Package Visualization

Module Plot1D2D

This file is part of pyCSAMT.

pyCSAMT is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

pyCSAMT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with pyCSAMT. If not, see <https://www.gnu.org/licenses/>.

---

Created on Mon Dec 28 14:28:06 2020

@author: KLaurent alias @Daniel03

class pycsamt.viewer.plot.Plot1d(**kwargs)

plot 1d class Deal with all 1D plots.

Key Words	Description
fig_dpi	dots-per-inch resolution of the figure default is 300
fig_num	number of the figure instance default is ‘Mesh’
fig_size	size of figure in inches (width, height) default is [5, 5]
fs	size of font of axis tick labels, axis labels are fs+2. default is 6
ls	[ ‘-’ | ‘.’ | ‘:’ ] line style of mesh lines default is ‘-’
marker	marker of stations default is r”$lacktriangledown$”
ms	size of marker in points. default is 5

Methods	Description
plot_topo_sep_azim	plot_topography , station separation and azimuth profile can plot individually or grouped by.
penetrated1D	skindepth plot. penetration depth at different frequencies
plot_static_correction	plot rho and rho corrected by different filter defalut filter is TMA.
plot_freqVSRhoPhase	Resistivity and phase plot.
plot_curves	plot data curves : specific for Zonge Engineering AVG file.
plot_RhoPhase errors	plot errors bar of resistivities in ohm.m and phase in degree.

Methods

penetration1D([fn, profile_fn, ...])	Pentration1D depth : Show skin depth at selected frequencies .
plotRMS([fn, target, savefig])	Plot RMS .
plot_curves([fn, savefig, selected_stations])	Plot Zonge Engineering AVG file with different components E and H at differents frequencies.
plot_freqVSRhoPhase([fn, profile_fn, ...])	Method to plot apparent resistivity |phase vs frequency .
plot_multiStations([X, Y, path, profile_lines])	Plot multisations of site sof survey area
plot_multiple_corrections(data_fn[, ...])	Plot multiples static correction for a line using two options like.
plot_static_correction(data_fn[, ...])	Plot corrected apparent resistivities at different stations to solve the problem of static shift by adding either Trimimg Moving average (TMA)filter or fixed-length-moving-average(FLMA) filter or Adaptative moving-average (AMA).
plot_station_profile([fn, straighten_type, ...])	Method to plot original station profile and coordinate reajustment
plot_topo_sep_azim([fn, profile_fn, savefig])	Method to plot topographic , stations separation and azimuth profiles .

penetration1D(fn=None, profile_fn=None, selected_frequency=None, **kwargs)

Pentration1D depth : Show skin depth at selected frequencies . for multiples frequencies , put argument selected_frequency on list. If frequency provided is not on the frequency range , it will be interpolated.

Parameters

• fn (str) – full path to [AVG|EDI|J] file

• profile_fn (str) – full path to stn station file . If user used EDI or J files , Dont need to add profile_file

• selected_frequency (list) – list , list of freauency want to see the penetration depth. must be on a list . i.e [8, 511,1024 ]

Params	Default	Description
rename_station	list	Bring the station name . Be sure the length of station name you provided match the size of the data station name .
rotate_station	int	rotation station name . Default is 90 degree.
fs	float	can change the size of marker. Default is .7 : eg ms =9*fs
lw	float	change the linewdth
plot_grid	bool	add grid on your plot . Default is False

Note

browse to see others plot config.

Example

>>> from viewer.plot import Plot1d
>>> path =  os.path.join(os.environ["pyCSAMT"],
...              'pycsamt','data', file_1)
>>> plot_1d_obj =Plot1d()
... plot1d_depth = plot_1d_obj.penetrated1D(fn =path ,
...                    profile_fn= os.path.join(
...                        os.path.dirname(path), 'K1.stn'),
...                    selected_frequency =511)

plotRMS(fn=None, target=1.0, savefig=None, **kwargs)

Plot RMS . If occamlogfile is not available , set rms value , iteration value at each rms and|or roughness.

Parameters

* fnstr

full path to occam2D logfile

• savefigstr

  full directory to save fig

• targetfloat

  target supposed RMS to reach . Default is 1.

Returns

obj , plot_RMS obj

Note

If occam2d logfile is availbale , dont need other parameters , except the path “fn” and as possible the “target”.

plot_curves(fn=None, savefig=None, selected_stations=1, **kws)

Plot Zonge Engineering AVG file with different components E and H at differents frequencies.

Parameters

• fn (str) – full path to Zonge Engineering file

• profile_fn (str) – full path to profile file .

• savefig (str) – path to figure plot

Params	Default	Description
fs	float	can change the size of marker. *Default is .7 : eg ms =9*fs
lw	float	change the linewdth
error_bar	bool	set to false to let invisible. Default is True

:Example :

>>> from viewer.plot import Plot1d
>>>path =  os.path.join(os.environ["pyCSAMT"],
...          'pycsamt','data', file_1)
>>> plot_1d_obj =Plot1d()
>>> plotcurves = plot_1d_obj .plot_curves(fn = path,
                                        selected_stations=[1,10, 20],
                                          error_bar=True)

plot_freqVSRhoPhase(fn=None, profile_fn=None, station_id=1, rename_stations=None, **kwargs)

Method to plot apparent resistivity |phase vs frequency .

Parameters

• fn (str) – full path to [AVG|EDI|J] file

• profile_fn (str) – full path to station profile .

Note

if user use drectly AVG data must provide station profile ‘.stn’

Others params	Default	Description
station_id	str or int	plot the name of station if string is povided make be sure that the station name is on the station list eg : station_id = 1 means plot S00 station =[1,13] means plot >S00,S12station [S05, 7, 8] – [ S05, S06, S07]
rename_stations	list	bring the station name . Be sure the length of station name you provided match the data station name
show_error	bool	if True , see errobar plot. Default is False.

plot_multiStations(X=None, Y=None, path=None, profile_lines=None, **kwargs)

Plot multisations of site sof survey area

Parameters

* pathstr

full path to station profile path . In the case where Zonge avg file is provided , use stn profile files. Group all stn file on a folder will call automatically

• profile_lineslist

  name of profile lines . if profile lines is NOne will tale all stn profiles in the path directory

• Xlist

  list of arrays array of X coordinates values for each

  survey line. Can be easting or Northing

• Y: list

  list of arrays of Y coordinates valuescan be easting

  or northing

.. note:: `X` and `Y` MUST be the same length

plot_multiple_corrections(data_fn, profile_fn=None, dipole_length=50.0, filter_type='ama', siteOrfreq='S00', refreq=None, **kws)

Plot multiples static correction for a line using two options like::

• plot rho|phase VS frequency `kind`= linear

• plot rho|phase VS station `kind`= site

default is ``line`

Parameters

• data_fn (str) – full path to file , can be [AVG|EDI|J] files

• siteOrfreq –

  list of station or list of frequency number to visualize.

  Mx list tolorate is 4. can be:

  -`siteOrfreq`=['S00', 'S04', 'S08', 'S12']
  -`siteOrfreq`=[1, 82, 1024, 8192]  in Hz
  

• kind – Type of plot. can be:: - kind =1 or ‘line’ - kind =2 or ‘site’

• profile_fn (str) – pathLike full path to Zonge Engeneering *.station file .If *.edi file or jfile is given, dont need to provide profile_fn

• dipole_length (float, int) – length of dipole in meters

Example

>>> from pycsamt.viewer.plot import Plot1d
>>> data='data/avg/K1.AVG'
>>> viewfreq=[80, 1024,2000,  8192] # set `kind` to ``1``.
>>> viewsite= ['S00', 's04', 's08', 'S12'] # set `kind` to ``2``
>>> plotObj = Plot1d()
>>> plotObj. plot_multiple_corrections(data_fn= data, kind=2,
                          filter_type ='ama',
                           siteOrfreq=viewfreq
                          )

plot_static_correction(data_fn, profile_fn=None, dipole_length=50.0, frequency_id=1, ADD_FILTER='tma', **kwargs)

Plot corrected apparent resistivities at different stations to solve the problem of static shift by adding either Trimimg Moving average (TMA)filter or fixed-length-moving-average(FLMA) filter or Adaptative moving-average (AMA). Actually FLMA and TMA filter are available and default filTer is TMA. To plot all filter into one figure add the joker * to arguments ADD_FILER.

Parameters

• data_fn (str) – full path to file , can be [AVG|EDI|J] files

• profile_fn (str) – pathLike full path to Zonge Engeneering *.station file .

• dipole_length (float, int) – length of dipole in meters when user applied for FLMA

Holding others informations

Params	Default	Description
frequency_id	str,int	plot the filtered frequency, eg frequency_id = 1023 means plot uncorrected rho and static rho at that frequency . set on list to plot multiple frequency [8,1101 ].
ADD_FILTER	str	name of filter to apply . TMA Trimming moving average AMA Adaptative moving average FLMA Fixed Length moving average

Note

Profile file (*.stn) is compolsory when provide raw Zonge AVG otherwise no need to profile for EDI or J file. In addition when FLMA filter is used m, provided dipole_length and number_of_points for window width are necessaries.

Example

>>> from from viewer.plot import Plot1d
>>> path =  os.path.join(os.environ["pyCSAMT"],
...              'pycsamt','data', file_1)
>>> plot_1d_obj =Plot1d()
... plot_1d_obj.plot_static_correction(data_fn =path ,
...                                   profile_fn= os.path.join(
...                                    os.path.dirname(path),
...                                            'K1.stn'),
...                                   frequency_id =1023)

plot_station_profile(fn=None, straighten_type='classic', reajust_coordinates=(0, 0), savefig=None, **kwargs)

Method to plot original station profile and coordinate reajustment

profiles. Deal with Zonge AVG file .

Parameters

* fnstr

full path to profile station file of Zonge Engineering station profile file . format egal to *.stn

• straighten_typestr

  type of straingther profile it may be classic, equisistant or distord Default is ‘classic’

• reajust_coordinateslist

  list of float x, y values

:Example:

>>> path =  os.path.join(os.environ["pyCSAMT"],
...          'pycsamt','data', 'avg', 'K1.stn')
>>> plot_1d_obj= Plot1d()
>>> plot_1d_obj.plot_station_profile(fn = path)

plot_topo_sep_azim(fn=None, profile_fn=None, savefig=None, **kwargs)

Method to plot topographic , stations separation and azimuth profiles . User can add station_names and and set _it to let the program to plot on the corresponding figure. He can alse force the program to plot its dipole length otherwise the program will compute it automatically.

If “set_station_name” is False , No Name of station will be visible.

User has the possibility to plot one by one figure or all by using a “*” symbol or 123. To polt one figure , it may use keyword argument “plot” following the king [‘topo’, azimuth’, ‘sep’] or integer 1|2|3. Method is flexible .User can customize the plot , marker and line as he wants by putting on list the matplotlib labels properties . The program uses the label properties on order to set configuration lines and other properties .Topography plot correspond to index 0 , stations-separation to index 1 and azimuth to index 2.To plot individually

, User doesnt need to put properties on list. Programm will

recognize and set the poperties provided according the figure He wants.

Parameters

* fnstr

full path to [EDI|J|AVG] file.

• profile_fnstr

  path to file may Zonge Engineering *.stn file

• plotstr

  type of plot , default is ‘*’ mean of three profile.

• Station_Names: list

  list of station names , User could provide. Default is None compute automatically

• set_station_namesbool

  display the station name on figure axis . Default is False.

• elevation(ndarray,1)

  Array_like of elevation

• station_pkarray_like,

  array_like station dipole center value.

• savefigstr

  path to save figure.

Returns

obj,

plot_obj azim- topo and station separation.

Keywords	Description
lw	line width . default is 1.5
ls	line style of lines,[ ‘-’ | ‘.’ | ‘:’ ] default is “[‘-’, ‘:’, ‘-.’]” for 3 profiles.
marker	marker of stations default is ‘o’
ms	size of marker in points. default is 6
color	color of line .*Default* is ‘k’
alpha	Marker transparence .*Defaut* is .2
markerfacecolor	facecolor or markers .*Default* is ‘k’
markeredgecolor	eadgecolor of markers . default is “[‘w’,’r’’gray’]”
xtick_label_rotation	xtick rotation angle . default* is 45.
ytick_label_rotation	ytick rotatoion angle .default * is 45
xtick_labelsize	xtick label size .defalut* is 12.
ytick_labelsize	ytick label size .defalut* is 12.

Example

>>> import os
>>> file_stn='K6.stn'
>>> path =  os.path.join(os.environ["pyCSAMT"],
...                          'pycsamt','data', file_stn)
...  plot_1d_obj= Plot1d()
.... plot_1d_obj.plot_topo_sep_azim(profile_fn= path , plot='*',
                                    set_station_names=True,
                                   dipole_length_curve=False)

class pycsamt.viewer.plot.Plot2d(**kws)

class to plot 2D map Deal with all 2D plots

keywords	Description
cb_pad	padding between axes edge and color bar
cb_shrink	percentage to shrink the color bar
climits	limits of the color scale for resistivity in log scale (min, max)
cmap	name of color map for resistivity values
fig_aspect	aspect ratio between width and height of resistivity image. 1 for equal axes
fig_dpi	resolution of figure in dots-per-inch
fig_num	number of figure instance
fig_size	size of figure in inches (width, height)
font_size	size of axes tick labels, axes labels is +2
grid	[ ‘both’ | ‘major’ |’minor’ | None ] string to tell the program to make a grid on the specified axes.
ms	size of station marker
plot_yn	[ ‘y’ | ‘n’] ‘y’ –> to plot on instantiation ‘n’ –> to not plot on instantiation
station_color	color of station marker
station_font_color	color station label
station_font_pad	padding between station label and marker
station_font_rotation	angle of station label in degrees 0 is horizontal
station_font_size	font size of station label
station_font_weight	font weight of station label
station_id	index to take station label from station name
station_marker	station marker. if inputing a LaTex marker be sure to input as r”LaTexMarker” otherwise might not plot properly
title	title of plot. If None then the name of the iteration file and containing folder will be the title with RMS and Roughness.
xlimits	limits of plot in x-direction in (km)
xminorticks	increment of minor ticks in x direction
xpad	padding in x-direction in km
ylimits	depth limits of plot positive down (km)
yminorticks	increment of minor ticks in y-direction
ypad	padding in negative y-direction (km)
yscale	[ ‘km’ | ‘m’ ] scale of plot, if ‘m’ everything will be scaled accordingly.

Methods

penetration2D([fn, profile_fn, savefig, doi])	Plot penetration 2D.
plot_Pseudolog([station_id, iter_fn, ...])	Build pseudodrill from the model resistivity .
plot_Response([data_fn, response_fn, mode])	Function to plot forward value , and residual value from Occam 2D
plot_occam2dModel([model_fn, iter_fn, ...])	Plotoccam Model form Occam Model class
pseudocrossResPhase(fn[, profile_fn, ...])	Plot Pseudocrossection of resistivity and phase.

penetration2D(fn=None, profile_fn=None, savefig=None, doi='2km', **kwargs)

Plot penetration 2D.

Parameters

* fnstr

full path to [EDI|AVG|J] files.

• doifloat

  depth assumed to be imaged , default is 2000m For CSAMT , 2km is enought to have more info about near surface.

  • Default* unit is “m”.

• profile_fnstr

  full path to profile *stn file

• savefigstr

  outdir

Returns

obj ,

plot penetration obj.

Example

>>> path =  os.path.join(os.environ["pyCSAMT"],
...      'pycsamt','data', K1.AVG)
>>> plot2d_obj = plot2d()
>>> plot2d_obj.penetration2D(fn = path,
...                        profile_fn=os.path.join(
...                            os.path.dirname(path),'K1.stn'),
...                         plot_style='imshow',  doi='10000m')

plot_Pseudolog(station_id='S00', iter_fn=None, mesh_fn=None, data_fn=None, iter2dat_fn=None, bln_fn=None, model_fn=None, **kwargs)

Build pseudodrill from the model resistivity .

Deal with true value of ressitivity obtained during survey .In fact , How to input these values into our model to produce an accuracy underground map is the chalenge.Building pseudolog allow to know how layers are disposal in underground so to emphasize the large conductive zone in the case of groundwater exploration. It is combinaison with geophysic data especially inversion data with geological data. Actually the program deal with Occam 2D inverison file or Bo Yang (x,y,z) file. We will extend this program later with other external softares files extension. If user have a golder software installed on its computer , can use the files generated by the software and to produce 2D map so to compare both . Model map and detail-sequences map to see the difference Details sequences map is most closest to the reality . When step descent parameter is small ,the detail sequences trend to model map . So More geological values are, more the accuracy of detail sequences logs becomes. Geological data allow to harmonize the value of resistivity produced by our model so to force the pogramm to make a correlation between data from true layers and the model values.

Parameters

station_id (str, int) – Number or the site id of the survey area number starts from 1 to the end .

Note

User caneither use Occam 2D inversions files to plot or BoYang (x, y, file)+ station location file (*bln) to plot if the two types of files are provided , program with give priority to Occam 2D inversion files.

Params	Type	Description
model_fn	str	full path to Occam model file .
iter_fn	str	full path to occam iteration file
data_fn	str	full path to occam_data file
doi	str	depth of investigation might be float or str like “1km” =1000
depth_scale	str	scale of imaging depth can be “km” or “m”. Default is”m”
step_descent	float	step to enforce the model resistivities to keep truth layers values as reference data . if step descentis egal to doi max, data looks like model at 99.99%.Step decent is function of depth and rho.
lc_AD_curves	tuple	customize line color of average curve and details sequneces logs eg : ((0.5, 0.8, 0.),’blue’)
default_unknow_lcolor	str	In the case the name of layer is notin our data base , customize the layer color . default is “(1.0, 1.0, 1.0)”.
default_unknow_lpatter	str	In the case the name of layer is not in our data base , customize the layer pattern default is “+.+.+.”

Note

constrained_electrical _properties_of_rocks param keeps the Truth layers resistivities as reference resistivities. If value is false will check in our data base to find the resistivities that match better the given resistivities of

the layers. Default is True.

Customize your plot using matplotlib properties.

Example

>>> from viewer.plot import Plot2d
>>> path =os.path.join(os.environ ['pyCSAMT'],
...                       'pycsamt', 'data', 'occam2D')
>>> plot2d_obj = Plot2d(station_label_rotation=None,
...                    show_grid=True,
...                    font_size =8,
...                    lc='r',
...                    fig_size=[5,8],
...                    markerfacecolor='k',
...                    markeredgecolor='k')
>>> plot2d_obj.plot_Pseudolog( station_id=[43],
...                          input_resistivities=[300, 500,
...                                             1000, 2000,
...                                             4000, 6000],
...                          input_layers =['alluvium',
...                                         'amphibolite',
...                                         'altered rock',
...                                          'augen gneiss',
...                                          'granite'],
...                            mesh_fn=os.path.join(path,
...                                                 'Occam2DMesh')
...                            iter_fn = os.path.join(path,
...                                                   'ITER17.iter'),
...                            model_fn =os.path.join(path,
...                                                   'Occam2DModel') ,
...                            data_fn =os.path.join(path,
...                                                  'OccamDataFile.dat'),
...                            doi='1km',
...                            step_descent=200.,
...                            plot_style= 'pcolormesh')

plot_Response(data_fn=None, response_fn=None, mode=None, **kws)

Function to plot forward value , and residual value from Occam 2D

list of params are below :

Params	Type	Description
response_fn	str	full path to occam iteration file
data_fn	str	full path to occam_data file
doi	str	depth of investigation might be float or str like “1km” =1000
show_station_id	str	show station names

Example

>>> from viewer.plot import Plot2d
>>> pathresp =os.path.join(os.environ ['pyCSAMT'],
...                           'pycsamt', 'data',
...         'occam2D','RESP17.resp')
>>> path_data =os.path.join(os.environ ['pyCSAMT'],
...                            'pycsamt', 'data',
...     'occam2D','OccamDataFile.dat' )
>>> plot2d_obj = plot2d()
... plot2d_obj.plot_Response(data_fn =path_data ,
...                             response_fn=  pathresp )

plot_occam2dModel(model_fn=None, iter_fn=None, mesh_fn=None, data_fn=None, doi=1000, **kwargs)

Plotoccam Model form Occam Model class

Parameters

model_fn (str) – full path to Occam 2Dmodel file

Params	Type	Description
iter_fn	str	full path to occam iteration file
mesh_fn	str	full path to mesh_fn file
data_fn	str	full path to occam_data file
doi	str	depth of investigation might be float or str like “1km” =1000
depth_scale	str	scale of imaging depth can be “km” or “m”. Default is”m”

Example

>>> data='OccamDataFile.dat'
>>> mesh = 'Occam2DMesh'
>>> model = 'Occam2DModel'
>>> iter_='ITER17.iter'
>>> path =os.path.join(os.environ ['pyCSAMT'],
...                       'data', 'occam2D', mesh)
>>> plot2d_obj = plot2d()
>>> plot2d_obj.plot_occam2dModel(mesh_fn=path,
...                            iter_fn = os.path.join(
...                                os.path.dirname(path), iter_),
...                            model_fn =os.path.join(
...                                os.path.dirname(path), model) ,
...                            data_fn =os.path.join(
...                                os.path.dirname(path), data ),
...                             doi='1km')

pseudocrossResPhase(fn, profile_fn=None, savefig=None, plot_style=None, **kws)

Plot Pseudocrossection of resistivity and phase.

Parameters

• fn (str) – full path to [‘AVG’, ‘EDI’, ‘J’] file .

• profile_fn (str) – full path to profile station file in the case fn is *AVG.

• savefig (str) – path to save figure

pycsamt.viewer.plot.plot_dataAndFits(data_fn=None, stations=None, **kws)

Plot error Apparent resistivity and phase and error in data for multiples zonge lines(AVG)

Parameters

• data_fn – Path to zonge *.avg file . Can be a list of avg files

• stations –

  station id . Can be a list of a staion or the station number. e.g.

  station =’S00’ sttion =’1’ station =[‘s00’, 13, 46]

• kws – keywords arguments. Please refer to pycsamt.ff.core.cs.CSAMT for further details

Returns

A list of: - z_lines: List of survey lines - z_stations: list of station to visualize - z_freq: list of frequency to plot on x-axis - z_appRHO: list of apparent resistivy in ohm.m to plot - z_phase: list of phase in degrees - z_appRho_err: list of error apparent resistivity - z_phase_err: list of error phase in %

Example

>>> from pycsamt.viewer.plot import plot_dataAndFits
>>> path =r'F:\ThesisImpvg'
>>> pathData = [os.path.join(path, file)
        for file in ['K1.AVG',
                     'K4.AVG', 'K6.AVG', 'K8.AVG'
                     ]]
>>> z_lines, z_stations, z_freq,  z_appRHO, z_phase,z_appRho_err,            z_phase_err=plot_dataAndFits(
        data_fn = pathData,
        stations=['S00', 'S04', 's06', 's10'])