tomo_Brazil.cnf

###############################################################################
#
# This is an example of configuration file, wherein global paths and parameters
# related to the seismic noise tomography procedure are defined. At least one
# configuration file should reside in the folder in which you intend to run
# your scripts. The configuration file(s) can have any name, as long as the
# extension is 'cnf': e.g., 'tomo.cnf', 'myconfig.cnf', 'test.cnf'...
#
# The parameters are divided in several sections:
# - [paths]             : default paths to input/output folders
# - [maps]              : parameters to plot maps
# - [cross-correlation] : parameters to calculate cross-correlations
# - [FTAN]              : parameters of the frequency-time analysis
# - [tomography]        : parameters of the tomographic inversion
#
# Before using the scripts and package pysismo, you should at least make sure
# that the paths in section [paths] and shapefiles in section [maps] are
# consistent with your own files and folders organization. And, of course, you
# should make sure to set the correct interval of dates to calculate the cross-
# correlations, in section [cross-correlation]. The other parameters can be
# fine-tuned later as you analyze your data.
#
# Module pysismo.psconfig takes care of reading the configuration file and
# defining the global parameters. If only one configuration file (*.cnf) is
# found in the current folder, then psconfig reads it silently. If
# several *.cnf files are found, then you'll be prompted to select one of
# them.
#
# Other modules then import from psconfig the parameters they need, e.g.:
# 
#   from psconfig import CROSSCORR_DIR, FTAN_DIR, PERIOD_BANDS, ...
#
# Note that most of (but not all) the global parameters are actually default 
# values that can be overridden in the functions where they are used. For
# example, ``PERIOD_BANDS`` is the default value of the input argument ``bands`` 
# of the function pscrosscorr.CrossCorrelation.plot_by_period_band(), but you
# can specify other bands by explicitly passing the argument, e.g.: 
# 
#   plot_by_period_band(bands=[[10, 30], [20, 50]])
#
# If, in one script, you want to modify a global parameter without touching
# the configuration file, you must first import psconfig, then modify the
# parameters as desired, and finally import other module(s), e.g.:
#
# >>> from pysismo import psconfig 
# >>> psconfig.FTAN_DIR = 'mydir'
# >>> from pysismo import pscrosscorr
# >>> pscrosscorr.FTAN_DIR
# 'mydir'   # ok the changes have been taken in account
#
# It is strongly discouraged to modify global parameters once psconfig (or a 
# module importing it) has been imported, as the effect can be highly
# imprevisible (immutable default values won't be affected, mutable default
# values can be affected, parameters used as is in the code will be affected).
#
###############################################################################


#======
[paths]
#======

# dir of miniseed, StationXML and dataless seed files. StationXML and dataless
# files can have any name, provided that the extension is 'xml' and 'dataless',
# respectively. One file can contain several stations.
#
# In the current version of the program, miniseed files MUST be
# organized inside their directory as:
# <year>-<month>/<network>.<station>.<channel>.mseed, e.g.:
# 1988-10/BL.JFOB.BHZ.mseed
# So, there is one sub-directory per month, and inside it, one miniseed
# file per month and per station.

MSEED_DIR = ../IRIS data
STATIONXML_DIR = ../StationXML files
DATALESS_DIR = ../Dataless seed

CROSSCORR_DIR = ./output/cross-correlation  ; dir of cross-correlation results
FTAN_DIR = ./output/FTAN                    ; dir of FTAN results (including dispersion curves)
TOMO_DIR = ./output/tomography              ; dir of tomographic inversion results
DEPTHMODELS_DIR = ./output/1D models        ; dir of 1D depth inversion results

# dir of the (binaries of the) Computer Programs in Seismology, used
# to calculate a theoretical dispersion curve given a 1D model
# (leave empty if you have not installed them)
COMPUTER_PROGRAMS_IN_SEISMOLOGY_DIR = /home/bruno/Data/Recherche/Utilitaires/Programmes/Computer Programs in Seismology/bin


#=====
[maps]
#=====

# paths to shapefiles (coasts, tectonic provinces and labels), used
# to plot maps:
#
# - ``COAST_SHP`` should be a shapefile containing lines or polygons
#   representing coasts (you can also include borders).
#
# - ``TECTO_SHP`` should be a shapefile containing polygons representing
#   tectonic provinces, AND AN ATTRIBUTE TABLE whose first field
#   contains the province's category, which will be used to affect
#   a color to the polygon (see below).
#
# - ``TECTO_LABELS`` should be a shapefile containing points representing
#   the location of the labels associated with the tectonic provinces,
#   AND AN ATTRIBUTE TABLE whose first field contains the label (characters
#   '\' will be replaced with line breaks), and the second field contains
#   the label's angle.
#
# Leave path empty if you don't have the corresponding shapefile.

COAST_SHP = ./shapefiles/SouthAmericaCoasts.shp
TECTO_SHP = ./shapefiles/SouthAmericaTectonicElements.shp
TECTO_LABELS = ./shapefiles/SouthAmericaTectonicElementsLabels.shp

# JSON dict giving the color of the tectonic provinces according to their
# category (first field of the attribute table of ``TECTO_SHP``, see above).
# A category not appearing in this dict will be filled with white.
# A color can be any object understood by matplotlib: a string (e.g., "green"),
# a grey shade (e.g., "0.5"), an html hex string (e.g., "#eeefff"),
# a R/G/B tuple (e.g., [0.5, 0.5, 0.5]) or a R/B/G/alpha tuple (e.g.,
# [0.5, 0.5, 0.5, 0.5]).

TECTO_COLORS = {
    "Archean": [1, 0.757, 0.757],
    "Phanerozoic": [1, 1, 0.878],
    "Neoproterozoic": "0.863"
    }

# bounding box of (large) global maps and (small) inset maps
# (min lon, max lon, min lat, max lat in JSON lists)

BBOX_LARGE = [-70, -30, -32, 8]
BBOX_SMALL = [-65, -35, -29, 1]


#==================
[cross-correlation]
#==================

USE_DATALESSPAZ = False             ; use dataless files to remove instrument response?
USE_STATIONXML = True               ; use stationXML files to remove instrument response?

FIRSTDAY = 1/1/1996                 ; first day of cross-correlation (d/m/y)
LASTDAY = 31/3/2012                 ; last day of cross-correlation (d/m/y)
MINFILL = 0.99                      ; minimum data fill within day

CROSSCORR_STATIONS_SUBSET = null    ; subset of stations (null if all, else JSON list)
CROSSCORR_TMAX = 2000               ; max time window (s) for cross-correlation
CROSSCORR_SKIPLOCS = ["50"]         ; locations to skip (JSON list)

PERIODMIN = 3.0                     ; bandpass parameters
PERIODMAX = 60.0
CORNERS = 2
ZEROPHASE = True
PERIOD_RESAMPLE = 1.0               ; resample period to decimate traces, after band-pass

ONEBIT_NORM = False                 ; one-bit normalization?
PERIODMIN_EARTHQUAKE = 15.0         ; earthquakes periods band
PERIODMAX_EARTHQUAKE = 50.0

WINDOW_FREQ = 0.0002                ; freq window (Hz) to smooth ampl spectrum


#=====
[FTAN]
#=====

# default period bands (JSON list), used to:
# - plot cross-correlation by period bands, in plot_FTAN(), plot_by_period_bands()
# - plot spectral SNR, in plot_spectral_SNR()
# - estimate min spectral SNR, in FTANs()

PERIOD_BANDS = [[4, 7], [7, 15], [10, 22], [15, 30], [20, 35]]
# (these bands focus on periods ~5, 10, 15, 20, 25 seconds)

# default parameters to define the signal and noise windows used to
# estimate the SNR:
# - the signal window is defined according to a min and a max velocity as:
#   dist/vmax < t < dist/vmin
# - the noise window has a fixed size and starts after a fixed trailing
#   time from the end of the signal window

SIGNAL_WINDOW_VMIN = 2.0
SIGNAL_WINDOW_VMAX = 4.0
SIGNAL2NOISE_TRAIL = 500.0
NOISE_WINDOW_SIZE = 500.0

# periods and velocities of the FTAN: start, stop and step (JSON lists)

RAWFTAN_PERIODS_STARTSTOPSTEP = [3.0, 45.1, 1.0]
CLEANFTAN_PERIODS_STARTSTOPSTEP = [3.0, 45.1, 1.0]
FTAN_VELOCITIES_STARTSTOPSTEP = [2.0, 5.51, 0.01]

# default width parameter of the narrow Gaussian bandpass filters
# applied in the FTAN. The bandpass filters take the form:
#
#  exp[-FTAN_ALPHA * ((f-f0)/f0)**2],
#
# where f is the frequency and f0 the center frequency of the filter.

FTAN_ALPHA = 20

# relative strength of the smoothing term in the penalty function that
# the dispersion curve seeks to minimize
STRENGTH_SMOOTHING = 1.0

# replace nominal frequency (i.e., center frequency of Gaussian filters)
# with instantaneous frequency (i.e., dphi/dt(t=arrival time) with phi the
# phase of the filtered analytic signal), in the FTAN and dispersion curves?
# See Bensen et al. (2007) for technical details.

USE_INSTANTANEOUS_FREQ = True

# if the instantaneous frequency (or period) is used, we need to discard bad
# values from instantaneous periods. So:
# - instantaneous periods whose relative difference with respect to
#   nominal period is greater than ``MAX_RELDIFF_INST_NOMINAL_PERIOD``
#   are discarded,
# - instantaneous periods lower than ``MIN_INST_PERIOD`` are discarded,
# - instantaneous periods whose relative difference with respect to the
#   running median is greater than ``MAX_RELDIFF_INST_MEDIAN_PERIOD`` are
#   discarded; the running median is calculated over
#   ``HALFWINDOW_MEDIAN_PERIOD`` points to the right and to the left
#   of each period.

MAX_RELDIFF_INST_NOMINAL_PERIOD = 0.8
MIN_INST_PERIOD = 1.5
HALFWINDOW_MEDIAN_PERIOD = 3
MAX_RELDIFF_INST_MEDIAN_PERIOD = 0.5

# ==========
[tomography]
# ==========

# Default parameters related to the velocity selection criteria

MINSPECTSNR = 7             ; min spectral SNR to retain velocity
MINSPECTSNR_NOSDEV = 15     ; min spectral SNR to retain velocity if no std dev
MAXSDEV = 0.1               ; max sdt dev (km/s) to retain velocity
MINNBTRIMESTER = 4          ; min nb of trimesters to estimate std dev
MAXPERIOD_FACTOR = 0.08333  ; max period = *MAXPERIOD_FACTOR* * pair distance

# Default internode spacing of grid

LONSTEP = 1
LATSTEP = 1

# Default correlation length of the smoothing kernel:
# S(r,r') = exp[-|r-r'|**2 / (2 * correlation_length**2)]

CORRELATION_LENGTH = 150

# Default strength of the spatial smoothing term (alpha) and the
# weighted norm penalization term (beta) in the penalty function

ALPHA = 400
BETA = 200

# Default parameter in the damping factor of the norm penalization term,
# such that the norm is weighted by exp(- lambda_*path_density)
# With a value of 0.15, penalization becomes strong when path density < ~20
# With a value of 0.30, penalization becomes strong when path density < ~10

LAMBDA = 0.3