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README.md

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+---
+title: Fastapi Dummy
+emoji: 🐢
+colorFrom: purple
+colorTo: blue
+sdk: docker
+pinned: false
+---
+
+# PhaseNet: A Deep-Neural-Network-Based Seismic Arrival Time Picking Method
+
+[![](https://github.com/AI4EPS/PhaseNet/workflows/documentation/badge.svg)](https://ai4eps.github.io/PhaseNet)
+
+## 1.  Install [miniconda](https://docs.conda.io/en/latest/miniconda.html) and requirements
+- Download PhaseNet repository
+```bash
+git clone https://github.com/wayneweiqiang/PhaseNet.git
+cd PhaseNet
+```
+- Install to default environment
+```bash
+conda env update -f=env.yml -n base
+```
+- Install to "phasenet" virtual envirionment
+```bash
+conda env create -f env.yml
+conda activate phasenet
+```
+
+## 2. Pre-trained model
+Located in directory: **model/190703-214543**
+
+## 3. Related papers
+- Zhu, Weiqiang, and Gregory C. Beroza. "PhaseNet: A Deep-Neural-Network-Based Seismic Arrival Time Picking Method." arXiv preprint arXiv:1803.03211 (2018).
+- Liu, Min, et al. "Rapid characterization of the July 2019 Ridgecrest, California, earthquake sequence from raw seismic data using machine‐learning phase picker." Geophysical Research Letters 47.4 (2020): e2019GL086189.
+- Park, Yongsoo, et al. "Machine‐learning‐based analysis of the Guy‐Greenbrier, Arkansas earthquakes: A tale of two sequences." Geophysical Research Letters 47.6 (2020): e2020GL087032.
+- Chai, Chengping, et al. "Using a deep neural network and transfer learning to bridge scales for seismic phase picking." Geophysical Research Letters 47.16 (2020): e2020GL088651.
+- Tan, Yen Joe, et al. "Machine‐Learning‐Based High‐Resolution Earthquake Catalog Reveals How Complex Fault Structures Were Activated during the 2016–2017 Central Italy Sequence." The Seismic Record 1.1 (2021): 11-19.
+
+## 4. Batch prediction
+See examples in the [notebook](https://github.com/wayneweiqiang/PhaseNet/blob/master/docs/example_batch_prediction.ipynb): [example_batch_prediction.ipynb](example_batch_prediction.ipynb)
+
+
+PhaseNet currently supports four data formats: mseed, sac, hdf5, and numpy. The test data can be downloaded here:
+```
+wget https://github.com/wayneweiqiang/PhaseNet/releases/download/test_data/test_data.zip
+unzip test_data.zip
+```
+
+- For mseed format:
+```
+python phasenet/predict.py --model=model/190703-214543 --data_list=test_data/mseed.csv --data_dir=test_data/mseed --format=mseed --amplitude --response_xml=test_data/stations.xml --batch_size=1 --sampling_rate=100 --plot_figure
+```
+```
+python phasenet/predict.py --model=model/190703-214543 --data_list=test_data/mseed2.csv --data_dir=test_data/mseed --format=mseed --amplitude --response_xml=test_data/stations.xml --batch_size=1 --sampling_rate=100 --plot_figure
+```
+
+- For sac format:
+```
+python phasenet/predict.py --model=model/190703-214543 --data_list=test_data/sac.csv --data_dir=test_data/sac --format=sac --batch_size=1 --plot_figure
+```
+
+- For numpy format:
+```
+python phasenet/predict.py --model=model/190703-214543 --data_list=test_data/npz.csv --data_dir=test_data/npz --format=numpy --plot_figure
+```
+
+- For hdf5 format:
+```
+python phasenet/predict.py --model=model/190703-214543 --hdf5_file=test_data/data.h5 --hdf5_group=data --format=hdf5 --plot_figure
+```
+
+- For a seismic array (used by [QuakeFlow](https://github.com/wayneweiqiang/QuakeFlow)):
+```
+python phasenet/predict.py --model=model/190703-214543 --data_list=test_data/mseed_array.csv --data_dir=test_data/mseed_array --stations=test_data/stations.json  --format=mseed_array --amplitude
+```
+
+Notes: 
+
+1. The reason for using "--batch_size=1" is because the mseed or sac files usually are not the same length. If you want to use a larger batch size for a good prediction speed, you need to cut the data to the same length.
+
+2. Remove the "--plot_figure" argument for large datasets, because plotting can be very slow.
+
+Optional arguments:
+```
+usage: predict.py [-h] [--batch_size BATCH_SIZE] [--model_dir MODEL_DIR]
+                  [--data_dir DATA_DIR] [--data_list DATA_LIST]
+                  [--hdf5_file HDF5_FILE] [--hdf5_group HDF5_GROUP]
+                  [--result_dir RESULT_DIR] [--result_fname RESULT_FNAME]
+                  [--min_p_prob MIN_P_PROB] [--min_s_prob MIN_S_PROB]
+                  [--mpd MPD] [--amplitude] [--format FORMAT]
+                  [--s3_url S3_URL] [--stations STATIONS] [--plot_figure]
+                  [--save_prob]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --batch_size BATCH_SIZE
+                        batch size
+  --model_dir MODEL_DIR
+                        Checkpoint directory (default: None)
+  --data_dir DATA_DIR   Input file directory
+  --data_list DATA_LIST
+                        Input csv file
+  --hdf5_file HDF5_FILE
+                        Input hdf5 file
+  --hdf5_group HDF5_GROUP
+                        data group name in hdf5 file
+  --result_dir RESULT_DIR
+                        Output directory
+  --result_fname RESULT_FNAME
+                        Output file
+  --min_p_prob MIN_P_PROB
+                        Probability threshold for P pick
+  --min_s_prob MIN_S_PROB
+                        Probability threshold for S pick
+  --mpd MPD             Minimum peak distance
+  --amplitude           if return amplitude value
+  --format FORMAT       input format
+  --stations STATIONS   seismic station info
+  --plot_figure         If plot figure for test
+  --save_prob           If save result for test
+```
+
+- The output picks are saved to "results/picks.csv" on default
+
+|file_name        |begin_time             |station_id|phase_index|phase_time             |phase_score|phase_amp             |phase_type|
+|-----------------|-----------------------|----------|-----------|-----------------------|-----------|----------------------|----------|
+|2020-10-01T00:00*|2020-10-01T00:00:00.003|CI.BOM..HH|14734      |2020-10-01T00:02:27.343|0.708      |2.4998866231208325e-14|P         |
+|2020-10-01T00:00*|2020-10-01T00:00:00.003|CI.BOM..HH|15487      |2020-10-01T00:02:34.873|0.416      |2.4998866231208325e-14|S         |
+|2020-10-01T00:00*|2020-10-01T00:00:00.003|CI.COA..HH|319        |2020-10-01T00:00:03.193|0.762      |3.708662269972206e-14 |P         |
+
+Notes:
+1. The *phase_index* means which data point is the pick in the original sequence. So *phase_time* = *begin_time* + *phase_index* / *sampling rate*. The default *sampling_rate* is 100Hz 
+
+
+## 5. QuakeFlow example
+A complete earthquake detection workflow can be found in the [QuakeFlow](https://wayneweiqiang.github.io/QuakeFlow/) project.
+
+## 6. Interactive example
+See details in the [notebook](https://github.com/wayneweiqiang/PhaseNet/blob/master/docs/example_gradio.ipynb): [example_interactive.ipynb](example_gradio.ipynb)
+
+## 7. Training
+- Download a small sample dataset:
+```bash
+wget https://github.com/wayneweiqiang/PhaseNet/releases/download/test_data/test_data.zip
+unzip test_data.zip
+```
+- Start training from the pre-trained model
+```
+python phasenet/train.py  --model_dir=model/190703-214543/ --train_dir=test_data/npz --train_list=test_data/npz.csv  --plot_figure --epochs=10 --batch_size=10
+```
+- Check results in the **log** folder
+