def test_reading_and_writing_different_byteorders(self):
"""
Writing different byte orders should not change
"""
# This file is little endian.
file = os.path.join(self.path, '1.su_first_trace')
with NamedTemporaryFile() as tf:
outfile = tf.name
# The following should both work.
su = _read_su(file)
data = su.traces[0].data
# Also read the original file.
with open(file, 'rb') as f:
org_data = f.read()
self.assertEqual(su.endian, '<')
# Write it little endian.
su.write(outfile, endian='<')
with open(outfile, 'rb') as f:
new_data = f.read()
self.assertEqual(org_data, new_data)
su2 = _read_su(outfile)
self.assertEqual(su2.endian, '<')
np.testing.assert_array_equal(data, su2.traces[0].data)
# Write it big endian.
su.write(outfile, endian='>')
with open(outfile, 'rb') as f:
new_data = f.read()
self.assertFalse(org_data == new_data)
su3 = _read_su(outfile)
self.assertEqual(su3.endian, '>')
np.testing.assert_array_equal(data, su3.traces[0].data)
def test_reading_and_writing_different_byteorders(self):
"""
Writing different byte orders should not change
"""
# This file is little endian.
file = os.path.join(self.path, "1.su_first_trace")
with NamedTemporaryFile() as tf:
outfile = tf.name
# The following should both work.
su = _read_su(file)
data = su.traces[0].data
# Also read the original file.
with open(file, "rb") as f:
org_data = f.read()
self.assertEqual(su.endian, "<")
# Write it little endian.
su.write(outfile, endian="<")
with open(outfile, "rb") as f:
new_data = f.read()
self.assertEqual(org_data, new_data)
su2 = _read_su(outfile)
self.assertEqual(su2.endian, "<")
np.testing.assert_array_equal(data, su2.traces[0].data)
# Write it big endian.
su.write(outfile, endian=">")
with open(outfile, "rb") as f:
new_data = f.read()
self.assertFalse(org_data == new_data)
su3 = _read_su(outfile)
self.assertEqual(su3.endian, ">")
np.testing.assert_array_equal(data, su3.traces[0].data)
def read_su2d(data):
"""Reads a Seismic Unix data file
input:
data: is a string with your data name
output:
sdata: matrix where each column represents a seismic trace
header: a dictionary with header words"""
st = _read_su(data)
#Get information from traces
ns = len(st.traces[0].data)
tracl = len(st.traces) #number of traces
dt = (st.traces[0].header.sample_interval_in_ms_for_this_trace
) / 1000000 # sampling rate in seconds
ft = (dt * ns) - dt #final time in seconds
header = {"dt": dt, "ns": ns, "tracl": tracl}
#Write the data into a matrix
dado = np.zeros((tracl, ns)) #empty matrix where I write the data
i = 0
while i < tracl:
dado[i][:] = st.traces[i].data
i = i + 1
sdata = np.transpose(dado)
return (sdata, header)
def test_enforcing_byteorders_while_reading(self):
"""
Tests whether or not enforcing the byte order while reading and writing
does something and works at all. Using the wrong byte order will most
likely raise an Exception.
"""
# This file is little endian.
file = os.path.join(self.path, '1.su_first_trace')
# The following should both work.
su = _read_su(file)
self.assertEqual(su.endian, '<')
su = _read_su(file, endian='<')
self.assertEqual(su.endian, '<')
# The following not because it will unpack the header and try to unpack
# the number of data samples specified there which will of course not
# correct.
self.assertRaises(SEGYTraceReadingError, _read_su, file, endian='>')
def test_enforcing_byteorders_while_reading(self):
"""
Tests whether or not enforcing the byte order while reading and writing
does something and works at all. Using the wrong byte order will most
likely raise an Exception.
"""
# This file is little endian.
file = os.path.join(self.path, "1.su_first_trace")
# The following should both work.
su = _read_su(file)
self.assertEqual(su.endian, "<")
su = _read_su(file, endian="<")
self.assertEqual(su.endian, "<")
# The following not because it will unpack the header and try to unpack
# the number of data samples specified there which will of course not
# correct.
self.assertRaises(SEGYTraceReadingError, _read_su, file, endian=">")
def test_read_bytes_io(self):
"""
Tests reading from BytesIO instances.
"""
# 1
filename = os.path.join(self.path, '1.su_first_trace')
with open(filename, 'rb') as fp:
data = fp.read()
st = _read_su(io.BytesIO(data))
self.assertEqual(len(st.traces[0].data), 8000)
def test_read_bytes_io(self):
"""
Tests reading from BytesIO instances.
"""
# 1
filename = os.path.join(self.path, "1.su_first_trace")
with open(filename, "rb") as fp:
data = fp.read()
st = _read_su(io.BytesIO(data))
self.assertEqual(len(st.traces[0].data), 8000)
def test_unpacking_su_data(self):
"""
Unpacks data and compares them to data unpacked by Madagascar.
"""
# This file has the same data as 1.sgy_first_trace.
file = os.path.join(self.path, '1.su_first_trace')
data_file = os.path.join(self.path, '1.sgy_first_trace.npy')
su = _read_su(file)
data = su.traces[0].data
# The data is written as integer so it is also converted to float32.
correct_data = np.require(np.load(data_file).ravel(), np.float32)
# Compare both.
np.testing.assert_array_equal(correct_data, data)
def test_unpacking_su_data(self):
"""
Unpacks data and compares them to data unpacked by Madagascar.
"""
# This file has the same data as 1.sgy_first_trace.
file = os.path.join(self.path, "1.su_first_trace")
data_file = os.path.join(self.path, "1.sgy_first_trace.npy")
su = _read_su(file)
data = su.traces[0].data
# The data is written as integer so it is also converted to float32.
correct_data = np.require(np.load(data_file).ravel(), np.float32)
# Compare both.
np.testing.assert_array_equal(correct_data, data)
def test_read_and_write_su(self):
"""
Reading and writing a SU file should not change it.
"""
file = os.path.join(self.path, '1.su_first_trace')
# Read the original file once.
with open(file, 'rb') as f:
org_data = f.read()
with NamedTemporaryFile() as tf:
outfile = tf.name
# Read the SU file.
su = _read_su(file)
# Write it.
su.write(outfile)
with open(outfile, 'rb') as f:
new_data = f.read()
# Should be identical!
self.assertEqual(org_data, new_data)
def test_read_and_write_su(self):
"""
Reading and writing a SU file should not change it.
"""
file = os.path.join(self.path, "1.su_first_trace")
# Read the original file once.
with open(file, "rb") as f:
org_data = f.read()
with NamedTemporaryFile() as tf:
outfile = tf.name
# Read the SU file.
su = _read_su(file)
# Write it.
su.write(outfile)
with open(outfile, "rb") as f:
new_data = f.read()
# Should be identical!
self.assertEqual(org_data, new_data)
def handleMsg(msgJ):
"""Process the message in msgJ.
Parameters:
msgJ: dict
Dictionary with command sent from client
Returns:
string
JSON string with command response
Commands are of the form:
{'cmd' : 'getCCC', 'param0': 'param0val', ...}
Response is a string of the form (note that JSON is picky that keys
and strings should be enclosed in double quotes:
'{"cmd" : "getCmd", "cmd" : "<response>"}'
{'cmd':'getHello'} -> {"cmd":"getHello", "hello": "world"}
{'cmd':'getSegyHdrs', filename: f} ->
{"cmd":"getSegyHdrs", "segyhdrs":
{ns:nsamps, dt:dt: hdrs:[hdr1, hdr2...]}}
FIXME FIXME - this currently returns "segy", not "ensemble" as the key
WARNING - you must call getSegyHdrs first
flo and fhi are optional. If they are not present, no filtering
{'cmd':'getEnsemble', filename:f, ensemble:n, [flo:flo, fhi: fhi]} ->
{"cmd":"getEnsemble", "segy":
{ns:nsamps, dt:dt: traces:[trc1, trc2...]}}
"""
print('msgJ: {}'.format(msgJ))
if msgJ['cmd'].lower() == 'getsegyhdrs':
filename = msgJ['filename']
print('getting segyhdr >{}<, filename: {}'.format(msgJ, filename))
t0 =datetime.now()
if segy.filename != filename:
# new file - open it
try:
s = _read_su(filename, endian='>', headonly=True)
segy.filename = filename
segy.segyfile = s
except:
ret = json.dumps({"cmd":"readSegy", "error": "Error reading file {}".format(filename)})
return ret
print("ntrcs = {}".format(len(segy.segyfile.traces)))
hdrs = [segy.getTrc(i, headonly=True) for i in range(len(segy.segyfile.traces))]
nsamps = segy.segyfile.traces[0].header.number_of_samples_in_this_trace
dt = segy.segyfile.traces[0].header.sample_interval_in_ms_for_this_trace/(1000.*1000.)
segy.nsamps = nsamps
segy.dt = dt
segy.hdrs = hdrs
ret = json.dumps({"cmd": "getSegyHdrs",
"segyHdrs" : json.dumps({"dt":dt, "ns":nsamps,
"filename": segy.filename,
"hdrs":hdrs})})
return ret
if msgJ['cmd'].lower() == 'getnmo':
# assumes getSegyHdrs called already. needed?
print('nmo getting ens', msgJ)
if segy.segyfile is None:
ret = json.dumps({"cmd":"getNMO", "error": "Error doing NMO: call getSegyHdrs first."})
return ret
try:
vnmo = msgJ['vnmo']
tnmo = msgJ['tnmo']
print('got nmo', vnmo, tnmo)
except:
vnmo = 'vnmo=2000'
tnmo = 'tnmo=0'
try:
ens = int(msgJ['ensemble'])
try:
# open a tmp file
tmpf = tempfile.NamedTemporaryFile(delete=False) # output
print('opened', tmpf.name)
# and the segy input file
with open(msgJ['filename'], 'rb') as sf: # input
# and do the nmo
p1 = sp.Popen(['suwind', 'key=cdp', 'min={}'.format(ens), 'max={}'.format(ens)], stdin=sf, stdout=sp.PIPE)
p2 = sp.Popen(['sugain', "tpow=1.5"], stdin=p1.stdout, stdout=sp.PIPE)
p3 = sp.Popen(['sunmo', vnmo, tnmo], stdin=p2.stdout, stdout=tmpf)
print('p2 ok')
p1.stdout.close()
p2.stdout.close()
out,err = p3.communicate()
print('suwind/sugain/nmo', out, err)
#print('nmo call', ret)
tmpf.close()
# nmo segy file
nsegy = Segy()
nsegy.filename = tmpf.name
nsegy.segyfile = _read_su(tmpf.name, headonly=False)
nmontrcs = len(nsegy.segyfile.traces)
#print('nmo ntrcs', nmontrcs)
nmotrcs = [nsegy.getTrc(i, headonly=False, trctype='seismic') for i in range(nmontrcs)]
# delete the tmp file
#os.unlink(tmpf.name)
print('nmo trcs', len(nmotrcs))
except:
print('err nmo', ens)
ret = json.dumps({"cmd":"getNMO", "error": "Error performing NMO"})
return ret
ntrc = len(nmotrcs)
except:
print('err ens', msgJ)
ret = json.dumps({"cmd":"getNMO", "error": "Error reading ensemble number"})
return ret
print("ens = {} ntrc={}".format(ens, len(nmotrcs)))
# dt/nsamps could change from the original due to decimation
dt = nmotrcs[0]["dt"]
nsamps = nmotrcs[0]["nsamps"]
print('dt, nsamps', dt, nsamps)
#print(json.dumps(traces[0]))
ret = json.dumps({"cmd": "getNMO",
"NMO" : json.dumps({"dt":dt, "ns":nsamps,
"filename": nsegy.filename,
"traces":nmotrcs})})
return ret
if msgJ['cmd'].lower() == 'getvelan':
if segy.segyfile is None:
ret = json.dumps({"cmd":"getEnsemble", "error": "Error reading ensemble"})
return ret
try:
ens = int(msgJ['ensemble'])
print('in velan', ens)
except:
print('no ens')
return json.dumps({"cmd":"getVelan", "error": "Error reading ensemble number"})
try:
dv = msgJ['dv']
fv = msgJ['fv']
nv = msgJ['nv']
except:
fv=1500
dv=100
nv=50
dvstr = "dv={}".format(dv)
fvstr = "fv={}".format(fv)
nvstr = "nv={}".format(nv)
tmpf = tempfile.NamedTemporaryFile(delete=False) # output
with open(segy.filename, 'rb') as sf:# input
#tmpfname = tmpf.name
p1 = sp.Popen(['suwind', 'key=cdp', 'min={}'.format(ens), 'max={}'.format(ens)], stdin=sf, stdout=sp.PIPE)
p2 = sp.Popen(['sugain', "tpow=1.5"], stdin=p1.stdout, stdout=sp.PIPE)
p3 = sp.Popen(['suvelan', dvstr, fvstr, nvstr], stdin=p2.stdout, stdout=tmpf)
print('p3 ok')
p1.stdout.close()
p2.stdout.close()
out,err = p3.communicate()
print('suwind/sugain/velan', out, err)
#ret = sp.call(['suvelan', dvstr, fvstr, nvstr], stdin=sf, stdout=tmpf)
#print('wrote suvelan file', ret, tmpf.name)
tmpf.close()
vsegy = Segy()
vsegy.filename=tmpf.name
vsegy.segyfile = _read_su(tmpf.name, headonly=False)
vtrcs = [vsegy.getTrc(i, headonly=False, trctype='velocity', v0=fv, dv=dv) for i in range(len(vsegy.segyfile.traces)) if vsegy.segyfile.traces[i].header.ensemble_number == ens]
print('nvel trcs', len(vtrcs))
dt = vtrcs[0]["dt"]
nsamps = vtrcs[0]["nsamps"]
print('dt, nsamps', dt, nsamps)
#print(json.dumps(traces[0]))
ret = json.dumps({"cmd": "getVelan",
"velan" : json.dumps({"dt":dt, "ns":nsamps, "fv":fv,
"dv":dv, "nv":nv,
"filename": vsegy.filename,
"traces":vtrcs})})
#ret = json.dumps({"cmd": "velan", "velan": "test"})
return ret
if msgJ["cmd"].lower() == "gethello":
ret = json.dumps({"cmd": "hello", "hello": "world"})
return ret
