def test_read_bytes_io(self):
"""
Tests reading from BytesIO instances.
"""
# 1
file = os.path.join(self.path, 'example.y_first_trace')
with open(file, 'rb') as f:
data = f.read()
st = _read_segy(io.BytesIO(data))
self.assertEqual(len(st.traces[0].data), 500)
# 2
file = os.path.join(self.path, 'ld0042_file_00018.sgy_first_trace')
with open(file, 'rb') as f:
data = f.read()
st = _read_segy(io.BytesIO(data))
self.assertEqual(len(st.traces[0].data), 2050)
# 3
file = os.path.join(self.path, '1.sgy_first_trace')
with open(file, 'rb') as f:
data = f.read()
st = _read_segy(io.BytesIO(data))
self.assertEqual(len(st.traces[0].data), 8000)
# 4
file = os.path.join(self.path, '00001034.sgy_first_trace')
with open(file, 'rb') as f:
data = f.read()
st = _read_segy(io.BytesIO(data))
self.assertEqual(len(st.traces[0].data), 2001)
# 5
file = os.path.join(self.path, 'planes.segy_first_trace')
with open(file, 'rb') as f:
data = f.read()
st = _read_segy(io.BytesIO(data))
self.assertEqual(len(st.traces[0].data), 512)
def load_SH_and_STH(filename, endian=None):
"""
Read and load headers from SEGY file. No data is loaded, saving time and memory.
Usage
-----
SH,STH = load_SH_and_STH(filename)
"""
# read file with obspy (headers only)
seis = _read_segy(filename, endian=endian, headonly=True)
traces = seis.traces
ntraces = len(traces)
# Load SEGY header
SH = load_SEGY_header(seis)
# additional headers for compatibility with older segy module
SH['filename'] = filename
SH["ntraces"] = ntraces
SH["ns"] = SH['number_of_samples_per_data_trace']
SH["dt"] = SH['sample_interval_in_microseconds'] / 1000 # in milliseconds
# Load all the Trace headers in arrays
STH = load_SEGY_trace_header(traces)
return SH, STH
def load_SEGY(filename, endian=None):
"""
Read and load data and headers from a SEGY file.
Usage
-----
data, SH, STH = load_SEGY(filename)
"""
# read file with obspy
seis = _read_segy(filename, endian=endian)
traces = seis.traces
ntraces = len(traces)
# Load SEGY header
SH = load_SEGY_header(seis)
# additional headers for compatibility with older segy module
SH['filename'] = filename
SH["ntraces"] = ntraces
SH["ns"] = SH['number_of_samples_per_data_trace']
SH["dt"] = SH['sample_interval_in_microseconds'] / 1000 # in milliseconds
# Load all the Trace headers in arrays
STH = load_SEGY_trace_header(traces)
# Load the data
data = np.vstack([t.data for t in traces]).T
return data, SH, STH
def dataload_segy(self, path_seis, size_vlm, idx0_vlm):
'''
This function loads a segy file and quary a subvolume defined by
size_vlm and idx0_vlm.
'''
t0 = time()
print('Start Loading Segy Data')
file_segy = _read_segy(path_seis).traces
traces = np.stack(t.data for t in file_segy)
inlines = np.stack(
t.header.for_3d_poststack_data_this_field_is_for_in_line_number
for t in file_segy)
xlines = np.stack(
t.header.for_3d_poststack_data_this_field_is_for_cross_line_number
for t in file_segy)
idx_inline = inlines - np.min(inlines)
idx_xline = xlines - np.min(xlines)
num_traces = len(traces)
num_inline = len(np.unique(inlines))
num_xline = len(np.unique(xlines))
num_sample = len(file_segy[0].data)
seis_vlm = np.zeros([num_inline, num_xline, num_sample])
for i in range(num_traces):
seis_vlm[idx_inline[i], idx_xline[i], :] = traces[i]
t1 = time()
print('\nCompleted Loading Segy Data')
print('\nElapsed time: ' + "{:.2f}".format(t1 - t0) + ' sec')
seis_vlm = seis_vlm[idx0_vlm[0]:idx0_vlm[0] + size_vlm[0],
idx0_vlm[1]:idx0_vlm[1] + size_vlm[1],
idx0_vlm[2]:idx0_vlm[2] + size_vlm[2]]
self.seis_vlm = seis_vlm
def plot_segy(segy_input, png=False, cmap='bone_r', log10=False):
'''
'''
import numpy as np
import matplotlib.pyplot as plt
from obspy.io.segy.segy import _read_segy
stream = _read_segy(segy_input, headonly=True)
data = np.stack(t.data for t in list(stream.traces))
fig = plt.subplots(figsize=(20,10))
if log10 == False:
plt.imshow(data.T, cmap=cmap, aspect='auto')
elif log10 == True:
plt.imshow(np.log10(data).T, cmap=cmap, aspect='auto')
plt.colorbar()
plt.show()
if png == True:
plt.savefig('test_segy_plot.png', dpi=200, bbox_inches='tight')
print('Saved Figure as ==> test_segy_plot.png')
else:
return fig
def __init__(self, filename, processor=None):
from obspy.io.segy.segy import _read_segy
self.stream = _read_segy(filename, unpack_headers=True)
self.dt = self.stream.binary_file_header.sample_interval_in_microseconds / 1000000
self.nsamp = len(self.stream.traces[0].data)
self.dt_synt = 0.004
self.dx_synt = 1
self.processor = processor
def __init__(self, segy_fn, pick_every=1):
'''
Class for reading 2D segy files. This class assumes that the traces are
CDP-ordered.
:param segy_fn: segy file name
:param pick_every: by default, every trace is read from the segy file, but
pick_every>1 allows skipping traces.
'''
self._sfn = segy_fn
self._sf = segy._read_segy(self._sfn)
self._pick_every = pick_every
# Read traces
self._mtraces = [] # trace samples
self._xs = [] # x coordinates
self._ys = [] # y coordinates
self._ns = [] # num samples
self._cdps = [] # ensemble number (cdps)
self._si = [] # sample interval
count = 0
for itr, tr in enumerate(self._sf.traces):
if (itr % self._pick_every == 0):
self._mtraces.append(tr.data)
self._xs.append(tr.header.source_coordinate_x)
self._ys.append(tr.header.source_coordinate_y)
self._ns.append(tr.header.number_of_samples_in_this_trace)
self._si.append(
tr.header.sample_interval_in_ms_for_this_trace /
1e6) # convert from micro seconds to s
self._cdps.append(tr.header.ensemble_number)
count += 1
# end for
self._ntraces = len(self._sf.traces)
self._ns = numpy.array(self._ns)
self._si = numpy.array(self._si)
self._xs = numpy.array(self._xs)
self._ys = numpy.array(self._ys)
self._cdps = numpy.array(self._cdps)
self._station_space = numpy.sqrt((self._xs[:-1] - self._xs[1:])**2 +
(self._ys[:-1] - self._ys[1:])**2)
self._dist = numpy.array([
numpy.sum(self._station_space[:i])
for i in range(len(self._station_space))
]) # compute euclidean distance along profile
self._ts = numpy.linspace(0, (numpy.max(self._ns) - 1) *
numpy.max(self._si), numpy.max(self._ns))
self._mtraces = numpy.array(self._mtraces)
self._mt, self._md = numpy.meshgrid(
self._ts, self._dist) # mesh grid of distance and time
self._mt, self._mc = numpy.meshgrid(
self._ts, self._cdps) # mesh grid of cdp and time
self._dist -= numpy.min(
self._dist) # distance along profile starts from 0
def read_segy(self, name):
"""
Read a SEGY file and places returns the data in an array of dimension
nt X nb traces
:param name: Name of the segyfile
:return: A numpy array containing the data
"""
segy = _read_segy(name)
return np.transpose(np.array([trace.data for trace in segy.traces]))
def get_trace_header_stuff(target):
# Copied verbatim from Seisplot
# Read the file.
section = segy._read_segy(target, unpack_headers=True)
# Make the data array.
data = np.vstack([t.data for t in section.traces]).T
# Collect some other data. Use a for loop because there are several.
elev, esp, ens, tsq = [], [], [], []
for i, trace in enumerate(section.traces):
elev.append(trace.header.receiver_group_elevation)
esp.append(trace.header.energy_source_point_number)
ens.append(trace.header.ensemble_number)
tsq.append(trace.header.trace_sequence_number_within_line)
return elev, esp, ens, tsq
def test_unpack_binary_file_header(self):
"""
Compares some values of the binary header with values read with
SeisView 2 by the DMNG.
"""
file = os.path.join(self.path, '1.sgy_first_trace')
segy = _read_segy(file)
header = segy.binary_file_header
# Compare the values.
self.assertEqual(header.job_identification_number, 0)
self.assertEqual(header.line_number, 0)
self.assertEqual(header.reel_number, 0)
self.assertEqual(header.number_of_data_traces_per_ensemble, 24)
self.assertEqual(header.number_of_auxiliary_traces_per_ensemble, 0)
self.assertEqual(header.sample_interval_in_microseconds, 250)
self.assertEqual(
header.sample_interval_in_microseconds_of_original_field_recording,
250)
self.assertEqual(header.number_of_samples_per_data_trace, 8000)
self.assertEqual(
header.
number_of_samples_per_data_trace_for_original_field_recording,
8000)
self.assertEqual(header.data_sample_format_code, 2)
self.assertEqual(header.ensemble_fold, 0)
self.assertEqual(header.trace_sorting_code, 1)
self.assertEqual(header.vertical_sum_code, 0)
self.assertEqual(header.sweep_frequency_at_start, 0)
self.assertEqual(header.sweep_frequency_at_end, 0)
self.assertEqual(header.sweep_length, 0)
self.assertEqual(header.sweep_type_code, 0)
self.assertEqual(header.trace_number_of_sweep_channel, 0)
self.assertEqual(header.sweep_trace_taper_length_in_ms_at_start, 0)
self.assertEqual(header.sweep_trace_taper_length_in_ms_at_end, 0)
self.assertEqual(header.taper_type, 0)
self.assertEqual(header.correlated_data_traces, 0)
self.assertEqual(header.binary_gain_recovered, 0)
self.assertEqual(header.amplitude_recovery_method, 0)
self.assertEqual(header.measurement_system, 0)
self.assertEqual(header.impulse_signal_polarity, 0)
self.assertEqual(header.vibratory_polarity_code, 0)
self.assertEqual(
header.number_of_3200_byte_ext_file_header_records_following,
0)
def load_img(self, img_path): """ reads and normalize a seismogram from the given segy file. :param img_path: a path to the segy file. :return: seismogram image as numpy array normalized between 0-1. """ segy = _read_segy(img_path) _traces = list() for trace in segy.traces: _traces.append(trace.data) x = np.asarray(_traces, dtype=np.float32) std = x.std() x -= x.mean() x /= std x *= 0.1 x += .5 x = np.clip(x, 0, 1) return x.T
def test_read_and_write_segy(self, headonly=False):
"""
Reading and writing again should not change a file.
"""
for file, attribs in self.files.items():
file = os.path.join(self.path, file)
non_normalized_samples = attribs['non_normalized_samples']
# Read the file.
with open(file, 'rb') as f:
org_data = f.read()
segy_file = _read_segy(file, headonly=headonly)
with NamedTemporaryFile() as tf:
out_file = tf.name
with warnings.catch_warnings(record=True):
segy_file.write(out_file)
# Read the new file again.
with open(out_file, 'rb') as f:
new_data = f.read()
# The two files should have the same length.
self.assertEqual(len(org_data), len(new_data))
# Replace the not normalized samples. The not normalized
# samples are already tested in test_packSEGYData and therefore not
# tested again here.
if len(non_normalized_samples) != 0:
# Convert to 4 byte integers. Any 4 byte numbers work.
org_data = from_buffer(org_data, np.int32)
new_data = from_buffer(new_data, np.int32)
# Skip the header (4*960 bytes) and replace the non normalized
# data samples.
org_data[960:][non_normalized_samples] = \
new_data[960:][non_normalized_samples]
# Create strings again.
org_data = org_data.tostring()
new_data = new_data.tostring()
# Just patch both headers - this tests something different.
org_data = _patch_header(org_data)
new_data = _patch_header(new_data)
# Always write the SEGY File revision number!
# org_data[3500:3502] = new_data[3500:3502]
# Test the identity without the SEGY revision number
self.assertEqual(org_data[:3500], new_data[:3500])
self.assertEqual(org_data[3502:], new_data[3502:])
def load_awi_segy(self,
segy_file='',
coordinate_file='',
dB=False,
correct_gps=True):
'''
'''
from obspy.io.segy.segy import _read_segy
import numpy as np
import pandas as pd
segy_file = segy_file
coordinate_file = coordinate_file
stream = _read_segy(segy_file, headonly=True)
data = pd.DataFrame(np.array([t.data for t in list(stream.traces)]))
header = stream.binary_file_header.__dict__
frame = header['line_number']
sample_interval = header['sample_interval_in_microseconds']
sample_interval = sample_interval * 10e-13
number_of_samples = header['number_of_samples_per_data_trace']
# build time array
time = np.repeat(sample_interval, number_of_samples)
time[0] = 0
time = np.cumsum(time)
self.Data = data.T
self.Stream = stream
self.Time = time
self.Frame = str(frame)
self.Domain = 'twt'
coords = pd.read_csv(coordinate_file, delim_whitespace=True)
self.Longitude = coords['GPSLon'].values
self.Latitude = coords['GPSLat'].values
self.Elevation = coords['GPSAlt'].values
self.GPS_time = coords['Time'].values
if correct_gps == True:
try:
self.Latitude = np.array(
pd.DataFrame(self.Latitude).mask(
pd.DataFrame(self.Latitude).duplicated(keep='first'),
np.nan).interpolate()).T[0]
self.Longitude = np.array(
pd.DataFrame(self.Longitude).mask(
pd.DataFrame(self.Longitude).duplicated(keep='first'),
np.nan).interpolate()).T[0]
except:
print('... could not correct gps positions.')
if dB == False:
self.dB = False
elif dB == True:
self.dB = True
else:
print('==> dB True or False? Is set to False.')
print('')
print('==> Loaded {}'.format(self.Frame))
return self
del stream, data, header, time, coords
"""Function to generate reflectivity for a wavelet with input accoustic velocity"""
""" input: Nx1 array
output: Nx1 array"""
nsamples = len(trace_velocity)
vfunct_imp = np.vectorize(get_impedance)
imp = vfunct_imp(trace_velocity.reshape(nsamples,))
rc = (imp[1:] - imp[:-1])/(imp[1:] + imp[:-1])
rc = np.append(rc,rc[-1])
return rc
xl = 676
il = 676
n_samples = 201
stream = _read_segy('../data/SEG_C3NA_Velocity.sgy', headonly=True)
full_data = np.stack(t.data for t in stream.traces).reshape(xl*il*n_samples,)
rc = np.apply_along_axis(get_reflectivity, 1, full_data.reshape(676*676,201))
w= bruges.filters.ricker(duration = 0.100, dt=0.001, f=120)
rc_f = np.apply_along_axis(lambda t:np.convolve(t, w, mode='same'),
axis=1,
arr=rc)
for i in range(676):
np.savetxt(f"../data/img_{i:03}.csv", rc_f.reshape(676,676,201)[i,:,:], delimiter = ",", fmt='%.2f')
def FBTime(inputfile):
""" Read the input SEG-Y files, 3D-VSP stacked file, sorted in SP, MD, Trace Number (output of stack)
save it to a stream object, the seismic format from the Obspy library.
Then create a total vector trace with X,Y and Z and pick the onset.
Save all first breaks to a text file."""
tic = timeit.default_timer()
print('The SEG-Y files is loading ... Please be patient')
stream = _read_segy(inputfile, headonly=True)
toc = timeit.default_timer()
print('The loading took {0:.0f} seconds'.format(toc - tic))
# Create a series of variable to be able to save each component of each geophone
# We will automatically figure out the following, number of geophone, number of shot points, number of components
nbr_of_geophone = np.count_nonzero(
np.unique(
np.array([
t.header.datum_elevation_at_receiver_group
for t in stream.traces
])))
nbr_of_SP = np.count_nonzero(
np.unique(
np.array(
[t.header.energy_source_point_number for t in stream.traces])))
nbr_of_components = np.count_nonzero(
np.unique(
np.array([
t.header.trace_number_within_the_ensemble
for t in stream.traces
])))
# We QC the variables by checking that the calculated number of traces is equal to the number of traces in the stream object (input SEG-Y file)
nbr_of_traces = nbr_of_geophone * nbr_of_SP * nbr_of_components
#nbr_of_samples_per_trace = stream.binary_file_header.number_of_samples_per_data_trace
if nbr_of_traces == int(str(stream).split()[0]):
print('All Shot Points, Components and Geophones accounted for.')
else:
print(
'Some traces are missing, please stop program and check SEG-Y file header'
)
# running_mean is a function with calculates the average in a moving window
def running_mean(x, N):
cumsum = np.cumsum(np.insert(x, 0, 0))
return (cumsum[N:] - cumsum[:-N]) / N
tic = timeit.default_timer(
) #to measure the time it takes to calculate the first break picking
#set up a series of variable for the automatic first break picker
first_arrival_time = np.empty(
0, dtype=np.int32) #empty array to store the first arrival time
fore_window = 10 #10 samples in the fore window
back_window = int(fore_window * 1.5) #15 samples in the back window
#the first ratio measurement is done at the end of the back window, therefore we need to add 'back_window - 1' sample to the ratio array to get the correct time of the maximum ratio sample
auto_pick_ratio_start = np.zeros(back_window - 1)
#set up a time array equal to 4 samples
time = np.linspace(0, 3, 4) - 2
#Start measuring first arrival time, source-receiver pair by source-receiver pair
for i in range(nbr_of_SP * nbr_of_geophone):
#create a total vector trace by summing the absolute values of all three components for all samples
data_to_vectorise = np.sum([
np.absolute(stream.traces[i * nbr_of_components + j].data)
for j in range(nbr_of_components)
],
axis=0)
#measure the average value in each window on the total vector trace
mean_back_window = running_mean(data_to_vectorise,
back_window)[:-fore_window]
mean_fore_window = running_mean(data_to_vectorise,
fore_window)[back_window:]
#calculate the ratio between fore and back window
auto_pick_ratio = mean_fore_window / mean_back_window
#add to the ratio array the 'back_window' samples with couldn't not be measured to have an array with an index equal to the time sample in the data
auto_pick_ratio = np.append(auto_pick_ratio_start, auto_pick_ratio)
#extract the first arrival time precise to the nearest sample
rough_first_arrival_time = auto_pick_ratio.argmax()
# interpolate around the rough first arrival time and find a better first break time
time_window = time + rough_first_arrival_time #time samples around the first arrival time -5/+4 samples
start = int(time_window[0]) #first time sample
end = int(time_window[-1]) #last time sample
amplitude_window = data_to_vectorise[
start:end +
1] #extract the amplitude of the total vector trace at these time samples
#set up the interpolation function to measure amplitude at any time with a cubic spline function
f = interp1d(time_window, amplitude_window, kind='cubic')
#interpolate every 0.1ms
interpolated_amp = np.array([f(t) for t in np.arange(start, end, 0.1)])
#measure the average value in each window on the total vector trace
mean_back_window = running_mean(interpolated_amp,
back_window)[:-fore_window]
mean_fore_window = running_mean(interpolated_amp,
fore_window)[back_window:]
#calculate the ratio between fore and back window
auto_pick_ratio = mean_fore_window / mean_back_window
##### previous interpolation was running too slowly with 100 samples, went down to 40 samples, which now takes about 3ms (+5ms to read the data in the first place)
#add the calculated first arrival time to the firt_arrival_time array n time (n = number of components)
first_arrival_time = np.append(
first_arrival_time,
np.repeat(auto_pick_ratio.argmax() / 10 + start,
nbr_of_components))
#every 2000 loops tell the users how much has been done of the calculation
if i % 2000 == 0:
print(
'The automatic first break picking has done {0:.1f}% of the work, almost there!'
.format(i / (nbr_of_SP * nbr_of_geophone) * 100))
tac = timeit.default_timer()
print('The automatic first break picking took {0:.1f} seconds'.format(tac -
tic))
# Save the first arrival time to a text file to import it later on
np.savetxt('FirstBreakTime.txt', first_arrival_time, fmt='%.2f')
plt.imshow(data,
cmap=cmap,
interpolation='bilinear',
vmin=0,
vmax=vm,
aspect='auto')
plt.colorbar(label="Amplitude", shrink=0.5)
#plt.xlim(xmin=400, xmax=800)
#plt.ylim(ymax=800,ymin=1200)
#%%
########################### main process ##############################
if __name__ == "__main__":
'''return a SEGYFile object '''
segy = _read_segy('Data/CX_pst_3710_3720.sgy', headonly=True)
'''read the header and trace'''
#print(segy.binary_file_header)
#print(segy.traces[492].header)
segy_inf(segy)
#print(segy.textual_file_header.decode(encoding='cp037'))
x = np.array(list(segy.textual_file_header.decode(encoding='cp037')))
print('\n'.join(''.join(row) for row in x.reshape((40, 80))))
print(segy.binary_file_header)
print(segy.traces[2].header)
'''etract line and plot the line'''
line3714 = extract_line(segy, 3714) #rows are traces
plot_line_attribute(line3714, cmap="seismic", percent=99)
#%%
try:
max_amp = float(sys.argv[5])
except:
print('Please enter a valid integer for the maximum amplitude:')
print("Use the following command to run this script")
print(
"python SEGY_filter_panels_multi.py \"[filename]\" [initial trace] [number of traces] [min amp] [max amp]"
)
max_amp = 1
# exit(0)
#just reading the SEGY
# #----------------------------------------------------------------------------------------
# stream = _read_su(filename,headonly=True)
stream = _read_segy(filename, headonly=True)
# stream = read(filename,format='segy')
# print(stream.textual_file_header)
# exit(0)
#print(stream)
print(stream.textual_file_header.decode())
#print(stream.binary_file_header)
print("Trace Length=",stream.traces[0].npts, \
'sampling interval=',stream.traces[0].header.sample_interval_in_ms_for_this_trace)
# init_trace=0
# num_trace=20
tlen = stream.traces[0].npts
dt = stream.traces[0].header.sample_interval_in_ms_for_this_trace
np.require(data, dtype=np.float32)
trace = Trace(data=data)
trace.stats.delta = 0.01
trace.stats.starttime = UTCDateTime(2011, 11, 11, 11, 11, 11)
if not hasattr(trace.stats, 'segy.trace_header'):
trace.stats.segy = {}
trace.stats.segy.trace_header = SEGYTraceHeader()
trace.stats.segy.trace_header = stream.traces[idx].header
out.append(trace)
inputfile = 'test.sgy'
print('The SEG-Y files is loading ... Please be patient')
tic = timeit.default_timer()
stream = _read_segy(inputfile, headonly=True)
toc = timeit.default_timer()
print('The loading took {0:.0f} seconds'.format(toc - tic))
""" extract all source and receiver (geophone) coordinates """
source_x = np.array([t.header.source_coordinate_x for t in stream.traces])[::3]
source_y = np.array([t.header.source_coordinate_y for t in stream.traces])[::3]
geo_x = np.array([t.header.group_coordinate_x for t in stream.traces])[::3]
geo_y = np.array([t.header.group_coordinate_x for t in stream.traces])[::3]
""" measures the source to receiver azimuth """
azimuth = np.round([(360 + math.degrees(
math.atan2((source_x[t] - geo_x[t]), (source_y[t] - geo_y[t])))) % 360
for t in range(source_x.size)],
decimals=2)
""" create a list of all the geophones' depth """
geophone_depths = (np.array(
[t.header.datum_elevation_at_receiver_group
num_epochs = 1
batch_size = 56
patch_size = 64
num_channels = 1
num_classes = 9
all_examples = 158812
num_examples = 7500
sampler = list(range(all_examples))
running_loss = 0.0
loss_list = []
##########################
### DATASET
##########################
filename = 'data/Seismic_data.sgy'
seismicdata = _read_segy(filename, headonly=True)
# train data and lable######
labeled_data = np.load('patchdata.npy')
labels = pd.read_csv('data/classification.ixz',
delimiter=" ",
names=["Inline", "Xline", "Time", "Class"])
labels["Xline"] -= 300 - 1
labels["Time"] = labels["Time"] // 4
# prediction data #########
inline_data = np.stack(
t.data for t in seismicdata.traces if
t.header.for_3d_poststack_data_this_field_is_for_in_line_number == 500).T
train_data, test_data, train_samples, test_samples = train_test_split(
labels, sampler, random_state=42)
print(train_data.shape, test_data.shape)
def test_unpack_trace_header(self):
"""
Compares some values of the first trace header with values read with
SeisView 2 by the DMNG.
"""
file = os.path.join(self.path, '1.sgy_first_trace')
segy = _read_segy(file)
header = segy.traces[0].header
# Compare the values.
self.assertEqual(header.trace_sequence_number_within_line, 0)
self.assertEqual(header.trace_sequence_number_within_segy_file, 0)
self.assertEqual(header.original_field_record_number, 1)
self.assertEqual(header.trace_number_within_the_original_field_record,
1)
self.assertEqual(header.energy_source_point_number, 0)
self.assertEqual(header.ensemble_number, 0)
self.assertEqual(header.trace_number_within_the_ensemble, 0)
self.assertEqual(header.trace_identification_code, 1)
self.assertEqual(
header.number_of_vertically_summed_traces_yielding_this_trace,
5)
self.assertEqual(
header.number_of_horizontally_stacked_traces_yielding_this_trace,
0)
self.assertEqual(header.data_use, 0)
self.assertEqual(getattr(
header, 'distance_from_center_of_the_' +
'source_point_to_the_center_of_the_receiver_group'), 0)
self.assertEqual(header.receiver_group_elevation, 0)
self.assertEqual(header.surface_elevation_at_source, 0)
self.assertEqual(header.source_depth_below_surface, 0)
self.assertEqual(header.datum_elevation_at_receiver_group, 0)
self.assertEqual(header.datum_elevation_at_source, 0)
self.assertEqual(header.water_depth_at_source, 0)
self.assertEqual(header.water_depth_at_group, 0)
self.assertEqual(
header.scalar_to_be_applied_to_all_elevations_and_depths, -100)
self.assertEqual(header.scalar_to_be_applied_to_all_coordinates, -100)
self.assertEqual(header.source_coordinate_x, 0)
self.assertEqual(header.source_coordinate_y, 0)
self.assertEqual(header.group_coordinate_x, 300)
self.assertEqual(header.group_coordinate_y, 0)
self.assertEqual(header.coordinate_units, 0)
self.assertEqual(header.weathering_velocity, 0)
self.assertEqual(header.subweathering_velocity, 0)
self.assertEqual(header.uphole_time_at_source_in_ms, 0)
self.assertEqual(header.uphole_time_at_group_in_ms, 0)
self.assertEqual(header.source_static_correction_in_ms, 0)
self.assertEqual(header.group_static_correction_in_ms, 0)
self.assertEqual(header.total_static_applied_in_ms, 0)
self.assertEqual(header.lag_time_A, 0)
self.assertEqual(header.lag_time_B, 0)
self.assertEqual(header.delay_recording_time, -100)
self.assertEqual(header.mute_time_start_time_in_ms, 0)
self.assertEqual(header.mute_time_end_time_in_ms, 0)
self.assertEqual(header.number_of_samples_in_this_trace, 8000)
self.assertEqual(header.sample_interval_in_ms_for_this_trace, 250)
self.assertEqual(header.gain_type_of_field_instruments, 0)
self.assertEqual(header.instrument_gain_constant, 24)
self.assertEqual(header.instrument_early_or_initial_gain, 0)
self.assertEqual(header.correlated, 0)
self.assertEqual(header.sweep_frequency_at_start, 0)
self.assertEqual(header.sweep_frequency_at_end, 0)
self.assertEqual(header.sweep_length_in_ms, 0)
self.assertEqual(header.sweep_type, 0)
self.assertEqual(header.sweep_trace_taper_length_at_start_in_ms, 0)
self.assertEqual(header.sweep_trace_taper_length_at_end_in_ms, 0)
self.assertEqual(header.taper_type, 0)
self.assertEqual(header.alias_filter_frequency, 1666)
self.assertEqual(header.alias_filter_slope, 0)
self.assertEqual(header.notch_filter_frequency, 0)
self.assertEqual(header.notch_filter_slope, 0)
self.assertEqual(header.low_cut_frequency, 0)
self.assertEqual(header.high_cut_frequency, 0)
self.assertEqual(header.low_cut_slope, 0)
self.assertEqual(header.high_cut_slope, 0)
self.assertEqual(header.year_data_recorded, 2005)
self.assertEqual(header.day_of_year, 353)
self.assertEqual(header.hour_of_day, 15)
self.assertEqual(header.minute_of_hour, 7)
self.assertEqual(header.second_of_minute, 54)
self.assertEqual(header.time_basis_code, 0)
self.assertEqual(header.trace_weighting_factor, 0)
self.assertEqual(
header.geophone_group_number_of_roll_switch_position_one, 2)
self.assertEqual(header.geophone_group_number_of_trace_number_one, 2)
self.assertEqual(header.geophone_group_number_of_last_trace, 0)
self.assertEqual(header.gap_size, 0)
self.assertEqual(header.over_travel_associated_with_taper, 0)
self.assertEqual(
header.x_coordinate_of_ensemble_position_of_this_trace, 0)
self.assertEqual(
header.y_coordinate_of_ensemble_position_of_this_trace, 0)
self.assertEqual(
header.for_3d_poststack_data_this_field_is_for_in_line_number, 0)
self.assertEqual(
header.for_3d_poststack_data_this_field_is_for_cross_line_number,
0)
self.assertEqual(header.shotpoint_number, 0)
self.assertEqual(
header.scalar_to_be_applied_to_the_shotpoint_number, 0)
self.assertEqual(header.trace_value_measurement_unit, 0)
self.assertEqual(header.transduction_constant_mantissa, 0)
self.assertEqual(header.transduction_constant_exponent, 0)
self.assertEqual(header.transduction_units, 0)
self.assertEqual(header.device_trace_identifier, 0)
self.assertEqual(header.scalar_to_be_applied_to_times, 0)
self.assertEqual(header.source_type_orientation, 0)
self.assertEqual(header.source_energy_direction_mantissa, 0)
self.assertEqual(header.source_energy_direction_exponent, 0)
self.assertEqual(header.source_measurement_mantissa, 0)
self.assertEqual(header.source_measurement_exponent, 0)
self.assertEqual(header.source_measurement_unit, 0)
plt.xlabel(u"Frequency(Hz)")
plt.ylabel(u"Time(ms)")
#plt.title(u"Time-frequency Spectrum")
plt.colorbar()
ax = plt.gca()
ax.invert_yaxis()
plt.tight_layout()
plt.show()
return cwtmatr, freqs
##################### Main processes #################################
if __name__ == "__main__":
import read_segy as rsegy
import resampling as rs
segy = _read_segy('data/seis/CX_ZJ_ori.SGY', headonly=True)
# time_start = 900.0
# time_stop = 1500.0
# time_step = 2.0 # ms
# inline = 3662
# xline = 1938
trace = rsegy.extract_seismic(segy, line=3662, xline=1938,
time_start = 810, time_stop= 1500, time_step=2, name='amp')
trace_res = rs.resample(trace.time, trace.amp,
time_start_re = 820,
time_stop_re = 1400,
time_step_re = 1,
kind="quadratic", plot=False,
logname='amp')
cc,ff = spectrum_cwt(trace_res.time, trace_res.amp/10000,
colorscale=1, widths=100, wavelet='morl', freqmax=100)
def get_nsamples(target):
section = segy._read_segy(target, unpack_headers=True)
return section.traces[0].header.number_of_samples_in_this_trace
def get_ntraces(target):
section = segy._read_segy(target, unpack_headers=True)
return len(section.traces)
def read_seismic():
try:
t0 = time.time()
data = segy_dir_path.get()
#use obspy to read data
stream = _read_segy(data, headonly=True)
#create stream object
num_trace = len(stream.traces)
#get ns from binary header
ns = stream.binary_file_header.number_of_samples_per_data_trace
min_il = int(min_inline.get())
max_il = int(int(max_inline.get()) + 1)
il_step = int(inline_step.get())
min_xl = int(min_xline.get())
max_xl = int(int(max_xline.get()) + 1)
xl_step = int(xline_step.get())
inline_range = np.arange(min_il, max_il, il_step)
xline_range = np.arange(min_xl, max_xl, xl_step)
total_traces_calculated = (len(inline_range) * len(xline_range))
total_missing_traces = int(total_traces_calculated - num_trace)
lines = [
"Total no of traces read : {}".format(num_trace),
"Total number of calculated traces :{}".format(
total_traces_calculated),
"Total traces to pad: {}".format(total_missing_traces)
]
tkinter.messagebox.showinfo("INFO", "\n".join(lines))
data = np.stack(t.data for t in stream.traces)
#get z dim
bounds, nt = data.shape
data_t = data.T
#Pad data with zero traces
data_padded = np.pad(data_t, [(0, 0), (0, total_missing_traces)],
mode='constant')
data_padded = data_padded.T
#Reshape data to a 3d cube
shaped_data = np.reshape(data_padded,
(inline_range.size, xline_range.size, nt))
#calculate the right colorbar scale
vm = np.percentile(shaped_data, 99)
#Define the mayavi data source
source = mlab.pipeline.scalar_field(shaped_data)
source.spacing = [il_step, xl_step, -4]
for axis in ['x', 'y', 'z']:
plane = mlab.pipeline.image_plane_widget(
source,
plane_orientation='{}_axes'.format(axis),
colormap="gray",
vmin=-vm,
vmax=vm,
slice_index=20)
plane.module_manager.scalar_lut_manager.reverse_lut = True
mlab.xlabel("XLINE")
mlab.ylabel("INLINE")
mlab.zlabel("TIME/DEPTH")
#mlab.title("3D Seismic Cube : {}".format(str(segy_dir_path.get())))
#mlab.colorbar()
mlab.show()
except ValueError:
tk.messagebox.showinfo("ERROR", "Please check your input bounds")
close_window()
except FileNotFoundError:
tk.messagebox.showinfo("ERROR", "Please check your input File")
close_window()
def get_tbase(target):
# Read the file.
section = segy._read_segy(target, unpack_headers=True)
nsamples = section.traces[0].header.number_of_samples_in_this_trace
dt = section.traces[0].header.sample_interval_in_ms_for_this_trace
return 0.001 * np.arange(0, nsamples * dt, dt)
def segy2segy(inSEGY,
outSEGY,
s_srs=23029,
t_srs=23030,
s_coord='Source',
t_coord='CDP',
force_scaling=False,
scaler=1.):
'''
Transform coordinates in SEGY files. This function makes use of the GDAL
library for processing coordinates and projections.
Parameters
----------
inSEGY : Filename
Input SEGY file.
outSEGY : Filename
Output SEGY file.
s_srs : Integer
Spatial reference system of the input (source) file. Must be defined as
a EPSG code, i.e. 23029 for ED50 / UTM Zone 29N
t_srs : Integer
Spatial reference system of the output (target) file. Must be defined
as a EPSG code, i.e. 23030 for ED50 / UTM Zone 30N
s_coord : String
Position of the coordinates in the input SEGY file. The field corresponds
to a byte position in the binary file.
t_coord : String
Position of the coordinates in the output SEGY file. The field corresponds
to a byte position in the binary file.
force_scaling : Boolean
If True, the program will use the number defined by the scaler argument
to calculate the coordinates. Default is False and so the program will read
the coordinate scaler from the SEGY file. It will use the same value for
writing coordinates in the new SEGY file.
scaler : Float
Used in combination with force_scaling. The scaler is defined like for
a SEGY file, for example -100 for dividing by 100 when reading.
'''
# read coordinates from input
XYarray, XYscale = segyXY(inSEGY, s_coord, force_scaling, scaler)
# transform coordinates
newXYarray = spatial.projectPoints(XYarray, s_srs, t_srs)
# Apply scaling
newXYarray = newXYarray / np.column_stack((XYscale, XYscale))
# load SEGY object (headers only)
seis = _read_segy(inSEGY, headonly=True)
traces = seis.traces
# get key for coordinates position in output file
Xcoord, Ycoord = coordKeys[t_coord.lower()]
# insert new coordinates in SEGY object
for i, trace in enumerate(traces):
trace.header.__setattr__(Xcoord, np.round(newXYarray[i, 0]))
trace.header.__setattr__(Ycoord, np.round(newXYarray[i, 1]))
# write output SEGY with new coordinates
seis.write(outSEGY)
def get_sample_rate_in_seconds(target):
section = segy._read_segy(target, unpack_headers=True)
return 1e-6 * section.traces[0].header.sample_interval_in_ms_for_this_trace