MSNoise Admin (Web Interface)

MSNoise Admin is a web interface that helps the user define the configuration for all the processing steps. It allows configuring the stations and filters to be used in the different steps of the workflow and provides a view on the database tables.

To start the admin:

$ msnoise admin

Which, by default, starts a web server listening on all interfaces on port 5000. This can be overridden by passing parameters to the command, e.g. for port 5099:

$ msnoise admin -p 5099

The next step consists of opening a web browser and open the ip address of the machine, by default on the current machine, it’ll be http://localhost:5000/ or http://127.0.0.1:5000/.

The top level menu shows four items:

Home

The index page shows

• The project location and its database

• Stats of the Data Availability, the CC, STACK, MWCS and DTT jobs.

• Quick action buttons for resetting or deleting jobs.

The name and the logo of the page can be overridden by setting an environment variable with a name and the HTML tag of the logo image:

set msnoise_brand="ROB|<img src='http://www.seismologie.be/img/oma/ROB-logo.svg' width=200 height=200>"

and then starting msnoise admin:

Configuration

Station

Stations appear as a table and are editable.

Stations are defined as:

class msnoise.msnoise_admin.Station(*args)

Station Object

Parameters:

• ref (int) – The Station ID in the database

• net (str) – The network code of the Station

• sta (str) – The station code

• X (float) – The X coordinate of the station

• Y (float) – The Y coordinate of the station

• altitude (float) – The altitude of the station

• coordinates (str) – The coordinates system. “DEG” is WGS84 latitude/ longitude in degrees. “UTM” is expressed in meters.

• instrument (str) – The instrument code, useful with PAZ correction

• used (bool) – Whether this station must be used in the computations.

Attributes:

X

Y

altitude

coordinates

net

ref

sta

used

used_channel_names

used_location_codes

Methods

chans
locs

Filter

Filters appear as a table and are editable. The filter parameters are validated before submission, so no errors should happen. Note: by default, the used parameter is set to False, don’t forget to change it!

Filters are defined as:

class msnoise.msnoise_admin.Filter(**kwargs)

Filter base class.

Parameters:

• ref (int) – The id of the Filter in the database

• low (float) – The lower frequency bound of the Whiten function (in Hz)

• high (float) – The upper frequency bound of the Whiten function (in Hz)

• mwcs_low (float) – The lower frequency bound of the linear regression done in MWCS (in Hz)

• mwcs_high (float) – The upper frequency bound of the linear regression done in MWCS (in Hz)

• mwcs_wlen (float) – Window length (in seconds) to perform MWCS

• mwcs_step (float) – Step (in seconds) of the windowing procedure in MWCS

• used (bool) – Is the filter activated for the processing

Attributes:

high

low

mwcs_high

mwcs_low

mwcs_step

mwcs_wlen

ref

used

Config

All configuration bits appear as a table and are editable. When editing one configuration item, the Edit tab shows extra information about the parameter, where it is used and its default value. Most of the configuration bits are case-sensitive!

Example view:

The table below lists the different fields:

Parameter Name	Description	Default Value
data_folder		Data Folder
output_folder	CROSS_CORRELATIONS	CC Output Folder in case keep_all=Y, to store the individual windows. The daily CCF will always be stored in the STACKS/001_DAYS folder.
data_structure	SDS	Either a predefined acronym [SDS]/BUD/IDDS, or /-separated path (e.g. NET/STA/YEAR/NET.STA.YEAR.DAY.MSEED).
archive_format		Force format of archive files to read? Leave empty for slightly slower auto-detection by Obspy, or specify any format supported by <a href=’https://docs.obspy.org/packages/autogen/obspy.core.stream.read.html’ target=’_blank’>obspy.core.stream.read()</a>.
network		Network to analyse
channels		Channels need to match the value (ex: [&ast;], &ast;Z, BH&ast;, HHZ,…)
startdate	1970-01-01	Start Date to process: [1970-01-01]=’since beginning of the archive’
enddate	2100-01-01	End Date to process: [2100-01-01]=’No end’
analysis_duration	86400	Duration of the Analysis in seconds (this shouldn’t be changed for now)
cc_sampling_rate	20	Sampling Rate for the CrossCorrelation (in Hz)
cc_normalisation	NO	Normalisation method for individual corr_duration) CCFs, default is not normalized (NO), but can be normalized based on the power of the two traces (POW), or by the maximum (MAX) or absolute maximum (ABSMAX) of the CCF
resampling_method	Decimate	Resampling method
preprocess_lowpass	8	Preprocessing Low-pass value (in Hz)
preprocess_highpass	0.01	Preprocessing High-pass value (in Hz)
preprocess_max_gap	10	Preprocessing maximum gap length that will be filled by interpolation (in seconds)
preprocess_taper_length	20	Duration of the taper applied at the beginning and end of trace during the preprocessing, to allow highpass filtering (in seconds)
remove_response	N	Remove instrument response
response_format	dataless	Remove instrument file format
response_path	inventory	Instrument correction file(s) location (path relative to db.ini), defaults to ‘./inventory’, i.e. a subfolder in the current project folder. All files in that folder will be parsed.
response_prefilt	(0.005, 0.006, 30.0, 35.0)	Remove instrument correction pre-filter (in Hz, see <a href=’https://docs.obspy.org/packages/autogen/obspy.core.trace.Trace.remove_response.html’ target=”_blank”>ObsPy Doc</a> for what it means.)
maxlag	120	Maximum lag (in seconds)
corr_duration	1800	Data windows to correlate (in seconds)
overlap	0	Amount of overlap between data windows [0:1[
winsorizing	3	Winsorizing at N time RMS , 0 disables winsorizing, -1 enables 1-bit normalization
whitening	A	Whiten Traces before cross-correlation: [A]ll (except for autocorr), [N]one, or only if [C]omponents are different
whitening_type	B	Type of spectral whitening function to use: [B]rutal (amplitude to 1.0), divide spectrum by its [PSD] or by band-passing the white spectrum with a hanning-window [HANN]. WARNING: only works for compute_cc, not compute_cc_rot, where it will always be B
clip_after_whiten	N	Do the clipping (winsorizing) after whitening?
stack_method	linear	Stack Method: Linear Mean or Phase Weighted Stack
pws_timegate	10	If stack_method =’pws’, width of the smoothing (in seconds)
pws_power	2	If stack_method =”pws”, Power of the Weighting
crondays	1	Number of days to monitor with scan_archive, typically used in cron (should be a float representing a number of days, or a string designating weeks, days, and/or hours using the format ‘Xw Xd Xh’)
components_to_compute	ZZ	List (comma separated) of components to compute between two different stations
cc_type	CC	Cross-Correlation type
components_to_compute_single_station		List (comma separated) of components within a single station. ZZ would be the autocorrelation of Z component, while ZE or ZN are the cross-components. Defaults to [], no single-station computations are done.
cc_type_single_station_AC	CC	Auto-Correlation type
cc_type_single_station_SC	CC	Cross-Correlation type for Cross-Components
keep_all	Y	Keep all cross-corr (length: corr_duration)
keep_days	Y	Keep all daily cross-corr
ref_begin	1970-01-01	Beginning or REF stacks. Can be absolute (2012-01-01) or relative (-100) days
ref_end	2100-01-01	End or REF stacks. Same as ref_begin
mov_stack	((‘1d’,’1d’))	A list of two parameters: the time to “roll” over (default 1 day) and the granularity (step) of the resulting stacked CCFs (default 1 day) to stack for the Moving-window stacks. This can be a list of tuples, e.g. ((‘1d’,’1d’),(‘2d’,’1d’)) corresponds to the MSNoise 1.6 “1,2” before. Time deltas can be anything pandas can interpret (“d”, “min”, “sec”, etc).
export_format	MSEED	Export stacks in which format(s) ?
sac_format	doublets	Format for SAC stacks ?
dtt_lag	static	How is the lag window defined
dtt_v	1	If dtt_lag =dynamic: what velocity to use to avoid ballistic wave (in km/s)
dtt_minlag	5	If dtt_lag =static: min lag time (in seconds)
dtt_width	30	Width of the time lag window (in seconds)
dtt_sides	both	Which sides to use
dtt_mincoh	0.65	Minimum coherence on dt measurement, MWCS points with values lower than that will not be used in the WLS, [0:1]
dtt_maxerr	0.1	Maximum error on dt measurement, MWCS points with values larger than that will not be used in the WLS [0:1]
dtt_maxdt	0.1	Maximum dt values, MWCS points with values larger than that will not be used in the WLS (in seconds)
wct_ns	5	smoothing parameter in frequency
wct_nt	5	smoothing parameter in time
wct_vpo	20	spacing param between discrete scales
wct_nptsfreq	300	number of freq points between min and max
dtt_codacycles	20	number of cycles of period (1/freq) between lag_min and lag_max
dvv_min_nonzero	0.25	percentage of data points with non-zero weighting required for regression otherwise nan (0 to 1)
wct_norm	Y	Is the REF and CCF are normalized before computing wavelet? [Y]/N
wavelet_type	(‘Morlet’,6.)	Wavelet type and optional associated parameter
plugins		Comma separated list of plugin names. Plugins names should be importable Python modules.
hpc	N	Is MSNoise going to run on an HPC?
stretching_max	0.01	Maximum stretching coefficient, e.g. 0.5 = 50%, 0.01 = 1%
stretching_nsteps	1000	Number of stretching steps between 1- stretching_max and 1+ stretching_max
qc_components	Z	Components to process for QC, defaults to [Z], but can be any comma separated list (e.g. ‘Z,E,N’)
qc_ppsd_length	3600	Length of data segments passed to psd in seconds. In the paper by McNamara et al (2004) a value of 3600 (1 hour) was chosen. Longer segments increase the upper limit of analyzed periods but decrease the number of analyzed segments.
qc_ppsd_overlap	0	Overlap of segments passed to psd. Overlap may take values between 0 and 1 and is given as fraction of the length of one segment, e.g. qc_ppsd_length=3600 and qc_ppsd_overlap=0.5 result in an overlap of 1800s of the segments.
qc_ppsd_period_smoothing_width_octaves	0.125	Determines over what period/frequency range the psd is smoothed around every central period/frequency. Given in fractions of octaves (default of 1 means the psd is averaged over a full octave at each central frequency).
qc_ppsd_period_step_octaves	0.0125	Step length on frequency axis in fraction of octaves (default of 0.125 means one smoothed psd value on the frequency axis is measured every 1/8 of an octave).
qc_ppsd_period_limits	(0.01,100)	Set custom lower and upper end of period range (e.g. (0.01, 100) seconds). The specified lower end of period range will be set as the central period of the first bin (geometric mean of left/right edges of smoothing interval). At the upper end of the specified period range, no more additional bins will be added after the bin whose center frequency exceeds the given upper end for the first time.
qc_ppsd_db_bins	(-200, -50, 1.)	Specify the lower and upper boundary and the width of the db bins. The bin width might get adjusted to fit a number of equally spaced bins in between the given boundaries.
qc_rms_frequency_ranges	[(1.0, 20.0), (4.0, 14.0), (4.0, 40.0), (4.0, 9.0)]	Specify the frequency bounds (in Hz) to compute the RMS from PSDs
qc_rms_type	DISP	What units do you want for the exported RMS

Database

Data Availability

Gives a view of the data_availability table. Allows to bulk edit/select rows. Its main goal is to check that the scan_archive procedure has successfully managed to list all files from one’s archive.

Jobs

Gives a view of the jobs table. Allows to bulk edit/select rows. Its main goal is to check the new_jobs or any other workflow step (or Plugins) successfully inserted/updated jobs.

Help

About

Shows some links and information about the package. Mostly the information present on the github readme file.

Bug Report

Web view of the msnoise bugreport -m, allows viewing if all required python modules are properly installed and available for MSNoise.