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PmagPy/PmagPy | programs/mk_redo.py | main | 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... | python | 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... | [
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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
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PmagPy/PmagPy | pmagpy/lcc_ticks.py | find_side | def find_side(ls, side):
"""
Given a shapely LineString which is assumed to be rectangular, return the
line corresponding to a given side of the rectangle.
"""
minx, miny, maxx, maxy = ls.bounds
points = {'left': [(minx, miny), (minx, maxy)],
'right': [(maxx, miny), (maxx, max... | python | def find_side(ls, side):
"""
Given a shapely LineString which is assumed to be rectangular, return the
line corresponding to a given side of the rectangle.
"""
minx, miny, maxx, maxy = ls.bounds
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PmagPy/PmagPy | pmagpy/lcc_ticks.py | lambert_xticks | def lambert_xticks(ax, ticks):
"""Draw ticks on the bottom x-axis of a Lambert Conformal projection."""
te = lambda xy: xy[0]
lc = lambda t, n, b: np.vstack((np.zeros(n) + t, np.linspace(b[2], b[3], n))).T
xticks, xticklabels = _lambert_ticks(ax, ticks, 'bottom', lc, te)
ax.xaxis.tick_bottom()
a... | python | def lambert_xticks(ax, ticks):
"""Draw ticks on the bottom x-axis of a Lambert Conformal projection."""
te = lambda xy: xy[0]
lc = lambda t, n, b: np.vstack((np.zeros(n) + t, np.linspace(b[2], b[3], n))).T
xticks, xticklabels = _lambert_ticks(ax, ticks, 'bottom', lc, te)
ax.xaxis.tick_bottom()
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PmagPy/PmagPy | pmagpy/lcc_ticks.py | lambert_yticks | def lambert_yticks(ax, ticks):
"""Draw ricks on the left y-axis of a Lamber Conformal projection."""
te = lambda xy: xy[1]
lc = lambda t, n, b: np.vstack((np.linspace(b[0], b[1], n), np.zeros(n) + t)).T
yticks, yticklabels = _lambert_ticks(ax, ticks, 'left', lc, te)
ax.yaxis.tick_left()
ax.set_y... | python | def lambert_yticks(ax, ticks):
"""Draw ricks on the left y-axis of a Lamber Conformal projection."""
te = lambda xy: xy[1]
lc = lambda t, n, b: np.vstack((np.linspace(b[0], b[1], n), np.zeros(n) + t)).T
yticks, yticklabels = _lambert_ticks(ax, ticks, 'left', lc, te)
ax.yaxis.tick_left()
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PmagPy/PmagPy | pmagpy/lcc_ticks.py | _lambert_ticks | def _lambert_ticks(ax, ticks, tick_location, line_constructor, tick_extractor):
"""Get the tick locations and labels for an axis of a Lambert Conformal projection."""
outline_patch = sgeom.LineString(ax.outline_patch.get_path().vertices.tolist())
axis = find_side(outline_patch, tick_location)
n_steps = ... | python | def _lambert_ticks(ax, ticks, tick_location, line_constructor, tick_extractor):
"""Get the tick locations and labels for an axis of a Lambert Conformal projection."""
outline_patch = sgeom.LineString(ax.outline_patch.get_path().vertices.tolist())
axis = find_side(outline_patch, tick_location)
n_steps = ... | [
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PmagPy/PmagPy | programs/deprecated/umich_magic.py | main | def main():
"""
NAME
umich_magic.py
DESCRIPTION
converts UMICH .mag format files to magic_measurements format files
SYNTAX
umich_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
... | python | def main():
"""
NAME
umich_magic.py
DESCRIPTION
converts UMICH .mag format files to magic_measurements format files
SYNTAX
umich_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
... | [
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umich_magic.py
DESCRIPTION
converts UMICH .mag format files to magic_measurements format files
SYNTAX
umich_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
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PmagPy/PmagPy | programs/dmag_magic.py | dmag_magic | def dmag_magic(in_file="measurements.txt", dir_path=".", input_dir_path="",
spec_file="specimens.txt", samp_file="samples.txt",
site_file="sites.txt", loc_file="locations.txt",
plot_by="loc", LT="AF", norm=True, XLP="",
save_plots=True, fmt="svg"):
"""
plots intensity decay ... | python | def dmag_magic(in_file="measurements.txt", dir_path=".", input_dir_path="",
spec_file="specimens.txt", samp_file="samples.txt",
site_file="sites.txt", loc_file="locations.txt",
plot_by="loc", LT="AF", norm=True, XLP="",
save_plots=True, fmt="svg"):
"""
plots intensity decay ... | [
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PmagPy/PmagPy | programs/dmag_magic.py | main | 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... | python | 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... | [
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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
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PmagPy/PmagPy | programs/watsons_v.py | main | def main():
"""
NAME
watsons_v.py
DESCRIPTION
calculates Watson's V statistic from input files
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files
SYNTAX
watsons_v.py [command line options]
OPTIONS
-h prints help message and quits
... | python | def main():
"""
NAME
watsons_v.py
DESCRIPTION
calculates Watson's V statistic from input files
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files
SYNTAX
watsons_v.py [command line options]
OPTIONS
-h prints help message and quits
... | [
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watsons_v.py
DESCRIPTION
calculates Watson's V statistic from input files
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files
SYNTAX
watsons_v.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE (with op... | [
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PmagPy/PmagPy | programs/deprecated/biplot_magic.py | main | def main():
"""
NAME
biplot_magic.py
DESCRIPTION
makes a biplot of specified variables from magic_measurements.txt format file
SYNTAX
biplot_magic.py [-h] [-i] [command line options]
INPUT
takes magic formated magic_measurments file
OPTIONS
-h prints h... | python | def main():
"""
NAME
biplot_magic.py
DESCRIPTION
makes a biplot of specified variables from magic_measurements.txt format file
SYNTAX
biplot_magic.py [-h] [-i] [command line options]
INPUT
takes magic formated magic_measurments file
OPTIONS
-h prints h... | [
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biplot_magic.py
DESCRIPTION
makes a biplot of specified variables from magic_measurements.txt format file
SYNTAX
biplot_magic.py [-h] [-i] [command line options]
INPUT
takes magic formated magic_measurments file
OPTIONS
-h prints help message and quits
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PmagPy/PmagPy | programs/strip_magic.py | main | 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 F... | python | 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 F... | [
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strip_magic.py
DESCRIPTION
plots various parameters versus depth or age
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strip_magic.py [command line optins]
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PmagPy/PmagPy | programs/site_edit_magic.py | main | def main():
"""
NAME
site_edit_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimens.txt file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
allows testing and reject... | python | def main():
"""
NAME
site_edit_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimens.txt file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
allows testing and reject... | [
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site_edit_magic.py
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makes equal area projections site by site
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PmagPy/PmagPy | programs/lowes.py | main | def main():
"""
NAME
lowes.py
DESCRIPTION
Plots Lowes spectrum for input IGRF-like file
SYNTAX
lowes.py [options]
OPTIONS:
-h prints help message and quits
-f FILE specify file name with input data
-d date specify desired date
-r read desired date... | python | def main():
"""
NAME
lowes.py
DESCRIPTION
Plots Lowes spectrum for input IGRF-like file
SYNTAX
lowes.py [options]
OPTIONS:
-h prints help message and quits
-f FILE specify file name with input data
-d date specify desired date
-r read desired date... | [
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lowes.py
DESCRIPTION
Plots Lowes spectrum for input IGRF-like file
SYNTAX
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PmagPy/PmagPy | data_files/LearningPython/main.py | main | def main():
"""This program prints doubled values!"""
import numpy
X=arange(.1,10.1,.2) #make a list of numbers
Y=myfunc(X) # calls myfunc with argument X
for i in range(len(X)):
print(X[i],Y[i]) | python | def main():
"""This program prints doubled values!"""
import numpy
X=arange(.1,10.1,.2) #make a list of numbers
Y=myfunc(X) # calls myfunc with argument X
for i in range(len(X)):
print(X[i],Y[i]) | [
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PmagPy/PmagPy | programs/common_mean.py | main | def main():
"""
NAME
common_mean.py
DESCRIPTION
calculates bootstrap statistics to test for common mean
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files
SYNTAX
common_mean.py [command line options]
OPTIONS
-h prints help m... | python | def main():
"""
NAME
common_mean.py
DESCRIPTION
calculates bootstrap statistics to test for common mean
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files
SYNTAX
common_mean.py [command line options]
OPTIONS
-h prints help m... | [
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PmagPy/PmagPy | SPD/lib/lib_curvature.py | AraiCurvature | def AraiCurvature(x=x,y=y):
"""
input: list of x points, list of y points
output: k, a, b, SSE. curvature, circle center, and SSE
Function for calculating the radius of the best fit circle to a set of
x-y coordinates.
Paterson, G. A., (2011), A simple test for the presence of multidomain
b... | python | def AraiCurvature(x=x,y=y):
"""
input: list of x points, list of y points
output: k, a, b, SSE. curvature, circle center, and SSE
Function for calculating the radius of the best fit circle to a set of
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PmagPy/PmagPy | SPD/lib/lib_curvature.py | TaubinSVD | def TaubinSVD(XY):
"""
algebraic circle fit
input: list [[x_1, y_1], [x_2, y_2], ....]
output: a, b, r. a and b are the center of the fitting circle, and r is the radius
Algebraic circle fit by Taubin
G. Taubin, "Estimation Of Planar Curves, Surfaces And Nonplanar
Space Cu... | python | def TaubinSVD(XY):
"""
algebraic circle fit
input: list [[x_1, y_1], [x_2, y_2], ....]
output: a, b, r. a and b are the center of the fitting circle, and r is the radius
Algebraic circle fit by Taubin
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PmagPy/PmagPy | SPD/lib/lib_curvature.py | VarCircle | def VarCircle(XY, Par): # must have at least 4 sets of xy points or else division by zero occurs
"""
computing the sample variance of distances from data points (XY) to the circle Par = [a b R]
"""
if type(XY) != numpy.ndarray:
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n = len(XY)
if n < 4:
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"""
computing the sample variance of distances from data points (XY) to the circle Par = [a b R]
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if type(XY) != numpy.ndarray:
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PmagPy/PmagPy | SPD/lib/lib_curvature.py | LMA | def LMA(XY,ParIni):
"""
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which is acquired by using an algebraic circle fit (TaubinSVD)
output: a, b, r. a and b are the center of the fitting circle, and r is the radius
% Geom... | python | def LMA(XY,ParIni):
"""
input: list of x and y values [[x_1, y_1], [x_2, y_2], ....], and a tuple containing an initial guess (a, b, r)
which is acquired by using an algebraic circle fit (TaubinSVD)
output: a, b, r. a and b are the center of the fitting circle, and r is the radius
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PmagPy/PmagPy | SPD/lib/lib_curvature.py | get_SSE | def get_SSE(a,b,r,x,y):
"""
input: a, b, r, x, y. circle center, radius, xpts, ypts
output: SSE
"""
SSE = 0
X = numpy.array(x)
Y = numpy.array(y)
for i in range(len(X)):
x = X[i]
y = Y[i]
v = (numpy.sqrt( (x -a)**2 + (y - b)**2 ) - r )**2
SSE += v
ret... | python | def get_SSE(a,b,r,x,y):
"""
input: a, b, r, x, y. circle center, radius, xpts, ypts
output: SSE
"""
SSE = 0
X = numpy.array(x)
Y = numpy.array(y)
for i in range(len(X)):
x = X[i]
y = Y[i]
v = (numpy.sqrt( (x -a)**2 + (y - b)**2 ) - r )**2
SSE += v
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PmagPy/PmagPy | programs/sundec.py | main | def main():
"""
NAME
sundec.py
DESCRIPTION
calculates calculates declination from sun compass measurements
INPUT FORMAT
GMT_offset, lat,long,year,month,day,hours,minutes,shadow_angle
where GMT_offset is the hours to subtract from local time for GMT.
SYNTAX
sun... | python | def main():
"""
NAME
sundec.py
DESCRIPTION
calculates calculates declination from sun compass measurements
INPUT FORMAT
GMT_offset, lat,long,year,month,day,hours,minutes,shadow_angle
where GMT_offset is the hours to subtract from local time for GMT.
SYNTAX
sun... | [
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sundec.py
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calculates calculates declination from sun compass measurements
INPUT FORMAT
GMT_offset, lat,long,year,month,day,hours,minutes,shadow_angle
where GMT_offset is the hours to subtract from local time for GMT.
SYNTAX
sundec.py [-i][-f FILE] [< ... | [
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PmagPy/PmagPy | programs/deprecated/sites_locations.py | main | def main():
"""
NAME
sites_locations.py
DESCRIPTION
reads in er_sites.txt file and finds all locations and bounds of locations
outputs er_locations.txt file
SYNTAX
sites_locations.py [command line options]
OPTIONS
-h prints help message and quits
-f... | python | def main():
"""
NAME
sites_locations.py
DESCRIPTION
reads in er_sites.txt file and finds all locations and bounds of locations
outputs er_locations.txt file
SYNTAX
sites_locations.py [command line options]
OPTIONS
-h prints help message and quits
-f... | [
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sites_locations.py
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reads in er_sites.txt file and finds all locations and bounds of locations
outputs er_locations.txt file
SYNTAX
sites_locations.py [command line options]
OPTIONS
-h prints help message and quits
-f: specimen input er_site... | [
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PmagPy/PmagPy | programs/zeq_magic2.py | main | def main():
"""
NAME
zeq_magic.py
DESCRIPTION
reads in magic_measurements formatted file, makes plots of remanence decay
during demagnetization experiments. Reads in prior interpretations saved in
a pmag_specimens formatted file and allows re-interpretations of best-fit l... | python | def main():
"""
NAME
zeq_magic.py
DESCRIPTION
reads in magic_measurements formatted file, makes plots of remanence decay
during demagnetization experiments. Reads in prior interpretations saved in
a pmag_specimens formatted file and allows re-interpretations of best-fit l... | [
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zeq_magic.py
DESCRIPTION
reads in magic_measurements formatted file, makes plots of remanence decay
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PmagPy/PmagPy | pmagpy/controlled_vocabularies2.py | Vocabulary.get_one_meth_type | def get_one_meth_type(self, mtype, method_list):
"""
Get all codes of one type (i.e., 'anisotropy_estimation')
"""
cond = method_list['dtype'] == mtype
codes = method_list[cond]
return codes | python | def get_one_meth_type(self, mtype, method_list):
"""
Get all codes of one type (i.e., 'anisotropy_estimation')
"""
cond = method_list['dtype'] == mtype
codes = method_list[cond]
return codes | [
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PmagPy/PmagPy | pmagpy/controlled_vocabularies2.py | Vocabulary.get_one_meth_category | def get_one_meth_category(self, category, all_codes, code_types):
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Get all codes in one category (i.e., all pmag codes).
This can include multiple method types (i.e., 'anisotropy_estimation', 'sample_prepartion', etc.)
"""
categories = Series(code_types[code_types[category] ==... | python | def get_one_meth_category(self, category, all_codes, code_types):
"""
Get all codes in one category (i.e., all pmag codes).
This can include multiple method types (i.e., 'anisotropy_estimation', 'sample_prepartion', etc.)
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PmagPy/PmagPy | programs/azdip_magic.py | main | def main():
"""
NAME
azdip_magic.py
DESCRIPTION
takes space delimited AzDip file and converts to MagIC formatted tables
SYNTAX
azdip_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify output file, default is: er_samples.t... | python | def main():
"""
NAME
azdip_magic.py
DESCRIPTION
takes space delimited AzDip file and converts to MagIC formatted tables
SYNTAX
azdip_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify output file, default is: er_samples.t... | [
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azdip_magic.py
DESCRIPTION
takes space delimited AzDip file and converts to MagIC formatted tables
SYNTAX
azdip_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify output file, default is: er_samples.txt/samples.txt
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PmagPy/PmagPy | programs/plot_geomagia.py | main | def main():
"""
NAME
plot_geomagia.py
DESCRIPTION
makes a map and VADM plot of geomagia download file
SYNTAX
plot_geomagia.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, specify geomagia download file
-res [c,l,i,h] s... | python | def main():
"""
NAME
plot_geomagia.py
DESCRIPTION
makes a map and VADM plot of geomagia download file
SYNTAX
plot_geomagia.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, specify geomagia download file
-res [c,l,i,h] s... | [
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plot_geomagia.py
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makes a map and VADM plot of geomagia download file
SYNTAX
plot_geomagia.py [command line options]
OPTIONS
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PmagPy/PmagPy | programs/conversion_scripts/k15_magic.py | main | def main():
"""
NAME
k15_magic.py
DESCRIPTION
converts .k15 format data to magic_measurements format.
assums Jelinek Kappabridge measurement scheme
SYNTAX
k15_magic.py [-h] [command line options]
OPTIONS
-h prints help message and quits
-DM DATA_MO... | python | def main():
"""
NAME
k15_magic.py
DESCRIPTION
converts .k15 format data to magic_measurements format.
assums Jelinek Kappabridge measurement scheme
SYNTAX
k15_magic.py [-h] [command line options]
OPTIONS
-h prints help message and quits
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k15_magic.py
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SYNTAX
k15_magic.py [-h] [command line options]
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PmagPy/PmagPy | programs/conversion_scripts2/cit_magic2.py | main | def main(command_line=True, **kwargs):
"""
NAME
cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify u... | python | def main(command_line=True, **kwargs):
"""
NAME
cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
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cit_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
cit_magic.py [command line options]
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PmagPy/PmagPy | programs/zeq.py | main | def main():
"""
NAME
zeq.py
DESCRIPTION
plots demagnetization data. The equal area projection has the X direction (usually North in geographic coordinates)
to the top. The red line is the X axis of the Zijderveld diagram. Solid symbols are lower hemisphere.
The solid ... | python | def main():
"""
NAME
zeq.py
DESCRIPTION
plots demagnetization data. The equal area projection has the X direction (usually North in geographic coordinates)
to the top. The red line is the X axis of the Zijderveld diagram. Solid symbols are lower hemisphere.
The solid ... | [
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zeq.py
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plots demagnetization data. The equal area projection has the X direction (usually North in geographic coordinates)
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PmagPy/PmagPy | programs/make_magic_plots.py | check_for_reqd_cols | def check_for_reqd_cols(data, reqd_cols):
"""
Check data (PmagPy list of dicts) for required columns
"""
missing = []
for col in reqd_cols:
if col not in data[0]:
missing.append(col)
return missing | python | def check_for_reqd_cols(data, reqd_cols):
"""
Check data (PmagPy list of dicts) for required columns
"""
missing = []
for col in reqd_cols:
if col not in data[0]:
missing.append(col)
return missing | [
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PmagPy/PmagPy | programs/make_magic_plots.py | main | def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available data and makes plots
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies inpu... | python | def main():
"""
NAME
make_magic_plots.py
DESCRIPTION
inspects magic directory for available data and makes plots
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies inpu... | [
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make_magic_plots.py
DESCRIPTION
inspects magic directory for available data and makes plots
SYNTAX
make_magic_plots.py [command line options]
INPUT
magic files
OPTIONS
-h prints help message and quits
-f FILE specifies input file name
-fmt... | [
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PmagPy/PmagPy | programs/core_depthplot.py | main | def main():
"""
NAME
core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth or age. plots data flagged as 'FS-SS-C' as discrete samples.
SYNTAX
core_depthplot.py [command line options]
# or, for Anaconda users:
core_depthplot_anaconda [comma... | python | def main():
"""
NAME
core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth or age. plots data flagged as 'FS-SS-C' as discrete samples.
SYNTAX
core_depthplot.py [command line options]
# or, for Anaconda users:
core_depthplot_anaconda [comma... | [
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core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth or age. plots data flagged as 'FS-SS-C' as discrete samples.
SYNTAX
core_depthplot.py [command line options]
# or, for Anaconda users:
core_depthplot_anaconda [command line options]
OP... | [
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PmagPy/PmagPy | programs/pca.py | main | def main():
"""
NAME
pca.py
DESCRIPTION
calculates best-fit line/plane through demagnetization data
INPUT FORMAT
takes specimen_name treatment intensity declination inclination in space delimited file
SYNTAX
pca.py [command line options][< filename]
OPTIONS
... | python | def main():
"""
NAME
pca.py
DESCRIPTION
calculates best-fit line/plane through demagnetization data
INPUT FORMAT
takes specimen_name treatment intensity declination inclination in space delimited file
SYNTAX
pca.py [command line options][< filename]
OPTIONS
... | [
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pca.py
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calculates best-fit line/plane through demagnetization data
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takes specimen_name treatment intensity declination inclination in space delimited file
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pca.py [command line options][< filename]
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PmagPy/PmagPy | programs/pt_rot.py | main | def main():
"""
NAME
pt_rot.py
DESCRIPTION
rotates pt according to specified age and plate
SYNTAX
pt_rot.py [command line options]
OPTIONS
-h prints help and quits
-f file with lon lat plate age Dplate as space delimited input
Dplate is the de... | python | def main():
"""
NAME
pt_rot.py
DESCRIPTION
rotates pt according to specified age and plate
SYNTAX
pt_rot.py [command line options]
OPTIONS
-h prints help and quits
-f file with lon lat plate age Dplate as space delimited input
Dplate is the de... | [
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pt_rot.py
DESCRIPTION
rotates pt according to specified age and plate
SYNTAX
pt_rot.py [command line options]
OPTIONS
-h prints help and quits
-f file with lon lat plate age Dplate as space delimited input
Dplate is the destination plate coordina... | [
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PmagPy/PmagPy | pmagpy/validate_upload3.py | requiredUnless | def requiredUnless(col_name, arg, dm, df, *args):
"""
Arg is a string in the format "str1, str2, ..."
Each string will be a column name.
Col_name is required in df unless each column from arg is present.
"""
# if column name is present, no need to check if it is required
if col_name in df.co... | python | def requiredUnless(col_name, arg, dm, df, *args):
"""
Arg is a string in the format "str1, str2, ..."
Each string will be a column name.
Col_name is required in df unless each column from arg is present.
"""
# if column name is present, no need to check if it is required
if col_name in df.co... | [
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PmagPy/PmagPy | pmagpy/validate_upload3.py | requiredUnlessTable | def requiredUnlessTable(col_name, arg, dm, df, con=None):
"""
Col_name must be present in df unless
arg (table_name) is present in contribution
"""
table_name = arg
if col_name in df.columns:
return None
elif not con:
return None
elif table_name in con.tables:
ret... | python | def requiredUnlessTable(col_name, arg, dm, df, con=None):
"""
Col_name must be present in df unless
arg (table_name) is present in contribution
"""
table_name = arg
if col_name in df.columns:
return None
elif not con:
return None
elif table_name in con.tables:
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PmagPy/PmagPy | pmagpy/validate_upload3.py | requiredIfGroup | def requiredIfGroup(col_name, arg, dm, df, *args):
"""
Col_name is required if other columns of
the group arg are present.
"""
group_name = arg
groups = set()
columns = df.columns
for col in columns:
if col not in dm.index:
continue
group = dm.loc[col]['group'... | python | def requiredIfGroup(col_name, arg, dm, df, *args):
"""
Col_name is required if other columns of
the group arg are present.
"""
group_name = arg
groups = set()
columns = df.columns
for col in columns:
if col not in dm.index:
continue
group = dm.loc[col]['group'... | [
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PmagPy/PmagPy | pmagpy/validate_upload3.py | required | def required(col_name, arg, dm, df, *args):
"""
Col_name is required in df.columns.
Return error message if not.
"""
if col_name in df.columns:
return None
else:
return '"{}" column is required'.format(col_name) | python | def required(col_name, arg, dm, df, *args):
"""
Col_name is required in df.columns.
Return error message if not.
"""
if col_name in df.columns:
return None
else:
return '"{}" column is required'.format(col_name) | [
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PmagPy/PmagPy | pmagpy/validate_upload3.py | isIn | def isIn(row, col_name, arg, dm, df, con=None):
"""
row[col_name] must contain a value from another column.
If not, return error message.
"""
#grade = df.apply(func, args=(validation_name, arg, dm), axis=1)
cell_value = row[col_name]
cell_value = str(cell_value)
if not cell_value:
... | python | def isIn(row, col_name, arg, dm, df, con=None):
"""
row[col_name] must contain a value from another column.
If not, return error message.
"""
#grade = df.apply(func, args=(validation_name, arg, dm), axis=1)
cell_value = row[col_name]
cell_value = str(cell_value)
if not cell_value:
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PmagPy/PmagPy | pmagpy/validate_upload3.py | checkMax | def checkMax(row, col_name, arg, *args):
"""
row[col_name] must be less than or equal to arg.
else, return error message.
"""
cell_value = row[col_name]
if not cell_value:
return None
elif isinstance(cell_value, float):
if np.isnan(cell_value):
return None
try... | python | def checkMax(row, col_name, arg, *args):
"""
row[col_name] must be less than or equal to arg.
else, return error message.
"""
cell_value = row[col_name]
if not cell_value:
return None
elif isinstance(cell_value, float):
if np.isnan(cell_value):
return None
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PmagPy/PmagPy | pmagpy/validate_upload3.py | cv | def cv(row, col_name, arg, current_data_model, df, con):
"""
row[col_name] must contain only values from the appropriate controlled vocabulary
"""
vocabulary = con.vocab.vocabularies
cell_value = str(row[col_name])
if not cell_value:
return None
elif cell_value == "None":
ret... | python | def cv(row, col_name, arg, current_data_model, df, con):
"""
row[col_name] must contain only values from the appropriate controlled vocabulary
"""
vocabulary = con.vocab.vocabularies
cell_value = str(row[col_name])
if not cell_value:
return None
elif cell_value == "None":
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PmagPy/PmagPy | pmagpy/validate_upload3.py | requiredOneInGroup | def requiredOneInGroup(col_name, group, dm, df, *args):
"""
If col_name is present in df, the group validation is satisfied.
If not, it still may be satisfied, but not by THIS col_name.
If col_name is missing, return col_name, else return None.
Later, we will validate to see if there is at least one... | python | def requiredOneInGroup(col_name, group, dm, df, *args):
"""
If col_name is present in df, the group validation is satisfied.
If not, it still may be satisfied, but not by THIS col_name.
If col_name is missing, return col_name, else return None.
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PmagPy/PmagPy | pmagpy/validate_upload3.py | validate_df | def validate_df(df, dm, con=None):
"""
Take in a DataFrame and corresponding data model.
Run all validations for that DataFrame.
Output is the original DataFrame with some new columns
that contain the validation output.
Validation columns start with:
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"""
Take in a DataFrame and corresponding data model.
Run all validations for that DataFrame.
Output is the original DataFrame with some new columns
that contain the validation output.
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PmagPy/PmagPy | pmagpy/validate_upload3.py | get_validation_col_names | def get_validation_col_names(df):
"""
Input: validated pandas DataFrame (using validate_df)
Output: names of all value validation columns,
names of all presence validation columns,
names of all type validation columns,
names of all missing group columns,
names... | python | def get_validation_col_names(df):
"""
Input: validated pandas DataFrame (using validate_df)
Output: names of all value validation columns,
names of all presence validation columns,
names of all type validation columns,
names of all missing group columns,
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PmagPy/PmagPy | pmagpy/validate_upload3.py | print_row_failures | def print_row_failures(failing_items, verbose=False, outfile_name=None):
"""
Take output from get_row_failures (DataFrame), and output it to
stdout, an outfile, or both.
"""
if outfile_name:
outfile = open(outfile_name, "w")
outfile.write("\t".join(["name", "row_number", "problem_typ... | python | def print_row_failures(failing_items, verbose=False, outfile_name=None):
"""
Take output from get_row_failures (DataFrame), and output it to
stdout, an outfile, or both.
"""
if outfile_name:
outfile = open(outfile_name, "w")
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PmagPy/PmagPy | pmagpy/validate_upload3.py | get_row_failures | def get_row_failures(df, value_cols, type_cols, verbose=False, outfile=None):
"""
Input: already validated DataFrame, value & type column names,
and output options.
Get details on each detected issue, row by row.
Output: DataFrame with type & value validation columns,
plus an "issues" column wit... | python | def get_row_failures(df, value_cols, type_cols, verbose=False, outfile=None):
"""
Input: already validated DataFrame, value & type column names,
and output options.
Get details on each detected issue, row by row.
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PmagPy/PmagPy | pmagpy/validate_upload3.py | get_bad_rows_and_cols | def get_bad_rows_and_cols(df, validation_names, type_col_names,
value_col_names, verbose=False):
"""
Input: validated DataFrame, all validation names, names of the type columns,
names of the value columns, verbose (True or False).
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"""
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names of the value columns, verbose (True or False).
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PmagPy/PmagPy | pmagpy/validate_upload3.py | validate_table | def validate_table(the_con, dtype, verbose=False, output_dir="."):
"""
Return name of bad table, or False if no errors found.
Calls validate_df then parses its output.
"""
print("-I- Validating {}".format(dtype))
# grab dataframe
current_df = the_con.tables[dtype].df
# grab data model
... | python | def validate_table(the_con, dtype, verbose=False, output_dir="."):
"""
Return name of bad table, or False if no errors found.
Calls validate_df then parses its output.
"""
print("-I- Validating {}".format(dtype))
# grab dataframe
current_df = the_con.tables[dtype].df
# grab data model
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PmagPy/PmagPy | pmagpy/validate_upload3.py | validate_contribution | def validate_contribution(the_con):
"""
Go through a Contribution and validate each table
"""
passing = True
for dtype in list(the_con.tables.keys()):
print("validating {}".format(dtype))
fail = validate_table(the_con, dtype)
if fail:
passing = False
print... | python | def validate_contribution(the_con):
"""
Go through a Contribution and validate each table
"""
passing = True
for dtype in list(the_con.tables.keys()):
print("validating {}".format(dtype))
fail = validate_table(the_con, dtype)
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passing = False
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PmagPy/PmagPy | pmagpy/validate_upload3.py | split_func | def split_func(string):
"""
Take a string like 'requiredIf("arg_name")'
return the function name and the argument:
(requiredIf, arg_name)
"""
ind = string.index("(")
return string[:ind], string[ind+1:-1].strip('"') | python | def split_func(string):
"""
Take a string like 'requiredIf("arg_name")'
return the function name and the argument:
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ind = string.index("(")
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PmagPy/PmagPy | pmagpy/validate_upload3.py | get_degree_cols | def get_degree_cols(df):
"""
Take in a pandas DataFrame, and return a list of columns
that are in that DataFrame AND should be between 0 - 360 degrees.
"""
vals = ['lon_w', 'lon_e', 'lat_lon_precision', 'pole_lon',
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'lon', 'lon_sigma', 'vgp_lon', ... | python | def get_degree_cols(df):
"""
Take in a pandas DataFrame, and return a list of columns
that are in that DataFrame AND should be between 0 - 360 degrees.
"""
vals = ['lon_w', 'lon_e', 'lat_lon_precision', 'pole_lon',
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PmagPy/PmagPy | pmagpy/validate_upload3.py | extract_col_name | def extract_col_name(string):
"""
Take a string and split it.
String will be a format like "presence_pass_azimuth",
where "azimuth" is the MagIC column name and "presence_pass"
is the validation.
Return "presence", "azimuth".
"""
prefixes = ["presence_pass_", "value_pass_", "type_pass_"]... | python | def extract_col_name(string):
"""
Take a string and split it.
String will be a format like "presence_pass_azimuth",
where "azimuth" is the MagIC column name and "presence_pass"
is the validation.
Return "presence", "azimuth".
"""
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PmagPy/PmagPy | pmagpy/validate_upload3.py | make_row_dict | def make_row_dict(row):
"""
Takes in a DataFrame row (Series),
and return a dictionary with the row's index as key,
and the row's values as values.
{col1_name: col1_value, col2_name: col2_value}
"""
ind = row[row.notnull()].index
values = row[row.notnull()].values
# to transformation... | python | def make_row_dict(row):
"""
Takes in a DataFrame row (Series),
and return a dictionary with the row's index as key,
and the row's values as values.
{col1_name: col1_value, col2_name: col2_value}
"""
ind = row[row.notnull()].index
values = row[row.notnull()].values
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PmagPy/PmagPy | programs/eq_di.py | main | def main():
"""
NAME
eq_di.py
DESCRIPTION
converts x,y pairs digitized from equal area projection to dec inc data
SYNTAX
eq_di.py [command line options] [< filename]
OPTIONS
-f FILE, input file
-F FILE, specifies output file name
-up if d... | python | def main():
"""
NAME
eq_di.py
DESCRIPTION
converts x,y pairs digitized from equal area projection to dec inc data
SYNTAX
eq_di.py [command line options] [< filename]
OPTIONS
-f FILE, input file
-F FILE, specifies output file name
-up if d... | [
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PmagPy/PmagPy | programs/chartmaker.py | main | def main():
"""
Welcome to the thellier-thellier experiment automatic chart maker.
Please select desired step interval and upper bound for which it is valid.
e.g.,
50
500
10
600
a blank entry signals the end of data entry.
which would generate steps with 50 degree in... | python | def main():
"""
Welcome to the thellier-thellier experiment automatic chart maker.
Please select desired step interval and upper bound for which it is valid.
e.g.,
50
500
10
600
a blank entry signals the end of data entry.
which would generate steps with 50 degree in... | [
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PmagPy/PmagPy | programs/conversion_scripts/s_magic.py | main | 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... | python | 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... | [
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s_magic.py
DESCRIPTION
converts .s format data to measurements format.
SYNTAX
s_magic.py [command line options]
OPTIONS
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-f SFILE specifies the .s file name
-s... | [
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PmagPy/PmagPy | programs/deprecated/basemap_magic.py | main | def main():
"""
NAME
basemap_magic.py
NB: this program no longer maintained - use plot_map_pts.py for greater functionality
DESCRIPTION
makes a map of locations in er_sites.txt
SYNTAX
basemap_magic.py [command line options]
OPTIONS
-h prints help message ... | python | def main():
"""
NAME
basemap_magic.py
NB: this program no longer maintained - use plot_map_pts.py for greater functionality
DESCRIPTION
makes a map of locations in er_sites.txt
SYNTAX
basemap_magic.py [command line options]
OPTIONS
-h prints help message ... | [
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basemap_magic.py
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makes a map of locations in er_sites.txt
SYNTAX
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PmagPy/PmagPy | programs/incfish.py | main | def main():
"""
NAME
incfish.py
DESCRIPTION
calculates fisher parameters from inc only data
INPUT FORMAT
takes inc data
SYNTAX
incfish.py [options] [< filename]
OPTIONS
-h prints help message and quits
-i for interactive filename entry
-f... | python | def main():
"""
NAME
incfish.py
DESCRIPTION
calculates fisher parameters from inc only data
INPUT FORMAT
takes inc data
SYNTAX
incfish.py [options] [< filename]
OPTIONS
-h prints help message and quits
-i for interactive filename entry
-f... | [
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incfish.py
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calculates fisher parameters from inc only data
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PmagPy/PmagPy | pmagpy/pmag.py | sort_diclist | def sort_diclist(undecorated, sort_on):
"""
Sort a list of dictionaries by the value in each
dictionary for the sorting key
Parameters
----------
undecorated : list of dicts
sort_on : str, numeric
key that is present in all dicts to sort on
Returns
---------
ordered lis... | python | def sort_diclist(undecorated, sort_on):
"""
Sort a list of dictionaries by the value in each
dictionary for the sorting key
Parameters
----------
undecorated : list of dicts
sort_on : str, numeric
key that is present in all dicts to sort on
Returns
---------
ordered lis... | [
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PmagPy/PmagPy | pmagpy/pmag.py | get_dictitem | def get_dictitem(In, k, v, flag, float_to_int=False):
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PmagPy/PmagPy | pmagpy/pmag.py | get_dictkey | def get_dictkey(In, k, dtype):
"""
returns list of given key (k) from input list of dictionaries (In) in data type dtype. uses command:
get_dictkey(In,k,dtype). If dtype =="", data are strings; if "int", data are integers; if "f", data are floats.
"""
Out = []
for d in In:
if... | python | def get_dictkey(In, k, dtype):
"""
returns list of given key (k) from input list of dictionaries (In) in data type dtype. uses command:
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"""
Out = []
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PmagPy/PmagPy | pmagpy/pmag.py | get_orient | def get_orient(samp_data, er_sample_name, **kwargs):
"""
samp_data : PmagPy list of dicts or pandas DataFrame
er_sample_name : sample name
"""
if isinstance(samp_data, pd.DataFrame):
samp_data = (samp_data.T.apply(dict))
# set orientation priorities
EX = ["SO-ASC", "SO-POM"]
samp... | python | def get_orient(samp_data, er_sample_name, **kwargs):
"""
samp_data : PmagPy list of dicts or pandas DataFrame
er_sample_name : sample name
"""
if isinstance(samp_data, pd.DataFrame):
samp_data = (samp_data.T.apply(dict))
# set orientation priorities
EX = ["SO-ASC", "SO-POM"]
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PmagPy/PmagPy | pmagpy/pmag.py | EI | def EI(inc):
"""
Given a mean inclination value of a distribution of directions, this
function calculates the expected elongation of this distribution using a
best-fit polynomial of the TK03 GAD secular variation model (Tauxe and
Kent, 2004).
Parameters
----------
inc : inclination in d... | python | def EI(inc):
"""
Given a mean inclination value of a distribution of directions, this
function calculates the expected elongation of this distribution using a
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Kent, 2004).
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----------
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PmagPy/PmagPy | pmagpy/pmag.py | find_f | def find_f(data):
"""
Given a distribution of directions, this function determines parameters
(elongation, inclination, flattening factor, and elongation direction) that
are consistent with the TK03 secular variation model.
Parameters
----------
data : array of declination, inclination pair... | python | def find_f(data):
"""
Given a distribution of directions, this function determines parameters
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data : array of declination, inclination pair... | [
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PmagPy/PmagPy | pmagpy/pmag.py | convert_lat | def convert_lat(Recs):
"""
uses lat, for age<5Ma, model_lat if present, else tries to use average_inc to estimate plat.
"""
New = []
for rec in Recs:
if 'model_lat' in list(rec.keys()) and rec['model_lat'] != "":
New.append(rec)
elif 'average_age' in list(rec.keys()) and ... | python | def convert_lat(Recs):
"""
uses lat, for age<5Ma, model_lat if present, else tries to use average_inc to estimate plat.
"""
New = []
for rec in Recs:
if 'model_lat' in list(rec.keys()) and rec['model_lat'] != "":
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PmagPy/PmagPy | pmagpy/pmag.py | convert_ages | def convert_ages(Recs, data_model=3):
"""
converts ages to Ma
Parameters
_________
Recs : list of dictionaries in data model by data_model
data_model : MagIC data model (default is 3)
"""
if data_model == 3:
site_key = 'site'
agekey = "age"
keybase = ""
else:
... | python | def convert_ages(Recs, data_model=3):
"""
converts ages to Ma
Parameters
_________
Recs : list of dictionaries in data model by data_model
data_model : MagIC data model (default is 3)
"""
if data_model == 3:
site_key = 'site'
agekey = "age"
keybase = ""
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PmagPy/PmagPy | pmagpy/pmag.py | convert_items | def convert_items(data, mapping):
"""
Input: list of dicts (each dict a record for one item),
mapping with column names to swap into the records.
Output: updated list of dicts.
"""
new_recs = []
for rec in data:
new_rec = map_magic.mapping(rec, mapping)
new_recs.append(new_re... | python | def convert_items(data, mapping):
"""
Input: list of dicts (each dict a record for one item),
mapping with column names to swap into the records.
Output: updated list of dicts.
"""
new_recs = []
for rec in data:
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PmagPy/PmagPy | pmagpy/pmag.py | convert_directory_2_to_3 | def convert_directory_2_to_3(meas_fname="magic_measurements.txt", input_dir=".",
output_dir=".", meas_only=False, data_model=None):
"""
Convert 2.0 measurements file into 3.0 measurements file.
Merge and convert specimen, sample, site, and location data.
Also translates crit... | python | def convert_directory_2_to_3(meas_fname="magic_measurements.txt", input_dir=".",
output_dir=".", meas_only=False, data_model=None):
"""
Convert 2.0 measurements file into 3.0 measurements file.
Merge and convert specimen, sample, site, and location data.
Also translates crit... | [
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PmagPy/PmagPy | pmagpy/pmag.py | convert_and_combine_2_to_3 | def convert_and_combine_2_to_3(dtype, map_dict, input_dir=".", output_dir=".", data_model=None):
"""
Read in er_*.txt file and pmag_*.txt file in working directory.
Combine the data, then translate headers from 2.5 --> 3.0.
Last, write out the data in 3.0.
Parameters
----------
dtype : stri... | python | def convert_and_combine_2_to_3(dtype, map_dict, input_dir=".", output_dir=".", data_model=None):
"""
Read in er_*.txt file and pmag_*.txt file in working directory.
Combine the data, then translate headers from 2.5 --> 3.0.
Last, write out the data in 3.0.
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----------
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PmagPy/PmagPy | pmagpy/pmag.py | convert_criteria_file_2_to_3 | def convert_criteria_file_2_to_3(fname="pmag_criteria.txt", input_dir=".",
output_dir=".", data_model=None):
"""
Convert a criteria file from 2.5 to 3.0 format and write it out to file
Parameters
----------
fname : string of filename (default "pmag_criteria.txt")
... | python | def convert_criteria_file_2_to_3(fname="pmag_criteria.txt", input_dir=".",
output_dir=".", data_model=None):
"""
Convert a criteria file from 2.5 to 3.0 format and write it out to file
Parameters
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fname : string of filename (default "pmag_criteria.txt")
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PmagPy/PmagPy | pmagpy/pmag.py | orient | def orient(mag_azimuth, field_dip, or_con):
"""
uses specified orientation convention to convert user supplied orientations
to laboratory azimuth and plunge
"""
or_con = str(or_con)
if mag_azimuth == -999:
return "", ""
if or_con == "1": # lab_mag_az=mag_az; sample_dip = -dip
... | python | def orient(mag_azimuth, field_dip, or_con):
"""
uses specified orientation convention to convert user supplied orientations
to laboratory azimuth and plunge
"""
or_con = str(or_con)
if mag_azimuth == -999:
return "", ""
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PmagPy/PmagPy | pmagpy/pmag.py | get_Sb | def get_Sb(data):
"""
returns vgp scatter for data set
"""
Sb, N = 0., 0.
for rec in data:
delta = 90. - abs(rec['vgp_lat'])
if rec['average_k'] != 0:
k = rec['average_k']
L = rec['average_lat'] * np.pi / 180. # latitude in radians
Nsi = rec['aver... | python | def get_Sb(data):
"""
returns vgp scatter for data set
"""
Sb, N = 0., 0.
for rec in data:
delta = 90. - abs(rec['vgp_lat'])
if rec['average_k'] != 0:
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PmagPy/PmagPy | pmagpy/pmag.py | get_sb_df | def get_sb_df(df, mm97=False):
"""
Calculates Sf for a dataframe with VGP Lat., and optional Fisher's k, site latitude and N information can be used to correct for within site scatter (McElhinny & McFadden, 1997)
Parameters
_________
df : Pandas Dataframe with columns
REQUIRED:
vgp_... | python | def get_sb_df(df, mm97=False):
"""
Calculates Sf for a dataframe with VGP Lat., and optional Fisher's k, site latitude and N information can be used to correct for within site scatter (McElhinny & McFadden, 1997)
Parameters
_________
df : Pandas Dataframe with columns
REQUIRED:
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PmagPy/PmagPy | pmagpy/pmag.py | grade | def grade(PmagRec, ACCEPT, type, data_model=2.5):
"""
Finds the 'grade' (pass/fail; A/F) of a record (specimen,sample,site) given the acceptance criteria
"""
GREATERTHAN = ['specimen_q', 'site_k', 'site_n', 'site_n_lines', 'site_int_n', 'measurement_step_min', 'specimen_int_ptrm_n', 'specimen_fvds', 'sp... | python | def grade(PmagRec, ACCEPT, type, data_model=2.5):
"""
Finds the 'grade' (pass/fail; A/F) of a record (specimen,sample,site) given the acceptance criteria
"""
GREATERTHAN = ['specimen_q', 'site_k', 'site_n', 'site_n_lines', 'site_int_n', 'measurement_step_min', 'specimen_int_ptrm_n', 'specimen_fvds', 'sp... | [
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PmagPy/PmagPy | pmagpy/pmag.py | flip | def flip(di_block, combine=False):
"""
determines 'normal' direction along the principle eigenvector, then flips the antipodes of
the reverse mode to the antipode
Parameters
___________
di_block : nested list of directions
Return
D1 : normal mode
D2 : flipped reverse mode as two DI ... | python | def flip(di_block, combine=False):
"""
determines 'normal' direction along the principle eigenvector, then flips the antipodes of
the reverse mode to the antipode
Parameters
___________
di_block : nested list of directions
Return
D1 : normal mode
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PmagPy/PmagPy | pmagpy/pmag.py | dia_vgp | def dia_vgp(*args): # new function interface by J.Holmes, SIO, 6/1/2011
"""
Converts directional data (declination, inclination, alpha95) at a given
location (Site latitude, Site longitude) to pole position (pole longitude,
pole latitude, dp, dm)
Parameters
----------
Takes input as (Dec, ... | python | def dia_vgp(*args): # new function interface by J.Holmes, SIO, 6/1/2011
"""
Converts directional data (declination, inclination, alpha95) at a given
location (Site latitude, Site longitude) to pole position (pole longitude,
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----------
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PmagPy/PmagPy | pmagpy/pmag.py | int_pars | def int_pars(x, y, vds, **kwargs):
"""
calculates York regression and Coe parameters (with Tauxe Fvds)
"""
# first do linear regression a la York
# do Data Model 3 way:
if 'version' in list(kwargs.keys()) and kwargs['version'] == 3:
n_key = 'int_n_measurements'
b_key = 'int_b'
... | python | def int_pars(x, y, vds, **kwargs):
"""
calculates York regression and Coe parameters (with Tauxe Fvds)
"""
# first do linear regression a la York
# do Data Model 3 way:
if 'version' in list(kwargs.keys()) and kwargs['version'] == 3:
n_key = 'int_n_measurements'
b_key = 'int_b'
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PmagPy/PmagPy | pmagpy/pmag.py | dovds | def dovds(data):
"""
calculates vector difference sum for demagnetization data
"""
vds, X = 0, []
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X.append(dir2cart(rec))
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ydif = X[k + 1][1] - X[k][1]
zdif = X[k + 1][2] - X[k][2]
v... | python | def dovds(data):
"""
calculates vector difference sum for demagnetization data
"""
vds, X = 0, []
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X.append(dir2cart(rec))
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PmagPy/PmagPy | pmagpy/pmag.py | vspec_magic | def vspec_magic(data):
"""
Takes average vector of replicate measurements
"""
vdata, Dirdata, step_meth = [], [], ""
if len(data) == 0:
return vdata
treat_init = ["treatment_temp", "treatment_temp_decay_rate", "treatment_temp_dc_on", "treatment_temp_dc_off", "treatment_ac_field", "treatm... | python | def vspec_magic(data):
"""
Takes average vector of replicate measurements
"""
vdata, Dirdata, step_meth = [], [], ""
if len(data) == 0:
return vdata
treat_init = ["treatment_temp", "treatment_temp_decay_rate", "treatment_temp_dc_on", "treatment_temp_dc_off", "treatment_ac_field", "treatm... | [
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PmagPy/PmagPy | pmagpy/pmag.py | get_specs | def get_specs(data):
"""
Takes a magic format file and returns a list of unique specimen names
"""
# sort the specimen names
speclist = []
for rec in data:
try:
spec = rec["er_specimen_name"]
except KeyError as e:
spec = rec["specimen"]
if spec not... | python | def get_specs(data):
"""
Takes a magic format file and returns a list of unique specimen names
"""
# sort the specimen names
speclist = []
for rec in data:
try:
spec = rec["er_specimen_name"]
except KeyError as e:
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PmagPy/PmagPy | pmagpy/pmag.py | vector_mean | def vector_mean(data):
"""
calculates the vector mean of a given set of vectors
Parameters
__________
data : nested array of [dec,inc,intensity]
Returns
_______
dir : array of [dec, inc, 1]
R : resultant vector length
"""
Xbar = np.zeros((3))
X = dir2cart(data).transpo... | python | def vector_mean(data):
"""
calculates the vector mean of a given set of vectors
Parameters
__________
data : nested array of [dec,inc,intensity]
Returns
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R : resultant vector length
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PmagPy/PmagPy | pmagpy/pmag.py | mark_dmag_rec | def mark_dmag_rec(s, ind, data):
"""
Edits demagnetization data to mark "bad" points with measurement_flag
"""
datablock = []
for rec in data:
if rec['er_specimen_name'] == s:
meths = rec['magic_method_codes'].split(':')
if 'LT-NO' in meths or 'LT-AF-Z' in meths or 'L... | python | def mark_dmag_rec(s, ind, data):
"""
Edits demagnetization data to mark "bad" points with measurement_flag
"""
datablock = []
for rec in data:
if rec['er_specimen_name'] == s:
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PmagPy/PmagPy | pmagpy/pmag.py | find_dmag_rec | def find_dmag_rec(s, data, **kwargs):
"""
Returns demagnetization data for specimen s from the data. Excludes other
kinds of experiments and "bad" measurements
Parameters
__________
s : specimen name
data : DataFrame with measurement data
**kwargs :
version : if not 3, assume da... | python | def find_dmag_rec(s, data, **kwargs):
"""
Returns demagnetization data for specimen s from the data. Excludes other
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PmagPy/PmagPy | pmagpy/pmag.py | open_file | def open_file(infile, verbose=True):
"""
Open file and return a list of the file's lines.
Try to use utf-8 encoding, and if that fails use Latin-1.
Parameters
----------
infile : str
full path to file
Returns
----------
data: list
all lines in the file
"""
t... | python | def open_file(infile, verbose=True):
"""
Open file and return a list of the file's lines.
Try to use utf-8 encoding, and if that fails use Latin-1.
Parameters
----------
infile : str
full path to file
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data: list
all lines in the file
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PmagPy/PmagPy | pmagpy/pmag.py | magic_read | def magic_read(infile, data=None, return_keys=False, verbose=False):
"""
Reads a Magic template file, returns data in a list of dictionaries.
Parameters
___________
Required:
infile : the MagIC formatted tab delimited data file
first line contains 'tab' in the firs... | python | def magic_read(infile, data=None, return_keys=False, verbose=False):
"""
Reads a Magic template file, returns data in a list of dictionaries.
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___________
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infile : the MagIC formatted tab delimited data file
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PmagPy/PmagPy | pmagpy/pmag.py | magic_read_dict | def magic_read_dict(path, data=None, sort_by_this_name=None, return_keys=False):
"""
Read a magic-formatted tab-delimited file and return a dictionary of
dictionaries, with this format:
{'Z35.5a': {'specimen_weight': '1.000e-03', 'er_citation_names': 'This study', 'specimen_volume': '', 'er_location_nam... | python | def magic_read_dict(path, data=None, sort_by_this_name=None, return_keys=False):
"""
Read a magic-formatted tab-delimited file and return a dictionary of
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{'Z35.5a': {'specimen_weight': '1.000e-03', 'er_citation_names': 'This study', 'specimen_volume': '', 'er_location_nam... | [
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PmagPy/PmagPy | pmagpy/pmag.py | sort_magic_data | def sort_magic_data(magic_data, sort_name):
'''
Sort magic_data by header (like er_specimen_name for example)
'''
magic_data_sorted = {}
for rec in magic_data:
name = rec[sort_name]
if name not in list(magic_data_sorted.keys()):
magic_data_sorted[name] = []
magic_... | python | def sort_magic_data(magic_data, sort_name):
'''
Sort magic_data by header (like er_specimen_name for example)
'''
magic_data_sorted = {}
for rec in magic_data:
name = rec[sort_name]
if name not in list(magic_data_sorted.keys()):
magic_data_sorted[name] = []
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PmagPy/PmagPy | pmagpy/pmag.py | upload_read | def upload_read(infile, table):
"""
Reads a table from a MagIC upload (or downloaded) txt file, puts data in a
list of dictionaries
"""
delim = 'tab'
hold, magic_data, magic_record, magic_keys = [], [], {}, []
f = open(infile, "r")
#
# look for right table
#
line = f.readline()[:-1]
... | python | def upload_read(infile, table):
"""
Reads a table from a MagIC upload (or downloaded) txt file, puts data in a
list of dictionaries
"""
delim = 'tab'
hold, magic_data, magic_record, magic_keys = [], [], {}, []
f = open(infile, "r")
#
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line = f.readline()[:-1]
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PmagPy/PmagPy | pmagpy/pmag.py | putout | def putout(ofile, keylist, Rec):
"""
writes out a magic format record to ofile
"""
pmag_out = open(ofile, 'a')
outstring = ""
for key in keylist:
try:
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except:
print(key, Rec[key])
# raw_input... | python | def putout(ofile, keylist, Rec):
"""
writes out a magic format record to ofile
"""
pmag_out = open(ofile, 'a')
outstring = ""
for key in keylist:
try:
outstring = outstring + '\t' + str(Rec[key]).strip()
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print(key, Rec[key])
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PmagPy/PmagPy | pmagpy/pmag.py | first_rec | def first_rec(ofile, Rec, file_type):
"""
opens the file ofile as a magic template file with headers as the keys to Rec
"""
keylist = []
opened = False
# sometimes Windows needs a little extra time to open a file
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while not opened:
try:
pma... | python | def first_rec(ofile, Rec, file_type):
"""
opens the file ofile as a magic template file with headers as the keys to Rec
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keylist = []
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# sometimes Windows needs a little extra time to open a file
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PmagPy/PmagPy | pmagpy/pmag.py | magic_write_old | def magic_write_old(ofile, Recs, file_type):
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Parameters
_________
ofile : path to output file
Recs : list of dictionaries in MagIC format
file_type : MagIC table type (e.g., specimens)
Effects :
writes a MagIC formatte... | python | def magic_write_old(ofile, Recs, file_type):
"""
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_________
ofile : path to output file
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PmagPy/PmagPy | pmagpy/pmag.py | magic_write | def magic_write(ofile, Recs, file_type):
"""
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_________
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Recs : list of dictionaries in MagIC format
file_type : MagIC table type (e.g., specimens)
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[True,False] : True if successful
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"""
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_________
ofile : path to output file
Recs : list of dictionaries in MagIC format
file_type : MagIC table type (e.g., specimens)
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PmagPy/PmagPy | pmagpy/pmag.py | dotilt | def dotilt(dec, inc, bed_az, bed_dip):
"""
Does a tilt correction on a direction (dec,inc) using bedding dip direction
and bedding dip.
Parameters
----------
dec : declination directions in degrees
inc : inclination direction in degrees
bed_az : bedding dip direction
bed_dip : beddi... | python | def dotilt(dec, inc, bed_az, bed_dip):
"""
Does a tilt correction on a direction (dec,inc) using bedding dip direction
and bedding dip.
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----------
dec : declination directions in degrees
inc : inclination direction in degrees
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PmagPy/PmagPy | pmagpy/pmag.py | dotilt_V | def dotilt_V(indat):
"""
Does a tilt correction on an array with rows of dec,inc bedding dip direction and dip.
Parameters
----------
input : declination, inclination, bedding dip direction and bedding dip
nested array of [[dec1, inc1, bed_az1, bed_dip1],[dec2,inc2,bed_az2,bed_dip2]...]
Re... | python | def dotilt_V(indat):
"""
Does a tilt correction on an array with rows of dec,inc bedding dip direction and dip.
Parameters
----------
input : declination, inclination, bedding dip direction and bedding dip
nested array of [[dec1, inc1, bed_az1, bed_dip1],[dec2,inc2,bed_az2,bed_dip2]...]
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----------
input : declination, inclination, bedding dip direction and bedding dip
nested array of [[dec1, inc1, bed_az1, bed_dip1],[dec2,inc2,bed_az2,bed_dip2]...]
Returns
-------
dec,inc : a... | [
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PmagPy/PmagPy | pmagpy/pmag.py | dogeo | def dogeo(dec, inc, az, pl):
"""
Rotates declination and inclination into geographic coordinates using the
azimuth and plunge of the X direction (lab arrow) of a specimen.
Parameters
----------
dec : declination in specimen coordinates
inc : inclination in specimen coordinates
Returns
... | python | def dogeo(dec, inc, az, pl):
"""
Rotates declination and inclination into geographic coordinates using the
azimuth and plunge of the X direction (lab arrow) of a specimen.
Parameters
----------
dec : declination in specimen coordinates
inc : inclination in specimen coordinates
Returns
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dec : declination in specimen coordinates
inc : inclination in specimen coordinates
Returns
-------
rotated_direction : tuple... | [
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PmagPy/PmagPy | pmagpy/pmag.py | dogeo_V | def dogeo_V(indat):
"""
Rotates declination and inclination into geographic coordinates using the
azimuth and plunge of the X direction (lab arrow) of a specimen.
Parameters
----------
indat: nested list of [dec, inc, az, pl] data
Returns
-------
rotated_directions : arrays of Decl... | python | def dogeo_V(indat):
"""
Rotates declination and inclination into geographic coordinates using the
azimuth and plunge of the X direction (lab arrow) of a specimen.
Parameters
----------
indat: nested list of [dec, inc, az, pl] data
Returns
-------
rotated_directions : arrays of Decl... | [
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Parameters
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indat: nested list of [dec, inc, az, pl] data
Returns
-------
rotated_directions : arrays of Declinations and Inclinations | [
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PmagPy/PmagPy | pmagpy/pmag.py | dodirot | def dodirot(D, I, Dbar, Ibar):
"""
Rotate a direction (declination, inclination) by the difference between
dec=0 and inc = 90 and the provided desired mean direction
Parameters
----------
D : declination to be rotated
I : inclination to be rotated
Dbar : declination of desired mean
... | python | def dodirot(D, I, Dbar, Ibar):
"""
Rotate a direction (declination, inclination) by the difference between
dec=0 and inc = 90 and the provided desired mean direction
Parameters
----------
D : declination to be rotated
I : inclination to be rotated
Dbar : declination of desired mean
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I : inclination to be rotated
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Ibar : inclination of desired mean
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PmagPy/PmagPy | pmagpy/pmag.py | dodirot_V | def dodirot_V(di_block, Dbar, Ibar):
"""
Rotate an array of dec/inc pairs to coordinate system with Dec,Inc as 0,90
Parameters
___________________
di_block : array of [[Dec1,Inc1],[Dec2,Inc2],....]
Dbar : declination of desired center
Ibar : inclination of desired center
Returns
__... | python | def dodirot_V(di_block, Dbar, Ibar):
"""
Rotate an array of dec/inc pairs to coordinate system with Dec,Inc as 0,90
Parameters
___________________
di_block : array of [[Dec1,Inc1],[Dec2,Inc2],....]
Dbar : declination of desired center
Ibar : inclination of desired center
Returns
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Returns
__________
array of rotated decs and incs: [[ro... | [
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PmagPy/PmagPy | pmagpy/pmag.py | find_samp_rec | def find_samp_rec(s, data, az_type):
"""
find the orientation info for samp s
"""
datablock, or_error, bed_error = [], 0, 0
orient = {}
orient["sample_dip"] = ""
orient["sample_azimuth"] = ""
orient['sample_description'] = ""
for rec in data:
if rec["er_sample_name"].lower() ... | python | def find_samp_rec(s, data, az_type):
"""
find the orientation info for samp s
"""
datablock, or_error, bed_error = [], 0, 0
orient = {}
orient["sample_dip"] = ""
orient["sample_azimuth"] = ""
orient['sample_description'] = ""
for rec in data:
if rec["er_sample_name"].lower() ... | [
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