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refactor: change freq_norm from string to enum #248

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merged 17 commits into from
Oct 27, 2023
Merged

refactor: change freq_norm from string to enum #248

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11d5171
refactor: change freq_norm from string to enum
anujsinha3 Oct 21, 2023
772e2d2
refactor: pre-commit hook format changes
anujsinha3 Oct 21, 2023
9c1afdf
refactor: change freq_norm from string to enum
anujsinha3 Oct 21, 2023
0cb9d69
refactor: correct import
anujsinha3 Oct 21, 2023
0858325
refactor: add parameterized test cases
anujsinha3 Oct 25, 2023
5879e7c
refactor: fix import
anujsinha3 Oct 25, 2023
b126be6
refactor: fix variable type
anujsinha3 Oct 25, 2023
2e69617
refactor: fix data sphinx error
anujsinha3 Oct 25, 2023
b79941e
refactor: revert the change
anujsinha3 Oct 25, 2023
a45da8d
refactor: change initialization of freq_norm from string to enum
anujsinha3 Oct 26, 2023
67057bc
refactor: change initialization of freq_norm from string to enum
anujsinha3 Oct 26, 2023
5107b2f
refactor: change initialization of freq_norm from string to enum
anujsinha3 Oct 26, 2023
bf24939
refactor: Fix navigation_with_keys warning.
anujsinha3 Oct 26, 2023
5d7d3fc
refactor: Fix navigation_with_keys warning.
anujsinha3 Oct 26, 2023
98a72c6
refactor: revert change
anujsinha3 Oct 26, 2023
c6ff331
refactor: set navigation_with_keys as false to prevent sphinx validat…
anujsinha3 Oct 27, 2023
b2f06d6
refactor: style consistency with \n
anujsinha3 Oct 27, 2023
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13 changes: 7 additions & 6 deletions script/test_whiten.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,8 @@
import scipy
from scipy.fftpack import next_fast_len

from noisepy.seis.noise_module import moving_ave, whiten
from src.noisepy.seis.datatypes import FreqNorm
from src.noisepy.seis.noise_module import moving_ave, whiten
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def whiten_original(data, fft_para):
Expand Down Expand Up @@ -62,9 +63,9 @@ def whiten_original(data, fft_para):
1j * np.angle(FFTRawSign[:, low:left])
)
# Pass band:
if freq_norm == "phase_only":
if freq_norm == FreqNorm.PHASE_ONLY:
FFTRawSign[:, left:right] = np.exp(1j * np.angle(FFTRawSign[:, left:right]))
elif freq_norm == "rma":
elif freq_norm == FreqNorm.RMA:
for ii in range(data.shape[0]):
tave = moving_ave(np.abs(FFTRawSign[ii, left:right]), smooth_N)
FFTRawSign[ii, left:right] = FFTRawSign[ii, left:right] / tave
Expand All @@ -82,9 +83,9 @@ def whiten_original(data, fft_para):
1j * np.angle(FFTRawSign[low:left])
)
# Pass band:
if freq_norm == "phase_only":
if freq_norm == FreqNorm.PHASE_ONLY:
FFTRawSign[left:right] = np.exp(1j * np.angle(FFTRawSign[left:right]))
elif freq_norm == "rma":
elif freq_norm == FreqNorm.RMA:
tave = moving_ave(np.abs(FFTRawSign[left:right]), smooth_N)
FFTRawSign[left:right] = FFTRawSign[left:right] / tave
# Right tapering:
Expand All @@ -109,7 +110,7 @@ def whiten_original(data, fft_para):
"freqmin": 0.01,
"freqmax": 0.2,
"smooth_N": 1,
"freq_norm": "phase_only",
"freq_norm": FreqNorm.PHASE_ONLY,
}

# 1 D case
Expand Down
8 changes: 7 additions & 1 deletion src/noisepy/seis/datatypes.py
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Expand Up @@ -110,6 +110,12 @@ class StackMethod(Enum):
ALL = "all"


class FreqNorm(Enum):
RMA = "rma"
NO = "no"
PHASE_ONLY = "phase_only"


class ConfigParameters(BaseModel):
model_config = ConfigDict(validate_default=True)

Expand Down Expand Up @@ -139,7 +145,7 @@ class ConfigParameters(BaseModel):
freqmin: float = Field(default=0.05)
freqmax: float = Field(default=2.0)
freq_norm: str = Field(
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default="rma", description="choose between 'rma' for a soft whitenning or 'no' for no whitening"
default=FreqNorm.RMA.value, description="choose between 'rma' for a soft whitenning or 'no' for no whitening"
)
# TODO: change "no"for "None", and add "one_bit"as an option
# TODO: change time_norm option from "no"to "None"
Expand Down
4 changes: 2 additions & 2 deletions src/noisepy/seis/noise_module.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
from scipy.fftpack import next_fast_len
from scipy.signal import hilbert

from .datatypes import ChannelData, ConfigParameters, StackMethod
from .datatypes import ChannelData, ConfigParameters, FreqNorm, StackMethod

logger = logging.getLogger(__name__)
"""
Expand Down Expand Up @@ -559,7 +559,7 @@ def noise_processing(fft_para: ConfigParameters, dataS):
white = dataS

# -----to whiten or not------
if fft_para.freq_norm != "no":
if fft_para.freq_norm != FreqNorm.NO:
source_white = whiten(white, fft_para) # whiten and return FFT
else:
Nfft = int(next_fast_len(int(dataS.shape[1])))
Expand Down
11 changes: 6 additions & 5 deletions tests/test_whiten.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
from scipy.fftpack import next_fast_len

from noisepy.seis.correlate import ConfigParameters
from noisepy.seis.datatypes import FreqNorm
from noisepy.seis.noise_module import moving_ave, whiten


Expand Down Expand Up @@ -56,9 +57,9 @@ def whiten_original(data, fft_para: ConfigParameters):
1j * np.angle(FFTRawSign[:, low:left])
)
# Pass band:
if fft_para.freq_norm == "phase_only":
if fft_para.freq_norm == FreqNorm.PHASE_ONLY:
FFTRawSign[:, left:right] = np.exp(1j * np.angle(FFTRawSign[:, left:right]))
elif fft_para.freq_norm == "rma":
elif fft_para.freq_norm == FreqNorm.RMA:
for ii in range(data.shape[0]):
tave = moving_ave(np.abs(FFTRawSign[ii, left:right]), fft_para.smooth_N)
FFTRawSign[ii, left:right] = FFTRawSign[ii, left:right] / tave
Expand All @@ -76,9 +77,9 @@ def whiten_original(data, fft_para: ConfigParameters):
1j * np.angle(FFTRawSign[low:left])
)
# Pass band:
if fft_para.freq_norm == "phase_only":
if fft_para.freq_norm == FreqNorm.PHASE_ONLY:
FFTRawSign[left:right] = np.exp(1j * np.angle(FFTRawSign[left:right]))
elif fft_para.freq_norm == "rma":
elif fft_para.freq_norm == FreqNorm.RMA:
tave = moving_ave(np.abs(FFTRawSign[left:right]), fft_para.smooth_N)
FFTRawSign[left:right] = FFTRawSign[left:right] / tave
# Right tapering:
Expand All @@ -103,7 +104,7 @@ def whiten_original(data, fft_para: ConfigParameters):
fft_para.freqmin = 0.01
fft_para.freqmax = 0.2
fft_para.smooth_N = 1
fft_para.freq_norm = "phase_only"
fft_para.freq_norm = FreqNorm.PHASE_ONLY


def whiten1d():
Expand Down
6 changes: 3 additions & 3 deletions tutorials/get_started.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@
"source": [
"from noisepy.seis import download, cross_correlate, stack, plotting_modules, __version__\n",
"from noisepy.seis.asdfstore import ASDFRawDataStore, ASDFCCStore, ASDFStackStore\n",
"from noisepy.seis.datatypes import ConfigParameters\n",
"from noisepy.seis.datatypes import ConfigParameters, FreqNorm\n",
"from dateutil.parser import isoparse\n",
"import os\n",
"print(f\"Using NoisePy version {__version__}\")\n",
Expand Down Expand Up @@ -119,7 +119,7 @@
"config.max_over_std = 10 # threshold to remove window of bad signals: set it to 10*9 if prefer not to remove them\n",
"\n",
"# TEMPORAL and SPECTRAL NORMALISATION\n",
"config.freq_norm= \"rma\" # choose between \"rma\" for a soft whitenning or \"no\" for no whitening. Pure whitening is not implemented correctly at this point.\n",
"config.freq_norm= FreqNorm.RMA # choose between \"rma\" for a soft whitenning or \"no\" for no whitening. Pure whitening is not implemented correctly at this point.\n",
"config.smoothspect_N = 10 # moving window length to smooth spectrum amplitude (points)\n",
" # here, choose smoothspect_N for the case of a strict whitening (e.g., phase_only)\n",
"\n",
Expand Down Expand Up @@ -248,7 +248,7 @@
},
"outputs": [],
"source": [
"config.freq_norm = \"rma\"\n",
"config.freq_norm = FreqNorm.RMA\n",
"raw_store = ASDFRawDataStore(raw_data_path) # Store for reading raw data\n",
"cc_store = ASDFCCStore(cc_data_path) # Store for writing CC data\n",
"\n",
Expand Down
4 changes: 2 additions & 2 deletions tutorials/noisepy_scedc_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@
"from noisepy.seis import cross_correlate, stack, plotting_modules, __version__ # noisepy core functions\n",
"from noisepy.seis.asdfstore import ASDFCCStore, ASDFStackStore # Object to store ASDF data within noisepy\n",
"from noisepy.seis.scedc_s3store import SCEDCS3DataStore, channel_filter # Object to query SCEDC data from on S3\n",
"from noisepy.seis.datatypes import ConfigParameters, StackMethod # Main configuration object\n",
"from noisepy.seis.datatypes import ConfigParameters, FreqNorm, StackMethod # Main configuration object\n",
"from noisepy.seis.channelcatalog import XMLStationChannelCatalog # Required stationXML handling object\n",
"import os\n",
"from datetime import datetime\n",
Expand Down Expand Up @@ -201,7 +201,7 @@
"config.max_over_std = 10 # threshold to remove window of bad signals: set it to 10*9 if prefer not to remove them\n",
"\n",
"################### SPECTRAL NORMALIZATION ############\n",
"config.freq_norm= \"rma\" # choose between \"rma\" for a soft whitening or \"no\" for no whitening. Pure whitening is not implemented correctly at this point.\n",
"config.freq_norm= FreqNorm.RMA # choose between \"rma\" for a soft whitening or \"no\" for no whitening. Pure whitening is not implemented correctly at this point.\n",
"config.smoothspect_N = 10 # moving window length to smooth spectrum amplitude (points)\n",
" # here, choose smoothspect_N for the case of a strict whitening (e.g., phase_only)\n",
"\n",
Expand Down
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