def test_read_gocad_sgrid_file(self):
if not os.path.isdir(self._model_dir):
self._model_dir = None
output_fn = os.path.basename(self._model_fn)
# read data file to get centre position
dObj = Data()
dObj.read_data_file(data_fn=self._data_fn)
# create a model object using the data object and read in gocad sgrid file
mObj = Model(data_obj=dObj, save_path=self._output_dir)
mObj.read_gocad_sgrid_file(self._sgrid_fn)
mObj.write_model_file()
output_data_file = os.path.normpath(
os.path.join(self._output_dir, output_fn))
self.assertTrue(os.path.isfile(output_data_file),
"output data file not found")
expected_data_file = os.path.normpath(self._model_fn_old_z_mesh)
self.assertTrue(
os.path.isfile(expected_data_file),
"Ref output data file does not exist, nothing to compare with")
is_identical, msg = diff_files(output_data_file, expected_data_file)
print(msg)
self.assertTrue(
is_identical,
"The output file is not the same with the baseline file.")
def _test_func(self):
if not os.path.isdir(edi_path):
# input file does not exist, skip test after remove the output dir
os.rmdir(self._output_dir)
self.skipTest("edi path does not exist: {}".format(edi_path))
# generate data
edi_list = glob.glob(edi_path + '/*.edi')
period_list = EdiCollection(edi_list).select_periods()
datob = Data(edi_list=edi_list,
inv_mode='1',
period_list=period_list,
epsg=epsg_code,
error_type_tipper='abs',
error_type_z='egbert',
comp_error_type=None,
error_floor=10)
datob.write_data_file(save_path=self._output_dir)
# create mesh grid model object
model = Model(
stations_object=datob.station_locations,
Data=datob,
epsg=epsg_code,
cell_size_east=10000,
cell_size_north=10000, # GA_VIC
pad_north=
8, # number of padding cells in each of the north and south directions
pad_east=8, # number of east and west padding cells
pad_z=8, # number of vertical padding cells
pad_stretch_v=
1.5, # factor to increase by in padding cells (vertical)
pad_stretch_h=
1.5, # factor to increase by in padding cells (horizontal)
n_air_layers=
0, # number of air layers 0, 10, 20, depend on topo elev height
res_model=
100, # halfspace resistivity value for initial reference model
n_layers=50, # total number of z layers, including air and pad_z
z1_layer=50, # first layer thickness metres, depend
z_target_depth=500000)
model.make_mesh(
) # the data file will be re-write in this method. No topo elev file used yet
model.plot_mesh()
model.plot_mesh_xy()
model.plot_mesh_xz()
# write a model file and initialise a resistivity model
model.write_model_file(save_path=self._output_dir)
# =============================================================================
import numpy as np
from mtpy.modeling.modem import Model
# =============================================================================
res_levels = [
(0, 2, 10),
(2, 5, 30),
(5, 25, 300),
(25, 60, 50),
(60, 150, 100),
(150, 1000, 10),
]
m = Model()
m.read_model_file(
r"c:\Users\jpeacock\OneDrive - DOI\MountainPass\modem_inv\mnp_03\mnp_z03_t02_c02_098.rho"
)
fwd = np.zeros_like(m.res_model)
for r in res_levels:
test = np.where((m.grid_z[:-1] >= r[0] * 1000)
& (m.grid_z[:-1] < r[1] * 1000))
fwd[:, :, test] = r[2]
# fwd[np.where(m.res_model <1)] = 0.3
m.write_model_file(model_fn_basename="mnp_fwd.rho", res_model=fwd)
pad_num=
3, # number of constant-width cells to add to outside of model before padding cells start
# this number is currently multiplied by 1.5 internally
n_air_layers=
10, #number of air layers, set to 0 to incorporate bathymetry only
res_model=100, # halfspace resistivity value for reference model
n_layers=100, # total number of z layers, including air
z1_layer=10, # first layer thickness
pad_method='stretch', # method for calculating padding
z_mesh_method='new',
z_target_depth=
120000 # depth to bottom of core model (padding after this depth)
)
mo.make_mesh()
mo.write_model_file(save_path=workdir)
# Add topography from EDI data.
# This function takes the same arguments as `add_topography_to_model2`
# but instead of a DEM file it takes a Data object.
mo.add_topography_from_data(do)
mo.write_model_file(save_path=workdir)
# update data elevations
do.project_stations_on_topography(mo)
# show the mesh
mo.plot_sealevel_resistivity()
co = Covariance()
co.smoothing_east = 0.4
def test_fun(self):
edipath = EDI_DATA_DIR # path where edi files are located
# period list (will not include periods outside of the range of the edi file)
start_period = -2
stop_period = 3
n_periods = 17
period_list = np.logspace(start_period, stop_period, n_periods)
# list of edi files, search for all files ending with '.edi'
edi_list = [
os.path.join(edipath, ff) for ff in os.listdir(edipath)
if (ff.endswith('.edi'))
]
do = Data(
edi_list=edi_list,
inv_mode='1',
save_path=self._output_dir,
period_list=period_list,
error_type_z='floor_egbert',
error_value_z=5,
error_type_tipper='floor_abs',
error_value_tipper=.03,
model_epsg=28354 # model epsg, currently set to utm zone 54
)
do.write_data_file()
do.data_array['elev'] = 0.
do.write_data_file(fill=False)
# create model file
mo = Model(
station_locations=do.station_locations,
cell_size_east=500,
cell_size_north=500,
pad_north=
7, # number of padding cells in each of the north and south directions
pad_east=7, # number of east and west padding cells
pad_z=6, # number of vertical padding cells
pad_stretch_v=
1.6, # factor to increase by in padding cells (vertical)
pad_stretch_h=
1.4, # factor to increase by in padding cells (horizontal)
n_air_layers=10, # number of air layers
res_model=100, # halfspace resistivity value for reference model
n_layers=90, # total number of z layers, including air
z1_layer=10, # first layer thickness
pad_method='stretch',
z_target_depth=120000)
mo.make_mesh()
mo.write_model_file(save_path=self._output_dir)
# add topography to res model
mo.add_topography_to_model2(AUS_TOPO_FILE)
# mo.add_topography_to_model2(r'E:/Data/MT_Datasets/concurry_topo/AussieContinent_etopo1.asc')
mo.write_model_file(save_path=self._output_dir)
do.project_stations_on_topography(mo)
co = Covariance()
co.write_covariance_file(model_fn=mo.model_fn)
for afile in ("ModEM_Data.dat", "covariance.cov",
"ModEM_Model_File.rho"):
output_data_file = os.path.normpath(
os.path.join(self._output_dir, afile))
self.assertTrue(os.path.isfile(output_data_file),
"output data file not found")
expected_data_file = os.path.normpath(
os.path.join(self._expected_output_dir, afile))
self.assertTrue(
os.path.isfile(expected_data_file),
"Ref output data file does not exist, nothing to compare with")
# print ("Comparing", output_data_file, "and", expected_data_file)
is_identical, msg = diff_files(output_data_file,
expected_data_file)
print msg
self.assertTrue(
is_identical,
"The output file is not the same with the baseline file.")
def test_fun_rotate(self):
# set the dir to the output from the previously correct run
self._expected_output_dir = os.path.join(SAMPLE_DIR, 'ModEM_rotate40')
edipath = EDI_DATA_DIR2
# example to specify a number of periods per decade
start_period = 0.002
stop_period = 2000
periods_per_decade = 4
period_list = get_period_list(start_period,
stop_period,
periods_per_decade,
include_outside_range=True)
# list of edi files, search for all files ending with '.edi'
edi_list = [
os.path.join(edipath, ff) for ff in os.listdir(edipath)
if (ff.endswith('.edi'))
]
do = Data(
edi_list=edi_list,
inv_mode='1',
save_path=self._output_dir,
period_list=period_list,
period_buffer=
2, # factor to stretch interpolation by. For example: if period_buffer=2
# then interpolated data points will only be included if they are
# within a factor of 2 of a true data point
error_type_z=
'floor_egbert', # error type (egbert is % of sqrt(zxy*zyx))
# floor means apply it as an error floor
error_value_z=5, # error floor (or value) in percent
error_type_tipper='floor_abs', # type of error to set in tipper,
# floor_abs is an absolute value set as a floor
error_value_tipper=.03,
rotation_angle=40,
model_epsg=28354 # model epsg, currently set to utm zone 54.
# See http://spatialreference.org/ to find the epsg code for your projection
)
do.write_data_file()
do.data_array['elev'] = 0.
do.write_data_file(fill=False)
# mesh rotation angle is the opposite direction to the rotation of the stations
if do.rotation_angle == 0:
mesh_rotation_angle = 0
else:
mesh_rotation_angle = -do.rotation_angle
# create model file
mo = Model(
stations_object=do.station_locations,
cell_size_east=8000,
cell_size_north=8000,
pad_north=
7, # number of padding cells in each of the north and south directions
pad_east=7, # number of east and west padding cells
pad_z=6, # number of vertical padding cells
pad_stretch_v=
1.6, # factor to increase by in padding cells (vertical)
pad_stretch_h=
1.4, # factor to increase by in padding cells (horizontal)
n_air_layers=10, #number of air layers
res_model=100, # halfspace resistivity value for reference model
n_layers=100, # total number of z layers, including air
z1_layer=10, # first layer thickness
pad_method='stretch', # method for calculating padding
z_mesh_method='new',
z_target_depth=
120000, # depth to bottom of core model (padding after this depth)
mesh_rotation_angle=mesh_rotation_angle)
mo.make_mesh()
mo.write_model_file(save_path=self._output_dir)
# add topography to res model
mo.add_topography_to_model2(AUS_TOPO_FILE)
mo.write_model_file(save_path=self._output_dir)
co = Covariance()
co.smoothing_east = 0.4
co.smoothing_north = 0.4
co.smoothing_z = 0.4
co.write_covariance_file(model_fn=mo.model_fn)
for afile in ("ModEM_Data.dat", "covariance.cov",
"ModEM_Model_File.rho"):
output_data_file = os.path.normpath(
os.path.join(self._output_dir, afile))
self.assertTrue(os.path.isfile(output_data_file),
"output data file not found")
expected_data_file = os.path.normpath(
os.path.join(self._expected_output_dir, afile))
self.assertTrue(
os.path.isfile(expected_data_file),
"Ref output data file does not exist, nothing to compare with")
# print ("Comparing", output_data_file, "and", expected_data_file)
is_identical, msg = diff_files(output_data_file,
expected_data_file)
print(msg)
self.assertTrue(
is_identical,
"The output file is not the same with the baseline file.")
n_airlayers=
10, # number of air layers 0, 10, 20, depend on topo elev height
res_model=100, # halfspace resistivity value for initial reference model
n_layers=55, # total number of z layers, including air and pad_z
z1_layer=50, # first layer thickness metres, depend
z_target_depth=500000)
model.make_mesh(
) # the data file will be re-write in this method. No topo elev file used yet
model.plot_mesh()
model.plot_mesh_xy()
model.plot_mesh_xz()
# write a model file and initialise a resistivity model
model.write_model_file(save_path=outputdir)
#=========== now add topo data, with or without air layers?
# 1) the data file will be changed in 3 columns sxi, syi and szi meters
# 2) The covariance file will be written.
# 3) the model file not changed?? No air layers can be seen in the .ws file.
# add topography, define an initial resistivity model, modify and re-write the data file, define covariance mask
# dat file will be changed and rewritten,
# grid centre is used as the new origin of coordinate system, topo data used in the elev column.
# model.add_topography(topofile, interp_method='nearest') # dat file will be written again as elevation updated
model.add_topography_2mesh(
topofile, interp_method='nearest'
) # dat file will be written again as elevation updated
def build_modem_inputfiles(edi_path, output_path):
"""
For a given se to edi files in edi_path, build the ModEM input files into output_path
:param edi_path: # path where edi files are located r'C:\mtpywin\mtpy\examples\data\edi_files_2'
:param output_path: # path to save to r'C:\test\ModEM'
:return:
"""
# not nece os.chdir(r'C:\mtpywin\mtpy') # change this path to the path where mtpy is installed
## period list (won't include periods outside of the range of the edi file) ###
## comment/uncomment your desired method ######################################
###############################################################################
## example to specify start, stop and total number of periods
# start_period = 0.001
# stop_period = 1000
# n_periods = 25
# period_list = np.logspace(np.log10(start_period),
# np.log10(stop_period),
# n_periods)
# example to specify a number of periods per decade
start_period = 0.002
stop_period = 2000
periods_per_decade = 4
period_list = get_period_list(start_period,
stop_period,
periods_per_decade,
include_outside_range=True)
## an example to use the periods from a particular edi file
# edifile_periods = op.join(edipath,'Synth00.edi')
# eobj = Edi(edifile_periods)
# period_list = 1./eobj.freq
###############################################################################
workdir = output_path
edipath = edi_path
# list of edi files, search for all files ending with '.edi'
edi_list = [
op.join(edipath, ff) for ff in os.listdir(edipath)
if (ff.endswith('.edi'))
]
# make the save path if it doesn't exist
if not op.exists(workdir):
os.mkdir(workdir)
do = Data(
edi_list=edi_list,
inv_mode='1',
save_path=workdir,
period_list=period_list,
period_buffer=
2, # factor to stretch interpolation by. For example: if period_buffer=2
# then interpolated data points will only be included if they are
# within a factor of 2 of a true data point
error_type_z=np.array([
['floor_percent', 'floor_egbert'],
# error type, options are 'egbert', 'percent', 'mean_od', 'eigen', 'median', 'off_diagonals'
['floor_egbert', 'percent']
]), # add floor to apply it as an error floor
# can supply a 2 x 2 array for each component or a single value
error_value_z=np.array([
[20., 5.], # error floor value in percent
[5., 20.]
]), # can supply a 2 x 2 array for each component or a single value
error_type_tipper='floor_abs', # type of error to set in tipper,
# floor_abs is an absolute value set as a floor
error_value_tipper=.03,
model_epsg=28354 # model epsg, currently set to utm zone 54.
# See http://spatialreference.org/ to find the epsg code for your projection
)
do.write_data_file()
# set elevations to zero as we need to ensure the stations are on the topography
do.data_array['elev'] = 0.
do.write_data_file(fill=False)
# create model file
mo = Model(
station_locations=do.station_locations,
cell_size_east=8000,
cell_size_north=8000,
pad_north=
7, # number of padding cells in each of the north and south directions
pad_east=7, # number of east and west padding cells
pad_z=6, # number of vertical padding cells
pad_stretch_v=1.6, # factor to increase by in padding cells (vertical)
pad_stretch_h=1.4, # factor to increase by in padding cells (horizontal)
pad_num=
3, # number of constant-width cells to add to outside of model before padding cells start
# this number is currently multiplied by 1.5 internally
n_air_layers=
10, # number of air layers, set to 0 to incorporate bathymetry only
res_model=100, # halfspace resistivity value for reference model
n_layers=100, # total number of z layers, including air
z1_layer=10, # first layer thickness
pad_method='stretch', # method for calculating padding
z_mesh_method='new',
z_target_depth=
120000 # depth to bottom of core model (padding after this depth)
)
mo.make_mesh()
mo.write_model_file(save_path=workdir)
# add topography to res model
# if the number of air layers is zero - bathymetry only will be added.
# if the number of air layers is nonzero - topography will be added, discretised into that number of cells
# mo.add_topography_to_model2(r'C:\mtpywin\mtpy\examples\data\AussieContinent_etopo1.asc')
mo.add_topography_to_model2(
r'C:\Githubz\mtpy\examples\data\AussieContinent_etopo1.asc')
mo.write_model_file(save_path=workdir)
# update data elevations
do.project_stations_on_topography(mo)
# show the mesh
mo.plot_sealevel_resistivity()
co = Covariance()
co.smoothing_east = 0.4
co.smoothing_north = 0.4
co.smoothing_z = 0.4
co.write_covariance_file(model_fn=mo.model_fn)
data_fn = r'C:\mtpywin\mtpy\examples\model_files\ModEM\ModEM_Data.dat'
dObj = Data()
dObj.read_data_file(data_fn=data_fn)
### option 2 ####
stationxyfile = r'C:\mtpywin\mtpy\examples\model_files\gocad\stationxy.txt'
xy = np.loadtxt(stationxyfile, usecols=(1, 2))
station_names = np.loadtxt(stationxyfile, usecols=(0, ), dtype='S10')
period_list = np.logspace(1, 4, 19) # change to your period list
# create data file
dObj = Data(epsg=epsg)
dObj._initialise_empty_data_array(xy,
period_list,
location_type='LL',
station_names=station_names)
dObj.write_data_file(fill=False, save_path=workdir)
# Create model file
mObj = Model(Data=dObj, save_path=workdir)
mObj.read_gocad_sgrid_file(gocad_sgrid_file)
mObj.model_fn_basename = op.join(workdir, 'ModEM_Model_forward.ws')
mObj.write_model_file()
# create covariance file
cov = Covariance(save_path=workdir,
smoothing_east=0.3,
smoothing_north=0.3,
smoothing_z=0.3)
cov.write_covariance_file(model_fn=mObj.model_fn)
def run(self):
# monkey patch plt.show() so the plot is not displayed in worker thread
true_plt_show = plt.show
plt.show = _fake_plt_show
self._figures = []
try:
if not os.path.exists(self.output_dir):
os.mkdir(self.output_dir)
# get period_list list
self.status_updated.emit("Selecting Periods...")
period_list = EdiCollection(self._edi_list).select_periods(**self._select_period_kwargs)
# save period plot for reference
figure = plt.gcf()
figure.savefig(os.path.join(self.output_dir, self._period_image_name))
if self.show:
self.figure_updated.emit('Period Distribution', figure)
# data object
self.status_updated.emit("Creating ModEM Data Object...")
self._data_kwargs['period_list'] = period_list
data = Data(edi_list=self._edi_list, **self._data_kwargs)
# write data file
self.status_updated.emit("Writing Initial ModEM Data File...")
data.write_data_file()
# create model
self.status_updated.emit("Creating Mesh Model...")
model = Model(data_object=data, **self._mesh_kwagrs)
model.make_mesh()
# plot mesh
model.plot_mesh(fig_num=plt.gcf().number + 1)
figure = plt.gcf()
figure.savefig(os.path.join(self.output_dir, self._mesh_image_name))
if self.show:
self.figure_updated.emit("Mesh", figure)
# model.plot_mesh_xy()
# self.figure_updated.emit("Mesh XY", plt.gcf())
# model.plot_mesh_xz()
# self.figure_updated.emit("Mesh XZ", plt.gcf())
model.write_model_file()
# add topography
self.status_updated.emit("Adding Topography...")
model.add_topography_to_mesh(**self._topo_args)
if self.show:
model.plot_topograph() # this is too slow so only plot and save image when asked
figure = plt.gcf()
figure.savefig(os.path.join(self.output_dir, self._topo_image_name))
self.figure_updated.emit("Topography", figure)
self.status_updated.emit("Updating Mesh Model...")
model.write_model_file()
# covariance
self.status_updated.emit("Creating Covariance File...")
self._covariance_kwargs['mask_arr'] = model.covariance_mask
cov = Covariance(**self._covariance_kwargs)
self.status_updated.emit("Writing Covariance File...")
cov.write_covariance_file(model_fn=model.model_fn, sea_water=self._topo_args['sea_resistivity'],
air=self._topo_args['air_resistivity'])
self.status_updated.emit("Creating README File...")
self.write_readme(os.path.join(self.output_dir, self._readme_name))
# done
self.status_updated.emit("Finishing...")
except Exception as e:
frm = inspect.trace()[-1]
mod = inspect.getmodule(frm[0])
self.export_error.emit("{}: {}".format(mod.__name__, e.message))
# restore plt.show()
plt.show = true_plt_show
def test_fun_edi_elevation(self):
edipath = EDI_DATA_DIR # path where edi files are located
# set the dir to the output from the previously correct run
self._expected_output_dir = os.path.join(SAMPLE_DIR, 'ModEM')
# period list (will not include periods outside of the range of the edi file)
start_period = -2
stop_period = 3
n_periods = 17
period_list = np.logspace(start_period, stop_period, n_periods)
# list of edi files, search for all files ending with '.edi'
edi_list = [
os.path.join(edipath, ff) for ff in os.listdir(edipath)
if (ff.endswith('.edi'))
]
do = Data(
edi_list=edi_list,
inv_mode='1',
save_path=self._output_dir,
period_list=period_list,
error_type_z='floor_egbert',
error_value_z=5,
error_type_tipper='floor_abs',
error_value_tipper=.03,
model_epsg=28354 # model epsg, currently set to utm zone 54
)
do.write_data_file()
# create model file
mo = Model(
station_locations=do.station_locations,
cell_size_east=500,
cell_size_north=500,
pad_north=
7, # number of padding cells in each of the north and south directions
pad_east=7, # number of east and west padding cells
pad_z=6, # number of vertical padding cells
pad_stretch_v=
1.6, # factor to increase by in padding cells (vertical)
pad_stretch_h=
1.4, # factor to increase by in padding cells (horizontal)
n_air_layers=10, # number of air layers
res_model=100, # halfspace resistivity value for reference model
n_layers=90, # total number of z layers, including air
z1_layer=10, # first layer thickness
pad_method='stretch',
z_target_depth=120000)
mo.make_mesh()
mo.write_model_file(save_path=self._output_dir)
# Add topography from EDI data
mo.add_topography_from_data(do)
mo.write_model_file(save_path=self._output_dir)
# BM: note this function makes a call to `write_data_file` and this is the datafile being
# compared!
do.project_stations_on_topography(mo)
co = Covariance()
co.write_covariance_file(model_fn=mo.model_fn)
# BM: if this test is failing check that the correct filenames are being selected
# for comparison
for test_output, expected_output in (
("ModEM_Data_topo.dat", "ModEM_Data_EDI_elev.dat"),
("covariance.cov", "covariance_EDI_elev.cov"),
("ModEM_Model_File.rho", "ModEM_Model_File_EDI_elev.rho")):
output_data_file = os.path.normpath(
os.path.join(self._output_dir, test_output))
self.assertTrue(os.path.isfile(output_data_file),
"output data file not found")
expected_data_file = os.path.normpath(
os.path.join(self._expected_output_dir, expected_output))
self.assertTrue(
os.path.isfile(expected_data_file),
"Ref output data file '{}' does not exist, nothing to compare with"
.format(expected_data_file))
is_identical, msg = diff_files(output_data_file,
expected_data_file)
print(msg)
self.assertTrue(
is_identical,
"The output file '{}' is not the same with the baseline file '{}'."
.format(output_data_file, expected_data_file))