
pmagplotlib.save_plots(EQ, files)
if ans == "q":
sys.exit()
else:
pmagplotlib.save_plots(EQ, files)
else:
print('skipping site - not enough data with specified coordinate system')
def main():
"""
NAME
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-f AFILE, specify specimens.txt formatted file for input
-fsa SAMPFILE, specify samples.txt file (required to plot by site)
-fsi SITEFILE, specify site file (required to include location information)
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just fill in the specimens, samples, sites tables
-sav don't make the tables - just save all the plots
-fmt [svg, jpg, eps] format for output images, png default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-n N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: specimens.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
args = sys.argv
if '-h' in args:
print(new.__doc__)
return
dir_path = pmag.get_named_arg("-WD", ".")
if '-ID' in args and dir_path == '.':
dir_path = pmag.get_named_arg("-ID", ".")
iboot, vec = 1, 0
num_bootstraps = pmag.get_named_arg("-n", 1000)
ipar = pmag.get_flag_arg_from_sys("-par", true=1, false=0)
ihext = pmag.get_flag_arg_from_sys("-x", true=1, false=0)
ivec = pmag.get_flag_arg_from_sys("-v", true=1, false=0)
if ivec:
vec = 3
#iplot = pmag.get_flag_arg_from_sys("-P", true=0, false=1)
isite = pmag.get_flag_arg_from_sys("-sit", true=1, false=0)
infile = pmag.get_named_arg('-f', 'specimens.txt')
samp_file = pmag.get_named_arg('-fsa', 'samples.txt')
site_file = pmag.get_named_arg('-fsi', 'sites.txt')
#outfile = pmag.get_named_arg("-F", "rmag_results.txt")
fmt = pmag.get_named_arg("-fmt", "png")
crd = pmag.get_named_arg("-crd", "s")
comp, Dir, PDir = 0, [], []
user = pmag.get_named_arg("-usr", "")
if '-B' in args:
iboot, ihext = 0, 1
save_plots, verbose, interactive = False, True, True
if '-sav' in args:
save_plots = True
verbose = False
interactive = False
if '-gtc' in args:
ind = args.index('-gtc')
d, i = float(args[ind+1]), float(args[ind+2])
PDir.append(d)
PDir.append(i)
if '-d' in args:
comp = 1
ind = args.index('-d')
vec = int(args[ind+1])-1
Dir = [float(args[ind+2]), float(args[ind+3])]
ipmag.aniso_magic_nb(infile, samp_file, site_file, verbose,
ipar, ihext, ivec, isite, False, iboot,
vec, Dir, PDir, crd, num_bootstraps,
dir_path, save_plots=save_plots, interactive=interactive,
fmt=fmt)
def main():
"""
NAME
chi_magic.py
DESCRIPTION
plots magnetic susceptibility as a function of frequency and temperature and AC field
SYNTAX
chi_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, specify measurements format file, default "measurements.txt"
-T IND, specify temperature step to plot
-e EXP, specify experiment name to plot
-fmt [svg,jpg,png,pdf] set figure format [default is svg]
-sav save figure and quit
"""
if "-h" in sys.argv:
print(main.__doc__)
return
infile = pmag.get_named_arg("-f", "measurements.txt")
dir_path = pmag.get_named_arg("-WD", ".")
infile = pmag.resolve_file_name(infile, dir_path)
fmt = pmag.get_named_arg("-fmt", "svg")
show_plots = True
if "-sav" in sys.argv:
show_plots = False
experiments = pmag.get_named_arg("-e", "")
# read in data from data model 3 example file
chi_data_all = pd.read_csv(infile, sep='\t', header=1)
if not experiments:
try:
experiments = chi_data_all.experiment.unique()
except Exception as ex:
print(ex)
experiments = ["all"]
else:
experiments = [experiments]
plotnum = 0
figs = {}
fnames = {}
for exp in experiments:
if exp == "all":
chi_data = chi_data_all
chi_data = chi_data_all[chi_data_all.experiment == exp]
if len(chi_data) <= 1:
print('Not enough data to plot {}'.format(exp))
continue
plotnum += 1
pmagplotlib.plot_init(plotnum, 5, 5) # set up plot
figs[str(plotnum)] = plotnum
fnames[str(plotnum)] = exp + '_temperature.{}'.format(fmt)
# get arrays of available temps, frequencies and fields
Ts = np.sort(chi_data.meas_temp.unique())
Fs = np.sort(chi_data.meas_freq.unique())
Bs = np.sort(chi_data.meas_field_ac.unique())
# plot chi versus temperature at constant field
b = Bs.max()
for num, f in enumerate(Fs):
this_f = chi_data[chi_data.meas_freq == f]
this_f = this_f[this_f.meas_field_ac == b]
plt.plot(this_f.meas_temp,
1e6 * this_f.susc_chi_volume,
label='%i' % (f) + ' Hz')
plt.legend()
plt.xlabel('Temperature (K)')
plt.ylabel('$\chi$ ($\mu$SI)')
plt.title('B = ' + '%7.2e' % (b) + ' T')
plotnum += 1
figs[str(plotnum)] = plotnum
fnames[str(plotnum)] = exp + '_frequency.{}'.format(fmt)
pmagplotlib.plot_init(plotnum, 5, 5) # set up plot
## plot chi versus frequency at constant B
b = Bs.max()
t = Ts.min()
this_t = chi_data[chi_data.meas_temp == t]
this_t = this_t[this_t.meas_field_ac == b]
plt.semilogx(this_t.meas_freq,
1e6 * this_t.susc_chi_volume,
label='%i' % (t) + ' K')
plt.legend()
plt.xlabel('Frequency (Hz)')
plt.ylabel('$\chi$ ($\mu$SI)')
plt.title('B = ' + '%7.2e' % (b) + ' T')
if show_plots:
pmagplotlib.draw_figs(figs)
ans = input("enter s[a]ve to save files, [return] to quit ")
if ans == 'a':
pmagplotlib.save_plots(figs, fnames)
sys.exit()
else:
sys.exit()
else:
pmagplotlib.save_plots(figs, fnames)
def main():
"""
NAME
plotXY.py
DESCRIPTION
Makes simple X,Y plots
INPUT FORMAT
X,Y data in columns
SYNTAX
plotxy.py [command line options]
OPTIONS
-h prints this help message
-f FILE to set file name on command line
-c col1 col2 specify columns to plot
-xsig col3 specify xsigma if desired
-ysig col4 specify xsigma if desired
-b xmin xmax ymin ymax, sets bounds
-sym SYM SIZE specify symbol to plot: default is red dots, 10 pt
-S don't plot the symbols
-xlab XLAB
-ylab YLAB
-l connect symbols with lines
-fmt [svg,png,pdf,eps] specify output format, default is svg
-sav saves plot and quits
-poly X plot a degree X polynomial through the data
-skip n Number of lines to skip before reading in data
"""
fmt, plot = 'svg', 0
col1, col2 = 0, 1
sym, size = 'ro', 50
xlab, ylab = '', ''
lines = 0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-sav' in sys.argv: plot = 1
if '-c' in sys.argv:
ind = sys.argv.index('-c')
col1 = int(sys.argv[ind + 1]) - 1
col2 = int(sys.argv[ind + 2]) - 1
if '-xsig' in sys.argv:
ind = sys.argv.index('-xsig')
col3 = int(sys.argv[ind + 1]) - 1
if '-ysig' in sys.argv:
ind = sys.argv.index('-ysig')
col4 = int(sys.argv[ind + 1]) - 1
if '-xlab' in sys.argv:
ind = sys.argv.index('-xlab')
xlab = sys.argv[ind + 1]
if '-ylab' in sys.argv:
ind = sys.argv.index('-ylab')
ylab = sys.argv[ind + 1]
if '-b' in sys.argv:
ind = sys.argv.index('-b')
xmin = float(sys.argv[ind + 1])
xmax = float(sys.argv[ind + 2])
ymin = float(sys.argv[ind + 3])
ymax = float(sys.argv[ind + 4])
if '-poly' in sys.argv:
ind = sys.argv.index('-poly')
degr = sys.argv[ind + 1]
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = sys.argv[ind + 1]
size = int(sys.argv[ind + 2])
if '-l' in sys.argv: lines = 1
if '-S' in sys.argv: sym = ''
skip = int(pmag.get_named_arg('-skip', default_val=0))
X, Y = [], []
Xerrs, Yerrs = [], []
f = open(file, 'r')
for num in range(skip):
f.readline()
data = f.readlines()
for line in data:
line.replace('\n', '')
line.replace('\t', ' ')
rec = line.split()
X.append(float(rec[col1]))
Y.append(float(rec[col2]))
if '-xsig' in sys.argv: Xerrs.append(float(rec[col3]))
if '-ysig' in sys.argv: Yerrs.append(float(rec[col4]))
if '-poly' in sys.argv:
pylab.plot(xs, ys)
coeffs = numpy.polyfit(X, Y, degr)
correl = numpy.corrcoef(X, Y)**2
polynomial = numpy.poly1d(coeffs)
xs = numpy.linspace(numpy.min(X), numpy.max(X), 10)
ys = polynomial(xs)
pylab.plot(xs, ys)
print(polynomial)
if degr == '1': print('R-square value =', '%5.4f' % (correl[0, 1]))
if sym != '':
pylab.scatter(X, Y, marker=sym[1], c=sym[0], s=size)
else:
pylab.plot(X, Y)
if '-xsig' in sys.argv and '-ysig' in sys.argv:
pylab.errorbar(X, Y, xerr=Xerrs, yerr=Yerrs, fmt=None)
if '-xsig' in sys.argv and '-ysig' not in sys.argv:
pylab.errorbar(X, Y, xerr=Xerrs, fmt=None)
if '-xsig' not in sys.argv and '-ysig' in sys.argv:
pylab.errorbar(X, Y, yerr=Yerrs, fmt=None)
if xlab != '': pylab.xlabel(xlab)
if ylab != '': pylab.ylabel(ylab)
if lines == 1: pylab.plot(X, Y, 'k-')
if '-b' in sys.argv: pylab.axis([xmin, xmax, ymin, ymax])
if plot == 0:
pylab.show()
else:
pylab.savefig('plotXY.' + fmt)
print('Figure saved as ', 'plotXY.' + fmt)
sys.exit()
def main():
"""
NAME
agm_magic.py
DESCRIPTION
converts Micromag agm files to magic format
SYNTAX
agm_magic.py [-h] [command line options]
OPTIONS
-usr USER: identify user, default is "" - put in quotation marks!
-bak: this is a IRM backfield curve
-f FILE, specify input file, required
-fsa SAMPFILE, specify er_samples.txt file relating samples, site and locations names,default is none
-F MFILE, specify magic measurements formatted output file, default is agm_measurements.txt
-spn SPEC, specimen name, default is base of input file name, e.g. SPECNAME.agm
-spc NUM, specify number of characters to designate a specimen, default = 0
-Fsp SPECFILE : name of er_specimens.txt file for appending data to
[default: er_specimens.txt]
-ncn NCON,: specify naming convention: default is #1 below
-syn SYN, synthetic specimen name
-loc LOCNAME : specify location/study name,
should have either LOCNAME or SAMPFILE (unless synthetic)
-ins INST : specify which instrument was used (e.g, SIO-Maud), default is ""
-u units: [cgs,SI], default is cgs
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column -- NOT CURRENTLY SUPPORTED
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
[8] specimen is a synthetic - it has no sample, site, location information
NB: all others you will have to customize your self
or e-mail [email protected] for help.
OUTPUT
MagIC format files: magic_measurements, er_specimens, er_sample, er_site
"""
citation='This study'
MeasRecs=[]
units='cgs'
meth="LP-HYS"
version_num=pmag.get_version()
args=sys.argv
fmt='old'
er_sample_name,er_site_name,er_location_name="","",""
inst=""
er_location_name="unknown"
er_synthetic_name=""
user=""
er_site_name=""
dir_path='.'
dm=3
if "-WD" in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-ID" in args:
ind = args.index("-ID")
input_dir_path = args[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
specfile = output_dir_path+'/er_specimens.txt'
output = output_dir_path+"/agm_measurements.txt"
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-bak" in args:
meth="LP-IRM-DCD"
output = output_dir_path+"/irm_measurements.txt"
if "-new" in args: fmt='new'
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
output = output_dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
agm_file= input_dir_path+'/'+args[ind+1]
er_specimen_name=args[ind+1].split('.')[0]
else:
print("agm_file field is required option")
print(main.__doc__)
sys.exit()
if '-Fsp' in args:
ind=args.index("-Fsp")
specfile= output_dir_path+'/'+args[ind+1]
specnum,samp_con,Z=0,'1',1
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-spn" in args:
ind=args.index("-spn")
er_specimen_name=args[ind+1]
#elif "-syn" not in args:
# print "you must specify a specimen name"
# sys.exit()
if "-syn" in args:
ind=args.index("-syn")
er_synthetic_name=args[ind+1]
er_specimen_name=""
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
sampfile = input_dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(sampfile)
print('sample_file successfully read in')
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print("option [4] must be in form 4-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print("option [7] must be in form 7-Z where Z is an integer")
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-u" in args:
ind=args.index("-u")
units=args[ind+1]
dm = pmag.get_named_arg("-DM", 2)
ErSpecRecs,filetype=pmag.magic_read(specfile)
ErSpecRec,MeasRec={},{}
ErSpecRec['er_citation_names']="This study"
ErSpecRec['er_specimen_name']=er_specimen_name
ErSpecRec['er_synthetic_name']=er_synthetic_name
if specnum!=0:
ErSpecRec["er_sample_name"]=er_specimen_name[:specnum]
else:
ErSpecRec["er_sample_name"]=er_specimen_name
if "-fsa" in args and er_synthetic_name=="":
for samp in Samps:
if samp["er_sample_name"] == ErSpecRec["er_sample_name"]:
ErSpecRec["er_location_name"]=samp["er_location_name"]
ErSpecRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6 and int(samp_con)!=8:
site=pmag.parse_site(ErSpecRec['er_sample_name'],samp_con,Z)
ErSpecRec["er_site_name"]=site
ErSpecRec["er_location_name"]=er_location_name
ErSpecRec['er_scientist_mail_names']=user.strip()
insert=1
for rec in ErSpecRecs:
if rec['er_specimen_name']==er_specimen_name:
insert=0
break
if insert==1:
ErSpecRecs.append(ErSpecRec)
ErSpecRecs,keylist=pmag.fillkeys(ErSpecRecs)
pmag.magic_write(specfile,ErSpecRecs,'er_specimens')
print("specimen name put in ",specfile)
f=open(agm_file,'r')
Data=f.readlines()
if "ASCII" not in Data[0]:fmt='new'
measnum,start=1,""
if fmt=='new': # new Micromag formatted file
end=2
for skip in range(len(Data)):
line=Data[skip]
rec=line.split()
if 'Units' in line:units=rec[-1]
if "Raw" in rec:
start=skip+2
if "Field" in rec and "Moment" in rec and start=="":
start=skip+2
break
else:
start = 2
end=1
for i in range(start,len(Data)-end): # skip header stuff
MeasRec={}
for key in list(ErSpecRec.keys()):
MeasRec[key]=ErSpecRec[key]
MeasRec['magic_instrument_codes']=inst
MeasRec['magic_method_codes']=meth
if 'er_synthetic_name' in list(MeasRec.keys()) and MeasRec['er_synthetic_name']!="":
MeasRec['magic_experiment_name']=er_synthetic_name+':'+meth
else:
MeasRec['magic_experiment_name']=er_specimen_name+':'+meth
line=Data[i]
rec=line.split(',') # data comma delimited
if rec[0]!='\n':
if units=='cgs':
field =float(rec[0])*1e-4 # convert from oe to tesla
else:
field =float(rec[0]) # field in tesla
if meth=="LP-HYS":
MeasRec['measurement_lab_field_dc']='%10.3e'%(field)
MeasRec['treatment_dc_field']=''
else:
MeasRec['measurement_lab_field_dc']=''
MeasRec['treatment_dc_field']='%10.3e'%(field)
if units=='cgs':
MeasRec['measurement_magn_moment']='%10.3e'%(float(rec[1])*1e-3) # convert from emu to Am^2
else:
MeasRec['measurement_magn_moment']='%10.3e'%(float(rec[1])) # Am^2
MeasRec['treatment_temp']='273' # temp in kelvin
MeasRec['measurement_temp']='273' # temp in kelvin
MeasRec['measurement_flag']='g'
MeasRec['measurement_standard']='u'
MeasRec['measurement_number']='%i'%(measnum)
measnum+=1
MeasRec['magic_software_packages']=version_num
MeasRecs.append(MeasRec)
# now we have to relabel LP-HYS method codes. initial loop is LP-IMT, minor loops are LP-M - do this in measurements_methods function
if meth=='LP-HYS':
recnum=0
while float(MeasRecs[recnum]['measurement_lab_field_dc'])<float(MeasRecs[recnum+1]['measurement_lab_field_dc']) and recnum+1<len(MeasRecs): # this is LP-IMAG
MeasRecs[recnum]['magic_method_codes']='LP-IMAG'
MeasRecs[recnum]['magic_experiment_name']=MeasRecs[recnum]['er_specimen_name']+":"+'LP-IMAG'
recnum+=1
#
if int(dm)==2:
pmag.magic_write(output,MeasRecs,'magic_measurements')
else:
print ('MagIC 3 is not supported yet')
sys.exit()
pmag.magic_write(output,MeasRecs,'measurements')
print("results put in ", output)