def __init__(self, title, liste, alpha, unit, opt):
self.title = title
self.dirs = liste
N = len(self.dirs)
self.rows = math.ceil(N/4)
self.columns = 4
self.cbunit = units.get_label(unit)
self.load_grid(alpha)
self.create_figure(opt)
self.cm(unit)
def plot_data(self, ov_plot, opt, i, j):
self.ax = ov_plot.axs[i, j]
# add data to plotman
if opt.cmaglin and self.type == 'mag':
self.cid = self.plotman.parman.add_data(np.power(10, self.data))
ov_plot.cbunit = 'rho'
else:
self.cid = self.plotman.parman.add_data(self.data)
# handle options
cblabel = units.get_label(ov_plot.cbunit)
zlabel = 'z [' + opt.xunit + ']'
xlabel = 'x [' + opt.xunit + ']'
if self.type == 'mag':
vmin = opt.mag_vmin
vmax = opt.mag_vmax
elif self.type == 'pha':
vmin = opt.pha_vmin
vmax = opt.pha_vmax
elif self.type == 'imag':
vmin = opt.imag_vmin
vmax = opt.imag_vmax
else:
vmin = opt.real_vmin
vmax = opt.real_vmax
xmin, xmax, zmin, zmax, vmin, vmax = check_minmax(ov_plot.plotman,
self.cid,
opt.xmin, opt.xmax,
opt.zmin, opt.zmax,
vmin, vmax,
)
# plot
fig, ax, cnorm, cmap, cb = ov_plot.plotman.plot_elements_to_ax(
cid=self.cid,
cid_alpha=ov_plot.alpha,
ax=self.ax,
xmin=xmin,
xmax=xmax,
zmin=zmin,
zmax=zmax,
cblabel=cblabel,
cbnrticks=opt.cbtiks,
title=self.title[3:],
zlabel=zlabel,
xlabel=xlabel,
plot_colorbar=True,
cmap_name=ov_plot.cm,
cbmin=vmin,
cbmax=vmax,
)
def plot_pha(cid, ax, plotman, title, alpha, vmin, vmax,
xmin, xmax, zmin, zmax, xunit, cbtiks, elecs):
'''Plot phase of the complex resistivity using the pha_options.
'''
# handle options
cblabel = units.get_label('phi')
zlabel = 'z [' + xunit + ']'
xlabel = 'x [' + xunit + ']'
cm = 'plasma'
cm = 'jet_r'
xmin, xmax, zmin, zmax, vmin, vmax = check_minmax(
plotman,
cid,
xmin, xmax,
zmin, zmax,
vmin, vmax,
)
# plot
fig, ax, cnorm, cmap, cb, scalarMap = plotman.plot_elements_to_ax(
cid=cid,
ax=ax,
cid_alpha=alpha,
xmin=xmin,
xmax=xmax,
zmin=zmin,
zmax=zmax,
cblabel=cblabel,
cbnrticks=cbtiks,
title=title,
zlabel=zlabel,
xlabel=xlabel,
plot_colorbar=True,
cmap_name=cm,
no_elecs=elecs,
cbmin=vmin,
cbmax=vmax,
)
return fig, ax, cnorm, cmap, cb
def plot_imag(cid, ax, plotman, title, alpha, vmin, vmax,
xmin, xmax, zmin, zmax, xunit, cbtiks, elecs):
'''Plot imag parts of the complex conductivity using the imag_options.
'''
# handle options
cblabel = units.get_label('log_imag')
zlabel = 'z [' + xunit + ']'
xlabel = 'x [' + xunit + ']'
cm = 'plasma_r'
xmin, xmax, zmin, zmax, vmin, vmax = check_minmax(
plotman,
cid,
xmin, xmax,
zmin, zmax,
vmin, vmax,
)
print('IMAG vmin/vmax', vmin, vmax)
# plot
fig, ax, cnorm, cmap, cb, scalarMap = plotman.plot_elements_to_ax(
cid=cid,
cid_alpha=alpha,
ax=ax,
xmin=xmin,
xmax=xmax,
zmin=zmin,
zmax=zmax,
cblabel=cblabel,
cbnrticks=cbtiks,
title=title,
zlabel=zlabel,
xlabel=xlabel,
plot_colorbar=True,
cmap_name=cm,
no_elecs=elecs,
cbmin=vmin,
cbmax=vmax,
)
return fig, ax, cnorm, cmap, cb
def plot_histograms(ertobj, keys, **kwargs):
"""Generate histograms for one or more keys in the given container.
Parameters
----------
ertobj : container instance or :class:`pandas.DataFrame`
data object which contains the data.
keys : str or list of strings
which keys (column names) to plot
merge : bool, optional
if True, then generate only one figure with all key-plots as columns
(default True)
log10plot : bool, optional
default: True
extra_dims : list, optional
Examples
--------
>>> from reda.plotters import plot_histograms
>>> from reda.testing import ERTContainer
>>> figs_dict = plot_histograms(ERTContainer, "r", merge=False)
Generating histogram plot for key: r
Returns
-------
figures : dict
dictionary with the generated histogram figures
"""
# you can either provide a DataFrame or an ERT object
if isinstance(ertobj, pd.DataFrame):
df = ertobj
else:
df = ertobj.data
if df.shape[0] == 0:
raise Exception('No data present, cannot plot')
if isinstance(keys, str):
keys = [
keys,
]
figures = {}
merge_figs = kwargs.get('merge', True)
if merge_figs:
nr_x = 2
nr_y = len(keys)
size_x = 15 / 2.54
size_y = 5 * nr_y / 2.54
fig, axes_all = plt.subplots(nr_y, nr_x, figsize=(size_x, size_y))
axes_all = np.atleast_2d(axes_all)
for row_nr, key in enumerate(keys):
print('Generating histogram plot for key: {0}'.format(key))
subdata_raw = df[key].values
subdata = subdata_raw[~np.isnan(subdata_raw)]
subdata = subdata[np.isfinite(subdata)]
subdata_log10_with_nan = np.log10(subdata[subdata > 0])
subdata_log10 = subdata_log10_with_nan[~np.isnan(subdata_log10_with_nan
)]
subdata_log10 = subdata_log10[np.isfinite(subdata_log10)]
if merge_figs:
axes = axes_all[row_nr].squeeze()
else:
fig, axes = plt.subplots(1, 2, figsize=(10 / 2.54, 5 / 2.54))
ax = axes[0]
ax.hist(
subdata,
_get_nr_bins(subdata.size),
)
ax.set_xlabel(units.get_label(key))
ax.set_ylabel('count')
ax.xaxis.set_major_locator(mpl.ticker.MaxNLocator(5))
ax.tick_params(axis='both', which='major', labelsize=6)
ax.tick_params(axis='both', which='minor', labelsize=6)
if subdata_log10.size > 0:
ax = axes[1]
ax.hist(
subdata_log10,
_get_nr_bins(subdata.size),
)
ax.set_xlabel(r'$log_{10}($' + units.get_label(key) + ')')
ax.set_ylabel('count')
ax.xaxis.set_major_locator(mpl.ticker.MaxNLocator(5))
else:
pass
# del(axes[1])
fig.tight_layout()
if not merge_figs:
figures[key] = fig
if merge_figs:
figures['all'] = fig
return figures
def plot_histograms_extra_dims(dataobj, keys, primary_dim=None, **kwargs):
"""Produce histograms grouped by one extra dimensions. Produce additional
figures for all extra dimensions.
The dimension to spread out along subplots is called the primary extra
dimension.
Extra dimensions are:
* timesteps
* frequency
If only "timesteps" are present, timesteps will be plotted as subplots.
If only "frequencies" are present, frequencies will be plotted as subplots.
If more than one extra dimensions is present, multiple figures will be
generated.
Test cases:
* not extra dims present (primary_dim=None, timestep, frequency)
* timestep (primary_dim=None, timestep, frequency)
* frequency (primary_dim=None, timestep, frequency)
* timestep + frequency (primary_dim=None, timestep, frequency)
check nr of returned figures.
Parameters
----------
dataobj : :py:class:`pandas.DataFrame` or reda container
The data container/data frame which holds the data
keys : string|list|tuple|iterable
The keys (columns) of the dataobj to plot
primary_dim : string
primary extra dimension to plot along subplots. If None, the first
extra dimension found in the data set is used, in the following order:
timestep, frequency.
subquery : str, optional
if provided, apply this query statement to the data before plotting
log10 : bool
Plot only log10 transformation of data (default: False)
lin_and_log10 : bool
Plot both linear and log10 representation of data (default: False)
Nx : int, optional
Number of subplots in x direction
Returns
-------
dim_name : str
name of secondary dimensions, i.e. the dimensions for which separate
figures were created
figures : dict
dict containing the generated figures. The keys of the dict correspond
to the secondary dimension grouping keys
Examples
--------
>>> import reda.testing.containers
>>> ert = reda.testing.containers.ERTContainer_nr
>>> import reda.plotters.histograms as RH
>>> dim_name, fig = RH.plot_histograms_extra_dims(ert, ['r', ])
>>> import reda.testing.containers
>>> ert = reda.testing.containers.ERTContainer_nr
>>> import reda.plotters.histograms as RH
>>> dim_name, fig = RH.plot_histograms_extra_dims(ert, ['r', 'a'])
"""
if isinstance(dataobj, pd.DataFrame):
df_raw = dataobj
else:
df_raw = dataobj.data
if kwargs.get('subquery', False):
df = df_raw.query(kwargs.get('subquery'))
else:
df = df_raw
# define some labels
edim_labels = {
'timestep': ('time', ''),
'frequency': (
'frequency',
'Hz',
),
}
# prepare data columns to plot
if isinstance(keys, str):
keys = [
keys,
]
columns = keys
N_c = len(columns)
# create log10 plots?
if kwargs.get('lin_and_log10', False):
transformers = ['lin', 'log10']
N_trafo = 2
elif kwargs.get('log10', False):
transformers = [
'log10',
]
N_trafo = 1
else:
transformers = [
'lin',
]
N_trafo = 1
# available extra dimensions
extra_dims = ('timestep', 'frequency')
# select dimension to plot into subplots
if primary_dim is None or primary_dim not in df.columns:
for extra_dim in extra_dims:
if extra_dim in df.columns:
primary_dim = extra_dim
# now primary_dim is either None (i.e., we don't have any extra dims to
# group), or it contains a valid column to group
# now prepare the secondary dimensions for which we create extra figures
secondary_dimensions = []
for extra_dim in extra_dims:
if extra_dim in df.columns and extra_dim != primary_dim:
secondary_dimensions.append(extra_dim)
# group secondary dimensions, or create a tuple with all the data
if secondary_dimensions:
group_secondary = df.groupby(secondary_dimensions)
else:
group_secondary = (('all', df), )
figures = {}
for sec_g_name, sec_g in group_secondary:
# group over primary dimension
if primary_dim is None:
group_primary = (('all', sec_g), )
N_primary = 1
else:
group_primary = sec_g.groupby(primary_dim)
N_primary = group_primary.ngroups
# determine layout of Figure
Nx_max = kwargs.get('Nx', 4)
N = N_primary * N_c * N_trafo
Nx = min(Nx_max, N)
Ny = int(np.ceil(N / Nx))
size_x = 5 * Nx / 2.54
size_y = 5 * Ny / 2.54
fig, axes = plt.subplots(Ny,
Nx,
figsize=(size_x, size_y),
sharex=True,
sharey=True)
axes = np.atleast_2d(axes)
index = 0
for p_name, pgroup in group_primary:
for column in columns:
for transformer in transformers:
# print('{0}-{1}-{2}'.format(ts_name, column, transformer))
subdata_raw = pgroup[column].values
subdata = subdata_raw[~np.isnan(subdata_raw)]
subdata = subdata[np.isfinite(subdata)]
if transformer == 'log10':
subdata_log10_with_nan = np.log10(subdata[subdata > 0])
subdata_log10 = subdata_log10_with_nan[
~np.isnan(subdata_log10_with_nan)]
subdata_log10 = subdata_log10[np.isfinite(
subdata_log10)]
subdata = subdata_log10
ax = axes.flat[index]
ax.hist(
subdata,
_get_nr_bins(subdata.size),
)
ax.set_xlabel(units.get_label(column))
ax.set_ylabel('count')
ax.xaxis.set_major_locator(mpl.ticker.MaxNLocator(3))
ax.tick_params(axis='both', which='major', labelsize=6)
ax.tick_params(axis='both', which='minor', labelsize=6)
# depending on the type of pname, change the format
p_name_fmt = '{}'
from numbers import Number
if isinstance(p_name, Number):
p_name_fmt = '{:.4f}'
title_str = '{}: ' + p_name_fmt + ' {}'
ax.set_title(
title_str.format(
edim_labels[primary_dim][0],
p_name,
edim_labels[primary_dim][1],
),
fontsize=7.0,
)
index += 1
# remove some labels
for ax in axes[:, 1:].flat:
ax.set_ylabel('')
for ax in axes[:-1, :].flat:
ax.set_xlabel('')
fig.tight_layout()
for ax in axes.flat[index:]:
ax.set_visible(False)
figures[sec_g_name] = fig
return '_'.join(secondary_dimensions), figures
def plot_pseudosection_type2(dataobj, column, **kwargs):
"""Create a pseudosection plot of type 2.
For a given measurement data set, create plots that graphically show
the data in a 2D color plot. Hereby, x and y coordinates in the plot
are determined by the current dipole (x-axis) and voltage dipole
(y-axis) of the corresponding measurement configurations.
This type of rawdata plot can plot any type of measurement
configurations, i.e., it is not restricted to certain types of
configurations such as Dipole-dipole or Wenner configurations. However,
spatial inferences cannot be made from the plots for all configuration
types.
Coordinates are generated by separately sorting the dipoles
(current/voltage) along the first electrode, and then subsequently
sorting by the difference (skip) between both electrodes.
Note that this type of raw data plot does not take into account the
real electrode spacing of the measurement setup.
Type 2 plots can show normal and reciprocal data at the same time.
Hereby the upper left triangle of the plot area usually contains normal
data, and the lower right triangle contains the corresponding
reciprocal data. Therefore a quick assessment of normal-reciprocal
differences can be made by visually comparing the symmetry on the 1:1
line going from the lower left corner to the upper right corner.
Note that this interpretation usually only holds for Dipole-Dipole data
(and the related Wenner configurations).
Parameters
----------
dataobj: ERT container|pandas.DataFrame
Container or DataFrame with data to plot
column: string
Column key to plot
ax: matplotlib.Axes object, optional
axes object to plot to. If not provided, a new figure and axes
object will be created and returned
nocb: bool, optional
if set to False, don't plot the colorbar
cblabel: string, optional
label for the colorbar
cbmin: float, optional
colorbar minimum
cbmax: float, optional
colorbar maximum
xlabel: string, optional
xlabel for the plot
ylabel: string, optional
ylabel for the plot
do_not_saturate: bool, optional
if set to True, then values outside the colorbar range will not
saturate with the respective limit colors. Instead, values lower
than the CB are colored "cyan" and vaues above the CB limit are
colored "red"
log10: bool, optional
if set to True, plot the log10 values of the provided data
Returns
-------
fig:
figure object
ax:
axes object
cb:
colorbar object
Examples
--------
You can just supply a pandas.DataFrame to the plot function:
.. plot::
:include-source:
import numpy as np
configs = np.array((
(1, 2, 4, 3),
(1, 2, 5, 4),
(1, 2, 6, 5),
(2, 3, 5, 4),
(2, 3, 6, 5),
(3, 4, 6, 5),
))
measurements = np.random.random(configs.shape[0])
import pandas as pd
df = pd.DataFrame(configs, columns=['a', 'b', 'm', 'n'])
df['measurements'] = measurements
from reda.plotters.pseudoplots import plot_pseudosection_type2
fig, ax, cb = plot_pseudosection_type2(
dataobj=df,
column='measurements',
)
You can also supply axes to plot to:
.. plot::
:include-source:
import numpy as np
configs = np.array((
(1, 2, 4, 3),
(1, 2, 5, 4),
(1, 2, 6, 5),
(2, 3, 5, 4),
(2, 3, 6, 5),
(3, 4, 6, 5),
))
measurements = np.random.random(configs.shape[0])
measurements2 = np.random.random(configs.shape[0])
import pandas as pd
df = pd.DataFrame(configs, columns=['a', 'b', 'm', 'n'])
df['measurements'] = measurements
df['measurements2'] = measurements2
from reda.plotters.pseudoplots import plot_pseudosection_type2
fig, axes = plt.subplots(1, 2)
plot_pseudosection_type2(
df,
column='measurements',
ax=axes[0],
cblabel='this label',
xlabel='xlabel',
ylabel='ylabel',
)
plot_pseudosection_type2(
df,
column='measurements2',
ax=axes[1],
cblabel='measurement 2',
xlabel='xlabel',
ylabel='ylabel',
)
fig.tight_layout()
>>> from reda.testing.containers import ERTContainer_nr
>>> import reda.plotters.pseudoplots as ps
>>> fig, axes, cb = ps.plot_pseudosection_type2(ERTContainer_nr, 'r')
"""
if isinstance(dataobj, pd.DataFrame):
df = dataobj
else:
df = dataobj.data
c = df[['a', 'b', 'm', 'n']].values
AB_ids = _get_unique_identifiers(c[:, 0:2])
MN_ids = _get_unique_identifiers(c[:, 2:4])
ab_sorted = np.sort(c[:, 0:2], axis=1)
mn_sorted = np.sort(c[:, 2:4], axis=1)
AB_coords = [
AB_ids[x]
for x in (ab_sorted[:, 0] * 1e5 + ab_sorted[:, 1]).astype(int)
]
MN_coords = [
MN_ids[x]
for x in (mn_sorted[:, 0] * 1e5 + mn_sorted[:, 1]).astype(int)
]
# check for duplicate positions
ABMN_coords = np.vstack((AB_coords, MN_coords)).T.copy()
_, counts = np.unique(
ABMN_coords.view(ABMN_coords.dtype.descr * 2),
return_counts=True,
)
# import IPython
# IPython.embed()
# exit()
if np.any(counts > 1):
print('found duplicate coordinates!')
# duplicate_configs = np.where(counts > 1)[0]
# print('duplicate configs:')
# print('A B M N')
# for i in duplicate_configs:
# print(c[i, :])
# prepare matrix
plot_values = np.squeeze(df[column].values)
if kwargs.get('log10', False):
plot_values = np.log10(plot_values)
C = np.zeros((len(MN_ids.items()), len(AB_ids))) * np.nan
C[MN_coords, AB_coords] = plot_values
# for display purposes, reverse the first dimension
C = C[::-1, :]
ax = kwargs.get('ax', None)
if ax is None:
fig, ax = plt.subplots(1, 1, figsize=(15 / 2.54, 10 / 2.54))
fig = ax.get_figure()
cmap = mpl.cm.get_cmap('viridis')
if kwargs.get('do_not_saturate', False):
cmap.set_over(color='r')
cmap.set_under(color='c')
im = ax.matshow(
C,
interpolation='none',
cmap=cmap,
aspect='auto',
vmin=kwargs.get('cbmin', None),
vmax=kwargs.get('cbmax', None),
extent=[
0,
max(AB_coords),
0,
max(MN_coords),
],
)
max_xy = max((max(AB_coords), max(MN_coords)))
ax.plot(
(0, max_xy),
(0, max_xy),
'-',
color='k',
linewidth=1.0,
)
cb = None
if not kwargs.get('nocb', False):
cb = fig.colorbar(im, ax=ax)
label = units.get_label(column)
if mpl.rcParams['text.usetex']:
label = label.replace('_', '-')
cb.set_label(kwargs.get('cblabel', label))
ax.set_xlabel(kwargs.get('xlabel', 'current dipoles'))
ax.set_ylabel(kwargs.get('ylabel', 'voltage dipoles'))
return fig, ax, cb
def plot_pseudosection_type3(dataobj, column, **kwargs):
"""Create a pseudosection plot of type 3.
For a given measurement data set, create plots that graphically show
the data in a 2D pseudoplot. Hereby, x and y coordinates (pseudodistance
and pseudodepth) in the plot are determined by the corresponding measurement
configuration (after Roy and Apparao (1971) and Dahlin and Zou (2005)).
This type of rawdata plot can plot any type of measurement
configurations, i.e., it is not restricted to certain types of
configurations such as Dipole-dipole or Wenner configurations.
Parameters
----------
dataobj: ERT container|pandas.DataFrame
Container or DataFrame with data to plot
column: string
Column key to plot
ax: matplotlib.Axes object, optional
axes object to plot to. If not provided, a new figure and axes
object will be created and returned
nocb: bool, optional
if set to False, don't plot the colorbar
cblabel: string, optional
label for the colorbar
cbmin: float, optional
colorbar minimum
cbmax: float, optional
colorbar maximum
xlabel: string, optional
xlabel for the plot
ylabel: string, optional
ylabel for the plot
do_not_saturate: bool, optional
if set to True, then values outside the colorbar range will not
saturate with the respective limit colors. Instead, values lower
than the CB are colored "cyan" and vaues above the CB limit are
colored "red"
markersize: float, optional
size of plotted data points
spacing: float, optional
if set to True, the actual electrode spacing is used for the computation
of the pseudodepth and -distance; default value is 1 m
log10: bool, optional
if set to True, plot the log10 values of the provided data
Returns
-------
fig:
figure object
ax:
axes object
cb:
colorbar object
Examples
--------
You can just supply a pandas.DataFrame to the plot function:
.. plot::
:include-source:
import numpy as np
configs = np.array((
(1, 2, 4, 3),
(1, 2, 5, 4),
(1, 2, 6, 5),
(2, 3, 5, 4),
(2, 3, 6, 5),
(3, 4, 6, 5),
))
measurements = np.random.random(configs.shape[0])
import pandas as pd
df = pd.DataFrame(configs, columns=['a', 'b', 'm', 'n'])
df['measurements'] = measurements
from reda.plotters.pseudoplots import plot_pseudosection_type3
fig, ax, cb = plot_pseudosection_type3(
dataobj=df,
column='measurements',
)
You can also supply axes to plot to:
.. plot::
:include-source:
import numpy as np
configs = np.array((
(1, 2, 4, 3),
(1, 2, 5, 4),
(1, 2, 6, 5),
(2, 3, 5, 4),
(2, 3, 6, 5),
(3, 4, 6, 5),
))
measurements = np.random.random(configs.shape[0])
measurements2 = np.random.random(configs.shape[0])
import pandas as pd
df = pd.DataFrame(configs, columns=['a', 'b', 'm', 'n'])
df['measurements'] = measurements
df['measurements2'] = measurements2
from reda.plotters.pseudoplots import plot_pseudosection_type3
fig, axes = plt.subplots(1, 2)
plot_pseudosection_type3(
df,
column='measurements',
ax=axes[0],
cblabel='this label',
xlabel='xlabel',
ylabel='ylabel',
)
plot_pseudosection_type3(
df,
column='measurements2',
ax=axes[1],
cblabel='measurement 2',
xlabel='xlabel',
ylabel='ylabel',
)
fig.tight_layout()
"""
if isinstance(dataobj, pd.DataFrame):
df = dataobj
else:
df = dataobj.data
c = (df[['a', 'b', 'm', 'n']] - 1) * kwargs.get('spacing', 1)
# define the configuration
# check on first quadrupole and assume the config is consistent
# dipole-dipole
if (sum(np.greater([c.a[0], c.b[0]], [c.m[0], c.n[0]])) == 2
or sum(np.greater([c.m[0], c.n[0]], [c.a[0], c.b[0]])) == 2):
c.loc[:, 'xp'] = ((c.a + c.b) / 2 + (c.n + c.m) / 2) / 2
c.loc[:, 'zp'] = -((c.n - c.b) * 0.195) # Roi and Appparo
# multiple gradient
else:
xmn = (c.m + c.n) / 2
c.loc[:, 'xp'] = xmn
c.loc[:, 'zp'] = np.abs(
np.min([xmn - c.a, c.b - xmn], axis=0) / 3) * -1 # Dahlin, Zhou
# extract the values to plot
c['plot_values'] = df[column]
if kwargs.get('log10', False):
c['plot_values'] = np.log10(c['plot_values'])
# sort after the pseudodistance and pseudodepth
pseudocoords = c[['xp', 'zp', 'plot_values']].sort_values(by=['xp', 'zp'])
ax = kwargs.get('ax', None)
if ax is None:
fig, ax = plt.subplots(1, 1, figsize=(15 / 2.54, 10 / 2.54))
fig = ax.get_figure()
cmap = mpl.cm.get_cmap('viridis')
if kwargs.get('do_not_saturate', False):
cmap.set_over(color='r')
cmap.set_under(color='c')
pseudocoords['markersize'] = kwargs.get('markersize', 10)
# check for same pseudocoordinates
common_pscoords = pseudocoords[['xp', 'zp']].drop_duplicates()
def smallify(markersize_array):
"""
For a given array of markersizes (with same size) compute a stepwise
decreasing factor for the plotting size based on the length of the array.
"""
nelems = len(markersize_array)
factor = 1 / nelems
return markersize_array * np.flip(np.arange(1, nelems + 1) * factor)
# check for overlapping points and adjust markersize accordingly
for _, common in common_pscoords.iterrows():
subset = pseudocoords.query('xp == {} and zp == {}'.format(
common.xp, common.zp))
pseudocoords.loc[subset.index, 'markersize'] = smallify(
pseudocoords.loc[subset.index, 'markersize'].values)
scat = ax.scatter(pseudocoords['xp'],
pseudocoords['zp'],
s=pseudocoords['markersize'],
c=pseudocoords['plot_values'],
marker='o',
edgecolors='none',
cmap=cmap,
vmin=kwargs.get('cbmin', None),
vmax=kwargs.get('cbmax', None),
alpha=1)
ax.set_xlim([
np.min(c['xp']) - 1 * kwargs.get('spacing', 1),
np.max(c['xp']) + 1 * kwargs.get('spacing', 1)
])
ax.set_ylim([
np.min(c['zp']) - 1 * kwargs.get('spacing', 1),
np.max(c['zp']) + 1 * kwargs.get('spacing', 1)
])
cb = None
if not kwargs.get('nocb', False):
cb = fig.colorbar(scat, ax=ax)
cb.set_label(kwargs.get('cblabel', units.get_label(column)))
ax.set_xlabel(kwargs.get('xlabel', 'Pseudodistance'))
ax.set_ylabel(kwargs.get('ylabel', 'Pseudodepth'))
return fig, ax, cb
def plot_histograms_extra_dims(dataobj, keys, **kwargs):
"""Produce histograms grouped by the extra dims.
Parameters
----------
Examples
--------
>>> import reda.testing.containers
>>> ert = reda.testing.containers.ERTContainer_nr
>>> import reda.plotters.histograms as RH
>>> fig = RH.plot_histograms_extra_dims(ert, ['R', ])
>>> fig
<matplotlib.figure.Figure object at ...>
>>> import reda.testing.containers
>>> ert = reda.testing.containers.ERTContainer_nr
>>> import reda.plotters.histograms as RH
>>> fig = RH.plot_histograms_extra_dims(ert, ['R', 'A'])
>>> fig
<matplotlib.figure.Figure object at ...>
"""
if isinstance(dataobj, pd.DataFrame):
df_raw = dataobj
else:
df_raw = dataobj.data
if kwargs.get('subquery', False):
df = df_raw.query(kwargs.get('subquery'))
else:
df = df_raw
split_timestamps = True
if split_timestamps:
group_timestamps = df.groupby('timestep')
N_ts = len(group_timestamps.groups.keys())
else:
group_timestamps = ('all', df)
N_ts = 1
columns = keys
N_c = len(columns)
plot_log10 = kwargs.get('log10plot', False)
if plot_log10:
transformers = ['lin', 'log10']
N_log10 = 2
else:
transformers = ['lin', ]
N_log10 = 1
# determine layout of plots
Nx_max = kwargs.get('Nx', 4)
N = N_ts * N_c * N_log10
Nx = min(Nx_max, N)
Ny = int(np.ceil(N / Nx))
size_x = 4 * Nx / 2.54
size_y = 5 * Ny / 2.54
fig, axes = plt.subplots(Ny, Nx, figsize=(size_x, size_y))
axes = np.atleast_2d(axes)
index = 0
for ts_name, tgroup in group_timestamps:
for column in columns:
for transformer in transformers:
# print('{0}-{1}-{2}'.format(ts_name, column, transformer))
subdata_raw = tgroup[column].values
subdata = subdata_raw[~np.isnan(subdata_raw)]
subdata = subdata[np.isfinite(subdata)]
if transformer == 'log10':
subdata_log10_with_nan = np.log10(subdata[subdata > 0])
subdata_log10 = subdata_log10_with_nan[~np.isnan(
subdata_log10_with_nan)
]
subdata_log10 = subdata_log10[np.isfinite(subdata_log10)]
subdata = subdata_log10
ax = axes.flat[index]
ax.hist(
subdata,
_get_nr_bins(subdata.size),
)
ax.set_xlabel(
units.get_label(column)
)
ax.set_ylabel('count')
ax.xaxis.set_major_locator(mpl.ticker.MaxNLocator(3))
index += 1
# remove some labels
for ax in axes[:, 1:].flat:
ax.set_ylabel('')
fig.tight_layout()
return fig
def create_singleplots(plotman, cov, mag, pha, pha_fpi, alpha, options):
'''Plot the data of the tomodir in individual plots.
'''
if cov is None:
cov = np.ones_like(mag) * np.nan
magunit = 'log_rho'
if not pha == []:
[real, imag] = calc_complex(mag, pha)
if options.c_in_log:
real = np.log10(real)
with np.errstate(divide='ignore'):
imag = np.log10(imag)
imag[np.isinf(imag)] = np.nan
if not pha_fpi == []:
[real_fpi, imag_fpi] = calc_complex(mag, pha_fpi)
if options.cmaglin:
mag = np.power(10, mag)
magunit = 'rho'
if options.c_in_log:
real_fpi = np.log10(real_fpi)
with np.errstate(divide='ignore'):
imag_fpi = np.log10(imag_fpi)
imag_fpi[np.isinf(imag_fpi)] = np.nan
# import IPython
# IPython.embed()
# print(imag_fpi, np.nanmin(imag_fpi), np.nanmax(imag_fpi))
# print(options.imag_vmin, options.imag_vmax)
# exit()
data = np.column_stack((
mag, cov, pha, real, imag,
pha_fpi, real_fpi, imag_fpi
))
titles = [
'Magnitude', 'Coverage',
'Phase', 'Real Part', 'Imaginary Part',
'FPI Phase', 'FPI Real Part', 'FPI Imaginary Part'
]
unites = [
magunit, 'cov',
'phi', 'log_real', 'log_imag',
'phi', 'log_real', 'log_imag'
]
vmins = [
options.mag_vmin, options.cov_vmin,
options.pha_vmin, options.real_vmin, options.imag_vmin,
options.pha_vmin, options.real_vmin, options.imag_vmin
]
vmaxs = [options.mag_vmax, options.cov_vmax,
options.pha_vmax, options.real_vmax, options.imag_vmax,
options.pha_vmax, options.real_vmax, options.imag_vmax]
cmaps = ['jet', 'GnBu',
'jet_r', 'jet_r', 'plasma_r',
'jet_r', 'jet_r', 'plasma_r']
saves = ['rho', 'cov',
'phi', 'real', 'imag',
'fpi_phi', 'fpi_real', 'fpi_imag']
else:
if options.cmaglin:
mag = np.power(10, mag)
magunit = 'rho'
data = np.column_stack((mag, cov, pha, real, imag))
titles = ['Magnitude', 'Coverage',
'Phase', 'Real Part', 'Imaginary Part']
unites = [magunit, 'cov',
'phi', 'log_real', 'log_imag']
vmins = [options.mag_vmin, options.cov_vmin,
options.pha_vmin, options.real_vmin, options.imag_vmin]
vmaxs = [options.mag_vmax, options.cov_vmax,
options.pha_vmax, options.real_vmax, options.imag_vmax]
cmaps = ['jet', 'GnBu',
'jet_r', 'jet_r', 'plasma_r']
saves = ['rho', 'cov',
'phi', 'real', 'imag']
else:
data = np.column_stack((mag, cov))
titles = ['Magnitude', 'Coverage']
unites = [magunit, 'cov']
vmins = [options.mag_vmin, options.cov_vmin]
vmaxs = [options.mag_vmax, options.cov_vmax]
cmaps = ['jet', 'GnBu']
saves = ['rho', 'cov']
try:
mod_rho = np.genfromtxt('rho/rho.dat', skip_header=1, usecols=([0]))
mod_pha = np.genfromtxt('rho/rho.dat', skip_header=1, usecols=([1]))
data = np.column_stack((data, mod_rho, mod_pha))
titles.append('Model')
titles.append('Model')
unites.append('rho')
unites.append('phi')
vmins.append(options.mag_vmin)
vmins.append(options.pha_vmin)
vmaxs.append(options.mag_vmax)
vmaxs.append(options.pha_vmax)
cmaps.append('jet')
cmaps.append('plasma')
saves.append('rhomod')
saves.append('phamod')
except Exception:
pass
for datum, title, unit, vmin, vmax, cm, save in zip(
np.transpose(data), titles, unites, vmins, vmaxs, cmaps, saves):
# print(save)
# if save == 'fpi_imag':
# import IPython
# IPython.embed()
sizex, sizez = getfigsize(plotman)
f, ax = plt.subplots(1, figsize=(sizex, sizez))
cid = plotman.parman.add_data(datum)
# handle options
cblabel = units.get_label(unit)
if options.title is not None:
title = options.title
zlabel = 'z [' + options.unit + ']'
xlabel = 'x [' + options.unit + ']'
xmin, xmax, zmin, zmax, vmin, vmax = check_minmax(
plotman,
cid,
options.xmin, options.xmax,
options.zmin, options.zmax,
vmin, vmax
)
# plot
cmap = mpl_cm.get_cmap(cm)
fig, ax, cnorm, cmap, cb, scalarMap = plotman.plot_elements_to_ax(
cid=cid,
cid_alpha=alpha,
ax=ax,
xmin=xmin,
xmax=xmax,
zmin=zmin,
zmax=zmax,
cblabel=cblabel,
title=title,
zlabel=zlabel,
xlabel=xlabel,
plot_colorbar=True,
cmap_name=cm,
over=cmap(1.0),
under=cmap(0.0),
no_elecs=options.no_elecs,
cbmin=vmin,
cbmax=vmax,
)
f.tight_layout()
f.savefig(save + '.png', dpi=300)