pmagpy 4.2.125__py3-none-any.whl → 4.3.1__py3-none-any.whl

pmagpy/ipmag.py

@@ -39,7 +39,6 @@ from . import data_model3 as data_model
 from .contribution_builder import Contribution
 from . import validate_upload3 as val_up3
 from numpy.linalg import inv, eig
-has_basemap, Basemap = pmag.import_basemap()
 has_cartopy, cartopy = pmag.import_cartopy()
 
 if has_cartopy == True:
@@ -2087,59 +2086,71 @@ def inc_from_lat(lat):
     return inc
 
 
-def plot_net(fignum=None,tick_spacing=10):
+def plot_net(fignum=None, tick_spacing=10, ax=None):
     """
     Draws circle and tick marks for equal area projection.
-    tick_spacing: interval for declination tick marks, default is 10
-    """
-    if fignum != None:
-        plt.figure(num=fignum,)
-        plt.clf()
-    plt.axis("off")
-    Dcirc = np.arange(0, 361.)
-    Icirc = np.zeros(361, 'f')
+
+    Parameters:
+        fignum: int or None
+            Figure number to use for creating a new figure if no axis is provided.
+        tick_spacing: int
+            Interval for declination tick marks, default is 10.
+        ax: matplotlib.axes.Axes or None
+            Axis to plot on. If None, the current axis will be used (or created if fignum is given).
+    """
+    if ax is None:
+        if fignum is not None:
+            plt.figure(num=fignum)
+            plt.clf()
+        ax = plt.gca()
+    ax.axis("off")
+    Dcirc = np.arange(0, 361.0)
+    Icirc = np.zeros(361, dtype=float)
     Xcirc, Ycirc = [], []
     for k in range(361):
         XY = pmag.dimap(Dcirc[k], Icirc[k])
         Xcirc.append(XY[0])
         Ycirc.append(XY[1])
-    plt.plot(Xcirc, Ycirc, 'k')
+    ax.plot(Xcirc, Ycirc, "k")
 
-# put on the tick marks
+    # Put on the tick marks
     Xsym, Ysym = [], []
     for I in range(tick_spacing, 100, tick_spacing):
-        XY = pmag.dimap(0., I)
+        XY = pmag.dimap(0.0, I)
         Xsym.append(XY[0])
         Ysym.append(XY[1])
-    plt.scatter(Xsym, Ysym, color='black',marker='_',s=10)
+    ax.scatter(Xsym, Ysym, color="black", marker="_", s=10)
+
     Xsym, Ysym = [], []
     for I in range(tick_spacing, 100, tick_spacing):
-        XY = pmag.dimap(90., I)
+        XY = pmag.dimap(90.0, I)
         Xsym.append(XY[0])
         Ysym.append(XY[1])
-    plt.scatter(Xsym, Ysym, color='black',marker='|',s=10)
+    ax.scatter(Xsym, Ysym, color="black", marker="|", s=10)
+
     Xsym, Ysym = [], []
     for I in range(tick_spacing, 90, tick_spacing):
-        XY = pmag.dimap(180., I)
+        XY = pmag.dimap(180.0, I)
         Xsym.append(XY[0])
         Ysym.append(XY[1])
-    plt.scatter(Xsym, Ysym, color='black',marker='_',s=10)
+    ax.scatter(Xsym, Ysym, color="black", marker="_", s=10)
+
     Xsym, Ysym = [], []
     for I in range(tick_spacing, 90, tick_spacing):
-        XY = pmag.dimap(270., I)
+        XY = pmag.dimap(270.0, I)
         Xsym.append(XY[0])
         Ysym.append(XY[1])
-    #plt.plot(Xsym, Ysym, 'k|')
-    plt.scatter(Xsym, Ysym, color='black',marker='|',s=10)
+    ax.scatter(Xsym, Ysym, color="black", marker="|", s=10)
+
     for D in range(0, 360, tick_spacing):
         Xtick, Ytick = [], []
         for I in range(4):
             XY = pmag.dimap(D, I)
             Xtick.append(XY[0])
             Ytick.append(XY[1])
-        plt.plot(Xtick, Ytick, 'k')
-    plt.axis("equal")
-    plt.axis((-1.05, 1.05, -1.05, 1.05))
+        ax.plot(Xtick, Ytick, "k")
+    ax.axis("equal")
+    ax.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='', connect_points=False, lw=0.25, lc='k', la=0.5, title=None, edge=None, alpha=1, zorder=2):
@@ -2588,44 +2599,6 @@ def plot_poles(map_axis, plon, plat, A95, label='', color='k', edgecolor='k',
     if legend == 'yes':
         plt.legend(loc=2)
 
-
-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 called, a plot needs to be initialized with code
-    that looks something like:
-    >from mpl_toolkits.basemap import Basemap
-    >mapname = Basemap(projection='ortho',lat_0=35,lon_0=200)
-    >plt.figure(figsize=(6, 6))
-    >mapname.drawcoastlines(linewidth=0.25)
-    >mapname.fillcontinents(color='bisque',lake_color='white',zorder=1)
-    >mapname.drawmapboundary(fill_color='white')
-    >mapname.drawmeridians(np.arange(0,360,30))
-    >mapname.drawparallels(np.arange(-90,90,30))
-    
-    Parameters:
-    mapname : the name of the current map that has been developed using basemap
-    plon : the longitude of the paleomagnetic pole being plotted (in degrees E)
-    plat : the latitude of the paleomagnetic pole being plotted (in degrees)
-    A95 : the A_95 confidence ellipse of the paleomagnetic pole (in degrees)
-    Optional Parameters (defaults are used if not specified)
-    -----------
-    color : the default color is black. Other colors can be chosen (e.g. 'r')
-    marker : the default is a circle. Other symbols can be chosen (e.g. 's')
-    markersize : the default is 20. Other size can be chosen
-    label : the default is no label. Labels can be assigned.
-    legend : the default is no legend ('no'). Putting 'yes' will plot a legend.
-    """
-    centerlon, centerlat = mapname(plon, plat)
-    A95_km = A95 * 111.32
-    mapname.scatter(centerlon, centerlat, marker=marker,
-                    color=color, edgecolors=edgecolor, s=markersize, label=label, zorder=101)
-    equi_basemap(mapname, plon, plat, A95_km, color)
-    if legend == 'yes':
-        plt.legend(loc=2)
-        
-        
 def plot_pole_ellipse(map_axis, dictionary, 
                       color='k', edgecolor='k', marker='s', 
                       markersize=20, label='', alpha=1.0, lw=1, lower=True, zorder=100):
@@ -2895,47 +2868,7 @@ def plot_vgp(map_axis, vgp_lon=None, vgp_lat=None, di_block=None, label='', colo
     if legend == True:
         plt.legend(loc=2)
 
-
-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 needs to be initialized with code
-    that looks something like:
-    >from mpl_toolkits.basemap import Basemap
-    >mapname = Basemap(projection='ortho',lat_0=35,lon_0=200)
-    >plt.figure(figsize=(6, 6))
-    >mapname.drawcoastlines(linewidth=0.25)
-    >mapname.fillcontinents(color='bisque',lake_color='white',zorder=1)
-    >mapname.drawmapboundary(fill_color='white')
-    >mapname.drawmeridians(np.arange(0,360,30))
-    >mapname.drawparallels(np.arange(-90,90,30))
-    Required Parameters
-    -----------
-    mapname : the name of the current map that has been developed using basemap
-    plon : the longitude of the paleomagnetic pole being plotted (in degrees E)
-    plat : the latitude of the paleomagnetic pole being plotted (in degrees)
-    Optional Parameters (defaults are used if not specified)
-    -----------
-    color : the color desired for the symbol and its A95 ellipse (default is 'k' aka black)
-    marker : the marker shape desired for the pole mean symbol (default is 'o' aka a circle)
-    label : the default is no label. Labels can be assigned.
-    legend : the default is no legend ('no'). Putting 'yes' will plot a legend.
-    """
-    if di_block != None:
-        di_lists = unpack_di_block(di_block)
-        if len(di_lists) == 3:
-            vgp_lon, vgp_lat, intensity = di_lists
-        if len(di_lists) == 2:
-            vgp_lon, vgp_lat = di_lists
-    centerlon, centerlat = mapname(vgp_lon, vgp_lat)
-    mapname.scatter(centerlon, centerlat, marker=marker,
-                    s=markersize, color=color, label=label, zorder=100)
-    if legend == 'yes':
-        plt.legend(loc=2)
-
-
-def vgp_calc(dataframe, tilt_correction='yes', site_lon='site_lon', site_lat='site_lat', 
+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',
              recalc_label=False):
     """
@@ -3433,7 +3366,7 @@ def shoot(lon, lat, azimuth, maxdist=None):
     return (glon2, glat2, baz)
 
 
-def equi(map_axis, centerlon, centerlat, radius, color, alpha=1.0, outline=True, fill=False):
+def equi(map_axis, centerlon, centerlat, radius, color, alpha=1.0, outline=True, fill=False, lw=1):
     """
     This function enables A95 error ellipses to be drawn in cartopy around
     paleomagnetic poles in conjunction with shoot
@@ -3470,7 +3403,7 @@ def equi(map_axis, centerlon, centerlat, radius, color, alpha=1.0, outline=True,
     # for non-filled ellipses
     if fill==False:
         plt.plot(X, Y, color=color,
-                 transform=ccrs.Geodetic(), alpha=alpha)
+                 transform=ccrs.Geodetic(), alpha=alpha, lw=lw)
 
     # for filled ellipses
     else:
@@ -3485,29 +3418,6 @@ def equi(map_axis, centerlon, centerlat, radius, color, alpha=1.0, outline=True,
                               transform=ccrs.Geodetic())
         map_axis.add_patch(circle_face)
 
-
-
-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
-    glat1 = centerlat
-    X = []
-    Y = []
-    for azimuth in range(0, 360):
-        glon2, glat2, baz = shoot(glon1, glat1, azimuth, radius)
-        X.append(glon2)
-        Y.append(glat2)
-    X.append(X[0])
-    Y.append(Y[0])
-
-    X, Y = m(X, Y)
-    plt.plot(X, Y, color)
-
-
 def ellipse(map_axis, centerlon, centerlat, major_axis, minor_axis, angle, n=360, filled=False,
             transform=None, **kwargs):
     """
@@ -5345,6 +5255,7 @@ def download_magic_from_doi(doi):
     else:
         return False, 'Error:', response.json()['err'][0]['message'], '\n'
 
+
 def validate_with_public_endpoint(contribution_file,verbose=False):
     """
     validate contribution to MagIC using public endpoint
@@ -5792,6 +5703,32 @@ def upload_magic(concat=False, dir_path='.',input_dir_path='.',validate=True,ver
             return False, "Could not create an upload file", None, None
     return new_up, val_response, None, None
 
+
+def contribution_to_magic(contribution, dir_path='.'):
+    """
+    Write a contribution object to MagIC-formatted files in the specified directory.
+    Compiles these files into a upload.txt file which can be uploaded into the 
+    MagIC database using the upload_magic function.
+    
+    Parameters
+    ----------
+    contribution : Contribution
+        A contribution object containing tables to be written to a MagIC-formatted file.
+    dir_path : str
+        The directory path where the MagIC-formatted file will be written.
+    """
+    if not os.path.exists(dir_path):
+        os.makedirs(dir_path)
+        
+    contribution.tables['specimens'].write_magic_file(dir_path=dir_path)
+    contribution.tables['samples'].write_magic_file(dir_path=dir_path)
+    contribution.tables['sites'].write_magic_file(dir_path=dir_path)
+    contribution.tables['locations'].write_magic_file(dir_path=dir_path)
+    contribution.tables['measurements'].write_magic_file(dir_path=dir_path)
+    
+    upload_magic(dir_path=dir_path, input_dir_path=dir_path)
+    
+
 def create_private_contribution(username="",password=""):
     """
     Create a private contribution on earthref.org/MagIC.
@@ -5999,7 +5936,6 @@ def validate_private_contribution(contribution_id,username="",password="",verbos
     return response
 
 
-
 def specimens_results_magic(infile='pmag_specimens.txt', measfile='magic_measurements.txt', sampfile='er_samples.txt', sitefile='er_sites.txt', agefile='er_ages.txt', specout='er_specimens.txt', sampout='pmag_samples.txt', siteout='pmag_sites.txt', resout='pmag_results.txt', critout='pmag_criteria.txt', instout='magic_instruments.txt', plotsites=False, fmt='svg', dir_path='.', cors=[], priorities=['DA-AC-ARM', 'DA-AC-TRM'], coord='g', user='', vgps_level='site', do_site_intensity=True, DefaultAge=["none"], avg_directions_by_sample=False, avg_intensities_by_sample=False, avg_all_components=False, avg_by_polarity=False, skip_directions=False, skip_intensities=False, use_sample_latitude=False, use_paleolatitude=False, use_criteria='default'):
     """
     Writes magic_instruments, er_specimens, pmag_samples, pmag_sites, pmag_criteria, and pmag_results. The data used to write this is obtained by reading a pmag_speciemns, a magic_measurements, a er_samples, a er_sites, a er_ages.
@@ -6912,14 +6848,14 @@ def orientation_magic(or_con=1, dec_correction_con=1, dec_correction=0, bed_corr
 
     # validate input
     if '4' in samp_con[0]:
-        pattern = re.compile('[4][-]\d')
+        pattern = re.compile(r'[4][-]\d')
         result = pattern.match(samp_con)
         if not result:
             raise Exception(
                 "If using sample naming convention 4, you must provide the number of characters with which to distinguish sample from site. [4-Z] XXXX[YYY]:  YYY is sample designation with Z characters from site XXX)")
 
     if '7' in samp_con[0]:
-        pattern = re.compile('[7][-]\d')
+        pattern = re.compile(r'[7][-]\d')
         result = pattern.match(samp_con)
         if not result:
             raise Exception(
@@ -8569,29 +8505,29 @@ def pmag_results_extract(res_file="pmag_results.txt", crit_file="", spec_file=""
         for k in range(len(SiteCols)):
             fstring = fstring + 'r'
         sf.write(fstring + '}\n')
-        sf.write('\hline\n')
+        sf.write(r'\hline\n')
         fstring = tabstring
         for k in range(len(DirCols)):
             fstring = fstring + 'r'
         f.write(fstring + '}\n')
-        f.write('\hline\n')
+        f.write(r'\hline\n')
         fstring = tabstring
         for k in range(len(IntCols)):
             fstring = fstring + 'r'
         fI.write(fstring + '}\n')
-        fI.write('\hline\n')
+        fI.write(r'\hline\n')
         fstring = tabstring
         if crit_file:
             for k in range(len(CritKeys)):
                 fstring = fstring + 'r'
             cr.write(fstring + '}\n')
-            cr.write('\hline\n')
+            cr.write(r'\hline\n')
         if spec_file:
             fstring = tabstring
             for k in range(len(SpecCols)):
                 fstring = fstring + 'r'
             fsp.write(fstring + '}\n')
-            fsp.write('\hline\n')
+            fsp.write(r'\hline\n')
     else:   # just set the tab and line endings for tab delimited
         sep = ' \t '
         end = ''
@@ -8625,13 +8561,13 @@ def pmag_results_extract(res_file="pmag_results.txt", crit_file="", spec_file=""
         Spoutstring = Spoutstring + end + "\n"
         fsp.write(Spoutstring)
     if latex:  # put in a horizontal line in latex file
-        f.write('\hline\n')
-        sf.write('\hline\n')
-        fI.write('\hline\n')
+        f.write(r'\hline\n')
+        sf.write(r'\hline\n')
+        fI.write(r'\hline\n')
         if crit_file:
-            cr.write('\hline\n')
+            cr.write(r'\hline\n')
         if spec_file:
-            fsp.write('\hline\n')
+            fsp.write(r'\hline\n')
  # do criteria
     if crit_file:
         for crit in Crits:
@@ -8743,23 +8679,23 @@ def pmag_results_extract(res_file="pmag_results.txt", crit_file="", spec_file=""
             fsp.write(outstring.strip(sep) + end + '\n')
     #
     if latex:  # write out the tail stuff
-        f.write('\hline\n')
-        sf.write('\hline\n')
-        fI.write('\hline\n')
-        f.write('\end{longtable}\n')
-        sf.write('\end{longtable}\n')
-        fI.write('\end{longtable}\n')
-        f.write('\end{document}\n')
-        sf.write('\end{document}\n')
-        fI.write('\end{document}\n')
+        f.write(r'\hline\n')
+        sf.write(r'\hline\n')
+        fI.write(r'\hline\n')
+        f.write(r'\end{longtable}\n')
+        sf.write(r'\end{longtable}\n')
+        fI.write(r'\end{longtable}\n')
+        f.write(r'\end{document}\n')
+        sf.write(r'\end{document}\n')
+        fI.write(r'\end{document}\n')
         if spec_file:
-            fsp.write('\hline\n')
-            fsp.write('\end{longtable}\n')
-            fsp.write('\end{document}\n')
+            fsp.write(r'\hline\n')
+            fsp.write(r'\end{longtable}\n')
+            fsp.write(r'\end{document}\n')
         if crit_file:
-            cr.write('\hline\n')
-            cr.write('\end{longtable}\n')
-            cr.write('\end{document}\n')
+            cr.write(r'\hline\n')
+            cr.write(r'\end{longtable}\n')
+            cr.write(r'\end{document}\n')
     f.close()
     sf.close()
     fI.close()
@@ -9314,7 +9250,7 @@ def find_ei(data, nb=1000, save=False, save_folder='.', fmt='svg',
 
     plt.figure(num=2, figsize=(4, 4))
     plt.plot(Is, Es, EI_color, zorder = nb+1, lw=3)
-    plt.xlabel("inclination ($^\circ$)", fontsize=12)
+    plt.xlabel(r"inclination ($^\circ$)", fontsize=12)
     plt.ylabel("elongation", fontsize=12)
     plt.ylim(.9,5)
     plt.text(Inc, Elong, ' %4.2f' % (flat_f), fontsize=12)
@@ -9356,7 +9292,7 @@ def find_ei(data, nb=1000, save=False, save_folder='.', fmt='svg',
 
     cdf_fig_num = 3
     plt.figure(num=cdf_fig_num, figsize=(4, 4))
-    pmagplotlib.plot_cdf(cdf_fig_num, I, 'inclination ($^\circ$)', 'r', title)
+    pmagplotlib.plot_cdf(cdf_fig_num, I, r'inclination ($^\circ$)', 'r', title)
     pmagplotlib.plot_vs(cdf_fig_num, [I[lower], I[upper]], 'b', '--')
     pmagplotlib.plot_vs(cdf_fig_num, [Inc], 'g', '-')
     pmagplotlib.plot_vs(cdf_fig_num, [Io], 'k', '-')
@@ -9479,7 +9415,7 @@ def find_ei_kent(data, site_latitude, site_longitude, kent_color='k', nb=1000, s
     # plot E/I figure
     plt.figure(num=1, figsize=(4, 4))
     plt.plot(Is, Es, EI_color, zorder = nb+1, lw=3)
-    plt.xlabel("inclination ($^\circ$)", fontsize=12)
+    plt.xlabel(r"inclination ($^\circ$)", fontsize=12)
     plt.ylabel("elongation", fontsize=12)
     plt.text(Inc, Elong, ' %4.2f' % (flat_f), fontsize=12)
 
@@ -9514,7 +9450,7 @@ def find_ei_kent(data, site_latitude, site_longitude, kent_color='k', nb=1000, s
         plt.savefig(save_folder+'/'+figprefix+'_bootstraps'+'.'+fmt, bbox_inches='tight', dpi=300)
 
     plt.figure(figsize=(4, 4))
-    pmagplotlib.plot_cdf(2, I, 'inclination ($^\circ$)', 'r', title)
+    pmagplotlib.plot_cdf(2, I, r'inclination ($^\circ$)', 'r', title)
     pmagplotlib.plot_vs(2, [I[lower], I[upper]], 'b', '--')
     pmagplotlib.plot_vs(2, [Inc], 'g', '-')
     pmagplotlib.plot_vs(2, [Io], 'k', '-')
@@ -9577,7 +9513,7 @@ def find_ei_kent(data, site_latitude, site_longitude, kent_color='k', nb=1000, s
     plt.title('%7.1f [%7.1f, %7.1f]' % (plat_mode, plat_lower, plat_upper) + '\nFit result: mu='+str(round(mu,2))+'\nstd='+str(round(std, 2)), fontsize=14)
     plt.xticks(fontsize=14)
     plt.yticks(fontsize=14)
-    plt.xlabel('paleolatitude ($^\circ$)', fontsize=16)
+    plt.xlabel(r'paleolatitude ($^\circ$)', fontsize=16)
     plt.ylabel('density', fontsize=16)
     
     if save:
@@ -9704,7 +9640,7 @@ def find_compilation_kent(plon, plat, A95, slon, slat,
     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.xlabel(r"compilation paleolatitudes ($^\circ$)", fontsize=16)
     plt.ylabel("density", fontsize=16)
 
     compilation_mean_lons = []
@@ -11106,13 +11042,13 @@ def plot_aniso(fignum, aniso_df, Dir=[], PDir=[], ipar=False, ihext=True, ivec=F
         if ihext:  # plot the Hext ellipses
             ellpars = [hpars["v1_dec"], hpars["v1_inc"], hpars["e12"], hpars["v2_dec"],
                        hpars["v2_inc"], hpars["e13"], hpars["v3_dec"], hpars["v3_inc"]]
-            pmagplotlib.plot_ell(fignum+1, ellpars, 'r-,', 1, 1)
+            v1_pts = pmagplotlib.plot_ell(fignum+1, ellpars, 'r,', 1, 1)
             ellpars = [hpars["v2_dec"], hpars["v2_inc"], hpars["e23"], hpars["v3_dec"],
                        hpars["v3_inc"], hpars["e12"], hpars["v1_dec"], hpars["v1_inc"]]
-            pmagplotlib.plot_ell(fignum+1, ellpars, 'b-,', 1, 1)
+            v2_pts = pmagplotlib.plot_ell(fignum+1, ellpars, 'b,', 1, 1)
             ellpars = [hpars["v3_dec"], hpars["v3_inc"], hpars["e13"], hpars["v1_dec"],
                        hpars["v1_inc"], hpars["e23"], hpars["v2_dec"], hpars["v2_inc"]]
-            pmagplotlib.plot_ell(fignum+1, ellpars, 'k-,', 1, 1)
+            v3_pts = pmagplotlib.plot_ell(fignum+1, ellpars, 'k,', 1, 1)
             if len(Dir) > 0:   # plot the comparison direction components
                     # put in dimap and plot as white symbol with axis color?
                 plot_di(di_block=[Dir], color='green',
@@ -11176,7 +11112,7 @@ def plot_aniso(fignum, aniso_df, Dir=[], PDir=[], ipar=False, ihext=True, ivec=F
                 pmagplotlib.plot_ell(fignum+1, ellpars, 'r-,', 1, 1)
                 ellpars = [hpars["v2_dec"], hpars["v2_inc"], bpars["v2_zeta"], bpars["v2_zeta_dec"],
                            bpars["v2_zeta_inc"], bpars["v2_eta"], bpars["v2_eta_dec"], bpars["v2_eta_inc"]]
-                pmagplotlib.plot_ell(fignum+1, ellpars, 'b-,', 1, 1)
+                pmagplotlib.plot_ell(fignum+1, ellpars, 'b-,', 1, 1)    
                 ellpars = [hpars["v3_dec"], hpars["v3_inc"], bpars["v3_zeta"], bpars["v3_zeta_dec"],
                            bpars["v3_zeta_inc"], bpars["v3_eta"], bpars["v3_eta_dec"], bpars["v3_eta_inc"]]
                 pmagplotlib.plot_ell(fignum+1, ellpars, 'k-,', 1, 1)
@@ -11674,12 +11610,11 @@ def get_matrix(n_pos=6):
 
     if n_pos == 15:
             positions = [[315., 0., 1.], [225., 0., 1.], [180., 0., 1.], [135., 0., 1.], [45., 0., 1.],
-                         [90., -45., 1.], [270., -45., 1.], [270.,
-                                                             0., 1.], [270., 45., 1.], [90., 45., 1.],
+                         [90., -45., 1.], [270., -45., 1.], [270., 0., 1.], [270., 45., 1.], [90., 45., 1.],
                          [180., 45., 1.], [180., -45., 1.], [0., -90., 1.], [0, -45., 1.], [0, 45., 1.]]
     if n_pos == 9:
             positions = [[315., 0., 1.], [225., 0., 1.], [180., 0., 1.],
-        [90., -45., 1.], [270., -45., 1.], [270., 0., 1.],
+                        [90., -45., 1.], [270., -45., 1.], [270., 0., 1.],
                          [180., 45., 1.], [180., -45., 1.], [0., -90., 1.]]
 
     tmpH = np.zeros((n_pos, 3), 'f')  # define tmpH
@@ -12630,14 +12565,14 @@ def zeq_magic(meas_file='measurements.txt', spec_file='',crd='s', dir_path = "."
         spec_df = meas_df[meas_df.specimen == s]
         # remove ARM data
         spec_df = spec_df[- spec_df.method_codes.str.contains(
-            'LP-*[\w]*-ARM')]
+            r'LP-*[\w]*-ARM')]
         # split data into NRM, thermal, and af dataframes
         spec_df_nrm = spec_df[spec_df.method_codes.str.contains(
             'LT-NO')]  # get the NRM data
         spec_df_th = spec_df[spec_df.method_codes.str.contains(
             'LT-T-Z')]  # zero field thermal demag steps
         try:
-            cond = spec_df.method_codes.str.contains('(^|[\s\:])LT-PTRM')
+            cond = spec_df.method_codes.str.contains(r'(^|[\s\:])LT-PTRM')
             spec_df_th = spec_df_th[-cond]  # get rid of some pTRM steps
         except ValueError:
             keep_inds = []
@@ -13483,13 +13418,13 @@ def sites_extract(site_file='sites.txt', directions_file='directions.xls',
             if dir_file.endswith('.xls'):
                 dir_file = dir_file[:-4] + ".tex"
             directions_out = open(dir_file, 'w+', errors="backslashreplace")
-            directions_out.write('\documentclass{article}\n')
+            directions_out.write(r'\documentclass{article}\n')
             directions_out.write('\\usepackage{booktabs}\n')
             directions_out.write('\\usepackage{longtable}\n')
             directions_out.write('\\begin{document}')
             directions_out.write(dir_df.to_latex(
                 index=False, longtable=True, multicolumn=False))
-            directions_out.write('\end{document}\n')
+            directions_out.write(r'\end{document}\n')
             directions_out.close()
         else:
             dir_df.to_excel(dir_file, index=False)
@@ -13504,13 +13439,13 @@ def sites_extract(site_file='sites.txt', directions_file='directions.xls',
                 intensity_file = intensity_file[:-4] + ".tex"
             intensities_out = open(intensity_file, 'w+',
                                    errors="backslashreplace")
-            intensities_out.write('\documentclass{article}\n')
+            intensities_out.write(r'\documentclass{article}\n')
             intensities_out.write('\\usepackage{booktabs}\n')
             intensities_out.write('\\usepackage{longtable}\n')
             intensities_out.write('\\begin{document}')
             intensities_out.write(int_df.to_latex(
                 index=False, longtable=True, multicolumn=False))
-            intensities_out.write('\end{document}\n')
+            intensities_out.write(r'\end{document}\n')
             intensities_out.close()
         else:
             int_df.to_excel(intensity_file, index=False)
@@ -13542,13 +13477,13 @@ def sites_extract(site_file='sites.txt', directions_file='directions.xls',
             if info_file.endswith('.xls'):
                 info_file = info_file[:-4] + ".tex"
             info_out = open(info_file, 'w+', errors="backslashreplace")
-            info_out.write('\documentclass{article}\n')
+            info_out.write(r'\documentclass{article}\n')
             info_out.write('\\usepackage{booktabs}\n')
             info_out.write('\\usepackage{longtable}\n')
             info_out.write('\\begin{document}')
             info_out.write(nfo_df.to_latex(
                 index=False, longtable=True, multicolumn=False))
-            info_out.write('\end{document}\n')
+            info_out.write(r'\end{document}\n')
             info_out.close()
         else:
             nfo_df.to_excel(info_file, index=False)
@@ -13605,7 +13540,7 @@ def specimens_extract(spec_file='specimens.txt', output_file='specimens.xls', la
             if out_file.endswith('.xls'):
                 out_file = out_file.rsplit('.')[0] + ".tex"
             info_out = open(out_file, 'w+', errors="backslashreplace")
-            info_out.write('\documentclass{article}\n')
+            info_out.write(r'\documentclass{article}\n')
             info_out.write('\\usepackage{booktabs}\n')
             if landscape:
                 info_out.write('\\usepackage{lscape}')
@@ -13617,8 +13552,8 @@ def specimens_extract(spec_file='specimens.txt', output_file='specimens.xls', la
             info_out.write(table_df.to_latex(index=False, longtable=longtable,
                                              escape=True, multicolumn=False))
             if landscape:
-                info_out.write('\end{landscape}\n')
-            info_out.write('\end{document}\n')
+                info_out.write(r'\end{landscape}\n')
+            info_out.write(r'\end{document}\n')
             info_out.close()
         else:
             table_df.to_excel(out_file, index=False)
@@ -13680,7 +13615,7 @@ def criteria_extract(crit_file='criteria.txt', output_file='criteria.xls',
                 '>'), 'operation'] = 'minimum'
             crit_df.loc[crit_df['Operation'] == '=', 'operation'] = 'equal to'
             info_out = open(out_file, 'w+', errors="backslashreplace")
-            info_out.write('\documentclass{article}\n')
+            info_out.write(r'\documentclass{article}\n')
             info_out.write('\\usepackage{booktabs}\n')
             # info_out.write('\\usepackage{longtable}\n')
             # T1 will ensure that symbols like '<' are formatted correctly
@@ -13688,7 +13623,7 @@ def criteria_extract(crit_file='criteria.txt', output_file='criteria.xls',
             info_out.write('\\begin{document}')
             info_out.write(crit_df.to_latex(index=False, longtable=False,
                                             escape=True, multicolumn=False))
-            info_out.write('\end{document}\n')
+            info_out.write(r'\end{document}\n')
             info_out.close()
         else:
             crit_df.to_excel(out_file, index=False)
@@ -14654,7 +14589,7 @@ def chi_magic(infile="measurements.txt", dir_path=".", experiments="",
                      label='%i' % (f)+' Hz')
         plt.legend()
         plt.xlabel('Temperature (K)')
-        plt.ylabel('$\chi$ ($\mu$SI)')
+        plt.ylabel(r'$\chi$ ($\mu$SI)')
         plt.title('B = '+'%7.2e' % (b) + ' T')
 
         plotnum += 1
@@ -14674,7 +14609,7 @@ def chi_magic(infile="measurements.txt", dir_path=".", experiments="",
                      this_t.susc_chi_volume, label='%i' % (t)+' K')
         plt.legend()
         plt.xlabel('Frequency (Hz)')
-        plt.ylabel('$\chi$ ($\mu$SI)')
+        plt.ylabel(r'$\chi$ ($\mu$SI)')
         plt.title('B = '+'%7.2e' % (b) + ' T')
 
     if interactive:
@@ -15616,10 +15551,7 @@ def simul_correlation_prob(alpha, k1, k2, trials=10000, print_result=False):
     The function runs an algorithm from Bogue and Coe (1981; doi: 10.1029/JB086iB12p11883) 
     for probabilistic correlation, evaluating the probability that the similarity between 
     two paleomagnetic directions is due to simultaneous sampling of the ancient magnetic 
-    field. This can be compared with the probability that the two directions were sampled 
-    at random times with the companion function (ipmag.random_correlation_prob; to come). 
-    k1 and k2 can be estimated the kappa of the  directions, or one can use the companion 
-    function (ipmag.full_kappa; to come) as in the original publication. 
+    field. Original written in Python by S. Bogue, translated to PmagPy functionality by AFP. 
     
     Parameters:
         alpha : angle between paleomagnetic directions (site means)
@@ -15631,24 +15563,32 @@ def simul_correlation_prob(alpha, k1, k2, trials=10000, print_result=False):
     Returns:
         float 
             number indicating probability value
+
+    Example:
+        Provide an angle and two precision parameter estimates to get the probability of
+        simultaneity, compare to RC / 11 comparison from Table 2 of the original publication
+        (exact value may differ due to RNG):
+
+        >>> ipmag.simul_correlation_prob(3.6, 391, 146)
+        0.8127
     """
     #sets initial value for counters
     hit = 0
     miss = 0
     
-    #trial loop
+    # trial loop
     for i in range(trials):
-        #generates two synthetic directions, using the estimated kappas
-        lontp1,lattp1 = ipmag.fishrot(k1, 1, 0, 90, di_block=False)
-        lontp2,lattp2 = ipmag.fishrot(k2, 1, 0, 90, di_block=False)
-        #determines the angle between the generated directions 
+        # generates two synthetic directions, using the estimated kappas
+        lontp1,lattp1 = fishrot(k1, 1, 0, 90, di_block=False)
+        lontp2,lattp2 = fishrot(k2, 1, 0, 90, di_block=False)
+        # determines the angle between the generated directions
         angle=pmag.angle([lontp1[0], lattp1[0]], [lontp2[0], lattp2[0]])
-        #checks if angle between synthetic directions meets or exceeds 'known' angle from directions to be tested
-        if (angle >= alpha):
+        # checks if angle between synthetic directions meets or exceeds 'known' angle from directions to be tested
+        if angle >= alpha:
             hit = hit + 1
         else:
             miss = miss + 1
-    #calculates probability based on how often the angle between the 'real' datasets is met or exceeded
+    # calculates probability based on how often the angle between the 'real' datasets is met or exceeded
     simul_prob = 1.0 * hit / trials
     
     if print_result == True:
@@ -15659,25 +15599,12 @@ def simul_correlation_prob(alpha, k1, k2, trials=10000, print_result=False):
 def rand_correlation_prob(sec_var, delta1, delta2, alpha, trials=10000, print_result=False):
 
     """
-    This function does a brute force numerical simulation of the 'random' 
-    hypothesis of Bogue + Coe (1981). Basically asks and answers the question:
-    if we randomly sampled the ancient field, how frequently would we get two
-    VGPs that are both this far from the time-averaged pole and this close 
-    together?  Approach is, assume VGP1 observed first, pull a random 
-    direction from Fisher distribution about mean pole with k. If it is within
-    alpha of VGP1, hit. If not, miss. Repeat many (10,000?) times. 
-    P(Hr)1 = hit/(trials). Then, repeat this process with VGP2, getting
-    P(Hr)2. The returned probability is the average of the two.
-    
-    A version of this function was written in Python by S. Bogue, translated
-    to PmagPy functionality by A. Pivarunas
-    
-    Bogue, S.W., and Coe, R.S., 1981, Paleomagnetic correlation of Columbia 
-    River basalt flows using secular variation. Journal of Geophysical
-    Research, v. 86, p. 11883-11897.
+    The function runs an algorithm from Bogue and Coe (1981; doi: 10.1029/JB086iB12p11883) 
+    for probabilistic correlation, evaluating the probability that the similarity between 
+    two paleomagnetic directions is due to random sampling of the ancient magnetic 
+    field. Original written in Python by S. Bogue, translated to PmagPy functionality by AFP.
     
-    Parameters
-    ----------
+    Parameters:
     sec_var: kappa estimate of regional secular variation (probably 30 or 40)
     alpha: angle between paleomagnetic directions (or poles)
     delta1: distance of direction 1 from mean direction
@@ -15685,18 +15612,26 @@ def rand_correlation_prob(sec_var, delta1, delta2, alpha, trials=10000, print_re
     trials: the number of simulations, default=10,000
     print_result: the probability value printed as a sentence, default=False 
     
-    Returns
-    --------------------------
-    rand_prob 
+    Returns:
+        float 
+            number indicating probability value
     
+    Example:
+        Provide estimate of regional secular variation, angle between directions, 
+        distance of each direction from a mean direction (like GAD) to return probability
+        of random field sampling, compare to RC / 11 comparison from Table 2 of the original
+        publication (exact value may differ due to RNG):
+
+        >>> ipmag.rand_correlation_prob(40, 17.2, 20, 3.6)
+        np.float64(0.0103)
     """
 
-    #calc probability of getting vgp within alpha of vgp1
+    # calc probability of getting vgp within alpha of vgp1
     i = 0
     miss = 0
     hit = 0
     for i in range(trials):
-        dec,inc = ipmag.fishrot(sec_var, 1, 0, 0, di_block=False)
+        dec,inc = fishrot(sec_var, 1, 0, 0, di_block=False)
         angle = pmag.angle([dec[0], inc[0]], [0, delta1])
         if (angle <= alpha):
             hit = hit + 1
@@ -15711,7 +15646,7 @@ def rand_correlation_prob(sec_var, delta1, delta2, alpha, trials=10000, print_re
     hit = 0
     miss = 0
     for i in range(trials):
-        dec, inc = ipmag.fishrot(sec_var, 1, 0, 0, di_block=False)
+        dec, inc = fishrot(sec_var, 1, 0, 0, di_block=False)
         angle = pmag.angle([dec[0], inc[0]], [0,delta2])
         if (angle <= alpha):
             hit = hit + 1