From 55650818caf514922eb5d6ddb59edbd275aefe3f Mon Sep 17 00:00:00 2001 From: Dongdong Tian Date: Tue, 25 Jun 2024 23:40:54 +0800 Subject: [PATCH] Add the JOSS paper (#120) --- paper/paper.bib | 94 ++++++++++++++++++++++++++++ paper/paper.md | 161 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 255 insertions(+) create mode 100644 paper/paper.bib create mode 100644 paper/paper.md diff --git a/paper/paper.bib b/paper/paper.bib new file mode 100644 index 00000000..333b2831 --- /dev/null +++ b/paper/paper.bib @@ -0,0 +1,94 @@ +@article{Obara2005, + title={{A densely distributed high-sensitivity seismograph network in Japan: Hi-net by National Research Institute for Earth Science and Disaster Prevention}}, + author={Obara, Kazushige and Kasahara, Keiji and Hori, Sadaki and Okada, Yoshimitsu}, + journal={Review of Scientific Instruments}, + volume={76}, + number={2}, + pages={021301}, + year={2005}, + month=feb, + DOI={10.1063/1.1854197} +} + +@article{Ishii2005, + title={{Extent, duration and speed of the 2004 Sumatra–Andaman earthquake imaged by the Hi-Net array}}, + author={Ishii, Miaki and Shearer, Peter M. and Houston, Heidi and Vidale, John E.}, + journal={Nature}, + volume={435}, + number={7044}, + pages={933–936}, + year={2005}, + month=jun, + DOI={10.1038/nature03675} +} + +@article{Peng2007, + title={{Seismicity rate immediately before and after main shock rupture from high‐frequency waveforms in Japan}}, + author={Peng, Zhigang and Vidale, John E. and Ishii, Miaki and Helmstetter, Agnes}, + journal={Journal of Geophysical Research: Solid Earth}, + volume={112}, + number={B3}, + pages={2006JB004386}, + year={2007}, + month=mar, + DOI={10.1029/2006JB004386}, +} + +@article{Okada2014, + title={{Recent progress of seismic observation networks in Japan —Hi-net, F-net, K-NET and KiK-net—}}, + author={Okada, Yoshimitsu and Kasahara, Keiji and Hori, Sadaki and Obara, Kazushige and Sekiguchi, Shoji and Fujiwara, Hiroyuki and Yamamoto, Akira}, + journal={Earth, Planets and Space}, + volume={56}, + number={8}, + pages={xv–xxviii}, + year={2014}, + month=jun, + DOI={10.1186/BF03353076}, +} + +@article{ObsPy2015, + title={{ObsPy: a bridge for seismology into the scientific Python ecosystem}}, + author={Krischer, Lion and Megies, Tobias and Barsch, Robert and Beyreuther, Moritz and Lecocq, Thomas and Caudron, Corentin and Wassermann, Joachim}, + journal={Computational Science & Discovery}, + volume={8}, + number={1}, + pages={014003}, + year={2015}, + month=may, + DOI={10.1088/1749-4699/8/1/014003}, +} + +@article{Yee2014, + title={{Regionally heterogeneous uppermost inner core observed with Hi‐net array}}, + journal={Journal of Geophysical Research: Solid Earth}, + author={Yee, Tae‐Gyu and Rhie, Junkee and Tkalčić, Hrvoje}, + volume={119}, + number={10}, + pages={7823–7845}, + year={2014}, + month=oct, + DOI={10.1002/2014JB011341}, +} +@article{Niu2005, + title={{Mapping the subducting Pacific slab beneath southwest Japan with Hi-net receiver functions}}, + journal={Earth and Planetary Science Letters}, + author={Niu, Fenglin and Levander, Alan and Ham, Sangwon and Obayashi, Masayuki}, + volume={239}, + number={1–2}, + pages={9–17}, + year={2005}, + month=oct, + DOI={10.1016/j.epsl.2005.08.009}, +} + +@article{Tian2017, + title={{Seismological evidence for a localized mushy zone at the Earth's inner core boundary}}, + journal={Nature Communications}, + author={Tian, Dongdong and Wen, Lianxing}, + volume={8}, + pages={165}, + number={1}, + year={2017}, + month=aug, + DOI={10.1038/s41467-017-00229-9}, +} diff --git a/paper/paper.md b/paper/paper.md new file mode 100644 index 00000000..b19961a3 --- /dev/null +++ b/paper/paper.md @@ -0,0 +1,161 @@ +--- +title: 'HinetPy: A Python package for accessing and processing NIED Hi-net seismic data' +tags: + - Python + - geophysics + - seismology +authors: + - name: Dongdong Tian + orcid: 0000-0001-7967-1197 + affiliation: 1 +affiliations: + - name: Hubei Subsurface Multi-scale Imaging Key Laboratory, School of Geophysics and Geomatics, China University of Geosciences, Wuhan 430074, China + index: 1 +date: 3 April 2024 +bibliography: paper.bib +--- + +# Summary + +HinetPy is a Python package designed for researchers working with seismic data from the +National Research Institute for Earth Science and Disaster Resilience (NIED) Hi-net +(High-sensitivity seismograph network) in Japan. The seismic network comprises approximately +800 stations with high-quality seismic data. Accessing and processing the data can be +challenging due to the limited functionality of the web UI and backend data server. +Additionally, the seismic data is stored in a non-standard format, which adds an extra +layer of complexity. HinetPy solves these challenges by offering a user-friendly interface +for accessing seismic data from NIED Hi-net and converting it to commonly used data +formats. It streamlines the workflow for seismologists, enabling them to more effectively +utilize this valuable dataset. + +# Statement of need + +The National Research Institute for Earth Science and Disaster Resilience (NIED) operates +and maintains NIED Hi-net, a nationwide high-sensitivity seismograph network in Japan. +Since its establishment in October 2000, NIED Hi-net has grown to include approximately +800 seismic stations equipped with three-component short-period seismometers [@Obara2005; @Okada2014]. +The NIED Hi-net website ([https://www.hinet.bosai.go.jp/](https://www.hinet.bosai.go.jp/)) +provides access to high-quality seismic data from 2004 onwards, including data from +other seismic networks such as F-net, S-net, V-net, and more. The NIED Hi-net data has +been widely used in various research from the study of earthquakes [e.g., @Ishii2005; @Peng2007] +to the structure of the Earth's deep interior [e.g., @Niu2005; @Yee2014; @Tian2017]. +Despite the value of the data provided by NIED Hi-net, accessing and processing it can be challenging. + +## Challenges in accessing NIED Hi-net data + +The NIED Hi-net data is available for free through the NIED Hi-net website after users +register for an account. However, accessing them can still be challenging. While most seismic +data centers have transitioned to standard FDSN web services +([https://www.fdsn.org/webservices/](https://www.fdsn.org/webservices/)) in recent years, +allowing users to request seismic data using open-source tools like ObsPy [@ObsPy2015], +NIED Hi-net has not yet upgraded to adopt these services. To request data +from the NIED Hi-net website, users must log in and click many buttons manually. +It is important to note that the NIED Hi-net website has limitations on the data +size and length in a single request. Specifically, the record length of a single channel +cannot exceed 60 minutes, and the total record length of +all channels cannot exceed 12,000 minutes. Considering that NIED Hi-net comprises about 800 seismic +stations and 2,400 channels (3 channels per station), the record length in a single +request must not exceed 5 minutes. If users require 30 minutes of data, they must divide the +time range into six subranges and submit six separate requests. The NIED Hi-net website +does not allow users to post multiple data requests simultaneously. Therefore, to obtain +the requested data, users must post a request, wait for the data to be prepared, and then +post subsequent requests. After all data is ready, users must manually download the files +and combine them into a single file. The entire process can be time-consuming and cumbersome. + +## Challenges in processing NIED Hi-net data + +NIED Hi-net stores seismic data in a non-standard format called WIN32, accompanied by a +'channels table' text file containing metadata for each channel. Most seismic data processing +software, such as ObsPy, cannot directly use these non-standard formats. Therefore, additional +processing is required to convert the data to commonly used formats, which poses challenges +for researchers. Although NIED Hi-net provides a set of commands in their win32tools package +to process WIN32 data and convert to the SAC format, there are currently no tools available +to convert the channels table to a more commonly used format, such as the SAC polezero file format. +This limitation hinders the broader utilization of NIED Hi-net data. + +# HinetPy for easy data accessing and processing + +HinetPy is designed to address specific challenges with accessing and processing +NIED Hi-net data through a user-friendly interface. It primarily offers two key components: +the `Client` class for data accessing and the `win32` module for data processing. + +The `Client` class utilizes the popular HTTP library [Requests](https://github.com/psf/requests) +to handle user authentication, data requests, status queries, and downloads. This simplifies +the process of accessing NIED Hi-net data, allowing users to access data without any +manual operations on the Hi-net website. + +The `win32` module provides several functions for processing WIN32 data, including: + +- Merging multiple small WIN32 data files into a single large WIN32 file. +- Converting data from WIN32 format to SAC format. +- Creating instrumental responses in SAC polezero format. + +Internally, the `win32` module currently relies on the `catwin32` and `win2sac_32` commands +from the NIED win32tools package for WIN32 data processing. Therefore, the win32tools package +(at least the two required commands) must be installed before using HinetPy. + +This is an example demonstrating how to request 20 minutes of waveform data of the Hi-net +network starting at 2010-01-01T00:00 (JST, GMT+0900), convert the data to SAC format +and extract SAC polezero files: +```python +from HinetPy import Client, win32 + +# You need to register a Hi-net account first +client = Client("username", "password") + +# Let's try to request 20-minute data of the Hi-net network (with an internal +# network code of '0101') starting at 2010-01-01T00:00 (JST, GMT+0900) +data, ctable = client.get_continuous_waveform("0101", "201001010000", 20) + +# The request and download process usually takes a few minutes. +# Be patient... +# Now you can see the data and channels table in your working directory +# Waveform data (in win32 format) : 0101_201001010000_20.cnt +# Channels table (plaintext file) : 0101_20100101.ch + +# Convert data from win32 format to SAC format +win32.extract_sac(data, ctable) +# Extract instrumental responses and save as SAC polezero files +win32.extract_sacpz(ctable) + +# Now you can see several SAC and SAC_PZ files in your working directory. +# +# N.NGUH.E.SAC ... +# N.NGUH.E.SAC_PZ ... +``` + +`"0101"` is the internal network code of the Hi-net network. The full list of supported +seismic networks and their internal network codes can be obtained via `client.info()`. + +# Key features + +The key features of HinetPy are: + +1. Facilitates easy access to NIED Hi-net seismic data, including continuous/event waveform + data and event catalogs. +2. Supports multiple seismic networks (e.g., F-net, S-net, MeSO-net and more in addition + to Hi-net) in Japan. +3. Selects a subset of stations based on geographical location or station name (Supports + Hi-net, F-net, S-net and MeSO-net only). +4. Converts waveform data to SAC format and instrumental responses to SAC polezero files. +5. Speeds up the downloading and processing workflow via the use of multithreading. + +# Important notes on the use of NIED Hi-net data + +1. Users must register an account on the NIED Hi-net website for accessing the data and + renew the account annually. +2. Users should report their research results using NIED Hi-net data to NIED. +3. Redistribution of any NIED Hi-net data is prohibited. + +# Acknowledgments + +The HinetPy package was first developed in 2013 by the author during the time as a graduate +student at the University of Science and Technology of China (USTC). It was later maintained +during the author's postdoctoral work at Michigan State University (MSU) and as a faculty +member at the China University of Geosciences, Wuhan. The authors would like to thank +users who report bugs and request features. The author is supported by +the National Natural Science Foundation of China under grant NSFC42274122, +the “CUG Scholar” Scientific Research Funds at China University of Geosciences (Wuhan) (Project No. 2022012), +and the Fundamental Research Funds for the Central Universities, China University of Geosciences (Wuhan) (No. CUG230604). + +# References