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PmagPy/PmagPy | pmagpy/pmag.py | initialize_acceptance_criteria | def initialize_acceptance_criteria(**kwargs):
'''
initialize acceptance criteria with NULL values for thellier_gui and demag_gui
acceptance criteria format is doctionaries:
acceptance_criteria={}
acceptance_criteria[crit]={}
acceptance_criteria[crit]['category']=
accept... | python | def initialize_acceptance_criteria(**kwargs):
'''
initialize acceptance criteria with NULL values for thellier_gui and demag_gui
acceptance criteria format is doctionaries:
acceptance_criteria={}
acceptance_criteria[crit]={}
acceptance_criteria[crit]['category']=
accept... | [
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PmagPy/PmagPy | pmagpy/pmag.py | read_criteria_from_file | def read_criteria_from_file(path, acceptance_criteria, **kwargs):
'''
Read accceptance criteria from magic criteria file
# old format:
multiple lines. pmag_criteria_code defines the type of criteria
to deal with old format this function reads all the lines and ignore empty cells.
i.e., the pro... | python | def read_criteria_from_file(path, acceptance_criteria, **kwargs):
'''
Read accceptance criteria from magic criteria file
# old format:
multiple lines. pmag_criteria_code defines the type of criteria
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PmagPy/PmagPy | pmagpy/pmag.py | add_flag | def add_flag(var, flag):
"""
for use when calling command-line scripts from withing a program.
if a variable is present, add its proper command_line flag.
return a string.
"""
if var:
var = flag + " " + str(var)
else:
var = ""
return var | python | def add_flag(var, flag):
"""
for use when calling command-line scripts from withing a program.
if a variable is present, add its proper command_line flag.
return a string.
"""
if var:
var = flag + " " + str(var)
else:
var = ""
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PmagPy/PmagPy | pmagpy/pmag.py | get_named_arg | def get_named_arg(name, default_val=None, reqd=False):
"""
Extract the value after a command-line flag such as '-f' and return it.
If the command-line flag is missing, return default_val.
If reqd == True and the command-line flag is missing, throw an error.
Parameters
----------
name : str
... | python | def get_named_arg(name, default_val=None, reqd=False):
"""
Extract the value after a command-line flag such as '-f' and return it.
If the command-line flag is missing, return default_val.
If reqd == True and the command-line flag is missing, throw an error.
Parameters
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name : str
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PmagPy/PmagPy | pmagpy/pmag.py | merge_recs_headers | def merge_recs_headers(recs):
'''
take a list of recs [rec1,rec2,rec3....], each rec is a dictionary.
make sure that all recs have the same headers.
'''
headers = []
for rec in recs:
keys = list(rec.keys())
for key in keys:
if key not in headers:
heade... | python | def merge_recs_headers(recs):
'''
take a list of recs [rec1,rec2,rec3....], each rec is a dictionary.
make sure that all recs have the same headers.
'''
headers = []
for rec in recs:
keys = list(rec.keys())
for key in keys:
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PmagPy/PmagPy | pmagpy/pmag.py | resolve_file_name | def resolve_file_name(fname, dir_path='.'):
"""
Parse file name information and output full path.
Allows input as:
fname == /path/to/file.txt
or
fname == file.txt, dir_path == /path/to
Either way, returns /path/to/file.txt.
Used in conversion scripts.
Parameters
----------
f... | python | def resolve_file_name(fname, dir_path='.'):
"""
Parse file name information and output full path.
Allows input as:
fname == /path/to/file.txt
or
fname == file.txt, dir_path == /path/to
Either way, returns /path/to/file.txt.
Used in conversion scripts.
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----------
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PmagPy/PmagPy | pmagpy/pmag.py | adjust_to_360 | def adjust_to_360(val, key):
"""
Take in a value and a key. If the key is of the type:
declination/longitude/azimuth/direction, adjust it to be within
the range 0-360 as required by the MagIC data model
"""
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adjust = False
for dec_... | python | def adjust_to_360(val, key):
"""
Take in a value and a key. If the key is of the type:
declination/longitude/azimuth/direction, adjust it to be within
the range 0-360 as required by the MagIC data model
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CheckDec = ['_dec', '_lon', '_azimuth', 'dip_direction']
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PmagPy/PmagPy | pmagpy/pmag.py | adjust_all_to_360 | def adjust_all_to_360(dictionary):
"""
Take a dictionary and check each key/value pair.
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adjust it to be within 0-360 as required by the MagIC data model
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"""
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PmagPy/PmagPy | pmagpy/pmag.py | do_mag_map | def do_mag_map(date, lon_0=0, alt=0, file="", mod="cals10k",resolution='low'):
"""
returns lists of declination, inclination and intensities for lat/lon grid for
desired model and date.
Parameters:
_________________
date = Required date in decimal years (Common Era, negative for Before Common E... | python | def do_mag_map(date, lon_0=0, alt=0, file="", mod="cals10k",resolution='low'):
"""
returns lists of declination, inclination and intensities for lat/lon grid for
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PmagPy/PmagPy | pmagpy/pmag.py | doeqdi | def doeqdi(x, y, UP=False):
"""
Takes digitized x,y, data and returns the dec,inc, assuming an
equal area projection
Parameters
__________________
x : array of digitized x from point on equal area projection
y : array of igitized y from point on equal area projection
UP : if... | python | def doeqdi(x, y, UP=False):
"""
Takes digitized x,y, data and returns the dec,inc, assuming an
equal area projection
Parameters
__________________
x : array of digitized x from point on equal area projection
y : array of igitized y from point on equal area projection
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PmagPy/PmagPy | pmagpy/pmag.py | separate_directions | def separate_directions(di_block):
"""
Separates set of directions into two modes based on principal direction
Parameters
_______________
di_block : block of nested dec,inc pairs
Return
mode_1_block,mode_2_block : two lists of nested dec,inc pairs
"""
ppars = doprinc(di_block)
... | python | def separate_directions(di_block):
"""
Separates set of directions into two modes based on principal direction
Parameters
_______________
di_block : block of nested dec,inc pairs
Return
mode_1_block,mode_2_block : two lists of nested dec,inc pairs
"""
ppars = doprinc(di_block)
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PmagPy/PmagPy | pmagpy/pmag.py | dovandamme | def dovandamme(vgp_df):
"""
determine the S_b value for VGPs using the Vandamme (1994) method
for determining cutoff value for "outliers".
Parameters
___________
vgp_df : pandas DataFrame with required column "vgp_lat"
This should be in the desired coordinate system and assumes one ... | python | def dovandamme(vgp_df):
"""
determine the S_b value for VGPs using the Vandamme (1994) method
for determining cutoff value for "outliers".
Parameters
___________
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PmagPy/PmagPy | pmagpy/pmag.py | scalc_vgp_df | def scalc_vgp_df(vgp_df, anti=0, rev=0, cutoff=180., kappa=0, n=0, spin=0, v=0, boot=0, mm97=0, nb=1000):
"""
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
____... | python | def scalc_vgp_df(vgp_df, anti=0, rev=0, cutoff=180., kappa=0, n=0, spin=0, v=0, boot=0, mm97=0, nb=1000):
"""
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
____... | [
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PmagPy/PmagPy | pmagpy/pmag.py | watsons_f | def watsons_f(DI1, DI2):
"""
calculates Watson's F statistic (equation 11.16 in Essentials text book).
Parameters
_________
DI1 : nested array of [Dec,Inc] pairs
DI2 : nested array of [Dec,Inc] pairs
Returns
_______
F : Watson's F
Fcrit : critical value from F table
"""
... | python | def watsons_f(DI1, DI2):
"""
calculates Watson's F statistic (equation 11.16 in Essentials text book).
Parameters
_________
DI1 : nested array of [Dec,Inc] pairs
DI2 : nested array of [Dec,Inc] pairs
Returns
_______
F : Watson's F
Fcrit : critical value from F table
"""
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PmagPy/PmagPy | pmagpy/pmag.py | apwp | def apwp(data, print_results=False):
"""
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Parameters
_________
data : [plate,lat,lon,age]
plate : [NA, SA, AF, IN, EU, AU, ANT, GL]
NA : North America
SA : South America... | python | def apwp(data, print_results=False):
"""
calculates expected pole positions and directions for given plate, location and age
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_________
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plate : [NA, SA, AF, IN, EU, AU, ANT, GL]
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PmagPy/PmagPy | pmagpy/pmag.py | chart_maker | def chart_maker(Int, Top, start=100, outfile='chart.txt'):
"""
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tape it to the oven. This chart will help keep track of the different
steps.
Z : performed in zero field - enter the temperature XXX.0 in the sio
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"""
Makes a chart for performing IZZI experiments. Print out the file and
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PmagPy/PmagPy | pmagpy/pmag.py | import_basemap | def import_basemap():
"""
Try to import Basemap and print out a useful help message
if Basemap is either not installed or is missing required
environment variables.
Returns
---------
has_basemap : bool
Basemap : Basemap package if possible else None
"""
Basemap = None
has_b... | python | def import_basemap():
"""
Try to import Basemap and print out a useful help message
if Basemap is either not installed or is missing required
environment variables.
Returns
---------
has_basemap : bool
Basemap : Basemap package if possible else None
"""
Basemap = None
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PmagPy/PmagPy | pmagpy/pmag.py | import_cartopy | def import_cartopy():
"""
Try to import cartopy and print out a help message
if it is not installed
Returns
---------
has_cartopy : bool
cartopy : cartopy package if available else None
"""
cartopy = None
has_cartopy = True
try:
import cartopy
WARNINGS['has_c... | python | def import_cartopy():
"""
Try to import cartopy and print out a help message
if it is not installed
Returns
---------
has_cartopy : bool
cartopy : cartopy package if available else None
"""
cartopy = None
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PmagPy/PmagPy | pmagpy/pmag.py | age_to_BP | def age_to_BP(age, age_unit):
"""
Convert an age value into the equivalent in time Before Present(BP) where Present is 1950
Returns
---------
ageBP : number
"""
ageBP = -1e9
if age_unit == "Years AD (+/-)" or age_unit == "Years Cal AD (+/-)":
if age < 0:
age = age+1 ... | python | def age_to_BP(age, age_unit):
"""
Convert an age value into the equivalent in time Before Present(BP) where Present is 1950
Returns
---------
ageBP : number
"""
ageBP = -1e9
if age_unit == "Years AD (+/-)" or age_unit == "Years Cal AD (+/-)":
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PmagPy/PmagPy | pmagpy/pmag.py | vocab_convert | def vocab_convert(vocab, standard, key=''):
"""
Converts MagIC database terms (method codes, geologic_types, etc) to other standards.
May not be comprehensive for each standard. Terms added to standards as people need them
and may not be up-to-date.
'key' can be used to distinguish vocab terms that... | python | def vocab_convert(vocab, standard, key=''):
"""
Converts MagIC database terms (method codes, geologic_types, etc) to other standards.
May not be comprehensive for each standard. Terms added to standards as people need them
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PmagPy/PmagPy | pmagpy/pmag.py | fix_directories | def fix_directories(input_dir_path, output_dir_path):
"""
Take arguments input/output directories and fixes them.
If no input_directory, default to output_dir_path for both.
Then return realpath for both values.
Parameters
----------
input_dir_path : str
output_dir_path : str
Retur... | python | def fix_directories(input_dir_path, output_dir_path):
"""
Take arguments input/output directories and fixes them.
If no input_directory, default to output_dir_path for both.
Then return realpath for both values.
Parameters
----------
input_dir_path : str
output_dir_path : str
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PmagPy/PmagPy | programs/conversion_scripts/magic_geomagia.py | main | def main():
"""
NAME
magic_geomagia.py
DESCRIPTION
Takes a MagIC file and outputs data for easier input into Max Brown's GEOMAGIA database
SYNTAX
magic_geomagia.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: the MagIC data fil... | python | def main():
"""
NAME
magic_geomagia.py
DESCRIPTION
Takes a MagIC file and outputs data for easier input into Max Brown's GEOMAGIA database
SYNTAX
magic_geomagia.py [command line options]
OPTIONS
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PmagPy/PmagPy | programs/conversion_scripts/magic_geomagia.py | method_codes_to_geomagia | def method_codes_to_geomagia(magic_method_codes,geomagia_table):
"""
Looks at the MagIC method code list and returns the correct GEOMAGIA code number depending
on the method code list and the GEOMAGIA table specified. Returns O, GEOMAGIA's "Not specified" value, if no match.
When mutiple codes are mat... | python | def method_codes_to_geomagia(magic_method_codes,geomagia_table):
"""
Looks at the MagIC method code list and returns the correct GEOMAGIA code number depending
on the method code list and the GEOMAGIA table specified. Returns O, GEOMAGIA's "Not specified" value, if no match.
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PmagPy/PmagPy | programs/microwave_magic.py | main | def main():
"""
NAME
microwave_magic.py
DESCRIPTION
plots microwave paleointensity data, allowing interactive setting of bounds.
Saves and reads interpretations
from a pmag_specimen formatted table, default: microwave_specimens.txt
SYNTAX
microwave_magic.py [com... | python | def main():
"""
NAME
microwave_magic.py
DESCRIPTION
plots microwave paleointensity data, allowing interactive setting of bounds.
Saves and reads interpretations
from a pmag_specimen formatted table, default: microwave_specimens.txt
SYNTAX
microwave_magic.py [com... | [
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plots microwave paleointensity data, allowing interactive setting of bounds.
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microwave_magic.py [command line options]
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PmagPy/PmagPy | programs/deprecated/odp_spn_magic.py | main | def main():
"""
NAME
odp_spn_magic.py
DESCRIPTION
converts ODP's Molspin's .spn format files to magic_measurements format files
SYNTAX
odp_spn_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify .spn format input ... | python | def main():
"""
NAME
odp_spn_magic.py
DESCRIPTION
converts ODP's Molspin's .spn format files to magic_measurements format files
SYNTAX
odp_spn_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
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PmagPy/PmagPy | programs/conversion_scripts/template_magic.py | convert | def convert(**kwargs):
"""
EXAMPLE DOCSTRING for function (you would usually put the discription here)
Parameters
-----------
user : colon delimited list of analysts (default : "")
magfile : input magnetometer file (required)
Returns
-----------
type - Tuple : (True or False indica... | python | def convert(**kwargs):
"""
EXAMPLE DOCSTRING for function (you would usually put the discription here)
Parameters
-----------
user : colon delimited list of analysts (default : "")
magfile : input magnetometer file (required)
Returns
-----------
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type - Tuple : (True or False indicating if conversion was sucessful, m... | [
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PmagPy/PmagPy | programs/b_vdm.py | main | def main():
"""
NAME
b_vdm.py
DESCRIPTION
converts B (in microT) and (magnetic) latitude to V(A)DM
INPUT (COMMAND LINE ENTRY)
B (microtesla), latitude (positive north)
OUTPUT
V[A]DM
SYNTAX
b_vdm.py [command line options] [< filename]
... | python | def main():
"""
NAME
b_vdm.py
DESCRIPTION
converts B (in microT) and (magnetic) latitude to V(A)DM
INPUT (COMMAND LINE ENTRY)
B (microtesla), latitude (positive north)
OUTPUT
V[A]DM
SYNTAX
b_vdm.py [command line options] [< filename]
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PmagPy/PmagPy | setup.py | do_walk | def do_walk(data_path):
"""
Walk through data_files and list all in dict format
"""
data_files = {}
def cond(File, prefix):
"""
Return True for useful files
Return False for non-useful files
"""
file_path = path.join(prefix, 'data_files', File)
return ... | python | def do_walk(data_path):
"""
Walk through data_files and list all in dict format
"""
data_files = {}
def cond(File, prefix):
"""
Return True for useful files
Return False for non-useful files
"""
file_path = path.join(prefix, 'data_files', File)
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PmagPy/PmagPy | programs/conversion_scripts2/bgc_magic2.py | main | def main(command_line=True, **kwargs):
"""
NAME
bgc_magic.py
DESCRIPTION
converts Berkeley Geochronology Center (BGC) format files to magic_measurements format files
SYNTAX
bgc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-... | python | def main(command_line=True, **kwargs):
"""
NAME
bgc_magic.py
DESCRIPTION
converts Berkeley Geochronology Center (BGC) format files to magic_measurements format files
SYNTAX
bgc_magic.py [command line options]
OPTIONS
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PmagPy/PmagPy | programs/deprecated/change_case_magic.py | main | def main():
"""
NAME
change_case_magic.py
DESCRIPTION
picks out key and converts to upper or lower case
SYNTAX
change_case_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-F FILE: s... | python | def main():
"""
NAME
change_case_magic.py
DESCRIPTION
picks out key and converts to upper or lower case
SYNTAX
change_case_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-F FILE: s... | [
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SYNTAX
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PmagPy/PmagPy | pmagpy/frp.py | get_pole | def get_pole(continent,age):
"""
returns rotation poles and angles for specified continents and ages
assumes fixed Africa.
Parameters
__________
continent :
aus : Australia
eur : Eurasia
mad : Madacascar
[nwaf,congo] : NW Africa [choose one... | python | def get_pole(continent,age):
"""
returns rotation poles and angles for specified continents and ages
assumes fixed Africa.
Parameters
__________
continent :
aus : Australia
eur : Eurasia
mad : Madacascar
[nwaf,congo] : NW Africa [choose one... | [
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PmagPy/PmagPy | programs/plot_magmap.py | main | def main():
"""
NAME
plot_magmap.py
DESCRIPTION
makes a color contour map of desired field model
SYNTAX
plot_magmap.py [command line options]
OPTIONS
-h prints help and quits
-f FILE specify field model file with format: l m g h
-fmt [pdf,eps,svg,... | python | def main():
"""
NAME
plot_magmap.py
DESCRIPTION
makes a color contour map of desired field model
SYNTAX
plot_magmap.py [command line options]
OPTIONS
-h prints help and quits
-f FILE specify field model file with format: l m g h
-fmt [pdf,eps,svg,... | [
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makes a color contour map of desired field model
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PmagPy/PmagPy | programs/download_magic.py | main | 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
ta... | python | 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
ta... | [
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unpacks a magic formatted smartbook .txt file from the MagIC database into the
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PmagPy/PmagPy | programs/quick_hyst.py | main | 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 t... | python | 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 t... | [
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makes plots of hysteresis data
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PmagPy/PmagPy | programs/curie.py | smooth | def smooth(x,window_len,window='bartlett'):
"""smooth the data using a sliding window with requested size.
This method is based on the convolution of a scaled window with the signal.
The signal is prepared by padding the beginning and the end of the signal
with average of the first (last) ten values of... | python | def smooth(x,window_len,window='bartlett'):
"""smooth the data using a sliding window with requested size.
This method is based on the convolution of a scaled window with the signal.
The signal is prepared by padding the beginning and the end of the signal
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PmagPy/PmagPy | programs/curie.py | deriv1 | def deriv1(x,y,i,n):
"""
alternative way to smooth the derivative of a noisy signal
using least square fit.
x=array of x axis
y=array of y axis
n=smoothing factor
i= position
in this method the slope in position i is calculated by least square fit of n points
before and after positi... | python | def deriv1(x,y,i,n):
"""
alternative way to smooth the derivative of a noisy signal
using least square fit.
x=array of x axis
y=array of y axis
n=smoothing factor
i= position
in this method the slope in position i is calculated by least square fit of n points
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PmagPy/PmagPy | programs/curie.py | main | def main():
"""
NAME
curie.py
DESCTIPTION
plots and interprets curie temperature data.
the 1st derivative is calculated from smoothed M-T curve
(convolution with trianfular window with width= <-w> degrees)
the 2nd derivative is calculated from smoothed 1st deriva... | python | def main():
"""
NAME
curie.py
DESCTIPTION
plots and interprets curie temperature data.
the 1st derivative is calculated from smoothed M-T curve
(convolution with trianfular window with width= <-w> degrees)
the 2nd derivative is calculated from smoothed 1st deriva... | [
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PmagPy/PmagPy | programs/conversion_scripts2/jr6_jr6_magic2.py | main | def main(command_line=True, **kwargs):
"""
NAME
jr6_jr6_magic.py
DESCRIPTION
converts JR6 .jr6 format files to magic_measurements format files
SYNTAX
jr6_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify i... | python | def main(command_line=True, **kwargs):
"""
NAME
jr6_jr6_magic.py
DESCRIPTION
converts JR6 .jr6 format files to magic_measurements format files
SYNTAX
jr6_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify i... | [
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converts JR6 .jr6 format files to magic_measurements format files
SYNTAX
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OPTIONS
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PmagPy/PmagPy | programs/deprecated/extract_methods.py | main | def main():
"""
NAME
extract_methods.py
DESCRIPTION
reads in a magic table and creates a file with method codes
SYNTAX
extract_methods.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify magic format input file, defaul... | python | def main():
"""
NAME
extract_methods.py
DESCRIPTION
reads in a magic table and creates a file with method codes
SYNTAX
extract_methods.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify magic format input file, defaul... | [
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reads in a magic table and creates a file with method codes
SYNTAX
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OPTIONS
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PmagPy/PmagPy | programs/gofish.py | main | def main():
"""
NAME
gofish.py
DESCRIPTION
calculates fisher parameters from dec inc data
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
gofish.py [options] [< filename]
OPTIONS
-h prints help message and quits
-i f... | python | def main():
"""
NAME
gofish.py
DESCRIPTION
calculates fisher parameters from dec inc data
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
gofish.py [options] [< filename]
OPTIONS
-h prints help message and quits
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calculates fisher parameters from dec inc data
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
gofish.py [options] [< filename]
OPTIONS
-h prints help message and quits
-i for interactive filename ... | [
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PmagPy/PmagPy | programs/trmaq_magic.py | main | 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 magi... | python | 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
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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
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PmagPy/PmagPy | programs/conversion_scripts/huji_sample_magic.py | main | def main():
"""
NAME
huji_sample_magic.py
DESCRIPTION
takes tab delimited Hebrew University sample file and converts to MagIC formatted tables
SYNTAX
huji_sample_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify sample o... | python | def main():
"""
NAME
huji_sample_magic.py
DESCRIPTION
takes tab delimited Hebrew University sample file and converts to MagIC formatted tables
SYNTAX
huji_sample_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify sample o... | [
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huji_sample_magic.py
DESCRIPTION
takes tab delimited Hebrew University sample file and converts to MagIC formatted tables
SYNTAX
huji_sample_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify sample output file, default is: ... | [
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PmagPy/PmagPy | programs/vector_mean.py | main | def main():
"""
NAME
vector_mean.py
DESCRIPTION
calculates vector mean of vector data
INPUT FORMAT
takes dec, inc, int from an input file
SYNTAX
vector_mean.py [command line options] [< filename]
OPTIONS
-h prints help message and quits
-f FILE, s... | python | def main():
"""
NAME
vector_mean.py
DESCRIPTION
calculates vector mean of vector data
INPUT FORMAT
takes dec, inc, int from an input file
SYNTAX
vector_mean.py [command line options] [< filename]
OPTIONS
-h prints help message and quits
-f FILE, s... | [
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vector_mean.py
DESCRIPTION
calculates vector mean of vector data
INPUT FORMAT
takes dec, inc, int from an input file
SYNTAX
vector_mean.py [command line options] [< filename]
OPTIONS
-h prints help message and quits
-f FILE, specify input file
... | [
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PmagPy/PmagPy | programs/scalc.py | main | def main():
"""
NAME
scalc.py
DESCRIPTION
calculates Sb from VGP Long,VGP Lat,Directional kappa,Site latitude data
SYNTAX
scalc -h [command line options] [< standard input]
INPUT
takes space delimited files with PLong, PLat,[kappa, N_site, slat]
OPTIONS
-h p... | python | def main():
"""
NAME
scalc.py
DESCRIPTION
calculates Sb from VGP Long,VGP Lat,Directional kappa,Site latitude data
SYNTAX
scalc -h [command line options] [< standard input]
INPUT
takes space delimited files with PLong, PLat,[kappa, N_site, slat]
OPTIONS
-h p... | [
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scalc.py
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calculates Sb from VGP Long,VGP Lat,Directional kappa,Site latitude data
SYNTAX
scalc -h [command line options] [< standard input]
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takes space delimited files with PLong, PLat,[kappa, N_site, slat]
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PmagPy/PmagPy | programs/irmaq_magic.py | main | def main():
"""
NAME
irmaq_magic.py
DESCRIPTION
plots IRM acquisition curves from measurements file
SYNTAX
irmaq_magic [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FIL... | python | def main():
"""
NAME
irmaq_magic.py
DESCRIPTION
plots IRM acquisition curves from measurements file
SYNTAX
irmaq_magic [command line options]
INPUT
takes magic formatted magic_measurements.txt files
OPTIONS
-h prints help message and quits
-f FIL... | [
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irmaq_magic.py
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plots IRM acquisition curves from measurements file
SYNTAX
irmaq_magic [command line options]
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takes magic formatted magic_measurements.txt files
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PmagPy/PmagPy | pmagpy/func.py | all_but_axis | def all_but_axis(i, axis, num_axes):
"""
Return a slice covering all combinations with coordinate i along
axis. (Effectively the hyperplane perpendicular to axis at i.)
"""
the_slice = ()
for j in range(num_axes):
if j == axis:
the_slice = the_slice + (i,)
else:
... | python | def all_but_axis(i, axis, num_axes):
"""
Return a slice covering all combinations with coordinate i along
axis. (Effectively the hyperplane perpendicular to axis at i.)
"""
the_slice = ()
for j in range(num_axes):
if j == axis:
the_slice = the_slice + (i,)
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PmagPy/PmagPy | pmagpy/func.py | array_map | def array_map(f, ar):
"Apply an ordinary function to all values in an array."
flat_ar = ravel(ar)
out = zeros(len(flat_ar), flat_ar.typecode())
for i in range(len(flat_ar)):
out[i] = f(flat_ar[i])
out.shape = ar.shape
return out | python | def array_map(f, ar):
"Apply an ordinary function to all values in an array."
flat_ar = ravel(ar)
out = zeros(len(flat_ar), flat_ar.typecode())
for i in range(len(flat_ar)):
out[i] = f(flat_ar[i])
out.shape = ar.shape
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PmagPy/PmagPy | dialogs/demag_dialogs.py | VGP_Dialog.on_plot_select | def on_plot_select(self,event):
"""
Select data point if cursor is in range of a data point
@param: event -> the wx Mouseevent for that click
"""
if not self.xdata or not self.ydata: return
pos=event.GetPosition()
width, height = self.canvas.get_width_height()
... | python | def on_plot_select(self,event):
"""
Select data point if cursor is in range of a data point
@param: event -> the wx Mouseevent for that click
"""
if not self.xdata or not self.ydata: return
pos=event.GetPosition()
width, height = self.canvas.get_width_height()
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PmagPy/PmagPy | dialogs/demag_dialogs.py | VGP_Dialog.on_change_plot_cursor | def on_change_plot_cursor(self,event):
"""
If mouse is over data point making it selectable change the shape of the cursor
@param: event -> the wx Mouseevent for that click
"""
if not self.xdata or not self.ydata: return
pos=event.GetPosition()
width, height = sel... | python | def on_change_plot_cursor(self,event):
"""
If mouse is over data point making it selectable change the shape of the cursor
@param: event -> the wx Mouseevent for that click
"""
if not self.xdata or not self.ydata: return
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PmagPy/PmagPy | dialogs/demag_dialogs.py | user_input.get_values | def get_values(self):
"""
Applies parsing functions to each input as specified in init before returning a tuple with first entry being a boolean which specifies if the user entered all values and a second entry which is a dictionary of input names to parsed values.
"""
return_dict = {}
... | python | def get_values(self):
"""
Applies parsing functions to each input as specified in init before returning a tuple with first entry being a boolean which specifies if the user entered all values and a second entry which is a dictionary of input names to parsed values.
"""
return_dict = {}
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PmagPy/PmagPy | programs/upload_magic.py | main | 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
OPTI... | python | 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
OPTI... | [
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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
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PmagPy/PmagPy | programs/forc_diagram.py | d2_func | def d2_func(x, y, z):
'''
#=================================================
/poly fit for every SF grid data
#=================================================
'''
X, Y = np.meshgrid(x, y, copy=False)
X = X.flatten()
Y = Y.flatten()
A = np.array([np.ones(len(X)), X, X**2, Y, Y**2, X... | python | def d2_func(x, y, z):
'''
#=================================================
/poly fit for every SF grid data
#=================================================
'''
X, Y = np.meshgrid(x, y, copy=False)
X = X.flatten()
Y = Y.flatten()
A = np.array([np.ones(len(X)), X, X**2, Y, Y**2, X... | [
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PmagPy/PmagPy | programs/forc_diagram.py | grid_list | def grid_list(data):
'''
#=================================================
/process the grid data
/convert to list data for poly fitting
#=================================================
'''
a = []
b = []
M = []
for i in data:
a.append(i[0]) # np.array([i[1] for i in d... | python | def grid_list(data):
'''
#=================================================
/process the grid data
/convert to list data for poly fitting
#=================================================
'''
a = []
b = []
M = []
for i in data:
a.append(i[0]) # np.array([i[1] for i in d... | [
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PmagPy/PmagPy | programs/forc_diagram.py | Forc.fit | def fit(self, SF, x_range, y_range, matrix_z):
'''
#=================================================
/the main fitting process
/xx,yy,zz = Hb,Ha,p
/p is the FORC distribution
/m0,n0 is the index of values on Ha = Hb
/then loop m0 and n0
/based on smooth f... | python | def fit(self, SF, x_range, y_range, matrix_z):
'''
#=================================================
/the main fitting process
/xx,yy,zz = Hb,Ha,p
/p is the FORC distribution
/m0,n0 is the index of values on Ha = Hb
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PmagPy/PmagPy | programs/forc_diagram.py | dataLoad.rawData | def rawData(self, fileAdres=None):
# skip skiprows
skiprows = None
skip_from = [b'Field', b'Moment']
with open(fileAdres, 'rb') as fr:
#f = fr.read()
for i, line in enumerate(fr, 1):
# print(line.split())
if skip_from == line.split(... | python | def rawData(self, fileAdres=None):
# skip skiprows
skiprows = None
skip_from = [b'Field', b'Moment']
with open(fileAdres, 'rb') as fr:
#f = fr.read()
for i, line in enumerate(fr, 1):
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PmagPy/PmagPy | pmagpy/validate_upload2.py | get_data_model | def get_data_model():
"""
try to grab the up to date data model document from the EarthRef site.
if that fails, try to get the data model document from the PmagPy directory on the user's computer.
if that fails, return False.
data_model is a set of nested dictionaries that looks like this:
{'mag... | python | def get_data_model():
"""
try to grab the up to date data model document from the EarthRef site.
if that fails, try to get the data model document from the PmagPy directory on the user's computer.
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PmagPy/PmagPy | pmagpy/validate_upload2.py | read_upload | def read_upload(up_file, data_model=None):
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print out warnings for any validation problems
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"""
take a file that should be ready for upload
using the data model, check that all required columns are full,
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print out warnings for any validation problems
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PmagPy/PmagPy | pmagpy/validate_upload2.py | split_lines | def split_lines(lines):
"""
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"""
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"""
split a MagIC upload format file into lists.
the lists are split by the '>>>' lines between file_types.
"""
container = []
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for line in lines:
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PmagPy/PmagPy | pmagpy/validate_upload2.py | get_dicts | def get_dicts(data):
"""
data must be a list of lists, from a tab delimited file.
in each list:
the first list item will be the type of data.
the second list item will be a tab delimited list of headers.
the remaining items will be a tab delimited list following the list of headers.
"""
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"""
data must be a list of lists, from a tab delimited file.
in each list:
the first list item will be the type of data.
the second list item will be a tab delimited list of headers.
the remaining items will be a tab delimited list following the list of headers.
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PmagPy/PmagPy | programs/lsq_redo.py | main | def main():
"""
NAME
lsq_redo.py
DESCRIPTION
converts a tab delimited LSQ format to PmagPy redo file and edits the magic_measurements table to mark "bad" measurements.
SYNTAX
lsq_redo.py [-h] [command line options]
OPTIONS
-h: prints help message and quits
... | python | def main():
"""
NAME
lsq_redo.py
DESCRIPTION
converts a tab delimited LSQ format to PmagPy redo file and edits the magic_measurements table to mark "bad" measurements.
SYNTAX
lsq_redo.py [-h] [command line options]
OPTIONS
-h: prints help message and quits
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PmagPy/PmagPy | pmagpy/ipmag.py | igrf | def igrf(input_list, mod='', ghfile=""):
"""
Determine Declination, Inclination and Intensity from the IGRF model.
(http://www.ngdc.noaa.gov/IAGA/vmod/igrf.html)
Parameters
----------
input_list : list with format [Date, Altitude, Latitude, Longitude]
date must be in decimal year format... | python | def igrf(input_list, mod='', ghfile=""):
"""
Determine Declination, Inclination and Intensity from the IGRF model.
(http://www.ngdc.noaa.gov/IAGA/vmod/igrf.html)
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input_list : list with format [Date, Altitude, Latitude, Longitude]
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PmagPy/PmagPy | pmagpy/ipmag.py | dms2dd | def dms2dd(degrees, minutes, seconds):
"""
Convert latitude/longitude of a location that is in degrees, minutes, seconds to decimal degrees
Parameters
----------
degrees : degrees of latitude/longitude
minutes : minutes of latitude/longitude
seconds : seconds of latitude/longitude
Retu... | python | def dms2dd(degrees, minutes, seconds):
"""
Convert latitude/longitude of a location that is in degrees, minutes, seconds to decimal degrees
Parameters
----------
degrees : degrees of latitude/longitude
minutes : minutes of latitude/longitude
seconds : seconds of latitude/longitude
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PmagPy/PmagPy | pmagpy/ipmag.py | fisher_mean | def fisher_mean(dec=None, inc=None, di_block=None):
"""
Calculates the Fisher mean and associated parameters from either a list of
declination values and a separate list of inclination values or from a
di_block (a nested list a nested list of [dec,inc,1.0]). Returns a
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"""
Calculates the Fisher mean and associated parameters from either a list of
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PmagPy/PmagPy | pmagpy/ipmag.py | fisher_angular_deviation | def fisher_angular_deviation(dec=None, inc=None, di_block=None, confidence=95):
'''
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lie can be calculated from the Fisher distribution. This function uses the
calculated Fisher concentration parameter to estimate this angle from... | python | def fisher_angular_deviation(dec=None, inc=None, di_block=None, confidence=95):
'''
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PmagPy/PmagPy | pmagpy/ipmag.py | bingham_mean | def bingham_mean(dec=None, inc=None, di_block=None):
"""
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either a list of declination values and a separate list of inclination
values or from a di_block (a nested list a nested list of [dec,inc,1.0]).
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"""
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PmagPy/PmagPy | pmagpy/ipmag.py | kent_mean | def kent_mean(dec=None, inc=None, di_block=None):
"""
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declination values and a separate list of inclination values or from a
di_block (a nested list a nested list of [dec,inc,1.0]). Returns a
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"""
Calculates the Kent mean and associated statistical parameters from either a list of
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PmagPy/PmagPy | pmagpy/ipmag.py | print_direction_mean | def print_direction_mean(mean_dictionary):
"""
Does a pretty job printing a Fisher mean and associated statistics for
directional data.
Parameters
----------
mean_dictionary: output dictionary of pmag.fisher_mean
Examples
--------
Generate a Fisher mean using ``ipmag.fisher_mean`` ... | python | def print_direction_mean(mean_dictionary):
"""
Does a pretty job printing a Fisher mean and associated statistics for
directional data.
Parameters
----------
mean_dictionary: output dictionary of pmag.fisher_mean
Examples
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PmagPy/PmagPy | pmagpy/ipmag.py | print_pole_mean | def print_pole_mean(mean_dictionary):
"""
Does a pretty job printing a Fisher mean and associated statistics for
mean paleomagnetic poles.
Parameters
----------
mean_dictionary: output dictionary of pmag.fisher_mean
Examples
--------
Generate a Fisher mean using ``ipmag.fisher_mean... | python | def print_pole_mean(mean_dictionary):
"""
Does a pretty job printing a Fisher mean and associated statistics for
mean paleomagnetic poles.
Parameters
----------
mean_dictionary: output dictionary of pmag.fisher_mean
Examples
--------
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PmagPy/PmagPy | pmagpy/ipmag.py | fishrot | def fishrot(k=20, n=100, dec=0, inc=90, di_block=True):
"""
Generates Fisher distributed unit vectors from a specified distribution
using the pmag.py fshdev and dodirot functions.
Parameters
----------
k : kappa precision parameter (default is 20)
n : number of vectors to determine (default... | python | def fishrot(k=20, n=100, dec=0, inc=90, di_block=True):
"""
Generates Fisher distributed unit vectors from a specified distribution
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Parameters
----------
k : kappa precision parameter (default is 20)
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PmagPy/PmagPy | pmagpy/ipmag.py | tk03 | def tk03(n=100, dec=0, lat=0, rev='no', G2=0, G3=0):
"""
Generates vectors drawn from the TK03.gad model of secular
variation (Tauxe and Kent, 2004) at given latitude and rotated
about a vertical axis by the given declination. Return a nested list of
of [dec,inc,intensity].
Parameters
-----... | python | def tk03(n=100, dec=0, lat=0, rev='no', G2=0, G3=0):
"""
Generates vectors drawn from the TK03.gad model of secular
variation (Tauxe and Kent, 2004) at given latitude and rotated
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Parameters
-----... | [
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PmagPy/PmagPy | pmagpy/ipmag.py | unsquish | def unsquish(incs, f):
"""
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data (incs) and returns 'unsquished' values.
Parameters
----------
incs : list of inclination values or a single value
f : unflattening factor (between 0.0 and 1.0)
Returns
------... | python | def unsquish(incs, f):
"""
This function applies uses a flattening factor (f) to unflatten inclination
data (incs) and returns 'unsquished' values.
Parameters
----------
incs : list of inclination values or a single value
f : unflattening factor (between 0.0 and 1.0)
Returns
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PmagPy/PmagPy | pmagpy/ipmag.py | squish | def squish(incs, f):
"""
This function applies an flattening factor (f) to inclination data
(incs) and returns 'squished' values.
Parameters
----------
incs : list of inclination values or a single value
f : flattening factor (between 0.0 and 1.0)
Returns
---------
incs_squishe... | python | def squish(incs, f):
"""
This function applies an flattening factor (f) to inclination data
(incs) and returns 'squished' values.
Parameters
----------
incs : list of inclination values or a single value
f : flattening factor (between 0.0 and 1.0)
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PmagPy/PmagPy | pmagpy/ipmag.py | do_flip | def do_flip(dec=None, inc=None, di_block=None):
"""
This function returns the antipode (i.e. it flips) of directions.
The function can take dec and inc as seperate lists if they are of equal
length and explicitly specified or are the first two arguments. It will then
return a list of flipped decs a... | python | def do_flip(dec=None, inc=None, di_block=None):
"""
This function returns the antipode (i.e. it flips) of directions.
The function can take dec and inc as seperate lists if they are of equal
length and explicitly specified or are the first two arguments. It will then
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PmagPy/PmagPy | pmagpy/ipmag.py | common_mean_bootstrap | def common_mean_bootstrap(Data1, Data2, NumSims=1000, save=False, save_folder='.', fmt='svg', figsize=(7, 2.3), x_tick_bins=4):
"""
Conduct a bootstrap test (Tauxe, 2010) for a common mean on two declination,
inclination data sets. Plots are generated of the cumulative distributions
of the Cartesian coo... | python | def common_mean_bootstrap(Data1, Data2, NumSims=1000, save=False, save_folder='.', fmt='svg', figsize=(7, 2.3), x_tick_bins=4):
"""
Conduct a bootstrap test (Tauxe, 2010) for a common mean on two declination,
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PmagPy/PmagPy | pmagpy/ipmag.py | common_mean_watson | def common_mean_watson(Data1, Data2, NumSims=5000, print_result=True, plot='no', save=False, save_folder='.', fmt='svg'):
"""
Conduct a Watson V test for a common mean on two directional data sets.
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Monte Carlo simulation in order to... | python | def common_mean_watson(Data1, Data2, NumSims=5000, print_result=True, plot='no', save=False, save_folder='.', fmt='svg'):
"""
Conduct a Watson V test for a common mean on two directional data sets.
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PmagPy/PmagPy | pmagpy/ipmag.py | fishqq | def fishqq(lon=None, lat=None, di_block=None):
"""
Test whether a distribution is Fisherian and make a corresponding Q-Q plot.
The Q-Q plot shows the data plotted against the value expected from a
Fisher distribution. The first plot is the uniform plot which is the
Fisher model distribution in terms... | python | def fishqq(lon=None, lat=None, di_block=None):
"""
Test whether a distribution is Fisherian and make a corresponding Q-Q plot.
The Q-Q plot shows the data plotted against the value expected from a
Fisher distribution. The first plot is the uniform plot which is the
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PmagPy/PmagPy | pmagpy/ipmag.py | lat_from_inc | def lat_from_inc(inc, a95=None):
"""
Calculate paleolatitude from inclination using the dipole equation
Required Parameter
----------
inc: (paleo)magnetic inclination in degrees
Optional Parameter
----------
a95: 95% confidence interval from Fisher mean
Returns
----------
... | python | def lat_from_inc(inc, a95=None):
"""
Calculate paleolatitude from inclination using the dipole equation
Required Parameter
----------
inc: (paleo)magnetic inclination in degrees
Optional Parameter
----------
a95: 95% confidence interval from Fisher mean
Returns
----------
... | [
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PmagPy/PmagPy | pmagpy/ipmag.py | lat_from_pole | def lat_from_pole(ref_loc_lon, ref_loc_lat, pole_plon, pole_plat):
"""
Calculate paleolatitude for a reference location based on a paleomagnetic pole
Required Parameters
----------
ref_loc_lon: longitude of reference location in degrees
ref_loc_lat: latitude of reference location
pole_plon:... | python | def lat_from_pole(ref_loc_lon, ref_loc_lat, pole_plon, pole_plat):
"""
Calculate paleolatitude for a reference location based on a paleomagnetic pole
Required Parameters
----------
ref_loc_lon: longitude of reference location in degrees
ref_loc_lat: latitude of reference location
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PmagPy/PmagPy | pmagpy/ipmag.py | inc_from_lat | def inc_from_lat(lat):
"""
Calculate inclination predicted from latitude using the dipole equation
Parameter
----------
lat : latitude in degrees
Returns
-------
inc : inclination calculated using the dipole equation
"""
rad = old_div(np.pi, 180.)
inc = old_div(np.arctan(2 ... | python | def inc_from_lat(lat):
"""
Calculate inclination predicted from latitude using the dipole equation
Parameter
----------
lat : latitude in degrees
Returns
-------
inc : inclination calculated using the dipole equation
"""
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_net | def plot_net(fignum):
"""
Draws circle and tick marks for equal area projection.
"""
# make the perimeter
plt.figure(num=fignum,)
plt.clf()
plt.axis("off")
Dcirc = np.arange(0, 361.)
Icirc = np.zeros(361, 'f')
Xcirc, Ycirc = [], []
for k in range(361):
XY = pmag.dimap(Dc... | python | def plot_net(fignum):
"""
Draws circle and tick marks for equal area projection.
"""
# make the perimeter
plt.figure(num=fignum,)
plt.clf()
plt.axis("off")
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_di | def plot_di(dec=None, inc=None, di_block=None, color='k', marker='o', markersize=20, legend='no', label='', title='', edge='',alpha=1):
"""
Plot declination, inclination data on an equal area plot.
Before this function is called a plot needs to be initialized with code that looks
something like:
>f... | python | def plot_di(dec=None, inc=None, di_block=None, color='k', marker='o', markersize=20, legend='no', label='', title='', edge='',alpha=1):
"""
Plot declination, inclination data on an equal area plot.
Before this function is called a plot needs to be initialized with code that looks
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>f... | [
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_di_mean | def plot_di_mean(dec, inc, a95, color='k', marker='o', markersize=20, label='', legend='no'):
"""
Plot a mean direction (declination, inclination) with alpha_95 ellipse on
an equal area plot.
Before this function is called, a plot needs to be initialized with code
that looks something like:
>fi... | python | def plot_di_mean(dec, inc, a95, color='k', marker='o', markersize=20, label='', legend='no'):
"""
Plot a mean direction (declination, inclination) with alpha_95 ellipse on
an equal area plot.
Before this function is called, a plot needs to be initialized with code
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>fi... | [
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>plt.figure(num=fignum,figsize=(10,10),dpi=160)
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_di_mean_bingham | def plot_di_mean_bingham(bingham_dictionary, fignum=1, color='k', marker='o', markersize=20, label='', legend='no'):
"""
see plot_di_mean_ellipse
"""
plot_di_mean_ellipse(bingham_dictionary, fignum=fignum, color=color,
marker=marker, markersize=markersize, label=label, legend=le... | python | def plot_di_mean_bingham(bingham_dictionary, fignum=1, color='k', marker='o', markersize=20, label='', legend='no'):
"""
see plot_di_mean_ellipse
"""
plot_di_mean_ellipse(bingham_dictionary, fignum=fignum, color=color,
marker=marker, markersize=markersize, label=label, legend=le... | [
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_di_mean_ellipse | def plot_di_mean_ellipse(dictionary, fignum=1, color='k', marker='o', markersize=20, label='', legend='no'):
"""
Plot a mean direction (declination, inclination) confidence ellipse.
Parameters
-----------
dictionary : a dictionary generated by the pmag.dobingham or pmag.dokent funcitons
"""
... | python | def plot_di_mean_ellipse(dictionary, fignum=1, color='k', marker='o', markersize=20, label='', legend='no'):
"""
Plot a mean direction (declination, inclination) confidence ellipse.
Parameters
-----------
dictionary : a dictionary generated by the pmag.dobingham or pmag.dokent funcitons
"""
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PmagPy/PmagPy | pmagpy/ipmag.py | make_orthographic_map | def make_orthographic_map(central_longitude=0, central_latitude=0, figsize=(8, 8),
add_land=True, land_color='tan', add_ocean=False, ocean_color='lightblue', grid_lines=True,
lat_grid=[-80., -60., -30.,
0., 30., 60., 80.],
... | python | def make_orthographic_map(central_longitude=0, central_latitude=0, figsize=(8, 8),
add_land=True, land_color='tan', add_ocean=False, ocean_color='lightblue', grid_lines=True,
lat_grid=[-80., -60., -30.,
0., 30., 60., 80.],
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_pole | def plot_pole(map_axis, plon, plat, A95, label='', color='k', edgecolor='k', marker='o', markersize=20, legend='no'):
"""
This function plots a paleomagnetic pole and A95 error ellipse on a cartopy map axis.
Before this function is called, a plot needs to be initialized with code
such as that in the ma... | python | def plot_pole(map_axis, plon, plat, A95, label='', color='k', edgecolor='k', marker='o', markersize=20, legend='no'):
"""
This function plots a paleomagnetic pole and A95 error ellipse on a cartopy map axis.
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Example
-------
>>> plon = 200
>>> plat = 60
>>> A95 = 6
>>> map_axis = ipm... | [
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_poles | def plot_poles(map_axis, plon, plat, A95, label='', color='k', edgecolor='k', marker='o', markersize=20, legend='no'):
"""
This function plots paleomagnetic poles and A95 error ellipses on a cartopy map axis.
Before this function is called, a plot needs to be initialized with code
such as that in the m... | python | def plot_poles(map_axis, plon, plat, A95, label='', color='k', edgecolor='k', marker='o', markersize=20, legend='no'):
"""
This function plots paleomagnetic poles and A95 error ellipses on a cartopy map axis.
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Examples
-------
>>> plons = [200, 180, 210]
>>> plats = [60, 40, 35]
>>> A95 =... | [
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_pole_basemap | def plot_pole_basemap(mapname, plon, plat, A95, label='', color='k', edgecolor='k', marker='o', markersize=20, legend='no'):
"""
This function plots a paleomagnetic pole and A95 error ellipse on whatever
current map projection has been set using the basemap plotting library.
Before this function is call... | python | def plot_pole_basemap(mapname, plon, plat, A95, label='', color='k', edgecolor='k', marker='o', markersize=20, legend='no'):
"""
This function plots a paleomagnetic pole and A95 error ellipse on whatever
current map projection has been set using the basemap plotting library.
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_pole_dp_dm | def plot_pole_dp_dm(map_axis, plon, plat, slon, slat, dp, dm, pole_label='pole', site_label='site',
pole_color='k', pole_edgecolor='k', pole_marker='o',
site_color='r', site_edgecolor='r', site_marker='s',
markersize=20, legend=True):
"""
This function... | python | def plot_pole_dp_dm(map_axis, plon, plat, slon, slat, dp, dm, pole_label='pole', site_label='site',
pole_color='k', pole_edgecolor='k', pole_marker='o',
site_color='r', site_edgecolor='r', site_marker='s',
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Example
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>>> dec = 280
>>> inc = 45
>>> a95 = 5
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_poles_colorbar | def plot_poles_colorbar(map_axis, plons, plats, A95s, colorvalues, vmin, vmax,
colormap='viridis', edgecolor='k', marker='o', markersize='20',
alpha=1.0, colorbar=True, colorbar_label='pole age (Ma)'):
"""
This function plots multiple paleomagnetic pole and A95 er... | python | def plot_poles_colorbar(map_axis, plons, plats, A95s, colorvalues, vmin, vmax,
colormap='viridis', edgecolor='k', marker='o', markersize='20',
alpha=1.0, colorbar=True, colorbar_label='pole age (Ma)'):
"""
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Example
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_vgp | def plot_vgp(map_axis, vgp_lon=None, vgp_lat=None, di_block=None, label='', color='k', marker='o',
edge='black', markersize=20, legend=False):
"""
This function plots a paleomagnetic pole position on a cartopy map axis.
Before this function is called, a plot needs to be initialized with code
... | python | def plot_vgp(map_axis, vgp_lon=None, vgp_lat=None, di_block=None, label='', color='k', marker='o',
edge='black', markersize=20, legend=False):
"""
This function plots a paleomagnetic pole position on a cartopy map axis.
Before this function is called, a plot needs to be initialized with code
... | [
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Example
-------
>>> vgps = ipmag.fishrot(dec=200,inc=30)
>>> vgp_lon_list,vgp_lat_list,intensiti... | [
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PmagPy/PmagPy | pmagpy/ipmag.py | plot_vgp_basemap | def plot_vgp_basemap(mapname, vgp_lon=None, vgp_lat=None, di_block=None, label='', color='k', marker='o', markersize=20, legend='no'):
"""
This function plots a paleomagnetic pole on whatever current map projection
has been set using the basemap plotting library.
Before this function is called, a plot n... | python | def plot_vgp_basemap(mapname, vgp_lon=None, vgp_lat=None, di_block=None, label='', color='k', marker='o', markersize=20, legend='no'):
"""
This function plots a paleomagnetic pole on whatever current map projection
has been set using the basemap plotting library.
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PmagPy/PmagPy | pmagpy/ipmag.py | vgp_calc | def vgp_calc(dataframe, tilt_correction='yes', site_lon='site_lon', site_lat='site_lat', dec_is='dec_is', inc_is='inc_is', dec_tc='dec_tc', inc_tc='inc_tc'):
"""
This function calculates paleomagnetic poles using directional data and site
location data within a pandas.DataFrame. The function adds the column... | python | def vgp_calc(dataframe, tilt_correction='yes', site_lon='site_lon', site_lat='site_lat', dec_is='dec_is', inc_is='inc_is', dec_tc='dec_tc', inc_tc='inc_tc'):
"""
This function calculates paleomagnetic poles using directional data and site
location data within a pandas.DataFrame. The function adds the column... | [
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"vgp_... | train | https://github.com/PmagPy/PmagPy/blob/c7984f8809bf40fe112e53dcc311a33293b62d0b/pmagpy/ipmag.py#L2183-L2272 |
PmagPy/PmagPy | pmagpy/ipmag.py | sb_vgp_calc | def sb_vgp_calc(dataframe, site_correction='yes', dec_tc='dec_tc', inc_tc='inc_tc'):
"""
This function calculates the angular dispersion of VGPs and corrects
for within site dispersion (unless site_correction = 'no') to return
a value S_b. The input data needs to be within a pandas Dataframe.
Param... | python | def sb_vgp_calc(dataframe, site_correction='yes', dec_tc='dec_tc', inc_tc='inc_tc'):
"""
This function calculates the angular dispersion of VGPs and corrects
for within site dispersion (unless site_correction = 'no') to return
a value S_b. The input data needs to be within a pandas Dataframe.
Param... | [
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Parameters
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dataframe : the name of the pandas.DataFrame containing the data
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PmagPy/PmagPy | pmagpy/ipmag.py | make_di_block | def make_di_block(dec, inc):
"""
Some pmag.py and ipmag.py functions require or will take a list of unit
vectors [dec,inc,1.] as input. This function takes declination and
inclination data and make it into such a nest list of lists.
Parameters
-----------
dec : list of declinations
inc ... | python | def make_di_block(dec, inc):
"""
Some pmag.py and ipmag.py functions require or will take a list of unit
vectors [dec,inc,1.] as input. This function takes declination and
inclination data and make it into such a nest list of lists.
Parameters
-----------
dec : list of declinations
inc ... | [
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dec : list of declinations
inc : list of inclinations
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PmagPy/PmagPy | pmagpy/ipmag.py | unpack_di_block | def unpack_di_block(di_block):
"""
This function unpacks a nested list of [dec,inc,mag_moment] into a list of
declination values, a list of inclination values and a list of magnetic
moment values. Mag_moment values are optional, while dec and inc values are
required.
Parameters
-----------
... | python | def unpack_di_block(di_block):
"""
This function unpacks a nested list of [dec,inc,mag_moment] into a list of
declination values, a list of inclination values and a list of magnetic
moment values. Mag_moment values are optional, while dec and inc values are
required.
Parameters
-----------
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PmagPy/PmagPy | pmagpy/ipmag.py | make_diddd_array | def make_diddd_array(dec, inc, dip_direction, dip):
"""
Some pmag.py functions such as the bootstrap fold test require a numpy array
of dec, inc, dip direction, dip [dec, inc, dd, dip] as input. This function
makes such an array.
Parameters
-----------
dec : paleomagnetic declination in d... | python | def make_diddd_array(dec, inc, dip_direction, dip):
"""
Some pmag.py functions such as the bootstrap fold test require a numpy array
of dec, inc, dip direction, dip [dec, inc, dd, dip] as input. This function
makes such an array.
Parameters
-----------
dec : paleomagnetic declination in d... | [
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-----------
dec : paleomagnetic declination in degrees
inc : paleomagnetic inclination in degrees
dip_di... | [
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PmagPy/PmagPy | pmagpy/ipmag.py | equi | def equi(map_axis, centerlon, centerlat, radius, color, alpha=1.0):
"""
This function enables A95 error ellipses to be drawn in cartopy around
paleomagnetic poles in conjunction with shoot
(modified from: http://www.geophysique.be/2011/02/20/matplotlib-basemap-tutorial-09-drawing-circles/).
"""
... | python | def equi(map_axis, centerlon, centerlat, radius, color, alpha=1.0):
"""
This function enables A95 error ellipses to be drawn in cartopy around
paleomagnetic poles in conjunction with shoot
(modified from: http://www.geophysique.be/2011/02/20/matplotlib-basemap-tutorial-09-drawing-circles/).
"""
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PmagPy/PmagPy | pmagpy/ipmag.py | equi_basemap | def equi_basemap(m, centerlon, centerlat, radius, color):
"""
This function enables A95 error ellipses to be drawn in basemap around
paleomagnetic poles in conjunction with shoot
(from: http://www.geophysique.be/2011/02/20/matplotlib-basemap-tutorial-09-drawing-circles/).
"""
glon1 = centerlon
... | python | def equi_basemap(m, centerlon, centerlat, radius, color):
"""
This function enables A95 error ellipses to be drawn in basemap around
paleomagnetic poles in conjunction with shoot
(from: http://www.geophysique.be/2011/02/20/matplotlib-basemap-tutorial-09-drawing-circles/).
"""
glon1 = centerlon
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PmagPy/PmagPy | pmagpy/ipmag.py | ellipse | def ellipse(map_axis, centerlon, centerlat, major_axis, minor_axis, angle, n=360, filled=False, **kwargs):
"""
This function enables general error ellipses to be drawn on the cartopy projection of the input map axis
using a center and a set of major and minor axes and a rotation angle east of north.
(Ad... | python | def ellipse(map_axis, centerlon, centerlat, major_axis, minor_axis, angle, n=360, filled=False, **kwargs):
"""
This function enables general error ellipses to be drawn on the cartopy projection of the input map axis
using a center and a set of major and minor axes and a rotation angle east of north.
(Ad... | [
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Parameters
-----------
map_axis : cartopy axis
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