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Merged
merged 3 commits into from
Mar 31, 2025
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Schaefferaj master #25

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ba52823
A Schaeffer.
Mar 28, 2025
5be0d75
Merge pull request #1 from schaefferaj/NFSI-OBS-Compatibility
schaefferaj Mar 31, 2025
ac516b1
changedGH actions and typo in tutorial doc
paudetseis Mar 31, 2025
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19 changes: 10 additions & 9 deletions .github/workflows/deploy.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,12 @@ on:
jobs:
# This workflow contains a single job called "build"
build:
name: ${{ matrix.os }} Python ${{ matrix.python-version }}
# The type of runner that the job will run on
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ["ubuntu-latest", "macos-latest"]
os: ["ubuntu-latest"]
python-version: ["3.10"]

steps:
Expand All @@ -38,19 +39,19 @@ jobs:
run: |
conda info
conda config --add channels conda-forge
conda install obspy pandas pytest
conda install obspy pandas pytest libstdcxx-ng
pip install stdb
pip install geographiclib
pip install -e .
conda list

- name: Tests
shell: bash -l {0}
run: |
mkdir empty
cd empty
conda install pytest
pytest ../orientpy/tests/
# - name: Tests
# shell: bash -l {0}
# run: |
# mkdir empty
# cd empty
# conda install pytest
# pytest ../orientpy/tests/
# conda install pytest-cov
# pytest -v --cov=orientpy ../orientpy/tests/
# bash <(curl -s https://codecov.io/bash)
Expand Down
6 changes: 3 additions & 3 deletions docs/tutorials.rst
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Expand Up @@ -10,13 +10,13 @@ LOBS3 and send the prompt to a logfile

.. code-block::

$ query_fdsn_stdb.py -N YH -C ?H? -S LOBS3 YH_list > logfile
$ query_fdsn_stdb -N YH -C ?H? -S LOBS3 YH_list > logfile

To check the station info for M08A, use the program ``ls_stdb.py``:
To check the station info for M08A, use the program ``ls_stdb``:

.. code-block::

$ ls_stdb.py YH_list.pkl
$ ls_stdb YH_list.pkl
Listing Station Pickle: YH_list.pkl
YH.LOBS3
--------------------------------------------------------------------------
Expand Down
73 changes: 41 additions & 32 deletions orientpy/classes.py
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Expand Up @@ -119,14 +119,15 @@ class Orient(object):

"""

def __init__(self, sta):
def __init__(self, sta, zcomp='Z'):

# Attributes from parameters
self.sta = sta

# Initialize meta and data objects as None
self.meta = None
self.data = None
self.zcomp = zcomp

def add_event(self, event, gacmin=None, gacmax=None,
depmax=1000., returned=False):
Expand Down Expand Up @@ -193,6 +194,9 @@ def download_data(self, client, stdata=[], ndval=np.nan, new_sr=None,
:class:`~obspy.core.UTCDateTime` object.
returned : bool
Whether or not to return the ``accept`` attribute
zcomp : str
Character representing the vertical component. Should be
a single character :str:. Default Z

Returns
-------
Expand Down Expand Up @@ -228,14 +232,19 @@ def download_data(self, client, stdata=[], ndval=np.nan, new_sr=None,
# Download data
err, stream = io.download_data(
client=client, sta=self.sta, start=tstart, end=tend,
stdata=stdata, ndval=ndval, new_sr=new_sr,
stdata=stdata, ndval=ndval, new_sr=new_sr, zcomp=self.zcomp,
verbose=verbose)

if err or stream is None:
print("* Waveform Request Failed...Skipping")
self.meta.accept = False
return self.meta.accept

# Store as attributes with traces in dictionary
try:
trE = stream.select(component='E')[0]
trN = stream.select(component='N')[0]
trZ = stream.select(component='Z')[0]
trZ = stream.select(component=self.zcomp)[0]
self.data = Stream(traces=[trZ, trN, trE])

# Filter Traces and resample
Expand All @@ -246,26 +255,24 @@ def download_data(self, client, stdata=[], ndval=np.nan, new_sr=None,

# If there is no ZNE, perhaps there is Z12?
except:
tr1 = stream.select(component='1')[0]
tr2 = stream.select(component='2')[0]
trZ = stream.select(component=self.zcomp)[0]
self.data = Stream(traces=[trZ, tr1, tr2])

try:
tr1 = stream.select(component='1')[0]
tr2 = stream.select(component='2')[0]
trZ = stream.select(component='Z')[0]
self.data = Stream(traces=[trZ, tr1, tr2])

# Filter Traces and resample
if new_sr:
self.data.filter('lowpass', freq=0.5*new_sr,
corners=2, zerophase=True)
self.data.resample(new_sr)

if not np.sum([np.std(tr.data) for tr in self.data]) > 0.:
print('Error: Data are all zeros')
self.meta.accept = False
# Filter Traces and resample
if new_sr:
self.data.filter('lowpass', freq=0.5*new_sr,
corners=2, zerophase=True)
self.data.resample(new_sr)

except:
if not np.sum([np.std(tr.data) for tr in self.data]) > 0.:
print('Error: Data are all zeros')
self.meta.accept = False

# except:
# self.meta.accept = False

if returned:
return self.meta.accept

Expand Down Expand Up @@ -311,9 +318,9 @@ class BNG(Orient):

"""

def __init__(self, sta):
def __init__(self, sta, zcomp='Z'):

Orient.__init__(self, sta)
Orient.__init__(self, sta, zcomp=zcomp)


def calc(self, dphi, dts, tt, bp=None, showplot=False):
Expand Down Expand Up @@ -366,21 +373,23 @@ def calc(self, dphi, dts, tt, bp=None, showplot=False):
test_sets = {
'ZNE':{'Z', 'N', 'E'},
'Z12':{'Z', '1', '2'},
'Z23':{'Z', '2', '3'},
'Z23':{'Z', '2', '3'},
'312':{'3', '1', '2'},
'123':{'1', '2', '3'} # probably should raise an exception if this is the case,
} # as no correction is estimated for the vertical component
for test_key in test_sets:
test_set = test_sets[test_key]
if test_set.issubset(set(comps_id)): # use sets to avoid sorting complications
comps_codes = list(test_key)
break

#-- temporarily modify channel codes, assuming that N/E are not oriented properly
channel_code_prefix = stream[0].stats.channel[:2] # prefix should be the same for all
# 3 components by now
stream.select(component=comps_codes[1])[0].stats.channel = channel_code_prefix + '1'
stream.select(component=comps_codes[2])[0].stats.channel = channel_code_prefix + '2'
stream.select(component=comps_codes[0])[0].stats.channel = channel_code_prefix + 'Z'
stream.select(component=comps_codes[0])[0].stats.channel = channel_code_prefix + self.zcomp.upper()


# Filter if specified
if bp:
Expand All @@ -396,8 +405,8 @@ def calc(self, dphi, dts, tt, bp=None, showplot=False):
# Define signal and noise
tr1 = stdata.select(component='1')[0].copy()
tr2 = stdata.select(component='2')[0].copy()
trZ = stdata.select(component='Z')[0].copy()
ntrZ = stnoise.select(component='Z')[0].copy()
trZ = stdata.select(component=self.zcomp.upper())[0].copy()
ntrZ = stnoise.select(component=self.zcomp.upper())[0].copy()

# Calculate and store SNR as attribute
self.meta.snr = 10.*np.log10(
Expand Down Expand Up @@ -517,9 +526,9 @@ class DL(Orient):

"""

def __init__(self, sta):
def __init__(self, sta, zcomp='Z'):

Orient.__init__(self, sta)
Orient.__init__(self, sta, zcomp=zcomp)


def calc(self, showplot=False):
Expand Down Expand Up @@ -609,15 +618,15 @@ def calc(self, showplot=False):

# R1 path
R1phi[k], R1cc[k] = utils.DLcalc(
stream.copy(), item[0], item[1],
stream, item[0], item[1],
item[2], self.meta.epi_dist, self.meta.baz, Ray1,
winlen=item[3], ptype=0)
winlen=item[3], ptype=0, zcomp=self.zcomp)

# R2 path
R2phi[k], R2cc[k] = utils.DLcalc(
stream.copy(), item[0], item[1],
stream, item[0], item[1],
item[2], dist2, baz2, Ray2,
winlen=item[4], ptype=0)
winlen=item[4], ptype=0, zcomp=self.zcomp)

# Store azimuths and CC values as attributes
self.meta.R1phi = R1phi
Expand Down
96 changes: 54 additions & 42 deletions orientpy/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -400,7 +400,8 @@ def parse_localdata_for_comp(comp='Z', stdata=[], sta=None,


def download_data(client=None, sta=None, start=UTCDateTime, end=UTCDateTime,
stdata=[], ndval=nan, new_sr=0., verbose=False):
stdata=[], ndval=nan, new_sr=0., verbose=False, zcomp='Z',
coordsys=2):
"""
Function to build a stream object for a seismogram in a given time window either
by downloading data from the client object or alternatively first checking if the
Expand Down Expand Up @@ -445,8 +446,7 @@ def download_data(client=None, sta=None, start=UTCDateTime, end=UTCDateTime,
from math import floor

# Output
print(("* {0:s}.{1:2s} - ZNE:".format(sta.station,
sta.channel.upper())))
print("* {0:s}.{1:2s}:".format(sta.station, sta.channel.upper()))

# Set Error Default to True
erd = True
Expand All @@ -456,7 +456,7 @@ def download_data(client=None, sta=None, start=UTCDateTime, end=UTCDateTime,
# Only a single day: Search for local data
# Get Z localdata
errZ, stZ = parse_localdata_for_comp(
comp='Z', stdata=stdata, sta=sta, start=start, end=end,
comp=zcomp, stdata=stdata, sta=sta, start=start, end=end,
ndval=ndval)
# Get N localdata
errN, stN = parse_localdata_for_comp(
Expand All @@ -481,53 +481,65 @@ def download_data(client=None, sta=None, start=UTCDateTime, end=UTCDateTime,
# Construct location name
if len(tloc) == 0:
tloc = "--"
# Construct Channel List
channelsZNE = sta.channel.upper() + 'Z,' + sta.channel.upper() + \
'N,' + sta.channel.upper() + 'E'
print(("* {1:2s}[ZNE].{2:2s} - Checking Network".format(
sta.station, sta.channel.upper(), tloc)))


# Get waveforms, with extra 1 second to avoid
# traces cropped too short - traces are trimmed later
st = None

try:
st = client.get_waveforms(
network=sta.network,
station=sta.station, location=loc,
channel=channelsZNE, starttime=start,
endtime=end+1., attach_response=False)
if len(st) == 3:
print("* - ZNE Data Downloaded")

# It's possible if len(st)==1 that data is Z12
else:
# Construct Channel List
channelsZ12 = sta.channel.upper() + 'Z,' + \
sta.channel.upper() + '1,' + \
sta.channel.upper() + '2'
msg = "* {1:2s}[Z12].{2:2s} - Checking Network".format(
sta.station, sta.channel.upper(), tloc)
print(msg)
try:
st = client.get_waveforms(
network=sta.network,
station=sta.station, location=loc,
channel=channelsZ12, starttime=start,
endtime=end, attach_response=False)
if len(st) == 3:
print("* - Z12 Data Downloaded")
else:
print("* Stream has less than 3 components")
st = None
except:
st = None
# Construct Channel List
channelsZNE = sta.channel.upper() + zcomp.upper() + ',' + sta.channel.upper() + 'N,' + sta.channel.upper() + 'E'
print("* {0:2s}[{1:1s}NE].{2:2s} - Checking FDSNWS".format(
sta.channel.upper(), zcomp.upper(), tloc))
st = client.get_waveforms(network=sta.network,station=sta.station, location=loc,channel=channelsZNE, starttime=start,endtime=end+1., attach_response=False)
except:
print("* - No Data Available")

#-- check if download got all needed data
if st is not None and len(st.select(component=zcomp)) >= 1 and len(st.select(component="N")) >= 1 and len(st.select(component='E')) >= 1:
print("* - "+zcomp.upper() + "NE Data Downloaded")
break


else:
# There was no data for above, so try other channels.
print("* - "+zcomp.upper() + "NE missing data")

# Construct Channel List
channelsZ12 = sta.channel.upper() + zcomp.upper() +',' + sta.channel.upper() + '1,' + sta.channel.upper() + '2'
print("* {0:2s}[{1:1s}12].{2:2s} - Checking Network".format(
sta.channel.upper(), zcomp.upper(), tloc))
try:
st = client.get_waveforms(
network=sta.network,
station=sta.station, location=loc,
channel=channelsZ12, starttime=start,
endtime=end, attach_response=False)
except:
print("* - No Data Available")
st = None
erd = True

#-- check if download got all needed data
if st is not None and len(st.select(component=zcomp)) >= 1 and len(st.select(component="1")) >= 1 and len(st.select(component='2')) >= 1:
print("* - "+zcomp.upper() + "12 Data Downloaded")
break
else:
print("* - "+zcomp.upper() + "12 missing data")


if st is None:
print("* - Stream is missing components")
st = None
erd = True


# Break if we successfully obtained 3 components in st
if not erd:

break

#print (st)

# Check the correct 3 components exist
if st is None:
print("* Error retrieving waveforms")
Expand Down Expand Up @@ -558,7 +570,7 @@ def download_data(client=None, sta=None, start=UTCDateTime, end=UTCDateTime,
str(tr.stats.starttime)+" " +
str(tr.stats.endtime)) for tr in st]
print("* True start: "+str(start))
print("* -> Shifting traces to true start")
print("* -> Shifting traces to true start")
delay = [tr.stats.starttime - start for tr in st]
st_shifted = Stream(
traces=[traceshift(tr, dt) for tr, dt in zip(st, delay)])
Expand Down
6 changes: 3 additions & 3 deletions orientpy/plotting.py
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Expand Up @@ -93,7 +93,7 @@ def plot_bng_waveforms(bng, stream, dts, tt):
"""

fig, ax = plt.subplots(5, 1, sharey=True)
cmpts = ['Z', 'R', 'T', '1', '2']
cmpts = [bng.zcomp.upper(), 'R', 'T', '1', '2']
taxis = np.linspace(-dts, dts, stream[0].stats.npts)

for item in list(zip(ax, cmpts)):
Expand Down Expand Up @@ -405,9 +405,9 @@ def plot_dl_results(stkey, R1phi, R1cc, R2phi, R2cc, ind, val,

# Add text as title
text = "Station "+stkey + \
": $\phi$ = {0:.1f} $\pm$ {1:.1f}".format(val, err)
": $\phi$ = {0:.1f} $\pm$ {1:.1f} (n={2:.0f}, cc={3:.2f})".format(val, err, sum(ind),cc0)
plt.suptitle(text, fontsize=12)
gs.tight_layout(f, rect=[0, 0, 1, 0.95])

return plt


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