pmagpy 4.2.122__py3-none-any.whl → 4.2.125__py3-none-any.whl

dialogs/thellier_gui_dialogs.py

@@ -29,7 +29,7 @@ import wx.lib.scrolledpanel
 import copy
 import os
 import scipy
-from scipy import arange
+from numpy import arange
 # only this one is nessesary.
 import wx
 from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigCanvas

pmag_env/__init__.py

@@ -1,4 +1,3 @@
-from __future__ import absolute_import
 from . import set_env
 
 __all__ = [set_env]

pmagpy/Fit.py

@@ -1,4 +1,3 @@
-from __future__ import print_function
 
 from builtins import map
 from builtins import str

pmagpy/__init__.py

@@ -1,4 +1,3 @@
-from __future__ import absolute_import
 
 import sys
 

pmagpy/builder2.py

@@ -3,7 +3,6 @@
 """
 Module for building or reading in specimen, sample, site, and location data.
 """
-from __future__ import print_function
 
 import os
 

pmagpy/cals10k.py

@@ -1,4 +1,3 @@
-from __future__ import print_function
 
 import sys
 

pmagpy/contribution_builder.py

@@ -2147,6 +2147,10 @@ class MagicDataFrame(object):
         name = self.get_singular_and_plural_dtype(self.dtype)[0]
         if name in self.df.columns:
             self.df[name] = self.df[name].astype(str)
+            
+        extra_name_col = name + "_name"
+        if extra_name_col in self.df.columns:
+            self.df = self.df.drop(extra_name_col, axis=1)
         #
         if df is None:
             df = self.df

pmagpy/controlled_vocabularies2.py

@@ -1,6 +1,4 @@
 #!/usr/bin/env python
-from __future__ import print_function
-from __future__ import absolute_import
 
 import json
 import os

pmagpy/convert_2_magic.py

@@ -1031,6 +1031,8 @@ def agm(agm_file, dir_path=".", input_dir_path="",
     # parse data
     stop = len(Data) - end
     for line in Data[start:stop]:  # skip header stuff
+        if 'T' in line: #some file formats end up with the first line is off by one. This skips the line
+            continue   
         MeasRec, SpecRec, SampRec, SiteRec, LocRec = {}, {}, {}, {}, {}
         # take care of some paper work
         if not syn:

pmagpy/demag_gui_utilities.py

@@ -1,6 +1,3 @@
-from __future__ import print_function
-from __future__ import absolute_import
-
 import os
 
 from builtins import zip

pmagpy/find_pmag_dir.py

@@ -1,7 +1,4 @@
-from __future__ import print_function
-from __future__ import absolute_import
-
-from imp import reload
+from importlib import reload
 import os
 import sys
 

pmagpy/gufm.py

@@ -1,4 +1,3 @@
-from __future__ import print_function
 
 def coeffs(date):
     if date < 1600:

pmagpy/ipmag.py

@@ -2142,7 +2142,7 @@ def plot_net(fignum=None,tick_spacing=10):
     plt.axis((-1.05, 1.05, -1.05, 1.05))
 
 
-def plot_di(dec=None, inc=None, di_block=None, color='k', marker='o', markersize=20, legend='no', label='', title=None, edge=None,alpha=1, zorder=2):
+def plot_di(dec=None, inc=None, di_block=None, color='k', marker='o', markersize=20, legend='no', label='', connect_points=False, lw=0.25, lc='k', la=0.5, title=None, edge=None, alpha=1, zorder=2):
     """
     Plot declination, inclination data on an equal area plot.
 
@@ -2159,8 +2159,13 @@ def plot_di(dec=None, inc=None, di_block=None, color='k', marker='o', markersize
         color : the default color is black. Other colors can be chosen (e.g. 'r')
         marker : the default marker is a circle ('o')
         markersize : default size is 20
-        label : the default label is blank ('')
         legend : the default is no legend ('no'). Putting 'yes' will plot a legend.
+        label : the default label is blank ('')
+        connect_points : option to connect points in order of plotting, default is False
+        lw : linewidth of connecting lines
+        lc : color of connecting lines
+        la : alpha of connecting lines
+        title : the default title is False
         edge : marker edge color - if blank, is color of marker
         alpha : opacity
         zorder : zorder of marker
@@ -2208,10 +2213,13 @@ def plot_di(dec=None, inc=None, di_block=None, color='k', marker='o', markersize
             color_up.append(color)
 
     if len(X_up) > 0:
+        if connect_points == True:
+            plt.plot(X_up, Y_up, ls = '-', linewidth=lw, color =lc, alpha = la, zorder=1)
         plt.scatter(X_up, Y_up, facecolors='none', edgecolors=color_up,
                     s=markersize, marker=marker, label=label,alpha=alpha, zorder=zorder)
-
     if len(X_down) > 0:
+        if connect_points == True:
+            plt.plot(X_down, Y_down, ls = '-', linewidth=lw, color =lc, alpha = la, zorder=1)
         plt.scatter(X_down, Y_down, facecolors=color_down, edgecolors=edge,
                     s=markersize, marker=marker, label=label,alpha=alpha, zorder=zorder)
     if legend == 'yes':
@@ -2464,7 +2472,6 @@ def make_robinson_map(central_longitude=0, figsize=(8, 8),
         ax.gridlines(xlocs=lon_grid, ylocs=lat_grid)
     return ax
 
-
 def plot_pole(map_axis, plon, plat, A95, label='', color='k', edgecolor='k',
               marker='o', markersize=20, legend='no',outline=True,
               filled_pole=False, fill_color='k', fill_alpha=1.0, 
@@ -2488,6 +2495,7 @@ def plot_pole(map_axis, plon, plat, A95, label='', color='k', edgecolor='k',
         filled_pole : if True, the A95 ellipse will be filled with color
         fill_color : color of fill; the default is black.
         fill_alpha : transparency of filled ellipse (the default is 1.0; no transparency).
+        mean_alpha : transparency of pole mean (the default is 1.0; no transparency).
         zorder : plotting order (default is 100; higher will move to top of plot)
 
     Examples:
@@ -2514,7 +2522,7 @@ def plot_pole(map_axis, plon, plat, A95, label='', color='k', edgecolor='k',
 
 def plot_poles(map_axis, plon, plat, A95, label='', color='k', edgecolor='k',
                marker='o', markersize=20, legend='no',outline=True,
-               filled_pole=False, fill_color='k', fill_alpha=1.0, zorder=101):
+               filled_pole=False, fill_color='k', fill_alpha=1.0, alpha=1.0, zorder=101, lw=1):
     """
     This function plots paleomagnetic poles and A95 error ellipses on a cartopy map axis.
 
@@ -2536,6 +2544,7 @@ def plot_poles(map_axis, plon, plat, A95, label='', color='k', edgecolor='k',
         filled_pole : if True, the A95 ellipse will be filled with color
         fill_color : color of fill; the default is black.
         fill_alpha : transparency of filled ellipse (the default is 1.0; no transparency).
+        alpha : transparency of pole mean (the default is 1.0; no transparency).
         zorder : plotting order (default is 100; higher will move to top of plot) 
 
     Examples:
@@ -2556,25 +2565,25 @@ def plot_poles(map_axis, plon, plat, A95, label='', color='k', edgecolor='k',
 
     map_axis.scatter(plon, plat, marker=marker,
                      color=color, edgecolors=edgecolor, s=markersize,
-                     label=label, zorder=zorder, transform=ccrs.PlateCarree())
+                     label=label, zorder=zorder, transform=ccrs.PlateCarree(), alpha=alpha)
     if filled_pole==False:
         if isinstance(color,str)==True:
             for n in range(0,len(A95)):
                 A95_km = A95[n] * 111.32
-                equi(map_axis, plon[n], plat[n], A95_km, color)
+                equi(map_axis, plon[n], plat[n], A95_km, color, alpha=alpha, lw=lw)
         else:
             for n in range(0,len(A95)):
                 A95_km = A95[n] * 111.32
-                equi(map_axis, plon[n], plat[n], A95_km, color[n])
+                equi(map_axis, plon[n], plat[n], A95_km, color[n], alpha=alpha, lw=lw)
     elif filled_pole==True:
         if isinstance(fill_color,str)==True:
             for n in range(0,len(A95)):
                 A95_km = A95[n] * 111.32
-                equi(map_axis, plon[n], plat[n], A95_km, fill_color, alpha=fill_alpha, outline=outline, fill=True)
+                equi(map_axis, plon[n], plat[n], A95_km, fill_color, alpha=fill_alpha, outline=outline, fill=True, lw=lw)
         else:
             for n in range(0,len(A95)):
                 A95_km = A95[n] * 111.32
-                equi(map_axis, plon[n], plat[n], A95_km, fill_color[n], alpha=fill_alpha, outline=outline, fill=True)
+                equi(map_axis, plon[n], plat[n], A95_km, fill_color[n], alpha=fill_alpha, outline=outline, fill=True, lw=lw)
 
     if legend == 'yes':
         plt.legend(loc=2)
@@ -2784,7 +2793,7 @@ def plot_pole_dp_dm(map_axis, plon, plat, slon, slat, dp, dm, pole_label='pole',
 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)',
-                        outline='True',filled_pole=False, fill_alpha=1.0):
+                        outline='True',filled_pole=False, fill_alpha=1.0, lw=1):
     """
     This function plots multiple paleomagnetic pole and A95 error ellipse on a cartopy map axis.
     The poles are colored by the defined colormap.
@@ -2827,7 +2836,7 @@ def plot_poles_colorbar(map_axis, plons, plats, A95s, colorvalues, vmin, vmax,
     plot_poles(map_axis, plons, plats, A95s,
                label='', color=colors, edgecolor=edgecolor, marker=marker,
                markersize=markersize,filled_pole=filled_pole,outline=outline,
-               fill_color=colors, fill_alpha=fill_alpha)
+               fill_color=colors, fill_alpha=fill_alpha, alpha=alpha, lw=lw)
 
     if colorbar == True:
         sm = plt.cm.ScalarMappable(
@@ -4192,7 +4201,7 @@ def ani_depthplot(spec_file='specimens.txt', samp_file='samples.txt',
             ax6 = plt.subplot(1, pcol, 5)
             Axs.append(ax6)
             ax6.plot(Bulks, BulkDepths, 'bo')
-            ax6.axis([bmin - 1, 1.1 * bmax, dmax, dmin])
+            ax6.set_ylim(dmax, dmin)
             ax6.set_xlabel('Bulk Susc. (uSI)')
             ax6.yaxis.set_major_locator(plt.NullLocator())
             if sum_file:
@@ -9613,6 +9622,138 @@ def find_ei_kent(data, site_latitude, site_longitude, kent_color='k', nb=1000, s
     else:
         return kent_stats
 
+
+def find_compilation_kent(plon, plat, A95, slon, slat,
+                          f_from_compilation=None, n=10000, n_fish=100,
+                          return_poles=False, return_kent_stats=True,
+                          return_paleolats=False, map_central_longitude=0,
+                          map_central_latitude=0):
+    
+    """
+    Applies flattening factors from the compilation to sedimentary paleomagnetic pole where only
+    pole longitude, pole latitude, A95, site longitude, and site latitude are available.
+
+    First, calculate the paleomagnetic direction at the site of the mean pole using plon, plat via
+    pmag.vgp_di. Then draw n resamples from the compiled f values in the compilation. The default
+    compilation of Pierce et al., 2022 can be used or the user can provide their own compilation.
+
+    Unsquish the directions with the resampled f factors, then convert the mean directions back to pole
+    space. Making the simplifying assumption that A95 is the same as the directions are unflattened.
+    Resample n_fish mean poles from the Fisher distribution given the unsquished plon, plat, and A95.
+    This will result in a total of n*n_fish number of resampled mean poles. Summarize the distribution
+    of the mean poles using a Kent distribution.
+
+    Parameters:
+        plon: legacy mean pole longitude
+        plat: legacy mean pole latitude
+        A95: legacy mean pole A95
+        slon: site longitude
+        slat: site latitude
+        f_from_compilation: list of f factors (default is None in which case the compilation of
+            Pierce et al., 2022 Table S1 will be used)
+        n: number of resamples from compilation (default is 10000)
+        n_fish: number of resamples from each Fisher mean pole position (default is 100)
+        return_poles: whether or not to return the resampled mean pole positions (default is False)
+        return_kent_stats: whether or not to return the calculated Kent distribution statistics of
+            the resampled mean poles (default is True)
+        return_paleolats: whether or not to return the computed compilation paleolatitudes (default is
+            False)
+        map_central_longitude: central longitude for the orthographic map (default is 0)
+        map_central_latitude: central latitude for the orthographic map (default is 0)
+
+    Returns:
+        Depending on the combination of boolean flags provided, returns one or more of:
+        - compilation_mean_lons, compilation_mean_lats: resampled mean pole positions
+        - f_compilation_kent_distribution_95: Kent distribution statistics
+        - compilation_paleolats: computed compilation paleolatitudes
+    """
+    # get the uncorrected declination and inclination from a given paleomagnetic pole
+    original_dec, original_inc = pmag.vgp_di(plat, plon, slat, slon)
+
+    if f_from_compilation is None:
+        # compilation f value list
+        f_from_compilation = pd.Series(
+            [
+                0.49, 0.77, 0.63, 0.59, 0.57, 0.4, 0.63, 0.66, 0.63, 0.49, 0.49,
+                0.58, 0.54, 0.73, 0.97, 0.59, 0.84, 0.9, 0.78, 0.83, 0.58, 0.94,
+                0.78, 0.9, 0.68, 0.48, 0.67, 0.66, 0.7, 0.43, 0.45, 0.58, 0.58,
+                0.53, 0.42, 0.51, 0.61, 0.52, 0.62, 0.73, 0.66, 0.55, 0.47, 0.77,
+                0.62, 0.54, 0.46, 0.56, 0.64, 0.47, 0.48, 0.44, 0.52, 0.65, 0.81,
+                0.64, 0.71, 0.79, 0.65, 0.56, 0.69, 0.43, 0.7, 0.67, 0.65, 0.49,
+                0.54, 0.64, 0.83, 0.68
+            ]
+        )
+    else:
+        f_from_compilation = pd.Series(f_from_compilation)
+
+    f_resample = f_from_compilation.sample(n=n, replace=True).tolist()
+
+    plt.figure(figsize=(6, 6))
+    plt.hist(f_resample, alpha=0.6, density=1)
+    plt.xticks(fontsize=14)
+    plt.yticks(fontsize=14)
+    plt.xlabel("resample of compilation f factors", fontsize=16)
+    plt.ylabel("density", fontsize=16)
+
+    # calculate corrected inclinations
+    compilation_incs = [pmag.unsquish(original_inc, f) for f in f_resample]
+    # calculate corrected paleolatitudes
+    compilation_paleolats = np.degrees(np.arctan(np.tan(np.radians(compilation_incs)) / 2))
+
+    plt.figure(figsize=(6, 6))
+    plt.hist(compilation_paleolats, alpha=0.6, density=1)
+    plt.xticks(fontsize=14)
+    plt.yticks(fontsize=14)
+    plt.xlabel("compilation paleolatitudes ($^\circ$)", fontsize=16)
+    plt.ylabel("density", fontsize=16)
+
+    compilation_mean_lons = []
+    compilation_mean_lats = []
+
+    for i in range(len(f_from_compilation)):
+        unsquish_plon, unsquish_plats, _, _ = pmag.dia_vgp(
+            original_dec, compilation_incs[i], A95, slat, slon)
+        resampled_lons, resampled_lats = fisher_mean_resample(
+            alpha95=A95,
+            n=n_fish,
+            dec=unsquish_plon,
+            inc=unsquish_plats,
+            di_block=0)
+        compilation_mean_lons.extend(resampled_lons)
+        compilation_mean_lats.extend(resampled_lats)
+
+    m = make_orthographic_map(map_central_longitude, map_central_latitude)
+    plot_vgp(
+        m,
+        compilation_mean_lons,
+        compilation_mean_lats,
+        color="lightgrey",
+        edge="none",
+        markersize=5,
+        alpha=0.002)
+
+    f_compilation_kent_distribution_95 = kent_distribution_95(
+        dec=compilation_mean_lons, inc=compilation_mean_lats)
+    print_kent_mean(f_compilation_kent_distribution_95)
+    plot_pole_ellipse(
+        m, f_compilation_kent_distribution_95, color="darkred", label="Kent mean pole")
+    plot_pole(
+        m, plon, plat, A95, label="uncorrected pole position", color="C0")
+    plt.legend(loc=8, fontsize=14)
+
+    results = []
+    if return_poles:
+        results.extend([compilation_mean_lons, compilation_mean_lats])
+    if return_kent_stats:
+        results.append(f_compilation_kent_distribution_95)
+    if return_paleolats:
+        results.append(compilation_paleolats)
+
+    if len(results) == 1:
+        return results[0]
+    return tuple(results)
+
+
 def pole_comparison_H2019(lon_1,lat_1,k_1,r_1,lon_2,lat_2,k_2,r_2):
     '''
     Calculate the Bhattacharyya Coefficient, Bayes error and the
@@ -12318,7 +12459,7 @@ def atrm_magic(meas_file, dir_path=".", input_dir_path="",
 
 
 
-def zeq_magic(meas_file='measurements.txt', spec_file='',crd='s',input_dir_path='.', angle=0,
+def zeq_magic(meas_file='measurements.txt', spec_file='',crd='s', dir_path = ".", input_dir_path="", angle=0,
               n_plots=5, save_plots=True, fmt="svg", interactive=False, specimen="",
               samp_file='samples.txt', contribution=None,fignum=1, image_records=False):
     """
@@ -12334,8 +12475,10 @@ def zeq_magic(meas_file='measurements.txt', spec_file='',crd='s',input_dir_path=
     crd : str
         coordinate system [s,g,t] for specimen, geographic, tilt corrected
         g,t options require a sample file with specimen and bedding orientation
+    dir_path : str
+        output directory for plots, default "."
     input_dir_path : str
-        input directory of meas_file, default "."
+        input directory, if different from dir_path, default ""
     angle : float
         angle of X direction with respect to specimen X
     n_plots : int, default 5
@@ -12673,7 +12816,7 @@ def zeq_magic(meas_file='measurements.txt', spec_file='',crd='s',input_dir_path=
                               'software_packages': version.version}
                 image_recs.append(image_rec)
         if save_plots:
-            saved.extend(pmagplotlib.save_plots(ZED, titles))
+            saved.extend(pmagplotlib.save_plots(ZED, titles, dir_path=dir_path))
         elif interactive:
             pmagplotlib.draw_figs(ZED)
             ans = pmagplotlib.save_or_quit()
@@ -14056,7 +14199,7 @@ def eqarea_magic(in_file='sites.txt', dir_path=".", input_dir_path="",
             FIG = pmagplotlib.add_borders(FIG, titles, con_id=con_id)
             saved_figs = pmagplotlib.save_plots(FIG, files)
         elif save_plots:
-            saved_figs = pmagplotlib.save_plots(FIG, files, incl_directory=True)
+            saved_figs = pmagplotlib.save_plots(FIG, files, dir_path = dir_path, incl_directory=True)
             #continue
         elif interactive:
             pmagplotlib.draw_figs(FIG)

pmagpy/mapping/__init__.py

@@ -3,7 +3,6 @@
 # 
 #  Copyright (c) 2014 Lori Jonestrask
 #  Author: Lori Jonestrask (mintblue87@gmail.com) .
-from __future__ import absolute_import
 #!/usr/bin/env python
 # __init__.py: -*- Python -*-  DESCRIPTIVE TEXT.
 # 

pmagpy/nlt.py

@@ -1,10 +1,7 @@
-from __future__ import division
-from __future__ import print_function
 from builtins import range
 
 import math
 
-from past.utils import old_div
 from scipy import optimize
 
 # some functions required by non-linear TRM programs
@@ -30,7 +27,7 @@ def funk(p, x, y):
     dev=0
     for i in range(len(x)):
       dev=dev+((y[i]-(alpha*math.tanh(beta*x[i])))**2)
-    rms=math.sqrt(old_div(dev,float(len(y))))
+    rms=math.sqrt(dev /float(len(y)))
     return rms
 #
 def compare(a, b):
@@ -63,12 +60,12 @@ def TRMinv(m,a,b):
     if float(b)==0:
         print('ERROR: TRMinv: b==0.')
         if not WARN : sys.exit()
-    x = (old_div(float(m), float(a)))
+    x = float(m) / float(a)
     if (1-x)<=0:
          print('ERROR:  TRMinv: (1-x)==0.')
          return -1
     if not WARN : sys.exit()
-    f = (old_div(1.,float(b))) * 0.5 * math.log (old_div((1+x), (1-x)))
+    f = (1. / float(b)) * 0.5 * math.log ((1+x) / (1-x))
     return float(f)
 
 def NRM(f,a,b,best):
@@ -80,7 +77,7 @@ def NRM(f,a,b,best):
     if float(f)==0:
         print('ERROR: NRM: f==0.')
     if not WARN : sys.exit()
-    m = (old_div(float(best),float(f))) * TRM(f,a,b)
+    m = (float(best) /float(f)) * TRM(f,a,b)
     return float(m)
 #
 def NLtrm(Bs,TRMs,best,blab,jackknife):
@@ -98,8 +95,8 @@ def NLtrm(Bs,TRMs,best,blab,jackknife):
     for i in range(len(TRMs)):
         if TRMs[i]>Tmax:Tmax=TRMs[i]    
         if Bs[i]>Bmax:Bmax=Bs[i]    
-    xi[0]=2.0*Tmax # maximum TRM
-    xi[1]=old_div(1.0,Bmax) # maximum field
+    xi[0] = 2.0 * Tmax # maximum TRM
+    xi[1] = 1.0 / Bmax # maximum field
 # Minimize tanh function using simplex
     xopt = optimize.fmin(funk, xi, args=(Bs, TRMs),xtol=FTOL,ftol=FTOL,maxiter=MAXITER)
     xopt2= optimize.fmin(funk, xopt, args=(Bs, TRMs),xtol=FTOL,ftol=FTOL,maxiter=MAXITER)
@@ -115,7 +112,7 @@ def NLtrm(Bs,TRMs,best,blab,jackknife):
         rms=0
         for ix in range(len(Bs)):
             rms = rms + (TRMs[ix]-(xopt2[0]*math.tanh(xopt2[1]*Bs[ix]))**2)
-        rms=math.sqrt(old_div(rms,len(Bs)))
+        rms=math.sqrt(rms / len(Bs))
     except ValueError:
 # If no fittanh data are available, return -Best
         rms=-1