def build_data(self):
"""
create data to write to an input file
"""
# read edi file to edi object
eo = mtedi.Edi()
eo.readfile(self.edipath)
self.edi_object = eo
# define z
zr = np.real(eo.Z.z)
# sign of imaginary component needs to be reversed for the pek1d inversion code
zi = -np.imag(eo.Z.z)
ze = eo.Z.zerr
z = zr + 1j * zi
# set errorfloors
if type(self.errorfloor) in [int, float]:
self.errorfloor = np.ones([2, 2]) * self.errorfloor
if self.errorfloor_type in ['relative', 'offdiagonals']:
zer = ze / np.abs(z)
for i in range(2):
for j in range(2):
zer[:, i, j][(zer[:, i, j] <
self.errorfloor[i, j])] = self.errorfloor[i,
j]
ze = np.abs(z) * zer
if self.errorfloor_type == 'offdiagonals':
for i in range(2):
for iz in range(len(z)):
if ze[iz, i, i] < ze[iz, i, 1 - i]:
ze[iz, i, i] = ze[iz, i, 1 - i]
elif self.errorfloor_type == 'absolute':
for i in range(2):
for j in range(2):
ze[:, i, j][(ze[:, i, j] <
self.errorfloor[i, j])] = self.errorfloor[i,
j]
# define header info for data file
header = '{:>5}\n{:>5}'.format(self.mode, len(eo.Z.resistivity))
# create data array
data_list = [1. / eo.freq]
for i in range(2):
for j in range(2):
if self.mode == 'I':
dd = [zr, ze, zi, ze]
for d in dd:
data_list.append(d[:, i, j])
self.header = header
self.data = np.vstack(data_list).T
self.z = zr + 1j * zi
self.zerr = ze
def _read_edi_file(self):
"""
read in edi file and set attributes accordingly
"""
self.edi_object = MTedi.Edi(self.fn, datatype=self._data_type)
self.lat = self.edi_object.lat
self.lon = self.edi_object.lon
self.elev = self.edi_object.elev
self.Z = self.edi_object.Z
self.Tipper = self.edi_object.Tipper
self.station = self.edi_object.station
#--> get utm coordinates from lat and lon
self._get_utm()
#--> make sure things are ordered from high frequency to low
self._check_freq_order()
#--> compute phase tensor
self.pt = MTpt.PhaseTensor(z_object=self.Z, freq=self.Z.freq)
#--> compute invariants
self.zinv = MTinv.Zinvariants(z_object=self.Z)
def convert2columns(fn):
try:
e_object = MTedi.Edi(filename=fn)
except:
print('invalid EDI file')
raise
filebase = op.splitext(fn)[0]
outfn = filebase + '.columns'
outstring = ''
for i, f in enumerate(e_object.freq):
outstring += '{0:> 10.5f} '.format(f)
for j in range(2):
for k in range(2):
outstring += '\t{0:.4f} {1:.4f} {2:.4f} '.format(float(np.real(e_object.Z.z[i, j, k])),
float(np.imag(e_object.Z.z[i, j, k])), e_object.Z.z_err[i, j, k])
outstring += '\n'
with open(outfn, 'w') as F:
F.write(outstring)
print('\tWritten data to file: {0}\n'.format(outfn))
return outfn
def __init__(self, fn=None, **kwargs):
self._fn = fn
self.station = kwargs.pop('station', None)
self._lat = kwargs.pop('lat', None)
self._lon = kwargs.pop('lon', None)
self._elev = kwargs.pop('elev', None)
self._Z = kwargs.pop('Z', MTz.Z())
self._Tipper = kwargs.pop('Tipper', MTz.Tipper())
self._utm_zone = kwargs.pop('utm_zone', None)
self._east = kwargs.pop('east', None)
self._north = kwargs.pop('north', None)
self._rotation_angle = kwargs.pop('rotation_angle', 0)
self.edi_object = MTedi.Edi()
self.pt = None
self.zinv = None
self._utm_ellipsoid = 23
#provide key words to fill values if an edi file does not exist
for key in kwargs.keys():
setattr(self, key, kwargs[key])
#--> read in the file name given
if self._fn is not None:
self._set_fn(fn)
def main():
if len(sys.argv) < 4:
print '\nNeed at least 2 arguments: <EDI file> '\
'<output directory> <#iterations> \n\n'\
'Optional arguments: \n [sigma scaling]\n'\
' [batch process flag "-b"] \n\n'
return
try:
fn_in = sys.argv[1]
fn_in = op.join(op.abspath(os.curdir), fn_in)
edi_object = MTedi.Edi(filename=fn_in)
except:
print '\n\tERROR - File is not a valid EDI file: {0}\n'.format(fn_in)
sys.exit()
try:
outdir = sys.argv[2]
outdir = op.join(op.abspath(os.curdir), outdir)
if not op.isdir(outdir):
os.makedirs(outdir)
except:
print '\n\tERROR - Output directory does not exist and cannot be'\
' generated: {0}\n'.format(outdir)
sys.exit()
try:
n_iterations = int(float(sys.argv[3]))
if n_iterations < 0:
raise
except:
print '\n\t ERROR - number of iterations must be a positive integer (incl. 0)\n'
sys.exit()
fn_out = None
sigma_scaling = 1
if len(sys.argv) > 4:
try:
sigma_scaling = float(sys.argv[4])
if sigma_scaling <= 0:
raise
except:
sigma_scaling = 1
print '\nWARNING - Invalid sigma scale ..using 1 instead\n'
try:
print
print 'Generating PTcross input data file'
if n_iterations != 0:
print '(evaluating {0} realisations of Z)'.format(n_iterations)
print '\t...'
generate_ptcrossdata_file(edi_object, n_iterations, sigma_scaling,
outdir, fn_out)
except:
raise
print '\n\tERROR - could not generate PT Cross Data file - check EDI file!\n'
def get_station_xy(edipath, savepath=None, basename='stationxy.dat'):
edilst = [ff for ff in os.listdir(edipath) if ff.endswith('.edi')]
xylst = []
for edifile in edilst:
eo = mtedi.Edi(op.join(edipath, edifile))
xylst.append([eo.station, eo.lon, eo.lat])
with open(op.join(savepath, basename), 'w') as xyfile:
xyfile.write('station x y\n')
xyfile.writelines(['{} {} {}\n'.format(*line) for line in xylst])
def read_edifiles(self):
"""
"""
self.find_edifiles()
if len(self.edifiles) > 0:
self.edi_objects = [mtedi.Edi(filename=efile) for efile in
list(self.edifiles.values())]
def convert_edi_coordinates_to_kml_file(edi_filelist, outfilename=None):
kml_string = ''
kml_string += '<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n'
kml_string += '<kml xmlns=\"http://www.opengis.net/kml/2.2\">\n'
kml_string += '<Document>\n'
for edi_idx, edi in enumerate(edi_filelist):
e = EDI.Edi()
e.readfile(edi)
lat = e.lat
lon = e.lon
ele = e.elev
station = e.head['dataid']
kml = []
description = 'File: {0}'.format(e.filename)
kml.append(' <Placemark>')
kml.append(' <name>%s</name>' % station)
kml.append(' <description>')
kml.append(' <p>%s</p>' % description)
kml.append(' </description>')
kml.append(' <Point>')
kml.append(' <coordinates>%f,%f,%f</coordinates>' %
(lon, lat, ele))
kml.append(' </Point>')
kml.append(' </Placemark>')
kml_string += '\n'.join(kml)
kml_string += '\n</Document>\n'
kml_string += '</kml>\n'
if outfilename is None:
outfilename = op.abspath('edi_coordinates.kml')
else:
try:
outfilename = op.abspath(op.join('.', outfilename))
except:
outfilename = op.abspath('edi_coordinates.kml')
outfilename = MTfh.make_unique_filename(outfilename)
fileObj = open(outfilename, 'w')
fileObj.write(kml_string)
fileObj.close()
return outfilename
def main():
if len(sys.argv) < 3:
print '\nNeed at least 2 arguments: <EDI file> '\
'<output directory> \n\n'\
'Optional arguments: \n [output filename]\n'\
' [batch process flag "-b"] \n\n'
return
try:
fn_in = sys.argv[1]
fn_in = op.join(op.abspath(os.curdir), fn_in)
edi_object = MTedi.Edi(filename=fn_in)
except:
print '\n\tERROR - File is not a valid EDI file: {0}\n'.format(fn_in)
sys.exit()
try:
outdir = sys.argv[2]
outdir = op.join(op.abspath(os.curdir), outdir)
if not op.isdir(outdir):
os.makedirs(outdir)
except:
print '\n\tERROR - Output directory does not exist and cannot be'\
' generated: {0}\n'.format(outdir)
sys.exit()
fn_out = None
if len(sys.argv) > 3:
try:
fn_out = sys.argv[3]
fn_out = op.join(outdir, fn_out)
except:
fn_out = None
print '\nWARNING - Invalid output filename...using default instead\n'
try:
generate_ptwiperdata_file(edi_object, outdir, fn_out)
except:
print '\n\tERROR - could not generate PT Cross Data file - check EDI file!\n'
def test_func():
# path to edis
epath = EDI_DATA_DIR2
svdir = TEMP_OUT_DIR
elst = [
op.join(epath, edi) for edi in os.listdir(epath)
if (edi.endswith('.edi'))
]
for efile in elst[-1:]:
eo = mtedi.Edi(efile)
pr = mtpr.PlotResponse(fn=efile,
plot_num=2,
plot_tipper='yri',
plot_pt='y')
figfile = os.path.join(svdir, os.path.basename(efile)[:-4] + '.png')
pr.save_plot(figfile)
assert (os.path.exists(figfile))
#==============================================================================
if not os.path.isfile(pkfn):
azimutharr = np.zeros((nf, ns))
phimaxarr = np.zeros((nf, ns))
phiminarr = np.zeros((nf, ns))
betaarr = np.zeros((nf, ns))
colorarr = np.zeros((nf, ns))
latlst = np.zeros(ns)
lonlst = np.zeros(ns)
stationlst = []
for ss, station in enumerate(edilst):
#make a data type Z
edi1 = mtedi.Edi(station[0])
edi2 = mtedi.Edi(station[1])
pt1 = mtpt.PhaseTensor(z_object=edi1.Z)
pt2 = mtpt.PhaseTensor(z_object=edi2.Z)
stationlst.append(edi1.station)
sz, se, sn = utm2ll.LLtoUTM(refe, edi1.lat, edi1.lon)
latlst[ss] = (sn - bhn) / 1000.
lonlst[ss] = (se - bhe) / 1000.
#calculate the difference between the two phase tensor ellipses
for ii in range(nf):
phi = np.eye(2) - (np.dot(np.linalg.inv(pt1.pt[ii]), pt2.pt[ii]))
z_target = 50000
n_layers = 50
res_err = 30
phase_err = 2.5
max_iter = 20
#==============================================================================
# loop over each edi inverting for TE and TM modes
#==============================================================================
edi_list = [os.path.join(edi_path, edi) for edi in os.listdir(edi_path)
if edi.find('.edi')>0]
log_fid = file(os.path.join(save_path, 'Occam1DLog.log'), 'w')
for edi in edi_list:
e1 = mtedi.Edi(edi)
#--> write occam1d data file
ocd = occam1d.Data()
if not os.path.exists(os.path.join(save_path, e1.station)):
os.mkdir(os.path.join(save_path, e1.station))
#--> write occam1d model file
ocm = occam1d.Model()
ocm.n_layers = n_layers
ocm.bottom_layer = z_depth
ocm.z1_layer = z1_thickness
ocm.target_depth = z_target
#--> write occam1d startup files
ocs = occam1d.Startup()
def makemap(edilist, mapstretchfactor, symbolsize, labelsize, showlabel):
#import of modules here due to warnings from Matplotlib packages
#these warnings distract the 'usage' information
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import matplotlib as mpl
import mtpy.utils.filehandling as MTfh
import mtpy.core.edi as EDI
import mtpy.utils.filehandling as MTfh
lats = []
lons = []
names = []
for i in edilist:
e = EDI.Edi()
e.readfile(i)
lats.append(e.lat)
lons.append(e.lon)
names.append(e.head['dataid'].lower())
coords = zeros((len(edilist), 2))
coords[:, 0] = lats
coords[:, 1] = lons
latrange = max(lats) - min(lats)
lonrange = max(lons) - min(lons)
#center point for projection:
c = [mean(lats), mean(lons)]
#-----------------------
#Matplotlib options
mpl.rcParams['font.size'] = 10.
mpl.rcParams['axes.labelsize'] = 8.
mpl.rcParams['xtick.labelsize'] = 6.
mpl.rcParams['ytick.labelsize'] = 6.
plt.close('all')
fig = plt.figure() #figsize=(5.7,4.3))
plt.subplots_adjust(left=0.2,
right=0.9,
top=0.90,
bottom=0.1,
wspace=0.15,
hspace=0.05)
ax = plt.subplot(111)
stretch = float(mapstretchfactor)
total_latmin = max((min(lats) - stretch * latrange), -90)
total_lonmin = max((min(lons) - stretch * lonrange), -180)
total_latmax = min((max(lats) + stretch * latrange), 90)
total_lonmax = min((max(lons) + stretch * lonrange), 180)
total_latrange = total_latmax - total_latmin
total_lonrange = total_lonmax - total_lonmin
#determine number of axes labels:
maximumlabels = 5
latnum = maximumlabels
lonnum = maximumlabels
lonlat_stretch = total_lonrange / total_latrange
if int(lonlat_stretch) > 2:
#significantly more long than lat
factor = int(int(lonlat_stretch) / 2.)
latnum = int(maximumlabels / factor) + 1
lonnum = maximumlabels
elif int(lonlat_stretch) < 0.5:
#significantly more long than lat
factor = int(int(1. / lonlat_stretch) / 2.)
lonnum = int(maximumlabels / factor) + 1
latnum = maximumlabels
m = Basemap(projection='merc',
lon_0=c[1],
lat_0=c[0],
lat_ts=c[0],
llcrnrlat=total_latmin,
urcrnrlat=total_latmax,
llcrnrlon=total_lonmin,
urcrnrlon=total_lonmax,
rsphere=6371200.,
resolution='h') #,ax=ax)
lons.append(total_lonmin)
lons.append(total_lonmax)
lats.append(total_latmin)
lats.append(total_latmax)
xgrid, ygrid = m(*meshgrid(lons, lats))
xdiff = xgrid.max() - xgrid.min()
ydiff = ygrid.max() - ygrid.min()
largest_extent = max(ydiff, xdiff)
m.drawcoastlines(linewidth=0.25, ax=ax)
m.drawcountries(linewidth=0.25, ax=ax)
m.fillcontinents(color='coral', lake_color='aqua', ax=ax)
m.drawmapboundary(fill_color='aqua', ax=ax)
m.drawparallels([
round(i, 3)
for i in linspace(total_latmin, total_latmax, latnum + 1, False)
][1:],
labels=[1, 0, 0, 0],
fmt='%.1f')
m.drawmeridians([
round(i, 3)
for i in linspace(total_lonmin, total_lonmax, lonnum + 1, False)
][1:],
labels=[0, 0, 0, 1],
fmt='%.1f')
m.drawrivers()
m.etopo()
m.drawmapscale(
total_lonmax - 0.15 * total_lonrange,
total_latmax - 0.2 * total_latrange,
c[1],
c[0],
2 * 10**(int(log10(largest_extent / 1000.)) - 1),
barstyle='simple',
labelstyle='simple',
fontsize=12,
fontcolor='k',
fillcolor1='r',
fillcolor2='g',
ax=None,
format='%d',
)
for x, y, name in zip(xgrid[0, :], ygrid[:, 0], names):
plt.plot(x, y, 'v', ms=symbolsize, color='k', label=name)
if showlabel is True:
plt.text(x,
y,
name,
fontsize=labelsize,
ha='center',
va='bottom',
color='k',
backgroundcolor='r') #, labelfontsize=5)
plt.title('locations of {0} MT stations'.format(len(names)))
f1 = 'station_locations_map.png'
f2 = 'station_locations_map.svg'
f1 = MTfh.make_unique_filename(f1)
f2 = MTfh.make_unique_filename(f2)
plt.savefig(f1, format='png', dpi=200)
plt.savefig(f2, format='svg', transparent=True)
return op.abspath(f1), op.abspath(f2)
def convert2edi(station,
directory,
survey_configfile,
instrument_response_file,
string2strip=None,
datestring=None):
basedir = op.abspath(os.curdir)
#name of intermediate coherence file:
infn_coh = '{0}.coh'.format(station.upper())
directory = op.abspath(directory)
os.chdir(directory)
print
#print station,directory, survey_configfile,None,instrument_response_file
print directory
if string2strip is not None:
j_filename_list = [
i for i in os.listdir(directory)
if op.basename(i).upper().endswith('.j'.upper())
]
j_filename_list = [
i for i in j_filename_list
if '{0}'.format(station.upper()) in op.basename(i).upper()
]
j_file = j_filename_list[0]
new_j_file = '%s.j' % (station.upper())
shutil.move(j_file, new_j_file)
print 'renamed j_file %s into %s' % (j_file, new_j_file)
coh_filenames_list = [
i for i in os.listdir(directory)
if op.basename(i).upper().endswith('c2'.upper())
]
for coh in coh_filenames_list:
suffix2 = op.splitext(coh)[-1]
suffix1 = op.splitext(op.splitext(coh)[-2])[-1]
newcoh = '%s' % (station.upper()) + suffix1 + suffix2
shutil.move(coh, newcoh)
print 'renamed coh file %s into %s' % (coh, newcoh)
edifn, cohfn = MTbp.convertbirrpoutput(station, directory,
survey_configfile, None,
instrument_response_file)
if edifn is None:
print
try:
os.remove(infn_coh)
except:
pass
os.chdir(basedir)
raise MTex.MTpyError_processing(
'\tERROR - could not write EDI file - check j-file!\n')
#sys.exit()
#parse the folder, find the j-file used before (the first one matching the
#specs), and determine the date from its name by stripping off the station names
j_filename_list = [
i for i in os.listdir(directory)
if op.basename(i).upper().endswith('.j'.upper())
]
j_filename_list = [
i for i in j_filename_list
if '{0}'.format(station.upper()) in op.basename(i).upper()
]
j_file = j_filename_list[0].upper()
#print j_file
if datestring is not None:
#try:
day = int(float(datestring))
day = int(float(datestring[-2:]))
month_num = int(float(datestring[-4:-2]))
year = int(float(datestring[-6:-4]))
#except:
# datestring = None
if datestring is None:
dateinfo = j_file.replace('.J', '')
dateinfo = dateinfo.replace(station.upper(), '')
#TODO : automatise these two steps if possible...!!!
#...maybe by agreeing on a common format for the date...??
#dateinfo = dateinfo.replace('_RR_B125_','')
if string2strip is not None:
for i in string2strip:
dateinfo = dateinfo.replace(i, '')
dateinfo = dateinfo.replace(i.upper(), '')
#split the date information
dateinfo = dateinfo.split('-')
try:
day = int(float(dateinfo[0]))
month = dateinfo[1].lower()
month_num = {
'jan': 1,
'feb': 2,
'mar': 3,
'apr': 4,
'may': 5,
'jun': 6,
'jul': 7,
'aug': 8,
'sep': 9,
'oct': 10,
'nov': 11,
'dec': 12,
}[month]
year = 14
except:
try:
datestring = int(float(dateinfo[0]))
day = int(float(dateinfo[0][-2:]))
month_num = int(float(dateinfo[0][-4:-2]))
# month_num = {'jan':1,'feb':2,'mar':3,'apr':4,'may':5,'jun':6,
# 'jul':7,'aug':8,'sep':9,'oct':10,'nov':11,'dec':12,}[month]
year = 14
except:
day = 0
month_num = 0
year = 0
# re read the edi file:
e_object = MTedi.Edi(filename=edifn)
e_object.head['loc'] = 'roma'
e_object.head['acqby'] = 'UofA'
e_object.head['acqdate'] = '2014/{0:02d}/{1:02d}'.format(month_num, day)
outfn_base = '{0}_{1}_{2:02d}{3:02d}{4:02d}'.format(
edi_prefix, station.upper(), year, month_num, day)
outfn = outfn_base + '.edi'
if 1:
outfn_true = e_object.writefile(outfn,
allow_overwrite=True,
use_info_string=True)
if outfn_true is None:
raise
print 'EDI file written: {0}\n'.format(outfn_true)
# except:
# print '\tERROR - could not write final EDI file {0}\n'.format(outfn)
outfn = outfn_true
#rename coherence file accordingly:
outfn_coh = outfn_base + '.coh'
try:
os.rename(infn_coh, outfn_coh)
except:
print 'Warning - could not find coherence file: {0}'.format(infn_coh)
#rename j file, so that another one can be found and processed, if this code
# is called within a loop:
os.rename(j_filename_list[0], j_filename_list[0] + '.done')
#remove intermediate EDI file
os.remove(edifn)
os.chdir(basedir)
return outfn, outfn_coh
# directory path where edi files are
dirpath = r"d:\Peacock\MTData\EDI_Files\Counts"
# path to save edi files that have distortion removed
drpath = os.path.join(dirpath, 'DR')
# make sure the drpath exists
if not os.path.exists(drpath):
os.mkdir(drpath)
#make a list of all edi files in the directory
edi_list = [
os.path.join(dirpath, edi) for edi in os.listdir(dirpath)
if edi.find('.edi') > 0
]
#loop over edi files and remove distortion
dlst = []
for edi in edi_list:
e1 = mtedi.Edi(filename=edi)
d, zd = distortion.remove_distortion(z_object=e1.Z)
e1.Z = zd
e1.writefile(os.path.join(dirpath, 'DR', e1.station.lower()))
dlst.append({'station': e1.station, 'd': d})
#print results for easy viewing
for dd in dlst:
print '--> Distortion tensor for {0} is:'.format(dd['station'])
print '{0}|{1: .2f} {2: .2f}|'.format('' * 5, dd['d'][0, 0], dd['d'][0, 1])
print '{0}|{1: .2f} {2: .2f}|'.format('' * 5, dd['d'][1, 0], dd['d'][1, 1])
def __init__(self, fn=None, **kwargs):
self._fn = fn
self.station = kwargs.pop('station', None)
self._lat = kwargs.pop('lat', None)
self._lon = kwargs.pop('lon', None)
self._elev = kwargs.pop('elev', None)
self._Z = kwargs.pop('Z', MTz.Z())
self._Tipper = kwargs.pop('Tipper', MTz.Tipper())
self._utm_zone = kwargs.pop('utm_zone', None)
self._east = kwargs.pop('east', None)
self._north = kwargs.pop('north', None)
self._rotation_angle = kwargs.pop('rotation_angle', 0)
self._data_type = kwargs.pop('data_type', 'z')
#provide key words to fill values if an edi file does not exist
if 'z_object' in kwargs:
self._Z = kwargs['z_object']
if 'z_array' in kwargs:
self._Z.z = kwargs['z_array']
if 'zerr_array' in kwargs:
self._Z.zerr = kwargs['zerr_array']
if 'freq' in kwargs:
self._Z.freq = kwargs['freq']
self._Tipper.freq = kwargs['freq']
if 'tipper_object' in kwargs:
self._Tipper = kwargs['tipper_object']
if 'tipper' in kwargs:
self._Tipper.tipper = kwargs['tipper']
if 'tippererr' in kwargs:
self._Tipper.tippererr = kwargs['tippererr']
if 'resisitivity' in kwargs:
self._Z.resistivity = kwargs['resistivity']
if 'resisitivity_err' in kwargs:
self._Z.resistivity_err = kwargs['resistivity_err']
if 'phase' in kwargs:
self._Z.phase = kwargs['phase']
if 'phase_err' in kwargs:
self._Z.phase = kwargs['phase_err']
self.edi_object = MTedi.Edi()
self.pt = None
self.zinv = None
self._utm_ellipsoid = 23
#--> read in the edi file if its given
if self._fn is not None:
if self._fn[-3:] == 'edi':
self._read_edi_file()
else:
not_fn = self._fn[os.path.basename(self._fn).find['.']:]
raise MTex.MTpyError_file_handling('File '+\
'type {0} not supported yet.'.format(not_fn))
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""
import sys
import matplotlib
#matplotlib.use('Qt4agg', force=True)
from pylab import *
import mtpy.core.edi as MTedi
fn = sys.argv[1]
edi = MTedi.Edi(edi_fn=fn)
try:
edi.read_edi_file()
except Exception, why:
print why
sys.exit(1)
res_te = []
res_tm = []
phi_te = []
phi_tm = []
reserr_te = []
reserr_tm = []
phierr_te = []
phierr_tm = []
@author: Alison Kirkby
plots edi files (res/phase vs period) for all edis in a directory and saves out as png files
"""
import os
os.chdir(r'C:\Git\mtpy')
import mtpy.imaging.plotresponse as mtpr
import mtpy.core.edi as mtedi
import os.path as op
# path to edis
epath = r'C:\Git\mtpy\examples\data\edi_files'
svdir = r'C:\Git\mtpy\examples\plots\edi_plots'
elst = [
op.join(epath, edi) for edi in os.listdir(epath) if (edi.endswith('.edi'))
]
for efile in elst[-1:]:
eo = mtedi.Edi(efile)
pr = mtpr.PlotResponse(fn=efile,
plot_num=2,
plot_tipper='yri',
plot_pt='y')
pr.save_plot(
op.join(svdir, op.join(svdir,
op.basename(efile)[:-4] + '.png')))
f_index += 1
if f_index == nf:
data_list.append({
'name': name,
'res': res,
'phase': phase,
'res_err': res_err,
'phase_err': phase,
'tipper': tipper,
'tipper_err': tipper_err
})
print 'Station = {0}, no. freq = {1}'.format(name, nf)
#write edi file
data_edi = mtedi.Edi()
data_z = mtz.Z()
data_z.freq = frequency
data_z.set_res_phase(res,
phase,
reserr_array=res_err,
phaseerr_array=phase_err)
data_T = mtz.Tipper(tipper_array=tipper, tippererr_array=tipper_err)
data_T.freq = frequency
data_edi.Z = data_z
data_edi.Tipper = data_T
#---------------HEADER----------------------------------------------
data_edi.head = dict([('dataid', name), ('acqby', 'P. E. Wannamaker'),
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""
import os, sys
import os.path as op
import mtpy.core.edi as MTedi
from pylab import *
fn = sys.argv[1]
edi = MTedi.Edi()
try:
edi.readfile(fn)
except:
print '\n\tFile does not exist: {0}\n'.format(fn)
sys.exit()
res_te = []
res_tm = []
phi_te = []
phi_tm = []
reserr_te = []
reserr_tm = []
phierr_te = []
phierr_tm = []
def generate_input_file(edifilename, outputdir=None):
eo = EDI.Edi()
eo.readfile(edifilename)
filebase = op.splitext(op.split(edifilename)[-1])[0]
outfilename1 = '{0}_bayesian1d_z.in'.format(filebase)
outfilename2 = '{0}_bayesian1d_zvar.in'.format(filebase)
outdir = op.split(edifilename)[0]
if outputdir is not None:
try:
if not op.isdir(outputdir):
os.makedirs(outputdir)
outdir = outputdir
except:
pass
outfn1 = op.join(outdir, outfilename1)
outfn2 = op.join(outdir, outfilename2)
outfn1 = MTfh.make_unique_filename(outfn1)
outfn2 = MTfh.make_unique_filename(outfn2)
freqs = eo.freq
z_array = eo.Z.z
z_err_array = eo.Z.z_err
if len(freqs) != len(z_array):
raise MTex.MTpyError_edi_file('ERROR in Edi file {0} - number of '
'freqs different from length of Z array'.format(eo.filename))
sorting = np.argsort(freqs)
outstring1 = ''
outstring2 = ''
for idx in sorting:
z = z_array[idx]
z_err = z_err_array[idx]
f = freqs[idx]
outstring1 += '{0}\t'.format(f)
outstring2 += '{0}\t'.format(f)
for i in np.arange(2):
for j in np.arange(2):
if np.imag(z[i % 2, (j + 1) / 2]) < 0:
z_string = '{0}-{1}i'.format(np.real(z[i % 2, (j + 1) / 2]),
np.abs(np.imag(z[i % 2, (j + 1) / 2])))
else:
z_string = '{0}+{1}i'.format(np.real(z[i % 2, (j + 1) / 2]),
np.imag(z[i % 2, (j + 1) / 2]))
z_err_string = '{0}'.format(z_err[i % 2, (j + 1) / 2])
outstring1 += '{0}\t'.format(z_string)
outstring2 += '{0}\t'.format(z_err_string)
outstring1 = outstring1.rstrip() + '\n'
outstring2 = outstring2.rstrip() + '\n'
Fout1 = open(outfn1, 'w')
Fout2 = open(outfn2, 'w')
Fout1.write(outstring1.expandtabs(4))
Fout2.write(outstring2.expandtabs(4))
Fout1.close()
Fout2.close()
return outfn1, outfn2
fn_inj = os.path.join(edipath_inj, station + '.edi')
if os.path.isfile(fn_base) == False or os.path.isfile(fn_inj) == False:
print station
station_list.remove(station)
ns = len(station_list)
nf = 43 # number of frequencies
z_base_arr = np.zeros((ns, nf, 2, 2), dtype='complex')
z_inj_arr = np.zeros((ns, nf, 2, 2), dtype='complex')
for ss, station in enumerate(station_list):
fn_base = os.path.join(edipath_base, station + '.edi')
fn_inj = os.path.join(edipath_inj, station + '.edi')
if os.path.isfile(fn_base) == True and os.path.isfile(fn_inj) == True:
edi_base = mtedi.Edi(fn_base)
edi_inj = mtedi.Edi(fn_inj)
z_err_base = np.sqrt(edi_base.Z.zerr.copy())
z_err_inj = np.sqrt(edi_inj.Z.zerr.copy())
#print z_err_base[0, 0, 1]
#compute a static shift correction
sx = np.sqrt(
np.mean(edi_base.Z.resistivity[0:15, 0, 1] /
edi_inj.Z.resistivity[0:15, 0, 1]))
sy = np.sqrt(
np.mean(edi_base.Z.resistivity[0:15, 1, 0] /
edi_inj.Z.resistivity[0:15, 1, 0]))
#remove the static shift from the injection survey
s, new_z = edi_inj.Z.no_ss(1 / sx, 1 / sy)
def plotedi(fn, saveplot=False, component=None):
edi = MTedi.Edi()
try:
edi.readfile(fn)
except:
print '\n\tERROR - not a valid EDI file: {0}\n'.format(fn)
sys.exit()
if saveplot is True:
import matplotlib
matplotlib.use('Agg')
from pylab import *
lo_comps = []
if component is not None:
'n' in component.lower()
try:
if 'n' in component.lower():
lo_comps.append('n')
except:
pass
try:
if 'e' in component.lower():
lo_comps.append('e')
except:
pass
if len(lo_comps) == 0:
lo_comps = ['n', 'e']
res_te = []
res_tm = []
phi_te = []
phi_tm = []
reserr_te = []
reserr_tm = []
phierr_te = []
phierr_tm = []
for r in edi.Z.resistivity:
res_te.append(r[0, 1])
res_tm.append(r[1, 0])
for p in edi.Z.phase:
phi_te.append(p[0, 1] % 90)
phi_tm.append(p[1, 0] % 90)
if np.mean(phi_te) > 90 and np.mean(phi_tm) > 90:
phi_te = [i % 90 for i in phi_te]
phi_tm = [i % 90 for i in phi_tm]
for r in edi.Z.resistivity_err:
reserr_te.append(r[0, 1])
reserr_tm.append(r[1, 0])
for p in edi.Z.phase_err:
phierr_te.append(p[0, 1])
phierr_tm.append(p[1, 0])
periods = 1. / edi.freq
resplotelement_xy = None
resplotelement_yx = None
ax1 = subplot(211)
if 'n' in lo_comps:
resplotelement_xy = errorbar(periods,
res_te,
reserr_te,
marker='x',
c='b',
fmt='x')
if 'e' in lo_comps:
resplotelement_yx = errorbar(periods,
res_tm,
reserr_tm,
marker='x',
c='r',
fmt='x')
xscale('log')
yscale('log')
minval = min(min(res_te, res_tm))
maxval = max(max(res_te, res_tm))
xlim(0.5 * min(periods), 2 * max(periods))
ylim([0.1, 100])
#ylim([minval/10,maxval*10])
autoscale(False)
ylabel('app.res. in Ohm m')
setp(ax1.get_xticklabels(), visible=False)
## share x only
ax2 = subplot(212, sharex=ax1)
autoscale(False)
#ylim(-45,135)
if 'n' in lo_comps:
errorbar(periods, phi_te, phierr_te, marker='x', c='b', fmt='x')
if 'e' in lo_comps:
errorbar(periods, phi_tm, phierr_tm, marker='x', c='r', fmt='x')
ylabel('phase')
xlabel('period (in s)')
plot([xlim()[0], xlim()[1]], [45, 45], '-.', c='0.7')
ylim([-0, 90])
ax1.legend([resplotelement_xy, resplotelement_yx],
['$E_{X}/B_Y$', '$E_Y/B_X$'],
loc=2,
ncol=1,
numpoints=1,
markerscale=0.8,
frameon=True,
labelspacing=0.3,
prop={'size': 8},
fancybox=True,
shadow=False)
tight_layout()
if saveplot is True:
ioff()
outfn = op.splitext(fn)[0] + '.png'
savefig(outfn, bbox_inches='tight')
close('all')
ion()
return outfn
else:
ion()
show(block=True)
return None
header_string = """#Data file \n# Period(s) Code GG_Lat GG_Lon X(m) Y(m) Z(m) Component Real Imag Error
> Full_Impedance \n> exp(-i\omega t)\n> [mV/km]/[nT]
> 0.00
"""
edilist = glob.glob(os.path.join(edipath, '*.[Ee][Dd][Ii]'))
edilist = [os.path.abspath(os.path.join(os.curdir, i)) for i in edilist]
lo_ediobjs = []
coord_list = []
utm_list = []
for edi in edilist:
e = E.Edi()
e.readfile(edi)
lo_ediobjs.append(e)
utm_list.append(conv.LLtoUTM(23, e.lat, e.lon))
coord_list.append([e.lat, e.lon])
lat0 = np.mean(np.array(coord_list)[:, 0])
lon0 = np.mean(np.array(coord_list)[:, 1])
coord_list = []
# check f\or utm zones...if different assign zone!
# for the moment assume all have the same zone
for utm in utm_list:
if os.path.isfile(os.path.join(edipath1, station + ediext)) == True:
imp1 = os.path.join(edipath1, station + ediext)
implst.append(imp1)
if os.path.isfile(os.path.join(edipath2, station + ediext)) == True:
imp2 = os.path.join(edipath2, station + ediext)
implst.append(imp2)
if os.path.isfile(os.path.join(edipath3, station + ediext)) == True:
imp3 = os.path.join(edipath3, station + ediext)
implst.append(imp3)
if implst == [] or len(implst) == 1:
stationclst.remove(station)
pass
else:
implst = [mtedi.Edi(implst[0]), mtedi.Edi(implst[1])]
period = implst[0].period
n = len(period)
z1 = implst[0].Z.z
z2 = implst[1].Z.z
rpdict1 = implst[0].Z.resistivity
rpdict2 = implst[1].Z.resistivity
# compute static shift for each x and y component
sx = np.sqrt(np.mean(rpdict1[0:10, 0, 1] / rpdict2[0:10, 0, 1]))
sy = np.sqrt(np.mean(rpdict1[0:10, 1, 0] / rpdict2[0:10, 1, 0]))
# remove static shift from 2nd set of files
z2[:, 0, 0] = z2[:, 0, 0] * sx
z2[:, 0, 1] = z2[:, 0, 1] * sx
def plotedi(fn, saveplot=False, component=None):
edi = MTedi.Edi()
try:
edi.readfile(fn)
except:
print '\n\tERROR - not a valid EDI file: {0}\n'.format(fn)
sys.exit()
# if saveplot is True:
# import matplotlib
# matplotlib.use('Agg')
import pylab
lo_comps = []
if component is not None:
'n' in component.lower()
try:
if 'n' in component.lower():
lo_comps.append('n')
except:
pass
try:
if 'e' in component.lower():
lo_comps.append('e')
except:
pass
if len(lo_comps) == 0:
lo_comps = ['n', 'e']
res_te = []
res_tm = []
phi_te = []
phi_tm = []
reserr_te = []
reserr_tm = []
phierr_te = []
phierr_tm = []
for r in edi.Z.resistivity:
res_te.append(r[0, 1])
res_tm.append(r[1, 0])
for p in edi.Z.phase:
phi_te.append(p[0, 1] % 90)
phi_tm.append(p[1, 0] % 90)
if pylab.np.mean(phi_te) > 90 and pylab.np.mean(phi_tm) > 90:
phi_te = [i % 90 for i in phi_te]
phi_tm = [i % 90 for i in phi_tm]
for r in edi.Z.resistivity_err:
reserr_te.append(r[0, 1])
reserr_tm.append(r[1, 0])
for p in edi.Z.phase_err:
phierr_te.append(p[0, 1])
phierr_tm.append(p[1, 0])
periods = 1. / edi.freq
resplotelement_xy = None
resplotelement_yx = None
axes = pylab.figure('EDI ' + fn)
ax1 = pylab.subplot(211)
if 'n' in lo_comps:
resplotelement_xy = pylab.errorbar(periods,
res_te,
reserr_te,
marker='x',
c='b',
fmt='x')
if 'e' in lo_comps:
resplotelement_yx = pylab.errorbar(periods,
res_tm,
reserr_tm,
marker='x',
c='r',
fmt='x')
pylab.xscale('log', nonposx='clip')
pylab.yscale('log', nonposy='clip')
minval = pylab.min(pylab.min(res_te, res_tm))
maxval = pylab.max(pylab.max(res_te, res_tm))
pylab.xlim(0.5 * pylab.min(periods), 2 * pylab.max(periods))
# ylim([0.1,100])
pylab.ylim([minval / 10, maxval * 10])
pylab.autoscale(False)
pylab.ylabel(r' $\rho$ (in $\Omega m$)')
pylab.setp(ax1.get_xticklabels(), visible=False)
# share x only
ax2 = pylab.subplot(212, sharex=ax1)
pylab.autoscale(False)
# ylim(-45,135)
if 'n' in lo_comps:
pylab.errorbar(periods, phi_te, phierr_te, marker='x', c='b', fmt='x')
if 'e' in lo_comps:
pylab.errorbar(periods, phi_tm, phierr_tm, marker='x', c='r', fmt='x')
pylab.ylabel('Phase angle ($\degree$)')
pylab.xlabel('Period (in s)')
pylab.plot([pylab.xlim()[0], pylab.xlim()[1]], [45, 45], '-.', c='0.7')
pylab.ylim([-0, 90])
ax1.legend([resplotelement_xy, resplotelement_yx],
['$E_{X}/B_Y$', '$E_Y/B_X$'],
loc=2,
ncol=1,
numpoints=1,
markerscale=0.8,
frameon=True,
labelspacing=0.3,
prop={'size': 8},
fancybox=True,
shadow=False)
pylab.tight_layout()
if saveplot is True:
pylab.ioff()
outfn = op.splitext(fn)[0] + '.png'
pylab.savefig(outfn, bbox_inches='tight')
pylab.close('all')
pylab.ion()
return outfn
else:
pylab.ion()
pylab.show(block=True)
return None
}
data_arr = np.zeros(
100,
dtype=[
("freq", np.float),
("z", (np.complex, (2, 2))),
("z_err", (np.float, (2, 2))),
("tipper", (np.complex, (2, 2))),
("tipper_err", (np.float, (2, 2))),
],
)
count = 0
for edi_fn in edi_fn_list:
edi_obj = mtedi.Edi(edi_fn)
# get sampling rate from directory path
for fkey in sorted(sr_dict.keys(), reverse=True):
if str(fkey) in edi_fn:
# locate frequency range
f_index = np.where((edi_obj.Z.freq >= sr_dict[fkey][1])
& (edi_obj.Z.freq <= sr_dict[fkey][0]))
data_arr["freq"][count:count +
len(f_index[0])] = edi_obj.Z.freq[f_index]
data_arr["z"][count:count + len(f_index[0])] = edi_obj.Z.z[f_index]
data_arr["z_err"][count:count +
len(f_index[0])] = edi_obj.Z.z_err[f_index]
if edi_obj.Tipper.tipper is not None:
data_arr["tipper"][count:count +
len(f_index[0]
def compute_spatial_median_ss(edi_file,
ss_tol=0.2,
freq_tol=0.15,
distance_radius=1000,
n_freq=20,
write_new_edi='y'):
"""
Compute the median of all stations within a given radius (distance_radius).
For each station only resistivities up to n_freq will be used to
estimate the median resistivity. The input station resistivity is then
divided by the median. The median is only calculated for the off-diagonal
terms. This works well if your station spacing is small <= 500m.
Arguments:
-----------
**edi_file** : string
full path to edi file to compute static shift for
Note that the other stations are assumed to be in
the same directory as edi_file.
**ss_tol** : float
tolerance or error about 1.0 to give to static shift
estimation. if 1-ss_tol < ss_estimation > 1+ss_tol then
the returned value is the ss_estimation, otherwise 1.0
is returned. *default* is 0.2
**freq_tol** : float
tolerance to look for frequencies in other edi files
that were found in edi_file. This is important if
the frequencies for each edi file are different.
frequency match occurs when
edi_file(freq)*(1-freq_tol) < edi_file2(freq) and
edi_file2(freq) > edi_file(freq)*(1+freq_tol)
*default* is 0.15
**distance_radius** : float
radius to search for other stations. Any
station that is within this radius is used
to calculate the median static shift.
*default* is 1000.
**n_freq** : int
number of frequencies to use to calculate median, assuming
the first frequency is the highest frequency.
*default* is 20.
**write_new_edi** : [ 'y' | 'n' ]
* 'y' will write a new edi file if there is a
static shift
* 'n' will not write a new edi_file
File will be saved to edi_path\SS\station.edi
Returns:
--------
**static_shift_x** : float
estimated median static shift in x direction
**static_shift_y** : float
estimated median static shift in y direction
**new_edi_fn** : string
full path to new edi file if write_new_edi == 'y'
otherwise None is returned.
"""
#convert meters to decimal degrees so we don't have to deal with zone
#changes
dm_deg = distance_radius * 8.994423457456377e-06
#get path to all the other edi_files
edi_path = os.path.dirname(edi_file)
#make a list of edi files in the directory
edi_list = [
os.path.join(edi_path, edi) for edi in os.listdir(edi_path)
if edi.find('.edi') > 0
]
#remove the edi_file to be estimated for
edi_list.remove(edi_file)
n_edi = len(edi_list)
#read the edi file
edi1 = mtedi.Edi(filename=edi_file)
#check to make sure the first frequency is the highest, if not flip
#things around
if edi1.freq[0] < edi1.freq[-1]:
edi1.freq = edi1.freq[::-1]
edi1.Z.z = edi1.Z.z[::-1]
#make a dictionary of frequencies
freq_dict = dict([('{:.6g}'.format(ff), ii)
for ii, ff in enumerate(edi1.freq[0:n_freq])])
#get resistivity and phase
res1, phase1, reserr1, phaseerr1 = edi1.Z.res_phase
#make a resistivity array invovling all stations that are within dm
res_array = np.zeros((n_edi, n_freq, 2, 2))
kk = 0
for kedi in edi_list:
edi2 = mtedi.Edi(kedi)
#check to make sure the first frequency is the highest, if not flip
#things around
if edi2.freq[0] < edi2.freq[-1]:
edi2.freq = edi2.freq[::-1]
edi2.Z.z = edi2.Z.z[::-1]
delta_d = np.sqrt((edi1.lat - edi2.lat)**2 + (edi1.lon - edi2.lon)**2)
if delta_d <= dm_deg:
print 'Station {0} is within dm'.format(edi2.station)
res2, phase2, reserr2, phaseerr2 = edi2.Z.res_phase
for jj, ff in enumerate(edi2.freq[0:n_freq]):
try:
ii = freq_dict['{0:.6g}'.format(ff)]
res_array[kk, ii, :, :] = res2[jj, :, :]
except KeyError:
freq_find = False
for fkey in freq_dict.keys():
if float(fkey) * (1 - freq_tol) < ff < float(fkey) * (
1 + freq_tol):
ii = freq_dict[fkey]
res_array[kk, ii, :, :] = res2[jj, :, :]
freq_find = True
break
else:
pass
if freq_find == False:
print 'Did not find frequency {0:.6g} for {1}'.format(
ff, edi2.station)
kk += 1
if kk == 0:
print '**** No stations with in {0} m'.format(distance_radius)
return 1.0, 1.0, None
#convert the res array into a masked array for averaging
res_array = np.ma.masked_equal(res_array, 0)
#compute the static shift of x-components
static_shift_x = res1[0:n_freq, 0, 1] / np.ma.extras.median(
res_array[:, :, 0, 1], axis=0)
static_shift_x = np.median(
static_shift_x[np.where(static_shift_x != np.inf)])
#check to see if the estimated static shift is within given tolerance
if 1.0 - ss_tol < static_shift_x < 1.0 + ss_tol:
static_shift_x = 1.0
#compute the static shift of y-components
static_shift_y = res1[0:n_freq, 1, 0] / np.ma.extras.median(
res_array[:, :, 1, 0], axis=0)
static_shift_y = np.median(
static_shift_y[np.where(static_shift_y != np.inf)])
#check to see if the estimated static shift is within given tolerance
if 1.0 - ss_tol < static_shift_y < 1.0 + ss_tol:
static_shift_y = 1.0
print 'Static shift in x-direction = {0:.2f}'.format(static_shift_x)
print 'Static shift in y-direction = {0:.2f}'.format(static_shift_y)
#write new edi file if there is a static shift correction
if write_new_edi == 'y':
svpath = os.path.join(edi_path, 'SS')
if not os.path.exists(svpath):
os.mkdir(svpath)
new_edi_fn = os.path.join(svpath,
os.path.basename(edi_file)[:-4] + '_ss.edi')
static_shift, new_z = edi1.Z.no_ss(static_shift_x, static_shift_y)
edi1.Z.z = new_z
edi1.writefile(new_edi_fn)
return static_shift_x, static_shift_y, new_edi_fn
else:
return static_shift_x, static_shift_y, None
