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chore: update tutorial for new io package and add more tests #305

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merged 4 commits into from
Mar 15, 2024
Merged

chore: update tutorial for new io package and add more tests #305

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a8cdd51
add more tests for noise module
niyiyu Mar 15, 2024
48b361b
update notebooks for io v0.1.13
niyiyu Mar 15, 2024
8c53854
fix pre-commit
niyiyu Mar 15, 2024
eb9ccab
update getstarted
niyiyu Mar 15, 2024
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ dependencies = [
"PyYAML==6.0",
"pydantic-yaml==1.0",
"psutil>=5.9.5,<6.0.0",
"noisepy-seis-io>=0.1.12",
"noisepy-seis-io>=0.1.13",
]


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8 changes: 3 additions & 5 deletions src/noisepy/seis/noise_module.py
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Expand Up @@ -164,8 +164,6 @@ def preprocess_raw(
# --reset the time to remove the discrepancy---
st[0].stats.starttime -= fric * 1e-6

# remove traces of too small length

# options to remove instrument response
if rm_resp != RmResp.NO:
if rm_resp != RmResp.INV:
Expand All @@ -188,14 +186,14 @@ def preprocess_raw(
st = []
return st

elif rm_resp == RmResp.SPECTRUM:
elif rm_resp == RmResp.SPECTRUM: # TODO: to be implement
logger.info("remove response using spectrum")
specfile = glob.glob(os.path.join(respdir, "*" + station + "*"))
if len(specfile) == 0:
raise ValueError("no response sepctrum found for %s" % station)
st = resp_spectrum(st, specfile[0], samp_freq, pre_filt)

elif rm_resp == RmResp.RESP:
elif rm_resp == RmResp.RESP: # TODO: to be implement
logger.info("remove response using RESP files")
resp = glob.glob(os.path.join(respdir, "RESP." + station + "*"))
if len(resp) == 0:
Expand All @@ -207,7 +205,7 @@ def preprocess_raw(
}
st.simulate(paz_remove=None, pre_filt=pre_filt, seedresp=seedresp)

elif rm_resp == RmResp.POLES_ZEROS:
elif rm_resp == RmResp.POLES_ZEROS: # TODO: to be implement
logger.info("remove response using poles and zeros")
paz_sts = glob.glob(os.path.join(respdir, "*" + station + "*"))
if len(paz_sts) == 0:
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226 changes: 226 additions & 0 deletions tests/data/CI/CI_CCA.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,226 @@
<?xml version='1.0' encoding='UTF-8'?>
<FDSNStationXML xmlns="http://www.fdsn.org/xml/station/1" schemaVersion="1.2">
<Source>IRIS-DMC</Source>
<Sender>IRIS-DMC</Sender>
<Module>IRIS WEB SERVICE: fdsnws-station | version: 1.1.52</Module>
<ModuleURI>http://service.iris.edu/fdsnws/station/1/query?starttime=2022-01-01T00%3A00%3A00.000000&amp;network=CI&amp;station=CCA&amp;channel=BHN&amp;level=response</ModuleURI>
<Created>2024-03-14T23:57:46.134100Z</Created>
<Network code="CI" startDate="1926-01-01T00:00:00.000000Z" restrictedStatus="open">
<Description>Southern California Seismic Network (SCSN)</Description>
<Identifier type="DOI">10.7914/SN/CI
</Identifier>
<TotalNumberStations>573</TotalNumberStations>
<SelectedNumberStations>1</SelectedNumberStations>
<Station code="CCA" startDate="2002-04-04T00:00:00.000000Z" restrictedStatus="open">
<Latitude unit="DEGREES">35.15252</Latitude>
<Longitude unit="DEGREES">-118.01649</Longitude>
<Elevation>710.0</Elevation>
<Site>
<Name>California City Airport</Name>
<Description>22636 Airport Way</Description>
<Town>California City</Town>
<Region>CA</Region>
<Country>USA</Country>
</Site>
<CreationDate>2002-04-04T00:00:00.000000Z</CreationDate>
<TotalNumberChannels>36</TotalNumberChannels>
<SelectedNumberChannels>1</SelectedNumberChannels>
<Channel code="BHN" startDate="2014-03-17T21:00:00.000000Z" restrictedStatus="open" locationCode="">
<Comment>
<Value>INSTALL NEW INSTRUMENTS</Value>
<BeginEffectiveTime>2014-03-17T21:00:00.000000Z</BeginEffectiveTime>
</Comment>
<Latitude unit="DEGREES">35.15252</Latitude>
<Longitude unit="DEGREES">-118.01649</Longitude>
<Elevation>710.0</Elevation>
<Depth>0.0</Depth>
<Azimuth unit="DEGREES">0.0</Azimuth>
<Dip unit="DEGREES">0.0</Dip>
<Type>CONTINUOUS</Type>
<Type>GEOPHYSICAL</Type>
<SampleRate unit="SAMPLES/S">40.0</SampleRate>
<ClockDrift unit="SECONDS/SAMPLE">0.002</ClockDrift>
<CalibrationUnits>
<Name>A</Name>
<Description>Electric Current in Amperes</Description>
</CalibrationUnits>
<Sensor>
<Type>EQMET</Type>
<Description>Velocity Sensor</Description>
<Manufacturer>EQMET</Manufacturer>
<Model>PBB-200S</Model>
<SerialNumber>255</SerialNumber>
</Sensor>
<DataLogger>
<Type>QUANTERRA</Type>
<Manufacturer>QUANTERRA</Manufacturer>
<Model>Q330S</Model>
<SerialNumber>5443</SerialNumber>
</DataLogger>
<Response>
<InstrumentSensitivity>
<Value>626915166.0349979</Value>
<Frequency>0.03</Frequency>
<InputUnits>
<Name>m/s</Name>
<Description>Velocity in meters per second</Description>
</InputUnits>
<OutputUnits>
<Name>counts</Name>
<Description>Digital Count in Digital counts</Description>
</OutputUnits>
</InstrumentSensitivity>
<Stage number="1">
<PolesZeros name="PBB200S-120SEC-HORIZONTAL">
<Description>METROZET</Description>
<InputUnits>
<Name>m/s</Name>
<Description>Velocity in meters per second</Description>
</InputUnits>
<OutputUnits>
<Name>V</Name>
<Description>Voltage in Volts</Description>
</OutputUnits>
<PzTransferFunctionType>LAPLACE (RADIANS/SECOND)</PzTransferFunctionType>
<NormalizationFactor>929399688.2971879</NormalizationFactor>
<NormalizationFrequency unit="HERTZ">0.03</NormalizationFrequency>
<Zero number="0">
<Real minusError="0.0" plusError="0.0">0.0</Real>
<Imaginary minusError="0.0" plusError="0.0">0.0</Imaginary>
</Zero>
<Zero number="1">
<Real minusError="0.0" plusError="0.0">0.0</Real>
<Imaginary minusError="0.0" plusError="0.0">0.0</Imaginary>
</Zero>
<Zero number="2">
<Real minusError="0.0" plusError="0.0">-247.651</Real>
<Imaginary minusError="0.0" plusError="0.0">0.0</Imaginary>
</Zero>
<Pole number="0">
<Real minusError="0.0" plusError="0.0">-0.037024</Real>
<Imaginary minusError="0.0" plusError="0.0">-0.037024</Imaginary>
</Pole>
<Pole number="1">
<Real minusError="0.0" plusError="0.0">-89.0321</Real>
<Imaginary minusError="0.0" plusError="0.0">342.287</Imaginary>
</Pole>
<Pole number="2">
<Real minusError="0.0" plusError="0.0">-1088.39</Real>
<Imaginary minusError="0.0" plusError="0.0">806.23</Imaginary>
</Pole>
<Pole number="3">
<Real minusError="0.0" plusError="0.0">-1088.39</Real>
<Imaginary minusError="0.0" plusError="0.0">-806.23</Imaginary>
</Pole>
<Pole number="4">
<Real minusError="0.0" plusError="0.0">-89.0321</Real>
<Imaginary minusError="0.0" plusError="0.0">-342.287</Imaginary>
</Pole>
<Pole number="5">
<Real minusError="0.0" plusError="0.0">-0.037024</Real>
<Imaginary minusError="0.0" plusError="0.0">0.037024</Imaginary>
</Pole>
</PolesZeros>
<StageGain>
<Value>1500.0</Value>
<Frequency>1.0</Frequency>
</StageGain>
</Stage>
<Stage number="2">
<StageGain>
<Value>1.0</Value>
<Frequency>0.03</Frequency>
</StageGain>
</Stage>
<Stage number="3">
<Coefficients>
<InputUnits>
<Name>V</Name>
<Description>Voltage in Volts</Description>
</InputUnits>
<OutputUnits>
<Name>counts</Name>
<Description>Digital Count in Digital counts</Description>
</OutputUnits>
<CfTransferFunctionType>DIGITAL</CfTransferFunctionType>
</Coefficients>
<Decimation>
<InputSampleRate unit="HERTZ">40.0</InputSampleRate>
<Factor>1</Factor>
<Offset>0</Offset>
<Delay>0.0</Delay>
<Correction>0.0</Correction>
</Decimation>
<StageGain>
<Value>419430.0</Value>
<Frequency>0.03</Frequency>
</StageGain>
</Stage>
<Stage number="4">
<FIR name="FIR_FLBELOW100_40">
<InputUnits>
<Name>counts</Name>
<Description>Digital Count in Digital counts</Description>
</InputUnits>
<OutputUnits>
<Name>counts</Name>
<Description>Digital Count in Digital counts</Description>
</OutputUnits>
<Symmetry>NONE</Symmetry>
<NumeratorCoefficient i="1">4.1895179e-13</NumeratorCoefficient>
<NumeratorCoefficient i="2">0.00033031761</NumeratorCoefficient>
<NumeratorCoefficient i="3">0.0010292126</NumeratorCoefficient>
<NumeratorCoefficient i="4">-0.003141228</NumeratorCoefficient>
<NumeratorCoefficient i="5">0.00020570927</NumeratorCoefficient>
<NumeratorCoefficient i="6">0.0015252131</NumeratorCoefficient>
<NumeratorCoefficient i="7">-0.0062319267</NumeratorCoefficient>
<NumeratorCoefficient i="8">0.010480133</NumeratorCoefficient>
<NumeratorCoefficient i="9">-0.013120247</NumeratorCoefficient>
<NumeratorCoefficient i="10">0.010782143</NumeratorCoefficient>
<NumeratorCoefficient i="11">-0.00144455</NumeratorCoefficient>
<NumeratorCoefficient i="12">-0.015872946</NumeratorCoefficient>
<NumeratorCoefficient i="13">0.039507404</NumeratorCoefficient>
<NumeratorCoefficient i="14">-0.06510363</NumeratorCoefficient>
<NumeratorCoefficient i="15">0.085371559</NumeratorCoefficient>
<NumeratorCoefficient i="16">-0.089191342</NumeratorCoefficient>
<NumeratorCoefficient i="17">0.050061889</NumeratorCoefficient>
<NumeratorCoefficient i="18">0.83723276</NumeratorCoefficient>
<NumeratorCoefficient i="19">0.26672305</NumeratorCoefficient>
<NumeratorCoefficient i="20">-0.16669311</NumeratorCoefficient>
<NumeratorCoefficient i="21">0.095283986</NumeratorCoefficient>
<NumeratorCoefficient i="22">-0.050921772</NumeratorCoefficient>
<NumeratorCoefficient i="23">0.016145837</NumeratorCoefficient>
<NumeratorCoefficient i="24">0.007063624</NumeratorCoefficient>
<NumeratorCoefficient i="25">-0.018387713</NumeratorCoefficient>
<NumeratorCoefficient i="26">0.01994141</NumeratorCoefficient>
<NumeratorCoefficient i="27">-0.015489507</NumeratorCoefficient>
<NumeratorCoefficient i="28">0.0085273541</NumeratorCoefficient>
<NumeratorCoefficient i="29">-0.0025578868</NumeratorCoefficient>
<NumeratorCoefficient i="30">-0.0018110264</NumeratorCoefficient>
<NumeratorCoefficient i="31">0.0024264926</NumeratorCoefficient>
<NumeratorCoefficient i="32">-0.0037576946</NumeratorCoefficient>
<NumeratorCoefficient i="33">0.00046729273</NumeratorCoefficient>
<NumeratorCoefficient i="34">0.00063307212</NumeratorCoefficient>
<NumeratorCoefficient i="35">-1.5687414e-06</NumeratorCoefficient>
<NumeratorCoefficient i="36">-1.2547978e-05</NumeratorCoefficient>
<NumeratorCoefficient i="37">3.2104054e-07</NumeratorCoefficient>
<NumeratorCoefficient i="38">-2.633241e-08</NumeratorCoefficient>
<NumeratorCoefficient i="39">-5.0999748e-08</NumeratorCoefficient>
</FIR>
<Decimation>
<InputSampleRate unit="HERTZ">40.0</InputSampleRate>
<Factor>1</Factor>
<Offset>0</Offset>
<Delay>0.430462</Delay>
<Correction>0.430462</Correction>
</Decimation>
<StageGain>
<Value>1.0</Value>
<Frequency>0.0</Frequency>
</StageGain>
</Stage>
</Response>
</Channel>
</Station>
</Network>
</FDSNStationXML>
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