### Install and Use an MSNoise Plugin

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.4.md

To use a plugin, install it as a Python package and declare its name in the project's configuration. This example shows how to invoke a command from an installed plugin.

```sh
$ msnoise plugin amazing

  Usage: msnoise-script.py plugin amazing [OPTIONS] COMMAND [ARGS]...

  Example Amazing Plugin for MSNoise

Options:
  --help  Show this message and exit.

Commands:
  sayhi  A Very Polite Command
```

```sh
$ msnoise plugin amazing sayhi

Hi
```

--------------------------------

### Implement Plugin Installation Logic

Source: https://github.com/robelgium/msnoise/blob/master/doc/plugins.md

Creates the database table and populates it with default values.

```python
from msnoise.api import *

from .amazing_table_def import AmazingConfig
from .default import default

def main():
    engine = get_engine()
    Session = sessionmaker(bind=engine)
    session = Session()

    AmazingConfig.__table__.create(bind=engine, checkfirst=True)
    for name in default.keys():
        session.add(AmazingConfig(name=name,value=default[name][-1]))

    session.commit()
```

--------------------------------

### Define Setup Entry Points

Source: https://github.com/robelgium/msnoise/blob/master/doc/plugins.md

Registers the plugin table definition in setup.py.

```python
'msnoise.plugins.table_def': [
        'AmazingConfig = msnoise_amazing.amazing_table_def:AmazingConfig',
    ],
```

--------------------------------

### List MSNoise plugins via CLI

Source: https://github.com/robelgium/msnoise/blob/master/doc/plugins.md

Verify installed and configured plugins using the command line interface.

```sh
$ msnoise plugin

  Usage: msnoise-script.py plugin [OPTIONS] COMMAND [ARGS]...

  Runs a command in a named plugin

Options:
  --help  Show this message and exit.

Commands:
  amazing  Example Amazing Plugin for MSNoise
```

--------------------------------

### MSNoise Reset Command Example

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.3.md

Example of how to use the `msnoise reset` command to change job status.

```APIDOC
## `msnoise reset` Command

The `msnoise reset` command is used to reset the status of jobs.

### Usage:
`msnoise reset [OPTIONS] JOBTYPE`

### Description:
Resets the job to "T"odo status. The `JOBTYPE` argument can be `CC` or `DTT`. By default, it only resets jobs that are currently "I"n progress.

### Options:

- **-a, --all**: Resets all jobs, regardless of their current status.
- **--help**: Shows this message and exit.
```

--------------------------------

### msnoise admin

Source: https://github.com/robelgium/msnoise/blob/master/doc/clickhelp/msnoise.md

Starts the Web Admin interface.

```APIDOC
## msnoise admin

### Description
Starts the Web Admin on http://localhost:5000 by default.

### Parameters
#### Options
- **-p, --port** (INTEGER) - Optional - Port to open
```

--------------------------------

### Test MariaDB Server

Source: https://github.com/robelgium/msnoise/blob/master/doc/installation.md

Verify the MariaDB server installation by running the executable in the console.

```sh
bin/mysqld --console
```

--------------------------------

### Verify MSNoise Installation

Source: https://github.com/robelgium/msnoise/blob/master/doc/installation.md

Use these commands to check for missing dependencies and run the built-in test suite to ensure the environment is configured correctly.

```sh
msnoise utils bugreport
msnoise utils test
```

--------------------------------

### Install Documentation Dependencies

Source: https://github.com/robelgium/msnoise/blob/master/doc/installation.md

Required packages for building the documentation using Conda and pip.

```sh
conda install -c conda-forge "sphinx<6" sphinx_bootstrap_theme numpydoc sphinx-gallery
pip install "sphinx_rtd_theme>1"
pip install pillow==9.0.0
```

--------------------------------

### Register CLI Command for Plugin

Source: https://github.com/robelgium/msnoise/blob/master/doc/plugins.md

Adds the install command to the plugin definition.

```python
@click.command()
def install():
    """ Create the Config table"""
    from .install import main
    main()

amazing.add_command(install)
```

--------------------------------

### Output File Path Structure

Source: https://github.com/robelgium/msnoise/blob/master/ARCHITECTURE.md

This example shows the standard output file path structure used in the msnoise project. It highlights the components like lineage names, step names, and output directories. Pay attention to the `lineage_names_upstream` and `step_name` for correct path construction.

```shell
OUTPUT/preprocess_1/cc_1/filter_1/_output/daily/ZZ/YA.UV05.00_YA.UV06.00/2010-09-01.nc
       ─────────────────────────── ────────────
       lineage_names_upstream       step_name (= filter_1 for cc)
```

```shell
OUTPUT/...stack_1/refstack_1/_output/REF/ZZ/YA.UV05.00_YA.UV06.00.nc
```

```shell
OUTPUT/...refstack_1/mwcs_1/_output/1D_1D/ZZ/YA.UV05.00_YA.UV06.00.nc
```

```shell
# DVV aggregates:
OUTPUT / upstream_lineage / dvv_step_name / _output / 1D_1D / dvv_CC_ZZ.nc
```

--------------------------------

### Install MSNoise and Dependencies via Conda

Source: https://github.com/robelgium/msnoise/blob/master/doc/installation.md

Use these commands to install the necessary Python packages and the MSNoise framework from the conda-forge channel.

```sh
conda install -c conda-forge flask-admin flask-wtf markdown folium pymysql logbook pandas pytables pip xarray
conda install -c conda-forge obspy
conda install -c conda-forge msnoise
```

--------------------------------

### Example msnoise bugreport output

Source: https://github.com/robelgium/msnoise/blob/master/doc/how_tos.md

This is an example output from the msnoise bugreport script, showing system details and the status of required Python modules. An '[X]' indicates presence, while '[ ]' indicates absence.

```sh
************* Computer Report *************

----------------+SYSTEM+-------------------
Windows
PC1577-as
10
10.0.17134
AMD64
Intel64 Family 6 Model 158 Stepping 9, GenuineIntel

----------------+PYTHON+-------------------
Python:3.7.3 | packaged by conda-forge | (default, Jul  1 2019, 22:01:29) [MSC v.1900 64 bit (AMD64)]

This script is at d:\pythonforsource\msnoise_stack\msnoise\msnoise\bugreport.py

---------------+MODULES+-------------------

Required:
[X] setuptools: 41.2.0
[X] numpy: 1.15.4
[X] scipy: 1.3.0
[X] pandas: 0.25.0
[X] matplotlib: 3.1.1
[X] sqlalchemy: 1.3.8
[X] obspy: 1.1.0
[X] click: 7.0
[X] pymysql: 0.9.3
[X] flask: 1.1.1
[X] flask_admin: 1.5.3
[X] markdown: 3.1.1
[X] wtforms: 2.2.1
[X] folium: 0.10.0
[X] jinja2: 2.10.1

Only necessary if you plan to build the doc locally:
[X] sphinx: 2.2.0
[X] sphinx_bootstrap_theme: 0.7.1

Graphical Backends: (at least one is required)
[ ] wx: not found
[ ] pyqt: not found
[ ] PyQt4: not found
[X] PyQt5: present (no version)
[ ] PySide: not found

Not required, just checking:
[X] json: 2.0.9
[X] psutil: 5.6.3
[ ] reportlab: not found
[ ] configobj: not found
[X] pkg_resources: present (no version)
[ ] paramiko: not found
[X] ctypes: 1.1.0
[X] pyparsing: 2.4.2
[X] distutils: 3.7.3
[X] IPython: 7.7.0
[ ] vtk: not found
[ ] enable: not found
[ ] traitsui: not found
[ ] traits: not found
[ ] scikits.samplerate: not found
```

--------------------------------

### Install Development Version of MSNoise

Source: https://github.com/robelgium/msnoise/blob/master/doc/installation.md

Commands to remove the current version and install the latest master branch of MSNoise.

```sh
pip uninstall msnoise
pip install http://msnoise.org/master.zip
```

--------------------------------

### Connect to MSNoise API and Get Configuration

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.3.md

Demonstrates how to connect to the MSNoise API and retrieve the configuration for a specific parameter like 'mov_stack'. This is useful for custom scripts or console interactions.

```python
from msnoise.api import connect, get_config
session = connect()
print get_config(session, "mov_stack")
```

--------------------------------

### Install Development Version of ObsPy

Source: https://github.com/robelgium/msnoise/blob/master/doc/installation.md

Commands to remove the current version and install the latest master branch of ObsPy.

```sh
pip uninstall obspy
pip install https://github.com/obspy/obspy/archive/master.zip
```

--------------------------------

### Run MSNoise Compute CC with Threading

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.4.md

Example of using the -t flag with msnoise compute_cc to enable multi-threading. Adjust thread count based on available cores and system RAM.

```bash
msnoise -t 4 compute_cc
```

--------------------------------

### Run MSNoise Compute MWCS with Threading

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.4.md

Example of using the -t flag with msnoise compute_mwcs to enable multi-threading. Ensure sufficient RAM is available if loading large datasets.

```bash
msnoise -t 16 compute_mwcs
```

--------------------------------

### MSNoise Compute Command Execution Output

Source: https://github.com/robelgium/msnoise/blob/master/doc/plugins.md

Example output from running the MSNoise plugin compute command. It shows the processing of specific station pairs for a given day and the details of the retrieved seismic data streams.

```shell
$ msnoise plugin amazing compute

Processing YA.UV05 for day 2010-09-01
1 Trace(s) in Stream:
YA.UV05.00.HHZ | 2010-09-01T00:00:00.000000Z - 2010-09-01T23:59:59.990000Z | 100.0 Hz, 8640000 samples
Processing YA.UV06 for day 2010-09-01
1 Trace(s) in Stream:
YA.UV06.00.HHZ | 2010-09-01T00:00:00.000000Z - 2010-09-01T23:59:59.990000Z | 100.0 Hz, 8640000 samples
Processing YA.UV10 for day 2010-09-01
1 Trace(s) in Stream:
YA.UV10.00.HHZ | 2010-09-01T00:00:00.000000Z - 2010-09-01T23:59:59.990000Z | 100.0 Hz, 8640000 samples
```

--------------------------------

### Configure plugin entry points in setup.py

Source: https://github.com/robelgium/msnoise/blob/master/doc/plugins.md

Use setuptools entry points to register plugin commands with the MSNoise CLI.

```python
from setuptools import setup, find_packages

setup(
    name='msnoise_amazing',
    version='0.1a',
    packages=find_packages(),
    include_package_data=True,
    install_requires=['msnoise',
                      'obspy'],
    entry_points = {
        'msnoise.plugins.commands': [
            'amazing = msnoise_amazing.plugin_definition:amazing',
            ],
        },
    author = "Thomas Lecocq & MSNoise dev team",
    author_email = "Thomas.Lecocq@seismology.be",
    description = "An example plugin",
    license = "EUPL-1.1",
    url = "http://www.msnoise.org",
    keywords="amazing seismology"
)
```

--------------------------------

### Display MSNoise help

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.3.md

Lists all available top-level commands and global options.

```sh
msnoise --help

Usage: msnoise-script.py [OPTIONS] COMMAND [ARGS]...

Options:
  -t, --threads INTEGER  Number of threads to use (only affects modules that
                         are designed to do parallel processing)
  --help                 Show this message and exit.

Commands:
  bugreport           This command launches the Bug Report script.
  compute_cc          Computes the CC jobs (based on the "New Jobs"...
  compute_dtt         Computes the dt/t jobs based on the new MWCS...
  compute_mwcs        Computes the MWCS based on the new stacked...
  compute_stretching  [experimental] Computes the stretching based...
  config              This command launches the Configurator.
  info                Outputs general information about the current...
  install             This command launches the installer.
  ipython             Launches an ipython notebook in the current...
  new_jobs            Determines if new CC jobs are to be defined
  plot                Top level command to trigger different plots
  populate            Rapidly scan the archive filenames and find...
  reset               Resets the job to "T"odo.
  scan_archive        Scan the archive and insert into the Data...
  stack               Stacks the [REF] and/or [MOV] windows
  test                Runs the test suite, should be executed in an...
  upgrade_db          Upgrade the database from pre-1.3 to MSNoise...
```

--------------------------------

### Build Documentation

Source: https://github.com/robelgium/msnoise/blob/master/doc/installation.md

Command to generate the HTML documentation.

```sh
make html
```

--------------------------------

### Register Plugin Job Types in setup.py

Source: https://github.com/robelgium/msnoise/blob/master/doc/plugins.md

This entry point in `setup.py` registers custom job types from a plugin. Ensure the path `msnoise_amazing.plugin_definition:register_job_types` correctly points to your registration function.

```python
'msnoise.plugins.jobtypes': [
'register = msnoise_amazing.plugin_definition:register_job_types',
],
```

--------------------------------

### Initialize MSNoise Project

Source: https://context7.com/robelgium/msnoise/llms.txt

Initializes a new MSNoise project, creating a database and configuration file. Use --auto-workflow to create default configurations and workflow steps. Requires a running server for MySQL/MariaDB and PostgreSQL.

```bash
# Create a new project directory and initialize
mkdir my_project && cd my_project

# Initialize with SQLite (simplest, no server needed)
msnoise db init --tech 1 --auto-workflow

# Initialize with MySQL/MariaDB (requires running server)
msnoise db init --tech 2 --auto-workflow
# Follow prompts for: hostname, database name, username, password

# Initialize with PostgreSQL
msnoise db init --tech 3 --auto-workflow

# After initialization, configure the project
msnoise config set data_folder=/path/to/seismic/archive
msnoise config set output_folder=./OUTPUT
msnoise config set startdate=2010-01-01
msnoise config set enddate=2010-12-31
```

--------------------------------

### msnoise db init

Source: https://github.com/robelgium/msnoise/blob/master/doc/clickhelp/msnoise.md

Initializes the current folder as an MSNoise project.

```APIDOC
## msnoise db init

### Description
Initializes the current folder to be a MSNoise Project by creating a database and a db.ini file.

### Parameters
#### Options
- **--tech** (TEXT) - Optional - Database technology: 1=SQLite 2=MySQL/MariaDB 3=PostgreSQL
- **--auto-workflow** (BOOLEAN) - Optional - Automatically create all default config sets, workflow steps and links without prompting.
```

--------------------------------

### Run the Simplest MSNoise Configuration

Source: https://github.com/robelgium/msnoise/blob/master/doc/how_tos.md

This recipe provides the most basic MSNoise run for rapidly checking data. It includes essential configuration steps and commands for cross-correlation and related analyses.

```sh
msnoise db init --tech 1

msnoise config set startdate=2019-01-01
msnoise config set enddate=2019-02-01
msnoise config set overlap=0.5
msnoise config set mov_stack=1,5,10

msnoise scan_archive --path /path/to/archive --recursively
msnoise populate --fromDA
msnoise db update_loc_chan
msnoise new_jobs --init

msnoise admin # add 1 filter in the Filter table
# or
msnoise db execute "insert into filters (ref, low, mwcs_low, high, mwcs_high, mwcs_wlen, mwcs_step, used) values (1, 0.1, 0.1, 1.0, 1.0, 12.0, 4.0, 1)"

msnoise cc compute_cc
msnoise cc stack -r
msnoise reset STACK
msnoise cc stack -m
msnoise cc dtt compute_mwcs
msnoise cc dtt compute_dtt
msnoise cc dtt compute_dvv
msnoise cc dtt plot dvv
```

--------------------------------

### Register Web Admin View

Source: https://github.com/robelgium/msnoise/blob/master/doc/plugins.md

Registers a new admin page via entry points in setup.py.

```python
'msnoise.plugins.admin_view': [
        'AmazingConfigView = msnoise_amazing.plugin_definition:AmazingConfigView',
        ],
```

--------------------------------

### Node Drag Start Function

Source: https://github.com/robelgium/msnoise/blob/master/msnoise/templates/admin/workflow_builder.html

Initiates the drag behavior for a node by raising it to the top of the SVG paint order.

```javascript
function dragstarted(event, d) {
    d3.select(this).raise(); // bring to front while dragging
}
```

--------------------------------

### Initialize MSNoise Database Session

Source: https://github.com/robelgium/msnoise/blob/master/examples/README.rst

Establishes a connection to the MSNoise database. This must be executed within a directory initialized with 'msnoise db init'.

```python
from msnoise.api import db
db = connect()
```

--------------------------------

### Dump and Import MSNoise Configuration

Source: https://github.com/robelgium/msnoise/blob/master/doc/how_tos.md

Export database tables to CSV and import them into a new project location.

```sh
msnoise db dump
```

```sh
msnoise db init
msnoise db import config --force
msnoise db import stations --force
msnoise db import filters --force
msnoise db import data_availability --force
msnoise db import jobs --force
```

--------------------------------

### Declare SQLAlchemy Tables

Source: https://github.com/robelgium/msnoise/blob/master/ARCHITECTURE.md

Always call declare_tables() to get a fresh Job class for DB queries. Do not use module-level imports.

```python
schema = declare_tables()
Job = schema.Job
```

--------------------------------

### PBS Job Script for Parallel CC

Source: https://github.com/robelgium/msnoise/blob/master/doc/how_tos.md

Example job script for running MSNoise cross-correlation tasks in parallel across an array of nodes.

```bash
#!/bin/bash
#PBS -N MSNoise_PDF_CC
#PBS -l walltime=01:00:00
#PBS -l select=1:ncpus=1:mem=1g
#PBS -l place=shared
#PBS -J 1-400
cd /scratch-a/thomas/2019_PDF
source /space/hpc-home/thomas/.profile
msnoise cc compute_cc
```

--------------------------------

### Implement plugin logic in plugin_definition.py

Source: https://github.com/robelgium/msnoise/blob/master/doc/plugins.md

Define CLI commands using the click library to extend MSNoise functionality.

```python
import click

@click.group()
def amazing():
    """Example Amazing Plugin for MSNoise"""
    pass

@click.command()
def sayhi():
    """A Very Polite Command"""
    print("Hi")

amazing.add_command(sayhi)
```

--------------------------------

### Handling No Configuration Sets Found

Source: https://github.com/robelgium/msnoise/blob/master/msnoise/templates/admin/config_sets_index.html

Displays a message and a link to create the first configuration set when no sets are found for a given category. This is a fallback UI element.

```html
{{ category_info.display_name }}

_No configuration sets found_ [Create first set]({{ url_for('.create_set', category=category_info.category) }})
```

--------------------------------

### Custom Plotting with MSNoise

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.4.md

Override default plot commands by using the -c argument before the plot command. Copy and edit plot scripts from the install directory to your project directory.

```bash
msnoise -c plot distance
```

--------------------------------

### Compute Wavelet Coherence Transform (WCT) in Python

Source: https://context7.com/robelgium/msnoise/llms.txt

Example of computing the Wavelet Coherence Transform (WCT) using Python, including parameters for smoothing, frequency, and wavelet type.

```python
from msnoise.core.signal import xwt, compute_wct_dtt

import numpy as np

# Example wavelet coherence computation
fs = 20.0  # Sampling rate
t = np.arange(0, 100, 1/fs)
ref_trace = np.sin(2 * np.pi * 0.5 * t)  # Reference
cur_trace = np.sin(2 * np.pi * 0.5 * (t * 1.001))  # Slightly stretched

# Compute wavelet coherence
WXamp, WXspec, WXangle, Wcoh, WXdt, freqs, coi = xwt(
    ref_trace, cur_trace, fs,
    ns=3,           # Smoothing parameter (scale)
    nt=0.25,        # Smoothing parameter (time)
    vpo=12,         # Voices per octave
    freqmin=0.1,    # Minimum frequency
    freqmax=8.0,    # Maximum frequency
    nptsfreq=100,   # Number of frequency points
    wavelet_type=("Morlet", 6.0)
)

print(f"Frequency range: {freqs.min():.2f} - {freqs.max():.2f} Hz")
print(f"WCT shape: {Wcoh.shape}")
```

--------------------------------

### Manage Workflow and Configuration

Source: https://context7.com/robelgium/msnoise/llms.txt

CLI commands for managing configuration sets, workflow steps, and job statuses.

```bash
# List all configuration sets
msnoise config list-sets

# Show details of a specific config set
msnoise config show-set mwcs 1

# Create a new configuration set
msnoise config create-set mwcs

# Copy an existing config set
msnoise config copy-set mwcs 1 mwcs 2

# List workflow steps
msnoise config list-workflow-steps

# Show workflow graph
msnoise config show-workflow-graph

# Create workflow links between steps
msnoise config create-workflow-links --verbose

# Reset jobs to Todo status
msnoise reset cc --all

# Get project info and job status
msnoise info
msnoise info --jobs
```

--------------------------------

### MSNoise Configuration Management

Source: https://context7.com/robelgium/msnoise/llms.txt

Retrieves and updates configuration values programmatically. Supports getting single values, all global configurations, and merged parameters for the workflow. Configuration is stored in the database.

```python
from msnoise.api import connect
from msnoise.core.config import get_config, update_config, get_params

db = connect()

# Get a single configuration value
maxlag = float(get_config(db, "maxlag"))
print(f"Maximum lag time: {maxlag} seconds")

# Get a boolean value
autocorr = get_config(db, "autocorr", isbool=True)
print(f"Autocorrelation enabled: {autocorr}")

# Get all global configuration as dictionary
all_config = get_config(db)
print(f"Data folder: {all_config['data_folder']}")

# Update a configuration value
update_config(db, "maxlag", "120")

# Get merged parameters for the full workflow (LayeredParams object)
params = get_params(db)
print(f"HPC mode: {params.global_.hpc}")
print(f"Sampling rate: {params.global_.cc_sampling_rate}")

db.close()
```

--------------------------------

### Custom Time Series Plotting with MSNoise

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.4.md

Example of customizing a specific plot (ccftime) with additional arguments using the -c flag. Modify the plot script to change visualization behavior.

```bash
msnoise -c plot ccftime YA.UV02 YA.UV06 -m 5
```

--------------------------------

### Compute MWCS (Moving Window Cross-Spectrum)

Source: https://context7.com/robelgium/msnoise/llms.txt

Commands for computing Moving Window Cross-Spectrum (MWCS) measurements, calculating dt/t, aggregating dv/v, and plotting results. Use 'compute_mwcs' to start.

```bash
# Compute MWCS measurements
msnoise cc dtt compute_mwcs
```

```bash
# Compute dt/t from MWCS measurements
msnoise cc dtt compute_mwcs_dtt
```

```bash
# Aggregate dv/v across all station pairs
msnoise cc dtt dvv compute_mwcs_dtt_dvv
```

```bash
# Plot MWCS results for a station pair
msnoise cc dtt plot mwcs YA.UV05.00 YA.UV06.00 --show True
```

```bash
# Plot dt/t timeseries
msnoise cc dtt plot mwcs_dtt_timing --filterid 1 --show True
```

--------------------------------

### Configure MariaDB Database

Source: https://github.com/robelgium/msnoise/blob/master/doc/installation.md

Commands for setting up the database password, testing the connection, and creating the MSNoise database schema.

```sh
mysqladmin -u root  flush-privileges password "SECRET"
mysql -u root -p
CREATE DATABASE msnoise;
SHOW DATABASES;
quit;
```

--------------------------------

### msnoise utils jupyter

Source: https://github.com/robelgium/msnoise/blob/master/doc/clickhelp/msnoise.md

Launches a Jupyter notebook environment in the current directory.

```APIDOC
## msnoise utils jupyter

### Description
Launches an jupyter notebook in the current folder.

### Method
CLI Command

### Endpoint
N/A (CLI command)

### Parameters
No specific parameters other than the command itself.

### Request Example
```sh
msnoise utils jupyter
```

### Response
N/A (CLI command launches Jupyter Notebook server)

### Error Handling
N/A (CLI command specific errors not detailed)
```

--------------------------------

### Customize MSNoise Plotting Scripts

Source: https://github.com/robelgium/msnoise/blob/master/doc/plotting.md

Override default plot commands using the `-c` argument before the plot command. To modify scripts, copy them from the install directory to your project and adjust the MSNoise API import.

```python
from ..api import *
to
from msnoise.api import *
```

--------------------------------

### msnoise config list-workflow-steps

Source: https://github.com/robelgium/msnoise/blob/master/doc/clickhelp/msnoise.md

Lists all workflow steps.

```APIDOC
## msnoise config list-workflow-steps

### Description
List all workflow steps.

### Method
Not applicable (CLI command)

### Endpoint
Not applicable (CLI command)

### Parameters
#### Options
- **--help** (boolean) - Optional - Show this message and exit.
```

--------------------------------

### Manage MSNoise Web Admin

Source: https://context7.com/robelgium/msnoise/llms.txt

Commands to launch the MSNoise web-based administration interface.

```bash
# Start the web admin on default port 5000
msnoise admin

# Use a custom port
msnoise admin --port 8080

# Then open http://localhost:5000 in your browser
```

--------------------------------

### Display command-specific help

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.3.md

Provides detailed usage information and options for a specific command.

```sh
msnoise reset --help

Usage: msnoise-script.py reset [OPTIONS] JOBTYPE

  Resets the job to "T"odo. ARG is [CC] or [DTT]. By default only resets
  jobs "I"n progress. --all resets all jobs, whatever the flag value

Options:
  -a, --all  Reset all jobs
  --help     Show this message and exit.
```

--------------------------------

### Load and Analyze MSNoise Results

Source: https://context7.com/robelgium/msnoise/llms.txt

Demonstrates loading results using MSNoiseResult from database IDs, retrieving CCF interferograms and reference stacks, and discovering downstream results.

```python
from msnoise.api import connect
from msnoise.results import MSNoiseResult

db = connect()

# Build result object from step IDs
result = MSNoiseResult.from_ids(
    db,
    preprocess=1, cc=1, filter=1, stack=1, refstack=1
)
print(result)  # Shows available methods

# Get CCF interferogram as xarray DataArray
ccf = result.get_ccf(
    pair="YA.UV05.00:YA.UV06.00",
    components="ZZ",
    mov_stack=("1D", "1D"),  # (window, step)
    format="xarray"
)

# Plot interferogram
import matplotlib.pyplot as plt
ccf.plot(robust=True, figsize=(10, 8))
plt.title("Cross-Correlation Function vs Time")
plt.savefig("interferogram.png")

# Get reference stack
ref = result.get_ref(pair="YA.UV05.00:YA.UV06.00", components="ZZ")
ref.REF.plot()
plt.savefig("reference.png")

# Discover downstream results (e.g., MWCS, stretching branches)
for branch in result.branches():
    print(f"Available: {branch.category} - {branch.lineage_names[-1]}")

db.close()
```

--------------------------------

### Create Processing Jobs

Source: https://context7.com/robelgium/msnoise/llms.txt

Analyzes data availability to create jobs for the workflow. Use --init for initial preprocessing and CC jobs, or --after to create jobs for subsequent steps.

```bash
# Create initial preprocessing and CC jobs
msnoise new_jobs --init
```

```bash
# Create jobs for subsequent workflow steps (after CC is done)
msnoise new_jobs --after cc
```

```bash
# Create stack jobs from completed CC jobs
msnoise new_jobs --after stack
```

```bash
# Check job status
msnoise info --jobs
```

--------------------------------

### Run MSNoise Test Suite

Source: https://github.com/robelgium/msnoise/blob/master/doc/clickhelp/msnoise.md

Executes the test suite in a temporary folder. Use the --fast option for a quick smoke test that uses stub compute functions and completes in under 30 seconds without requiring seismic data.

```sh
msnoise utils test --help
```

```sh
msnoise utils test --fast
```

```sh
msnoise utils test -p myprefix --tech 1
```

```sh
msnoise utils test -c
```

--------------------------------

### msnoise config create-all-sets

Source: https://github.com/robelgium/msnoise/blob/master/doc/clickhelp/msnoise.md

Creates a complete set of workflow configurations for each category.

```APIDOC
## msnoise config create-all-sets

### Description
Create one configuration set for each workflow category.

### Method
Not applicable (CLI command)

### Endpoint
Not applicable (CLI command)

### Parameters
#### Options
- **--force** (boolean) - Optional - Force creation even if config sets already exist
- **--dry-run** (boolean) - Optional - Show what would be created without actually creating it
```

--------------------------------

### Develop MSNoise Plugins

Source: https://context7.com/robelgium/msnoise/llms.txt

Structure for creating custom MSNoise plugins and discovering them via CLI.

```python
# Plugin structure example (in my_plugin/__init__.py)
"""
my_plugin
=========
Custom MSNoise plugin for specialized analysis.
"""

from flask_admin.contrib.sqla import ModelView

# Define plugin info
name = "My Plugin"
short_name = "myplugin"

# Define custom configuration parameters
def get_config():
    return {
        "my_param": {
            "default": "10",
            "definition": "My custom parameter",
        }
    }

# Define custom job types
def get_jobs():
    return {
        "MYPROCESS": {
            "description": "My custom processing step",
            "after": "CC",  # Run after CC step
        }
    }

# Register with MSNoise
def register(app):
    """Called when MSNoise loads the plugin."""
    pass
```

```bash
# Plugins are automatically discovered when installed via pip
# List available plugins
msnoise info
```

--------------------------------

### Document Ready Event Handlers

Source: https://github.com/robelgium/msnoise/blob/master/msnoise/templates/admin/psd-spectrogram.html

Initializes the web interface by fetching network data and setting up event listeners for dropdown changes and refresh button clicks. These handlers trigger data population and image updates.

```javascript
$(document).ready(function() {
  get_network_station(populate_network);
  $('#network').change(function() {
    $('#station')
      .find('option')
      .remove()
      .end();
    get_network_station(populate_stations);
  });
  $('#station').change(function() {
    $('#location')
      .find('option')
      .remove()
      .end();
    $('#channel')
      .find('option')
      .remove()
      .end();
    $('#file')
      .find('option')
      .remove()
      .end();
    $('#date')
      .find('option')
      .remove()
      .end();
    get_network_station(populate_locations);
  });
  $('#location').change(function() {
    update_images();
  });
  $('#channel').change(function() {
    update_images();
  });
  $('#refresh').click(function() {
    update_images();
  });
});
```

--------------------------------

### msnoise config create-workflow-steps-from-configs

Source: https://github.com/robelgium/msnoise/blob/master/doc/clickhelp/msnoise.md

Creates workflow steps automatically from all existing config sets.

```APIDOC
## msnoise config create-workflow-steps-from-configs

### Description
Create workflow steps automatically from all existing config sets.
This command scans all configuration sets in the database and creates corresponding workflow steps, sorted by natural workflow order.

### Method
Not applicable (CLI command)

### Endpoint
Not applicable (CLI command)

### Parameters
#### Options
- **-v, --verbose** (boolean) - Optional - Show detailed output
- **--help** (boolean) - Optional - Show this message and exit.
```

--------------------------------

### Initialize Graph and Update Stats on DOM Load

Source: https://github.com/robelgium/msnoise/blob/master/msnoise/templates/admin/workflow_builder.html

Sets up the workflow graph and initial statistics when the DOM is ready. Also configures event listeners for dynamic form element updates.

```javascript
document.addEventListener('DOMContentLoaded', function() { console.log('DOM loaded, initializing graph...'); initializeGraph(); updateStats(); // Update form dropdowns based on workflow logic const fromStepSelect = document.getElementById('from_step_select'); const toStepSelect = document.getElementById('to_step_select'); if (fromStepSelect && toStepSelect && workflowData.nodes) { fromStepSelect.addEventListener('change', function() { const fromStepId = parseInt(this.value); const fromNode = workflowData.nodes.find(n => n.id === fromStepId); // Clear options toStepSelect.innerHTML = '<option value="">Select target step...</option>'; if (fromNode) { const WORKFLOW_CHAINS = { 'global': ['preprocess', 'psd'], 'preprocess': ['cc'], 'cc': ['filter'], 'psd': ['psd_rms'], 'psd_rms': [], 'filter': ['stack'], 'stack': ['refstack'], 'refstack': ['mwcs', 'stretching', 'wavelet'], 'mwcs': ['mwcs_dtt'], 'mwcs_dtt': ['mwcs_dtt_dvv'], 'mwcs_dtt_dvv': [], 'stretching': ['stretching_dvv'], 'stretching_dvv': [], 'wavelet': ['wavelet_dtt'], 'wavelet_dtt': ['wavelet_dtt_dvv'], 'wavelet_dtt_dvv': [] }; const validNextCategories = WORKFLOW_CHAINS[fromNode.category] || []; workflowData.nodes.forEach(node => { if (node.id !== fromStepId && (validNextCategories.includes(node.category) || validNextCategories.length === 0)) { const existingLink = workflowData.edges.find(e => e.from === fromStepId && e.to === node.id ); const linkStatus = existingLink ? ' (already linked)' : ''; const option = document.createElement('option'); option.value = node.id; option.textContent = `${node.name} (${node.category}:${node.set_number})${linkStatus}`; if (existingLink) { option.style.color = '#6c757d'; option.style.fontStyle = 'italic'; } toStepSelect.appendChild(option); } }); } }); } }); }
```

--------------------------------

### Generate Power Spectral Densities and Spectrograms with MSNoise

Source: https://github.com/robelgium/msnoise/blob/master/doc/how_tos.md

Use this recipe to rapidly check noise content and generate Power Spectral Densities (PSDs) and spectrograms. Ensure response files are correctly configured.

```sh
msnoise db init --tech 1

msnoise config set startdate=2019-01-01
msnoise config set enddate=2019-02-01
msnoise config set response_path=/path/to/response_files

msnoise scan_archive --path /path/to/archive --recursively
msnoise populate --fromDA
msnoise db update_loc_chan
msnoise new_jobs --init --nocc

msnoise admin # check the qc_* parameters

msnoise qc compute_psd
msnoise qc plot_psd YA.UV05.00.HHZ
```

--------------------------------

### Define Default Plugin Parameters

Source: https://github.com/robelgium/msnoise/blob/master/doc/plugins.md

Stores default configuration values in an OrderedDict.

```python
from collections import OrderedDict
default = OrderedDict()

default['parameter1'] = ["Some really useful text",'1']
default['parameter2'] = ["Some really useful text",'1']
default['parameter3'] = ["Some really useful text",'1']
default['parameter4'] = ["Some really useful text",'1']

default['question1'] = ["Is this a useful text [Y]/N",'Y']
```

--------------------------------

### msnoise populate

Source: https://github.com/robelgium/msnoise/blob/master/doc/clickhelp/msnoise.md

Scans archive filenames to find Network/Stations.

```APIDOC
## msnoise populate

### Description
Rapidly scan the archive filenames and find Network/Stations, only works with known archive structures, or with a custom code provided by the user.

### Method
Not applicable (CLI command)

### Endpoint
Not applicable (CLI command)

### Parameters
#### Options
- **--fromDA** (boolean) - Optional - Populates the station table using network and station codes found in the data_availability table, overrides the default workflow step.
- **--help** (boolean) - Optional - Show this message and exit.
```

--------------------------------

### Connect to MSNoise Database

Source: https://context7.com/robelgium/msnoise/llms.txt

Establishes a database connection using SQLAlchemy. Reads connection parameters from 'db.ini'. Supports SQLite, MySQL/MariaDB, and PostgreSQL. Always close the session when done.

```python
from msnoise.api import connect

# Connect to database (reads db.ini from current directory)
db = connect()

# Alternatively, specify a custom db.ini path
db = connect(inifile="/path/to/project/db.ini")

# Use the session for queries
from msnoise.msnoise_table_def import Station
stations = db.query(Station).filter(Station.used == True).all()
for sta in stations:
    print(f"{sta.net}.{sta.sta}: {sta.X}, {sta.Y}")

# Always close when done
db.close()
```

--------------------------------

### Run MSNoise Plugin Command

Source: https://context7.com/robelgium/msnoise/llms.txt

This command is used to execute a plugin within the MSNoise framework. Ensure the plugin namespace is correctly specified.

```bash
msnoise myplugin process
```

--------------------------------

### msnoise config create-workflow-step

Source: https://github.com/robelgium/msnoise/blob/master/doc/clickhelp/msnoise.md

Creates a new workflow step interactively.

```APIDOC
## msnoise config create-workflow-step

### Description
Create a new workflow step interactively.

### Method
Not applicable (CLI command)

### Endpoint
Not applicable (CLI command)

### Parameters
#### Options
- **--help** (boolean) - Optional - Show this message and exit.
```

--------------------------------

### Display plot command help

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.3.md

Lists all available plotting sub-commands.

```sh
msnoise plot --help

Usage: msnoise-script.py plot [OPTIONS] COMMAND [ARGS]...

  Top level command to trigger different plots

Options:
  --help  Show this message and exit.

Commands:
  ccftime            Plots the dv/v (parses the dt/t results)
  data_availability  Plots the Data Availability vs time
  distance           Plots the REFs of all pairs vs distance
  dvv                Plots the dv/v (parses the dt/t results)
  interferogram      Plots the interferogram between sta1 and sta2...
  mwcs               Plots the mwcs results between sta1 and sta2...
  station_map        Plots the station map (very basic)
```

--------------------------------

### MSNoise Main Commands

Source: https://github.com/robelgium/msnoise/blob/master/doc/releasenotes/msnoise-1.3.md

Overview of the primary commands available in the MSNoise CLI.

```APIDOC
## MSNoise CLI Commands

MSNoise provides a top-level command-line interface for various operations. The general usage is `msnoise [COMMAND] [OPTIONS] [ARGS]`.

### Available Commands:

- **install**: Installs MSNoise.
- **config**: Configures MSNoise settings.
- **populate**: Scans the archive and populates the station table.
- **scan_archive**: Scans the archive for data.
- **new_jobs**: Defines new jobs for processing.
- **compute_cc**: Computes cross-correlations.
- **stack**: Stacks seismic data windows.
- **compute_mwcs**: Computes Moving Window Cross-Spectral analysis.
- **compute_dtt**: Computes time-domain difference analysis.
- **bugreport**: Launches the bug report script.
- **ipython**: Launches an IPython notebook.
- **reset**: Resets job status.
- **info**: Outputs general information.
- **test**: Runs the test suite.
- **upgrade_db**: Upgrades the database.
- **plot**: Triggers various plotting functions.

### Global Options:

- **-t, --threads INTEGER**: Number of threads to use for parallel processing.
- **--help**: Shows this message and exits.
```