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

pmagpy/pmag.py

@@ -16,7 +16,7 @@ from pmag_env import set_env
 import pandas as pd
 import SPD.lib.leastsq_jacobian as lib_k
 
-WARNINGS = {'basemap': False, 'cartopy': False}
+WARNINGS = {'cartopy': False}
 
 
 def get_version():
@@ -4502,7 +4502,7 @@ def fisher_mean(data):
         
     Examples
     --------
-    >>> data = [[150,-45],[151,-46],[145,-38],[146,-41]
+    >>> data = [[150,-45],[151,-46],[145,-38],[146,-41]]
     >>> pmag.fisher_mean(data)
     {'dec': 147.87247771265734,
     'inc': -42.52872729473035,
@@ -4512,7 +4512,9 @@ def fisher_mean(data):
     'alpha95': 4.865886096375297,
     'csd': 4.283846101842065}   
     """
-    N, fpars = len(data), {}
+    data = np.asarray(data)
+    N = data.shape[0]
+    fpars = {}
     
     if N < 2: 
         return {'dec': data[0][0], 
@@ -4520,10 +4522,9 @@ def fisher_mean(data):
     
     # use only dec, inc values even if intensity values are provided
     # so that calculations are on unit vectors
-    for i in range(N):
-        data[i] = data[i][:2]
+    dir_data = data[:, :2].copy()
 
-    X = np.array(dir2cart(data))
+    X = np.array(dir2cart(dir_data))
     Xbar = X.sum(axis=0)
     R = np.linalg.norm(Xbar)
     Xbar = Xbar/R
@@ -8975,10 +8976,16 @@ def designAARM(npos):
     if npos != 9:
         print('Sorry - only 9 positions available')
         return
-    Dec = [315., 225., 180., 135., 45., 90., 270.,
-           270., 270., 90., 0., 0., 0., 180., 180.]
-    Dip = [0., 0., 0., 0., 0., -45., -45., 0.,
-           45., 45., 45., -45., -90., -45., 45.]
+    Dec = [315., 225., 180., 
+           135., 45., 90., 
+           270., 270., 270., 
+           90., 180., 180., 
+           0., 0., 0.]
+    Dip = [0., 0., 0., 
+           0., 0., -45., 
+           -45., 0., 45., 
+           45., 45., -45., 
+           -90., -45., 45.]
     index9 = [0, 1, 2, 5, 6, 7, 10, 11, 12]
     H = []
     for ind in range(15):
@@ -13356,61 +13363,6 @@ def chart_maker(Int, Top, start=100, outfile='chart.txt'):
             f.close()
     print("output stored in: chart.txt")
 
-
-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_basemap = True
-    has_cartopy = import_cartopy()[0]
-    try:
-        from mpl_toolkits.basemap import Basemap
-        WARNINGS['has_basemap'] = True
-    except ImportError:
-        has_basemap = False
-        # if they have installed cartopy, no warning is needed
-        if has_cartopy:
-            return has_basemap, False
-        # if they haven't installed Basemap or cartopy, they need to be warned
-        if not WARNINGS['basemap']:
-            print(
-                "-W- You haven't installed a module for plotting maps (cartopy or Basemap)")
-            print("    Recommended: install cartopy.  With conda:")
-            print("    conda install cartopy")
-            print(
-                "    For more information, see http://earthref.org/PmagPy/Cookbook#getting_python")
-    except (KeyError, FileNotFoundError):
-        has_basemap = False
-        # if cartopy is installed, no warning is needed
-        if has_cartopy:
-            return has_basemap, False
-        if not WARNINGS['basemap']:
-            print('-W- Basemap is installed but could not be imported.')
-            print('    You are probably missing a required environment variable')
-            print(
-                '    If you need to use Basemap, you will need to run this program or notebook in a conda env.')
-            print('    For more on how to create a conda env, see: https://conda.io/docs/user-guide/tasks/manage-environments.html')
-            print(
-                '    Recommended alternative: install cartopy for plotting maps.  With conda:')
-            print('    conda install cartopy')
-    if has_basemap and not has_cartopy:
-        print("-W- You have installed Basemap but not cartopy.")
-        print("    In the future, Basemap will no longer be supported.")
-        print("    To continue to make maps, install using conda:")
-        print('    conda install cartopy')
-
-    WARNINGS['basemap'] = True
-    return has_basemap, Basemap
-
-
 def import_cartopy():
     """
     Try to import cartopy and print out a help message

pmagpy/pmagplotlib.py

@@ -29,7 +29,6 @@ if has_cartopy:
     from cartopy.mpl.gridliner import LONGITUDE_FORMATTER, LATITUDE_FORMATTER
     from cartopy import feature as cfeature
     from cartopy.feature import NaturalEarthFeature, LAND, COASTLINE, OCEAN, LAKES, BORDERS
-has_basemap, Basemap = pmag.import_basemap()
 
 import os
 import matplotlib
@@ -328,7 +327,7 @@ def plot_qq_norm(fignum, Y, title):
     Returns
     ___________
     d,dc : the values for D and Dc (the critical value)
-       if d>dc, likely to be normally distributed (95\% confidence)
+       if d>dc, likely to be normally distributed (95% confidence)
     """
     plt.figure(num=fignum)
     if type(Y) == list:
@@ -866,9 +865,6 @@ def plot_mag(fignum, datablock, s, num, units, norm):
     plt.title(tstring)
     plt.draw()
 
-#
-#
-
 
 def plot_zed(ZED, datablock, angle, s, units):
     """
@@ -1741,20 +1737,26 @@ def plot_ell(fignum, pars, col='k', lower=True, plot=True):
         PTS.append([pts[0], pts[1]])
         # put on an equal area projection
         R = np.sqrt(1. - abs(elli[2])) / (np.sqrt(elli[0]**2 + elli[1]**2))
-        if elli[2] <= 0:
+        if pts[1] <= 0:
             #            for i in range(3): elli[i]=-elli[i]
+            if len(X_ell) != 0:
+                X_ell.append(np.nan)
+                Y_ell.append(np.nan)
             X_up.append(elli[1] * R)
             Y_up.append(elli[0] * R)
         else:
+            if len(X_up) != 0:
+                X_up.append(np.nan)
+                Y_up.append(np.nan)
             X_ell.append(elli[1] * R)
             Y_ell.append(elli[0] * R)
     if plot == 1:
         plt.figure(num=fignum)
-        col = col[0]+'.'
+        col = col[0]
         if X_ell != []:
-            plt.plot(X_ell, Y_ell, col, markersize=3)
+            plt.plot(X_ell, Y_ell, color=col, lw=1)
         if X_up != []:
-            plt.plot(X_up, Y_up, col, markersize=3)
+            plt.plot(X_up, Y_up, color=col, lw=1, ls='--')
     else:
         return PTS
 
@@ -2944,183 +2946,6 @@ def add_borders(Figs, titles, border_color='#000000', text_color='#800080', con_
                        size=10)
     return Figs
 
-
-def plot_map_basemap(fignum, lats, lons, Opts):
-    """
-    plot_map_basemap(fignum, lats,lons,Opts)
-    makes a basemap with lats/lons
-        requires working installation of Basemap
-    Parameters:
-    _______________
-    fignum : matplotlib figure number
-    lats : array or list of latitudes
-    lons : array or list of longitudes
-    Opts : dictionary of plotting options:
-        Opts.keys=
-            latmin : minimum latitude for plot
-            latmax : maximum latitude for plot
-            lonmin : minimum longitude for plot
-            lonmax : maximum longitude
-            lat_0 : central latitude
-            lon_0 : central longitude
-            proj : projection [basemap projections, e.g., moll=Mollweide, merc=Mercator, ortho=orthorhombic,
-                lcc=Lambert Conformal]
-            sym : matplotlib symbol
-            symsize : symbol size in pts
-            edge : markeredgecolor
-            pltgrid : plot the grid [1,0]
-            res :  resolution [c,l,i,h] for crude, low, intermediate, high
-            boundinglat : bounding latitude
-            sym : matplotlib symbol for plotting
-            symsize : matplotlib symbol size for plotting
-            names : list of names for lats/lons (if empty, none will be plotted)
-            pltgrd : if True, put on grid lines
-            padlat : padding of latitudes
-            padlon : padding of longitudes
-            gridspace : grid line spacing
-            details : dictionary with keys:
-                coasts : if True, plot coastlines
-                rivers : if True, plot rivers
-                states : if True, plot states
-                countries : if True, plot countries
-                ocean : if True, plot ocean
-                fancy : if True, plot etopo 20 grid
-                    NB:  etopo must be installed
-        if Opts keys not set :these are the defaults:
-           Opts={'latmin':-90,'latmax':90,'lonmin':0,'lonmax':360,'lat_0':0,'lon_0':0,'proj':'moll','sym':'ro,'symsize':5,'pltgrid':1,'res':'c','boundinglat':0.,'padlon':0,'padlat':0,'gridspace':30,'details':all False,'edge':None}
-
-    """
-    if not has_basemap:
-        print('-W- Basemap must be installed to run plot_map_basemap')
-        return
-    fig = plt.figure(num=fignum)
-    rgba_land = (255, 255, 150, 255)
-    rgba_ocean = (200, 250, 255, 255)
-    ExMer = ['sinus', 'moll', 'lcc']
-    # draw meridian labels on the bottom [left,right,top,bottom]
-    mlabels = [0, 0, 0, 1]
-    plabels = [1, 0, 0, 0]  # draw parallel labels on the left
-    # set default Options
-    Opts_defaults = {'latmin': -90, 'latmax': 90, 'lonmin': 0, 'lonmax': 360,
-                     'lat_0': 0, 'lon_0': 0, 'proj': 'moll', 'sym': 'ro', 'symsize': 5,
-                     'edge': None, 'pltgrid': 1, 'res': 'c', 'boundinglat': 0.,
-                     'padlon': 0, 'padlat': 0, 'gridspace': 30,
-                     'details': {'fancy': 0, 'coasts': 0, 'rivers': 0, 'states': 0, 'countries': 0, 'ocean': 0}}
-    for key in Opts_defaults.keys():
-        if key not in Opts.keys() and key != 'details':
-            Opts[key] = Opts_defaults[key]
-        if key == 'details':
-            if key not in Opts.keys():
-                Opts[key] = Opts_defaults[key]
-            for detail_key in Opts_defaults[key].keys():
-                if detail_key not in Opts[key].keys():
-                    Opts[key][detail_key] = Opts_defaults[key][detail_key]
-
-    if Opts['proj'] in ExMer:
-        mlabels = [0, 0, 0, 0]
-    if Opts['proj'] not in ExMer:
-        m = Basemap(projection=Opts['proj'], lat_0=Opts['lat_0'],
-                    lon_0=Opts['lon_0'], resolution=Opts['res'])
-        plabels = [0, 0, 0, 0]
-    else:
-        m = Basemap(llcrnrlon=Opts['lonmin'], llcrnrlat=Opts['latmin'], urcrnrlat=Opts['latmax'], urcrnrlon=Opts['lonmax'],
-                    projection=Opts['proj'], lat_0=Opts['lat_0'], lon_0=Opts['lon_0'], lat_ts=0., resolution=Opts['res'], boundinglat=Opts['boundinglat'])
-    if 'details' in list(Opts.keys()):
-        if Opts['details']['fancy'] == 1:
-            from mpl_toolkits.basemap import basemap_datadir
-            EDIR = basemap_datadir + "/"
-            etopo = np.loadtxt(EDIR + 'etopo20data.gz')
-            elons = np.loadtxt(EDIR + 'etopo20lons.gz')
-            elats = np.loadtxt(EDIR + 'etopo20lats.gz')
-            x, y = m(*np.meshgrid(elons, elats))
-            cs = m.contourf(x, y, etopo, 30, cmap=color_map.jet)
-        if Opts['details']['coasts'] == 1:
-            m.drawcoastlines(color='k')
-        if Opts['details']['rivers'] == 1:
-            m.drawrivers(color='b')
-        if Opts['details']['states'] == 1:
-            m.drawstates(color='r')
-        if Opts['details']['countries'] == 1:
-            m.drawcountries(color='g')
-        if Opts['details']['ocean'] == 1:
-            try:
-                m.drawlsmask(land_color=rgba_land,
-                             ocean_color=rgba_ocean, lsmask_lats=None)
-            except TypeError:
-                # this is caused by basemap function: _readlsmask
-                # interacting with numpy
-                # (a float is provided, numpy wants an int).
-                # hopefully will be fixed eventually.
-                pass
-    if Opts['pltgrid'] == 0.:
-        circles = np.arange(Opts['latmin'], Opts['latmax'] + 15., 15.)
-        meridians = np.arange(Opts['lonmin'], Opts['lonmax'] + 30., 30.)
-    elif Opts['pltgrid'] > 0:
-        if Opts['proj'] in ExMer or Opts['proj'] == 'lcc':
-            circles = np.arange(-90, 180. +
-                                Opts['gridspace'], Opts['gridspace'])
-            meridians = np.arange(0, 360., Opts['gridspace'])
-        else:
-            g = Opts['gridspace']
-            latmin, lonmin = g * \
-                int(Opts['latmin'] / g), g * \
-                int(Opts['lonmin'] / g)
-            latmax, lonmax = g * \
-                int(Opts['latmax'] / g), g * \
-                int(Opts['lonmax'] / g)
-            # circles=np.arange(latmin-2.*Opts['padlat'],latmax+2.*Opts['padlat'],Opts['gridspace'])
-            # meridians=np.arange(lonmin-2.*Opts['padlon'],lonmax+2.*Opts['padlon'],Opts['gridspace'])
-            meridians = np.arange(0, 360, 30)
-            circles = np.arange(-90, 90, 30)
-    if Opts['pltgrid'] >= 0:
-        # m.drawparallels(circles,color='black',labels=plabels)
-        # m.drawmeridians(meridians,color='black',labels=mlabels)
-        # skip the labels - they are ugly
-        m.drawparallels(circles, color='black')
-        # skip the labels - they are ugly
-        m.drawmeridians(meridians, color='black')
-        m.drawmapboundary()
-    prn_name, symsize = 0, 5
-    if 'names' in Opts.keys() and len(Opts['names']) > 0:
-        names = Opts['names']
-        if len(names) > 0:
-            prn_name = 1
-#
-    X, Y, T, k = [], [], [], 0
-    if 'symsize' in list(Opts.keys()):
-        symsize = Opts['symsize']
-    if Opts['sym'][-1] != '-':  # just plot points
-        X, Y = m(lons, lats)
-        if prn_name == 1:
-            for pt in range(len(lats)):
-                T.append(plt.text(X[pt] + 5000, Y[pt] - 5000, names[pt]))
-        m.plot(X, Y, Opts['sym'], markersize=symsize,
-               markeredgecolor=Opts['edge'])
-    else:  # for lines,  need to separate chunks using lat==100.
-        chunk = 1
-        while k < len(lats) - 1:
-            if lats[k] <= 90:  # part of string
-                x, y = m(lons[k], lats[k])
-                if x < 1e20:
-                    X.append(x)
-                if y < 1e20:
-                    Y.append(y)  # exclude off the map points
-                if prn_name == 1:
-                    T.append(plt.text(x + 5000, y - 5000, names[k]))
-                k += 1
-            else:  # need to skip 100.0s and move to next chunk
-                # plot previous chunk
-                m.plot(X, Y, Opts['sym'], markersize=symsize,
-                       markeredgecolor=Opts['edge'])
-                chunk += 1
-                while lats[k] > 90. and k < len(lats) - 1:
-                    k += 1  # skip bad points
-                X, Y, T = [], [], []
-        if len(X) > 0:
-            m.plot(X, Y, Opts['sym'], markersize=symsize,
-                   markeredgecolor=Opts['edge'])  # plot last chunk
-
-
 def plot_map(fignum, lats, lons, Opts):
     """
     makes a cartopy map  with lats/lons
@@ -3398,73 +3223,6 @@ def plot_map(fignum, lats, lons, Opts):
     if Opts['global']:
         ax.set_global()
 
-
-def plot_mag_map_basemap(fignum, element, lons, lats, element_type, cmap='RdYlBu', lon_0=0, date=""):
-    """
-    makes a color contour map of geomagnetic field element
-
-    Parameters
-    ____________
-    fignum : matplotlib figure number
-    element : field element array from pmag.do_mag_map for plotting
-    lons : longitude array from pmag.do_mag_map for plotting
-    lats : latitude array from pmag.do_mag_map for plotting
-    element_type : [B,Br,I,D] geomagnetic element type
-        B : field intensity
-        Br : radial field intensity
-        I : inclinations
-        D : declinations
-    Optional
-    _________
-        cmap : matplotlib color map
-        lon_0 : central longitude of the Hammer projection
-        date : date used for field evaluation,
-               if custom ghfile was used, supply filename
-
-
-    Effects
-    ______________
-    plots a Hammer projection color contour with  the desired field element
-    """
-    if not has_basemap:
-        print('-W- Basemap must be installed to run plot_mag_map_basemap')
-        return
-    from matplotlib import cm  # matplotlib's color map module
-    lincr = 1
-    if type(date) != str:
-        date = str(date)
-    fig = plt.figure(fignum)
-    m = Basemap(projection='hammer', lon_0=lon_0)
-    x, y = m(*meshgrid(lons, lats))
-    m.drawcoastlines()
-    if element_type == 'B':
-        levmax = element.max()+lincr
-        levmin = round(element.min()-lincr)
-        levels = np.arange(levmin, levmax, lincr)
-        cs = m.contourf(x, y, element, levels=levels, cmap=cmap)
-        plt.title('Field strength ($\mu$T): '+date)
-    if element_type == 'Br':
-        levmax = element.max()+lincr
-        levmin = round(element.min()-lincr)
-        cs = m.contourf(x, y, element, levels=np.arange(
-            levmin, levmax, lincr), cmap=cmap)
-        plt.title('Radial field strength ($\mu$T): '+date)
-    if element_type == 'I':
-        levmax = element.max()+lincr
-        levmin = round(element.min()-lincr)
-        cs = m.contourf(
-            x, y, element, levels=np.arange(-90, 100, 20), cmap=cmap)
-        m.contour(x, y, element, levels=np.arange(-80, 90, 10), colors='black')
-        plt.title('Field inclination: '+date)
-    if element_type == 'D':
-        # cs=m.contourf(x,y,element,levels=np.arange(-180,180,10),cmap=cmap)
-        cs = m.contourf(
-            x, y, element, levels=np.arange(-180, 180, 10), cmap=cmap)
-        m.contour(x, y, element, levels=np.arange(-180, 180, 10), colors='black')
-        plt.title('Field declination: '+date)
-    cbar = m.colorbar(cs, location='bottom')
-
-
 def plot_mag_map(fignum, element, lons, lats, element_type, cmap='coolwarm', lon_0=0, date="", contours=False, proj='PlateCarree', min=False,max=False):
     """
     makes a color contour map of geomagnetic field element
@@ -3541,9 +3299,9 @@ def plot_mag_map(fignum, element, lons, lats, element_type, cmap='coolwarm', lon
                         colors='black', transform=ccrs.PlateCarree())
 
         if element_type == 'Br':
-            plt.title('Radial field strength ($\mu$T): '+date)
+            plt.title(r'Radial field strength ($\mu$T): '+date)
         else:
-            plt.title('Total field strength ($\mu$T): '+date)
+            plt.title(r'Total field strength ($\mu$T): '+date)
     if element_type == 'I':
         plt.contourf(xx, yy, element,
                      levels=np.arange(-90, 90, lincr),
@@ -3879,8 +3637,7 @@ def msp_magic(spec_df,axa="",axb="",site='site',labels=['a)','b)'],save_plots=Fa
      #        transform=axb.transAxes,fontsize=fontsize)
     res=stats.linregress(Q_DSC,Bs_uT)
     ts=tinv(0.05,len(Q_DSC)-2)
-    axb.text(.1,.9,f'Bmsp =: {res.intercept:.1f} $\pm$  {.5*ts*res.intercept_stderr:.1f} $\mu$T',
-    #axb.text(.1,.9,f'Bmsp =: {res.intercept:.1f} $\pm$  {res.intercept_stderr:.1f} $\mu$T',
+    axb.text(.1,.9,rf'Bmsp =: {res.intercept:.1f} $\pm$  {.5*ts*res.intercept_stderr:.1f} $\mu$T',
             transform=axb.transAxes,fontsize=fontsize)
     
     print(f"intercept (1 sigma): {res.intercept:.1f} +/- {res.intercept_stderr:.1f}")