def main(dr, tc=True):
import gmi_misc
import os
old_cwd = os.getcwd()
gmi_misc.info('Current directory: ' + old_cwd)
try:
os.chdir(dr)
except:
gmi_misc.error('CAN NOT OPEN WORKING DIRECTORY ' + dr +
', ABORTING...')
gmi_misc.info('WORKING DIRECTORY: ' + os.getcwd())
print("HASH TEST")
import gmi_config
gmi_config.read_config()
#**************** HASH TESTS **************************#
import gmi_hash
stages = [0, 0, 0]
stages, dict = gmi_hash.read_dict('checksums.npy', runcheck=tc)
#**************** ---------- **************************#
os.chdir(old_cwd)
return stages, dict
def convert_sht_grid_to_xyz(inp):
if isinstance(inp, str):
try:
grid = np.loadtxt(inp)
except:
gmi_misc.error('CAN NOT OPEN/WRONG FORMAT')
exit()
else:
grid = inp
lat_N = len(grid[:, 0])
lon_N = len(grid[0, :])
X = np.zeros(lat_N * lon_N)
Y = np.zeros(lat_N * lon_N)
Z = np.zeros(lat_N * lon_N)
k = 0
for i in range(0, lon_N):
for j in range(0, lat_N):
if (0.0 + float(i) * 360.0 / float(lon_N) < 180.0):
X[k] = 0.0 + float(i) * 360.0 / float(lon_N)
else:
X[k] = -360.0 + 0.0 + float(i) * 360.0 / float(lon_N)
Y[k] = 90.0 - float(j) * 180.0 / float(lat_N)
Z[k] = grid[j, i]
k += 1
return X, Y, Z
def switch_path(pth):
old_cwd = os.getcwd()
try:
os.chdir(pth)
except:
gmi_misc.error('CAN NOT OPEN WORKING DIRECTORY ' + pth +
', ABORTING...')
return old_cwd
def main(dr):
#**************** TESTING PARAMS (WOULD BE REMOVED)*******#
CREATE_VIM_MODEL = True
#**************** ---------------------------------*******#
import gmi_misc
#**************** PRINT HEADER ***************************#
gmi_misc.print_header()
print("Script no. 1: Creation of a tesseroid model")
#**************** ------------ ***************************#
#**************** GET WORKING DIRECTORY ******************#
import os
old_cwd = os.getcwd()
gmi_misc.info('Current directory: ' + old_cwd)
try:
os.chdir(dr)
except:
gmi_misc.error('CAN NOT OPEN WORKING DIRECTORY ' + dr +
', ABORTING...')
gmi_misc.message('Working directory: ' + os.getcwd())
#**************** --------------------- ******************#
#**************** read parameters from file **************#
import gmi_config
gmi_config.read_config()
#**************** ------------------------- **************#
result_folder = gmi_misc.init_result_folder()
import numpy as np
n_lon, n_lat, X, Y = gmi_misc.create_tess_cpoint_grid()
#*********************************************************#
Z_bot = gmi_misc.read_surf_grid(gmi_config.BOT_SURFACE)
Z_top = gmi_misc.read_surf_grid(gmi_config.TOP_SURFACE)
if gmi_config.MULTIPLICATOR != 1.0:
gmi_misc.warning(
"NOTE: SUSCEPTIBILITY OF EACH TESSEROID IS MULTIPLIED BY " +
str(gmi_config.MULTIPLICATOR))
_create_tess_model_file('model', 1.0 * gmi_config.MULTIPLICATOR, X, Y,
Z_top, Z_bot)
if CREATE_VIM_MODEL:
if ('.vim'
in gmi_config.INIT_SOLUTION) or ('.vis'
in gmi_config.INIT_SOLUTION):
sus_grid = gmi_misc.read_sus_grid(gmi_config.INIT_SOLUTION)
dm1, dm2, x0 = gmi_misc.convert_surf_grid_to_xyz(sus_grid)
_create_tess_model_file(result_folder + '/model_with_x0', x0, X, Y,
Z_top, Z_bot)
_create_tess_model_file(result_folder + '/model_with_x0_mult',
x0 * gmi_config.MULTIPLICATOR, X, Y, Z_top,
Z_bot)
np.savetxt(result_folder + '/init_solution.x0', x0)
gmi_misc.write_sus_grid_to_file(
x0, result_folder + 'init_solution.xyz')
#**************** WRITE MD5 PARAMS **************#
import hashlib
file_name = 'model.magtess'
with open(file_name, 'r') as file_to_check:
# read contents of the file
data = file_to_check.read()
# pipe contents of the file through
md5_returned = hashlib.md5(data.encode('utf-8')).hexdigest()
#Save
dictionary = {
'stage1': md5_returned,
'stage2': '',
'stage3': '',
'stage4': '',
}
np.save('checksums.npy', dictionary)
#**************** ---------------- **************#
#**************** RETURN BACK TO INITIAL PATH ***#
os.chdir(old_cwd)
def _create_tess_model_file(fname, suscept, x_grid, y_grid, z_topg, z_botg):
import numpy as np
import os
import gmi_config
gmi_config.read_config()
import gmi_misc
nlat, nlon = x_grid.shape
if gmi_config.T_DO_TILES:
width = gmi_config.T_WIDTH
minlon = gmi_config.T_LON_MIN - gmi_config.T_EDGE_EXT
maxlon = gmi_config.T_LON_MAX + gmi_config.T_EDGE_EXT
minlat = gmi_config.T_LAT_MIN - gmi_config.T_EDGE_EXT
maxlat = gmi_config.T_LAT_MAX + gmi_config.T_EDGE_EXT
else:
width = gmi_config.WIDTH
minlon = gmi_config.LON_MIN
maxlon = gmi_config.LON_MAX
minlat = gmi_config.LAT_MIN
maxlat = gmi_config.LAT_MAX
with open(fname + '.tess', 'w') as tessfile:
k = 0
for i in range(nlat - 1, -1, -1):
for j in range(nlon):
if isinstance(suscept, np.ndarray):
sus_curr = suscept[k]
elif isinstance(suscept, float):
sus_curr = suscept
else:
pass
if gmi_misc.check_if_in_boundary(x_grid[i, j], y_grid[i, j],
minlon, maxlon, minlat,
maxlat):
string = str(x_grid[i, j] - width / 2.0) + ' ' + str(
x_grid[i, j] + width / 2.0) + ' ' + str(
y_grid[i, j] - width / 2.0) + ' ' + str(
y_grid[i, j] + width / 2.0) + ' ' + str(
z_topg[i, j]) + ' ' + str(
z_botg[i, j]) + ' 1.0 ' + str(sus_curr)
tessfile.write(string + '\n')
k = k + 1
if not os.path.isfile(gmi_config.IGRF_COEFF_FILENAME):
gmi_misc.warning(
'main field SH model ' + gmi_config.IGRF_COEFF_FILENAME +
' is missing, downloading IGRF13 from https://www.ngdc.noaa.gov/IAGA/vmod/geomag70_linux.tar.gz as a substitute! Check your config file'
)
_download_igrf()
gmi_config.IGRF_COEFF_FILENAME = 'geomag70_linux/IGRF13.COF'
os.system(gmi_config.TESSUTIL_MAGNETIZE_MODEL_FILENAME + ' ' +
gmi_config.IGRF_COEFF_FILENAME + ' ' + fname + '.tess ' +
str(gmi_config.IGRF_DAY) + ' ' + str(gmi_config.IGRF_MONTH) +
' ' + str(gmi_config.IGRF_YEAR) + ' ' + fname + '.magtess')
if os.path.isfile(fname + '.tess'):
gmi_misc.ok("Magnetic tesseroid model " + '\033[1m' + fname + '.tess' +
'\033[0m' + " is created")
else:
gmi_misc.error("model.magtess WAS NOT CREATED, CHECK IF " + '\033[1m' +
gmi_config.TESSUTIL_MAGNETIZE_MODEL_FILENAME +
'\033[0m' + " IS WORKING PROPERLY")
#**************** GET WORKING DIRECTORY ******************#
import os
old_cwd = os.getcwd()
gmi_misc.info('Current directory: ' + old_cwd)
WORKING_DIR = ''
import sys
if len(sys.argv) == 1:
WORKING_DIR = ''
WORKING_DIR = sys.argv[1]
try:
os.chdir(WORKING_DIR)
except:
gmi_misc.error('CAN NOT OPEN WORKING DIRECTORY ' + WORKING_DIR +
', ABORTING...')
gmi_misc.info('WORKING DIRECTORY: ' + os.getcwd())
#**************** --------------------- ******************#
#**************** read parameters from file **************#
import gmi_config
gmi_config.read_config()
#**************** ------------------------- **************#
#************ check if previous stages were launched *****#
import gmi_hash
stages = [0, 0, 0]
stages, dictionary = gmi_hash.read_dict('checksums.npy')
err = 0
def main(dr):
import numpy as np
import gmi_misc
#**************** PRINT HEADER ***************************#
gmi_misc.print_header()
print ("Script no. 2: Calculation of the magnetic field of each tesseroid in the model")
#**************** ------------ ***************************#
#**************** GET WORKING DIRECTORY ******************#
import os
old_cwd = os.getcwd()
gmi_misc.info('Current directory: '+ old_cwd)
try:
os.chdir(dr)
except:
gmi_misc.error('CAN NOT OPEN WORKING DIRECTORY '+ dr + ', ABORTING...')
gmi_misc.info('WORKING DIRECTORY: '+ os.getcwd())
#**************** --------------------- ******************#
#**************** read parameters from file **************#
import gmi_config
gmi_config.read_config()
#**************** ------------------------- **************#
#************ check if previous stages were launched *****#
import gmi_hash
stages = [0,0,0]
stages, dictionary = gmi_hash.read_dict('checksums.npy')
if __name__ == '__main__':
err = 0
if stages[0] == -1:
gmi_misc.warning('model.magtess was changed after the run of Script 1, restart Script no. 1 first! ABORTING...')
elif stages[0] == 0:
gmi_misc.warning('model.magtess was changed after the run of Script 1, restart Script no. 1 first! ABORTING...')
else:
pass
if err > 0:
gmi_misc.error('CHECKSUM FAILED, ABORTING!')
#**************** --------------------- ******************#
#**************** CREATE CALCULATION GRID ****************#
gmi_misc.create_calc_grid('grid.txt')
#**************** --------------------- ******************#
#**************** OPEN TESSEROID MODEL *******************#
try:
mag_tesseroids = np.loadtxt('model.magtess', delimiter=" ")
except IOError as err:
gmi_misc.error("CAN NOT OPEN TESSEROID MODEL: {0}".format(err))
exit(-1)
#print mag_tesseroids
n_tess = len(mag_tesseroids)
print ('Number of tesseroids in the model: ' + str(n_tess))
#**************** --------------------- ******************#
from tqdm import tqdm
import pyshtools
coeff_info = pyshtools.SHCoeffs.from_zeros(1)
import os
if os.path.exists('model'):
if len(os.listdir('model') ) > 0:
if __name__ == '__main__':
gmi_misc.warning("MODEL FOLDER ALREADY EXIST! DO YOU WANT TO RECALCULATE?")
if gmi_misc.ask() == True:
pass
else:
gmi_misc.error("MODEL FOLDER WAS NOT OVERWRITEN, ABORTING!")
else:
os.mkdir('model')
if gmi_config.MULTIPLICATOR != 1.0:
gmi_misc.warning("NOTE: SUSCEPTIBILITY OF EACH TESSEROID IS MULTIPLIED BY " + str(gmi_config.MULTIPLICATOR))
n_cpu = os.cpu_count()
gmi_misc.message('Number of processors: '+ str(n_cpu))
gmi_misc.message('Calculating effects of each tesseroid...')
bar = tqdm(range(n_tess))
i = 0
while i < n_tess:
curr_max_j = 0
for j in range(0, n_cpu, 1):
if (i+j) < n_tess:
with open('dummy_' + str(j) + '.magtess', 'w') as tessfile:
string = str(mag_tesseroids[i+j, 0]) + ' ' + str(mag_tesseroids[i+j, 1]) + ' ' + str(mag_tesseroids[i+j, 2]) + ' ' + str(mag_tesseroids[i+j, 3]) + ' ' + str(mag_tesseroids[i+j, 4]) + ' ' + str(mag_tesseroids[i+j, 5]) + ' ' + str(mag_tesseroids[i+j, 6]) + ' ' + str(mag_tesseroids[i+j, 7]) + ' ' + str(mag_tesseroids[i+j, 8]) + ' ' + str(mag_tesseroids[i+j, 9]) + ' ' + str(mag_tesseroids[i+j, 10])
tessfile.write(string + '\n')
curr_max_j = curr_max_j + 1
command_bz = "" + gmi_config.TESSBZ_FILENAME + " dummy_" + str(0) + ".magtess < grid.txt > " + "out_" + str(0) + "_Bz.txt"
for j in range(1, n_cpu, 1):
if (i+j) < n_tess:
command_bz = command_bz + ' | '
command_bz = command_bz + "" + gmi_config.TESSBZ_FILENAME + " dummy_" + str(j) + ".magtess < grid.txt > " + "out_" + str(j) + "_Bz.txt"
command = command_bz + '\n'
os.system(command)
for j in range(0, n_cpu, 1):
if (i+j) < n_tess:
raw_grid = gmi_misc.read_data_grid("out_" + str(j) + "_Bz.txt")
shtools_inp_grid = pyshtools.SHGrid.from_array(raw_grid)
#get SH coefficients
shtools_coeff = shtools_inp_grid.expand(normalization='schmidt')
coeff_info = shtools_coeff
shtools_coeff.to_file('model/tess_n' + str(i) + '.coeff')
os.remove("out_" + str(j) + "_Bz.txt")
os.remove('dummy_' + str(j) + '.magtess')
i = i + 1
bar.update(curr_max_j)
gmi_misc.ok('...done')
gmi_misc.message('Properties of SHCoeffs:')
gmi_misc.message(str(coeff_info.info()))
gmi_misc.message("Max degree: " + str(coeff_info.lmax))
#**************** WRITE MD5 PARAMS **************#
dictionary['stage2'] = gmi_hash._gethashofdirs('model', verbose=1)
dictionary['stage3'] = ''
dictionary['stage4'] = ''
np.save('checksums.npy', dictionary)
#**************** ---------------- **************#
#**************** RETURN BACK TO INITIAL PATH ***#
os.chdir(old_cwd)
def main(dr):
#**************** TESTING PARAMS (WOULD BE REMOVED)*******#
CREATE_VIM_MODEL = True
#**************** ---------------------------------*******#
import gmi_misc
#**************** PRINT HEADER ***************************#
gmi_misc.print_header()
gmi_misc.message("Creation of a tesseroid model")
#**************** ------------ ***************************#
#**************** GET WORKING DIRECTORY ******************#
import os
old_cwd = os.getcwd()
gmi_misc.info('Current directory: ' + old_cwd)
try:
os.chdir(dr)
except:
gmi_misc.error('CAN NOT OPEN WORKING DIRECTORY ' + dr +
', ABORTING...')
gmi_misc.message('Working directory: ' + os.getcwd())
#**************** --------------------- ******************#
#**************** read parameters from file **************#
import gmi_config
gmi_config.read_config()
#**************** ------------------------- **************#
result_folder = gmi_misc.init_result_folder()
import numpy as np
n_lon, n_lat, X, Y = gmi_misc.create_tess_cpoint_grid()
#*********************************************************#
gmi_misc.message('Path to surfaces: ' + gmi_config.PATH_SURFACES)
import glob, re
surfaces_filenames = glob.glob(gmi_config.PATH_SURFACES + '/*')
try:
surfaces_filenames.sort(
key=lambda f: int(re.sub('\D', '', f))
) #good initial sort but doesnt sort numerically very well
sorted(surfaces_filenames) #sort numerically in ascending order
except:
gmi_misc.error(
'CHECK FILENAMES IN LAYERS FOLDER - THERE SHOULD BE INTEGER NUMBERS IN FILENAMES TO INDICATE THE ORDER OF SURFACES'
)
gmi_misc.message('All surfaces: ' + str(surfaces_filenames))
for li, this_surf, next_surf in zip(range(len(surfaces_filenames) - 1),
surfaces_filenames[0:-1],
surfaces_filenames[1:]):
gmi_misc.message('Layer ' + str(li) + ': upper surface ' + this_surf +
', lower surface: ' + next_surf)
Z_bot = gmi_misc.read_surf_grid(next_surf)
Z_top = gmi_misc.read_surf_grid(this_surf)
if gmi_config.MULTIPLICATOR != 1.0:
gmi_misc.warning(
"NOTE: SUSCEPTIBILITY OF EACH TESSEROID IS MULTIPLIED BY " +
str(gmi_config.MULTIPLICATOR))
_create_tess_model_file('layer' + str(li),
1.0 * gmi_config.MULTIPLICATOR, X, Y, Z_top,
Z_bot)
#**************** WRITE MD5 PARAMS **************#
#/fix it
'''
import hashlib
file_name = 'model.magtess'
with open(file_name, 'r') as file_to_check:
# read contents of the file
data = file_to_check.read()
# pipe contents of the file through
md5_returned = hashlib.md5(data.encode('utf-8')).hexdigest()
#Save
dictionary = {'stage1':md5_returned,
'stage2':'',
'stage3':'',
'stage4':'',
}
np.save('checksums.npy', dictionary)
#**************** ---------------- **************#
'''
#**************** RETURN BACK TO INITIAL PATH ***#
os.chdir(old_cwd)
def main(dr):
import gmi_misc
#**************** PRINT HEADER ***************************#
gmi_misc.print_header()
print("Script no. 4: Inversion")
#**************** ------------ ***************************#
#**************** GET WORKING DIRECTORY ******************#
import os
old_cwd = os.getcwd()
gmi_misc.info('Current directory: ' + old_cwd)
try:
os.chdir(dr)
except:
gmi_misc.error('CAN NOT OPEN WORKING DIRECTORY ' + dr +
', ABORTING...')
gmi_misc.info('WORKING DIRECTORY: ' + os.getcwd())
#**************** --------------------- ******************#
#**************** read parameters from file **************#
import gmi_config
gmi_config.read_config()
#**************** ------------------------- **************#
#************ check if previous stages were launched *****#
'''
import gmi_hash
stages = [0,0,0]
stages, dictionary = gmi_hash.read_dict('checksums.npy')
err = 0
if stages[0] == -1:
gmi_misc.warning('model.magtess was changed after the run of Script 1, restart Script no. 1 first! ABORTING...')
err += 1
elif stages[0] == 0:
gmi_misc.warning('model.magtess was changed after the run of Script 1, restart Script no. 1 first! ABORTING...')
err += 1
else:
pass
if stages[1] == -1:
gmi_misc.warning('Folder model was changed after the run of Script 2, restart Script no. 2 first! ABORTING...')
err += 1
elif stages[1] == 0:
gmi_misc.warning('Folder model was changed after the run of Script 2, restart Script no. 2 first! ABORTING...')
err += 1
else:
pass
if stages[2] == -1:
gmi_misc.warning('Design matrix was changed after the run of Script 3, restart Script no. 3 first! ABORTING...')
err += 1
elif stages[2] == 0:
gmi_misc.warning('Design matrix was changed after the run of Script 3, restart Script no. 3 first! ABORTING...')
err += 1
else:
pass
if err > 0:
gmi_misc.error('CHECKSUM FAILED, ABORTING!')
'''
#**************** --------------------- ******************#
import matplotlib.pyplot as plt
import pyshtools
import numpy as np
from scipy.interpolate import griddata
import convert_shtools_grids
gmi_misc.warning("INPUT GRID IS MULTIPLIED BY " +
str(gmi_config.MULTIPLICATOR))
##READ DESIGN MATRIX
A = np.load('design_matrix_shcoeff.npy')
A_alldeg = np.load('design_matrix_ufilt_shcoeff.npy')
import scipy.io
A = np.transpose(A)
A_alldeg = np.transpose(A_alldeg)
##READ INITIAL SOLUTION
#read initial solution
sus_grid = gmi_misc.read_sus_grid(gmi_config.INIT_SOLUTION)
dm1, dm2, x0 = gmi_misc.convert_surf_grid_to_xyz(sus_grid)
d_ideal = np.matmul(A, x0)
##READ OBSERVED GRID
obs_grid = gmi_misc.read_data_grid(
gmi_config.OBSERVED_DATA) #* gmi_config.MULTIPLICATOR
##READ SUBTRACTABLE FIELD
try:
sub_grid = gmi_misc.read_data_grid(
gmi_config.SUBTRACT_DATA) * gmi_config.MULTIPLICATOR
except IOError as err:
print("CAN NOT OPEN SUBTRACTEBLE DATAFILE: {0}".format(err))
sub_grid = obs_grid * 0.0
##REMOVE SUBTRACTABLE FIELD
obs_grid = obs_grid - sub_grid
def _save_powerspectrum(specname, shc):
spectrum = shc.spectrum()
deg = shc.degrees()
with open(specname, 'w') as f:
for i in range(len(deg)):
f.write(str(deg[i]) + ' ' + str(spectrum[i]) + '\n')
##CONVERT OBSERVED GRID INTO SHCOEFF
obs_sht_grid = pyshtools.SHGrid.from_array(obs_grid)
obs_sht_shcoeff = obs_sht_grid.expand(normalization='schmidt')
obs_sht_shcoeff.to_file("obs_sht_shcoeff.sht_shcoeff")
##save unfiltered input grid
obs_sht_grid = obs_sht_shcoeff.expand(grid='DH2')
glon, glat, gval = convert_shtools_grids.convert_sht_grid_to_xyz(
obs_sht_grid.to_array())
gmi_misc.write_xyz_grid_to_file(glon, glat, gval, 'obs_grid.xyz')
_save_powerspectrum('obs_sht_shcoeff.spec', obs_sht_shcoeff)
##FILTER OBSERVED GRID INTO SHCOEFF
obs_sht_shcoeff_trunc = gmi_misc.remove_lw_sh_coeff(
obs_sht_shcoeff, gmi_config.N_MIN_CUTOFF)
obs_sht_shcoeff_trunc.to_file("obs_sht_shcoeff_trunc.sht_shcoeff")
##save filtered input grid
obs_sht_grid_filt = obs_sht_shcoeff_trunc.expand(grid='DH2')
glon, glat, gval = convert_shtools_grids.convert_sht_grid_to_xyz(
obs_sht_grid_filt.to_array())
gmi_misc.write_xyz_grid_to_file(glon, glat, gval, 'obs_grid_filt.xyz')
_save_powerspectrum('obs_sht_shcoeff_trunc.spec', obs_sht_shcoeff_trunc)
d = gmi_misc.read_coeffs_from_text_file(
"obs_sht_shcoeff_trunc.sht_shcoeff", gmi_config.N_MIN_CUTOFF)
n_coeff = len(d)
#SOLVING
import gmi_inv_methods
print("d_ideal (np.matmul(A, x0)) = " + str(d_ideal))
print("d = " + str(d))
print("|d_ideal - d| = " + str(np.linalg.norm(d_ideal - d)))
h = gmi_inv_methods.Projected_Gradient(A, d, x0)
print("x0 = " + str(x0))
print("h = " + str(h))
print("|x0 - h| = " + str(np.linalg.norm(x0 - h)))
d_res = np.matmul(A_alldeg, h)
res_sht_shcoeff = gmi_misc.convert_result_into_shtools_format(
d_res, 'res_sht_shcoeff.sht_shcoeff')
res_sht_grid = res_sht_shcoeff.expand(grid='DH2')
glon, glat, gval = convert_shtools_grids.convert_sht_grid_to_xyz(
res_sht_grid.to_array())
gmi_misc.write_xyz_grid_to_file(glon, glat, gval, 'res_grid.xyz')
_save_powerspectrum('res_sht_shcoeff.spec', res_sht_shcoeff)
res_sht_shcoeff_trunc = gmi_misc.remove_lw_sh_coeff(
res_sht_shcoeff, gmi_config.N_MIN_CUTOFF)
res_sht_shcoeff_trunc.to_file("res_sht_shcoeff_trunc.sht_shcoeff")
res_sht_grid_filt = res_sht_shcoeff_trunc.expand(grid='DH2')
glon, glat, gval = convert_shtools_grids.convert_sht_grid_to_xyz(
res_sht_grid_filt.to_array())
gmi_misc.write_xyz_grid_to_file(glon, glat, gval, 'res_grid_filt.xyz')
_save_powerspectrum('res_sht_shcoeff_trunc.spec', res_sht_shcoeff_trunc)
######################
gmi_misc.write_sus_grid_to_file(h, 'res.xyz')
gmi_misc.write_sus_grid_to_file(
x0 - h,
'x0-res.xyz',
)
gmi_misc.write_sus_grid_to_file(x0, 'x0.xyz')
#save result
result_folder = gmi_misc.init_result_folder()
import shutil
shutil.copyfile('input.txt', './' + result_folder + '/' + 'input.txt')
shutil.copyfile('x0-res.xyz', './' + result_folder + '/' + 'x0-res.xyz')
shutil.copyfile('x0.xyz', './' + result_folder + '/' + 'x0.xyz')
shutil.copyfile('res.xyz', './' + result_folder + '/' + 'res.xyz')
shutil.copyfile('obs_grid_filt.xyz',
'./' + result_folder + '/' + 'obs_grid_filt.xyz')
shutil.copyfile('obs_sht_shcoeff_trunc.spec',
'./' + result_folder + '/' + 'obs_sht_shcoeff_trunc.spec')
shutil.copyfile(
'obs_sht_shcoeff_trunc.sht_shcoeff',
'./' + result_folder + '/' + 'obs_sht_shcoeff_trunc.sht_shcoeff')
shutil.copyfile('obs_grid.xyz',
'./' + result_folder + '/' + 'obs_grid.xyz')
shutil.copyfile('obs_sht_shcoeff.spec',
'./' + result_folder + '/' + 'obs_sht_shcoeff.spec')
shutil.copyfile('obs_sht_shcoeff.sht_shcoeff',
'./' + result_folder + '/' + 'obs_sht_shcoeff.sht_shcoeff')
shutil.copyfile('res_grid_filt.xyz',
'./' + result_folder + '/' + 'res_grid_filt.xyz')
shutil.copyfile('res_sht_shcoeff_trunc.spec',
'./' + result_folder + '/' + 'res_sht_shcoeff_trunc.spec')
shutil.copyfile(
'res_sht_shcoeff_trunc.sht_shcoeff',
'./' + result_folder + '/' + 'res_sht_shcoeff_trunc.sht_shcoeff')
shutil.copyfile('res_grid.xyz',
'./' + result_folder + '/' + 'res_grid.xyz')
shutil.copyfile('res_sht_shcoeff.spec',
'./' + result_folder + '/' + 'res_sht_shcoeff.spec')
shutil.copyfile('res_sht_shcoeff.sht_shcoeff',
'./' + result_folder + '/' + 'res_sht_shcoeff.sht_shcoeff')
shutil.copyfile('nlssubprob.dat',
'./' + result_folder + '/' + 'nlssubprob.dat')
try:
shutil.copyfile('video_log.mp4',
'./' + result_folder + '/' + 'video_log.mp4')
except:
print('could not cave video')
#**************** RETURN BACK TO INITIAL PATH ***#
os.chdir(old_cwd)
def start_main(self):
if not os.path.exists(self.cfg.get('PATH', 'GMI_PATH')):
gmi_misc.warning('Select new working folder path')
return
if not os.path.exists(self.cfg.get('PATH', 'GMI_MAGNETIZER')):
gmi_misc.warning('Select new path to tessutil_magnetize_model')
return
if not os.path.exists(self.cfg.get('PATH', 'GMI_TESSBZ')):
gmi_misc.warning('Select new path to tessbz')
return
HARDMODE = True
if not HARDMODE:
try:
shutil.copyfile(
self.cfg.get('PATH', 'GMI_MAGNETIZER'),
self.cfg.get('PATH', 'GMI_PATH') +
'/tessutil_magnetize_model')
os.chmod(
self.cfg.get('PATH', 'GMI_PATH') +
'/tessutil_magnetize_model', st.st_mode | stat.S_IEXEC)
except:
gmi_misc.warning('Could not copy executable ' +
self.cfg.get('PATH', 'GMI_MAGNETIZER') +
' to the working folder ' +
self.cfg.get('PATH', 'GMI_PATH'))
try:
shutil.copyfile(self.cfg.get('PATH', 'GMI_TESSBZ'),
self.cfg.get('PATH', 'GMI_PATH') + '/tessbz')
os.chmod(
self.cfg.get('PATH', 'GMI_PATH') + '/tessbz',
st.st_mode | stat.S_IEXEC)
except:
gmi_misc.warning('Could not copy executable ' +
self.cfg.get('PATH', 'GMI_TESSBZ') +
' to the working folder ' +
self.cfg.get('PATH', 'GMI_PATH'))
else:
os.system(
'cp ' +
self.cfg.get('PATH', 'GMI_MAGNETIZER').replace(' ', '\ ') +
' ' + self.cfg.get('PATH', 'GMI_PATH').replace(' ', '\ ') +
'/tessutil_magnetize_model')
os.system('cp ' +
self.cfg.get('PATH', 'GMI_TESSBZ').replace(' ', '\ ') +
' ' +
self.cfg.get('PATH', 'GMI_PATH').replace(' ', '\ ') +
'/tessbz')
CHMOD = ''
import sys
if sys.platform == 'linux':
CHMOD = 'chmod +x'
elif sys.platform == 'darwin':
CHMOD = 'chmod 755'
else:
gmi_misc.error('Unsupported operating system')
os.system(CHMOD + ' ' +
(self.cfg.get('PATH', 'GMI_PATH')).replace(' ', '\ ') +
'/tessutil_magnetize_model')
os.system(CHMOD + ' ' +
(self.cfg.get('PATH', 'GMI_PATH')).replace(' ', '\ ') +
'/tessbz')
with open('.config.ini', 'w') as configfile:
self.cfg.write(configfile)
self.accept()
def main(dr):
import gmi_misc
#**************** PRINT HEADER ***************************#
gmi_misc.print_header()
print("Grid reading test")
#**************** ------------ ***************************#
#**************** GET WORKING DIRECTORY ******************#
import os
old_cwd = os.getcwd()
gmi_misc.info('Current directory: ' + old_cwd)
try:
os.chdir(dr)
except:
gmi_misc.error('CAN NOT OPEN WORKING DIRECTORY ' + dr +
', ABORTING...')
gmi_misc.info('WORKING DIRECTORY: ' + os.getcwd())
#**************** --------------------- ******************#
#**************** read parameters from file **************#
import gmi_config
gmi_config.read_config()
#**************** ------------------------- **************#
#BODY*****************************************************#
import matplotlib.pyplot as plt
import pyshtools
import numpy as np
from scipy.interpolate import griddata
#read design matrices
try:
A = np.load('design_matrix_shcoeff.npy')
A = np.transpose(A)
except:
print("CAN NOT OPEN SH COEFF DESIGN MATRIX")
exit(-1)
#read initial solution
sus_grid = gmi_misc.read_sus_grid(gmi_config.INIT_SOLUTION)
dm1, dm2, x0 = gmi_misc.convert_surf_grid_to_xyz(sus_grid)
obs_matmul = np.matmul(A, x0)
#read PRECALCULATED observed grid all degrees
try:
raw_grid = gmi_misc.read_data_grid(gmi_config.OBSERVED_DATA)
except IOError as err:
print("CAN NOT OPEN OBSERVED DATAFILE: {0}".format(err))
exit(-1)
shtools_inp_grid = pyshtools.SHGrid.from_array(raw_grid)
sht_obs_tessfc_alldegrees = shtools_inp_grid.expand(
normalization='schmidt')
sht_obs_tessfc = gmi_misc.remove_lw_sh_coeff(sht_obs_tessfc_alldegrees,
gmi_config.N_MIN_CUTOFF)
sht_obs_tessfc.to_file("test_sht_obs_tessfc.coeff")
obs_tessfc = gmi_misc.read_coeffs_from_text_file(
"test_sht_obs_tessfc.coeff", gmi_config.N_MIN_CUTOFF)
obs_diff = (obs_matmul - obs_tessfc)
print(obs_diff)
print(np.linalg.norm(obs_diff))
#*********************************************************#
#**************** RETURN BACK TO INITIAL PATH ***#
os.chdir(old_cwd)
def read_config():
import os
import gmi_misc
#gmi_misc.debug('Reading config file ' + os.path.abspath("mydir/myfile.txt"))
import sys
this = sys.modules[__name__]
import configparser
config = configparser.ConfigParser()
try:
config.readfp(open(r'input.txt'))
except:
gmi_misc.warning('no input.txt file in the directory, creating an empty one...')
create_empty_config()
config.readfp(open(r'input.txt'))
#get project name
try:
this.PROJECT_NAME = str(config.get('Name', 'PROJECT_NAME'))
except:
gmi_misc.error('Necessary parameters in input.txt are missing! ABORTING')
try:
this.MULTILAYER = True
this.PATH_SURFACES = config.get('Global Tesseroid Model', 'PATH_SURFACES')
except:
gmi_misc.debug('Path to the list of surfaces in input.txt is missing! ABORTING')
this.MULTILAYER = False
if (this.MULTILAYER == False):
try:
this.TOP_SURFACE = config.get('Global Tesseroid Model', 'TOP_SURFACE')
this.BOT_SURFACE = config.get('Global Tesseroid Model', 'BOT_SURFACE')
except:
gmi_misc.error('Necessary parameters in input.txt are missing! ABORTING')
try:
#Global Tesseroid Model
this.LON_MIN = float(config.get('Global Tesseroid Model', 'LON_MIN'))
this.LON_MAX = float(config.get('Global Tesseroid Model', 'LON_MAX'))
this.LAT_MIN = float(config.get('Global Tesseroid Model', 'LAT_MIN'))
this.LAT_MAX = float(config.get('Global Tesseroid Model', 'LAT_MAX'))
this.WIDTH = float(config.get('Global Tesseroid Model', 'WIDTH'))
this.IGRF_DAY = int(config.get('Global Tesseroid Model', 'IGRF_DAY'))
this.IGRF_MONTH = int(config.get('Global Tesseroid Model', 'IGRF_MONTH'))
this.IGRF_YEAR = int(config.get('Global Tesseroid Model', 'IGRF_YEAR'))
this.IGRF_COEFF_FILENAME = config.get('Global Tesseroid Model', 'IGRF_COEFF_FILENAME')
#Global Grid
this.GRID_LON_MIN = float(config.get('Global Grid', 'GRID_LON_MIN'))
this.GRID_LON_MAX = float(config.get('Global Grid', 'GRID_LON_MAX'))
this.GRID_LAT_MIN = float(config.get('Global Grid', 'GRID_LAT_MIN'))
this.GRID_LAT_MAX = float(config.get('Global Grid', 'GRID_LAT_MAX'))
this.GRID_ALT = float(config.get('Global Grid', 'GRID_ALT'))
this.GRID_STEP = float(config.get('Global Grid', 'GRID_STEP'))
#Spherical Harmonics
this.N_MIN_CUTOFF = int(config.get('Spherical Harmonics', 'N_MIN_CUTOFF'))
#Inversion
this.OBSERVED_DATA = config.get('Inversion', 'OBSERVED_DATA')
this.SUBTRACT_DATA = config.get('Inversion', 'SUBTRACT_DATA')
this.INIT_SOLUTION = config.get('Inversion', 'INIT_SOLUTION')
this.MAX_ITER = int(config.get('Inversion', 'MAX_ITER'))
this.MULTIPLICATOR = float(config.get('Inversion', 'MULTIPLICATOR'))
except:
gmi_misc.error('Necessary parameters in input.txt are missing! ABORTING')
try:
#Tiles
this.T_DO_TILES = True
this.T_LON_MIN = float(config.get('Tiles', 'T_LON_MIN'))
this.T_LON_MAX = float(config.get('Tiles', 'T_LON_MAX'))
this.T_LAT_MIN = float(config.get('Tiles', 'T_LAT_MIN'))
this.T_LAT_MAX = float(config.get('Tiles', 'T_LAT_MAX'))
this.T_WIDTH = float(config.get('Tiles', 'T_WIDTH'))
this.T_EDGE_EXT = float(config.get('Tiles', 'T_EDGE_EXT'))
this.T_GRID_STEP = float(config.get('Tiles', 'T_GRID_STEP'))
except:
gmi_misc.debug('Tile inversion parameters are missing in input.txt')
this.T_DO_TILES = False
import platform
import os
oper_system = platform.system()
this.TESSUTIL_MAGNETIZE_MODEL_FILENAME = './tessutil_magnetize_model'
if os.path.isfile(this.TESSUTIL_MAGNETIZE_MODEL_FILENAME) == False:
gmi_misc.error("CAN NOT FIND " + this.TESSUTIL_MAGNETIZE_MODEL_FILENAME)
this.TESSBZ_FILENAME = './tessbz'
if os.path.isfile(this.TESSBZ_FILENAME) == False:
gmi_misc.error("CAN NOT FIND " + this.TESSBZ_FILENAME)
return config
def main(dr):
#**************** TESTING PARAMS (WOULD BE REMOVED)*******#
TRUNCATE = True
#**************** ---------------------------------*******#
import gmi_misc
#**************** PRINT HEADER ***************************#
gmi_misc.print_header()
print ("Script no. 3: Creation of design matrices")
#**************** ------------ ***************************#
#**************** GET WORKING DIRECTORY ******************#
import os
old_cwd = os.getcwd()
gmi_misc.info('Current directory: '+ old_cwd)
try:
os.chdir(dr)
except:
gmi_misc.error('CAN NOT OPEN WORKING DIRECTORY '+ dr + ', ABORTING...')
gmi_misc.info('WORKING DIRECTORY: '+ os.getcwd())
#**************** --------------------- ******************#
#**************** read parameters from file **************#
import gmi_config
gmi_config.read_config()
#**************** ------------------------- **************#
#************ check if previous stages were launched *****#
'''
import gmi_hash
stages = [0,0,0]
stages, dictionary = gmi_hash.read_dict('checksums.npy')
if __name__ == '__main__':
err = 0
if stages[0] == -1:
err += 1
gmi_misc.warning('model.magtess was changed after the run of Script 1, restart Script no. 1 first! ABORTING...')
elif stages[0] == 0:
err += 1
gmi_misc.warning('model.magtess was changed after the run of Script 1, restart Script no. 1 first! ABORTING...')
else:
pass
if stages[1] == -1:
err += 1
gmi_misc.warning('Folder model was changed after the run of Script 2, restart Script no. 2 first! ABORTING...')
elif stages[1] == 0:
err += 1
gmi_misc.warning('Folder model was changed after the run of Script 2, restart Script no. 2 first! ABORTING...')
else:
pass
if err > 0:
gmi_misc.error('CHECKSUM FAILED, ABORTING!')
'''
#**************** --------------------- ******************#
#**************** CREATE DESIGN MATRICES *****************#
import os
import glob
import pyshtools
import numpy as np
import glob, re
models_filenames = glob.glob('layer*.magtess')
try:
models_filenames.sort(key=lambda f: int(re.sub('\D', '', f))) #good initial sort but doesnt sort numerically very well
sorted(models_filenames) #sort numerically in ascending order
except:
gmi_misc.error('CHECK FILENAMES IN LAYERS FOLDER - THERE SHOULD BE INTEGER NUMBERS IN FILENAMES TO INDICATE THE ORDER OF SURFACES')
gmi_misc.message('All layers: ' + str(models_filenames))
for li,this_model in zip(range(len(models_filenames)), models_filenames):
this_model_noext = this_model.split('.')[0]
os.chdir(this_model_noext)
coefflist = glob.glob("*.coeff")
os.chdir('..')
n_tess = len(coefflist)
if n_tess == 0:
gmi_misc.error("NO CALCULATED SH MODELS OF EACH TESSEROID'S MAGNETIC FIELD")
exit(-1)
if gmi_config.MULTIPLICATOR != 1.0:
gmi_misc.warning("NOTE: SUSCEPTIBILITY OF EACH TESSEROID IS MULTIPLIED BY "+ str(gmi_config.MULTIPLICATOR))
coeff_filename = this_model_noext + '/tess_n' + str(0) + '.coeff'
b = gmi_misc.read_coeffs_from_text_file(coeff_filename, gmi_config.N_MIN_CUTOFF)
n_vals = len(b)
gmi_misc.message('Assemblying design matrices...')
from tqdm import tqdm
A = np.zeros((n_tess, n_vals))
A_ufilt = np.zeros((n_tess, n_vals))
#if __name__ == '__main__':
for i in tqdm(range(n_tess)):
coeff_filename = this_model_noext + '/tess_n' + str(i) + '.coeff'
b = gmi_misc.read_coeffs_from_text_file(coeff_filename, gmi_config.N_MIN_CUTOFF)
b_ufilt = gmi_misc.read_coeffs_from_text_file(coeff_filename, 0)
A[i, :] = b[:]
A_ufilt[i, :] = b_ufilt[:]
#**************** SAVE MATRICES *****************#
if((len(models_filenames)) == 1):
np.save('design_matrix_shcoeff', A)
np.save('design_matrix_ufilt_shcoeff', A_ufilt)
else:
np.save(this_model_noext + '_design_matrix_shcoeff', A)
np.save(this_model_noext + '_design_matrix_ufilt_shcoeff', A_ufilt)
#**************** ------------- *****************#
gmi_misc.ok('...done')
#**************** WRITE MD5 PARAMS **************#
'''
import hashlib
SHAhash = hashlib.md5()
f1 = open('design_matrix_shcoeff.npy', 'rb')
while 1:
# Read file in as little chunks
buf = f1.read(4096)
if not buf : break
SHAhash.update(hashlib.md5(buf).hexdigest().encode('utf-8'))
f1.close()
f2 = open('design_matrix_ufilt_shcoeff.npy', 'rb')
while 1:
# Read file in as little chunks
buf = f2.read(4096)
if not buf : break
SHAhash.update(hashlib.md5(buf).hexdigest().encode('utf-8'))
f2.close()
dictionary['stage3'] = SHAhash.hexdigest()
dictionary['stage4'] = ''
np.save('checksums.npy', dictionary)
'''
#**************** ---------------- **************#
#**************** RETURN BACK TO INITIAL PATH ***#
os.chdir(old_cwd)
def main(dr):
#**************** TESTING PARAMS (WOULD BE REMOVED)*******#
TRUNCATE = True
#**************** ---------------------------------*******#
import gmi_misc
#**************** PRINT HEADER ***************************#
gmi_misc.print_header()
print("Script no. 3: Creation of design matrices")
#**************** ------------ ***************************#
#**************** GET WORKING DIRECTORY ******************#
import os
old_cwd = os.getcwd()
gmi_misc.info('Current directory: ' + old_cwd)
try:
os.chdir(dr)
except:
gmi_misc.error('CAN NOT OPEN WORKING DIRECTORY ' + dr +
', ABORTING...')
gmi_misc.info('WORKING DIRECTORY: ' + os.getcwd())
#**************** --------------------- ******************#
#**************** read parameters from file **************#
import gmi_config
gmi_config.read_config()
#**************** ------------------------- **************#
#************ check if previous stages were launched *****#
import gmi_hash
stages = [0, 0, 0]
stages, dictionary = gmi_hash.read_dict('checksums.npy')
if __name__ == '__main__':
err = 0
if stages[0] == -1:
err += 1
gmi_misc.warning(
'model.magtess was changed after the run of Script 1, restart Script no. 1 first! ABORTING...'
)
elif stages[0] == 0:
err += 1
gmi_misc.warning(
'model.magtess was changed after the run of Script 1, restart Script no. 1 first! ABORTING...'
)
else:
pass
if stages[1] == -1:
err += 1
gmi_misc.warning(
'Folder model was changed after the run of Script 2, restart Script no. 2 first! ABORTING...'
)
elif stages[1] == 0:
err += 1
gmi_misc.warning(
'Folder model was changed after the run of Script 2, restart Script no. 2 first! ABORTING...'
)
else:
pass
if err > 0:
gmi_misc.error('CHECKSUM FAILED, ABORTING!')
#**************** --------------------- ******************#
#**************** CREATE DESIGN MATRICES *****************#
import os
import glob
os.chdir('model')
coefflist = glob.glob("*.coeff")
os.chdir('..')
n_tess = len(coefflist)
if n_tess == 0:
gmi_misc.error(
"NO CALCULATED SH MODELS OF EACH TESSEROID'S MAGNETIC FIELD")
exit(-1)
if gmi_config.MULTIPLICATOR != 1.0:
gmi_misc.warning(
"NOTE: SUSCEPTIBILITY OF EACH TESSEROID IS MULTIPLIED BY " +
str(gmi_config.MULTIPLICATOR))
import pyshtools
import numpy as np
coeff_filename = 'model/tess_n' + str(0) + '.coeff'
b = gmi_misc.read_coeffs_from_text_file(coeff_filename,
gmi_config.N_MIN_CUTOFF)
n_vals = len(b)
gmi_misc.message('Assemblying design matrices...')
from tqdm import tqdm
A = np.zeros((n_tess, n_vals))
A_ufilt = np.zeros((n_tess, n_vals))
#if __name__ == '__main__':
for i in tqdm(range(n_tess)):
coeff_filename = 'model/tess_n' + str(i) + '.coeff'
b = gmi_misc.read_coeffs_from_text_file(coeff_filename,
gmi_config.N_MIN_CUTOFF)
b_ufilt = gmi_misc.read_coeffs_from_text_file(coeff_filename, 0)
A[i, :] = b[:]
A_ufilt[i, :] = b_ufilt[:]
'''
else:
from PyQt5 import QtWidgets
app = QtWidgets.QApplication.instance()
if app is None:
# if it does not exist then a QApplication is created
app = QtWidgets.QApplication([])
from progress_bar import ProgressBar
pb = ProgressBar()
for i in range(n_tess):
coeff_filename = 'model/tess_n' + str(i) + '.coeff'
b = gmi_misc.read_coeffs_from_text_file(coeff_filename, gmi_config.N_MIN_CUTOFF)
b_ufilt = gmi_misc.read_coeffs_from_text_file(coeff_filename, 0)
A[i, :] = b[:]
A_ufilt[i, :] = b_ufilt[:]
pb.setValue(((i + 1) / n_tess) * 100)
app.processEvents()
pb.close()
'''
gmi_misc.ok('...done')
#**************** SAVE MATRICES *****************#
np.save('design_matrix_shcoeff', A)
np.save('design_matrix_ufilt_shcoeff', A_ufilt)
#**************** ------------- *****************#
#**************** WRITE MD5 PARAMS **************#
import hashlib
SHAhash = hashlib.md5()
f1 = open('design_matrix_shcoeff.npy', 'rb')
while 1:
# Read file in as little chunks
buf = f1.read(4096)
if not buf: break
SHAhash.update(hashlib.md5(buf).hexdigest().encode('utf-8'))
f1.close()
f2 = open('design_matrix_ufilt_shcoeff.npy', 'rb')
while 1:
# Read file in as little chunks
buf = f2.read(4096)
if not buf: break
SHAhash.update(hashlib.md5(buf).hexdigest().encode('utf-8'))
f2.close()
dictionary['stage3'] = SHAhash.hexdigest()
dictionary['stage4'] = ''
np.save('checksums.npy', dictionary)
#**************** ---------------- **************#
#**************** RETURN BACK TO INITIAL PATH ***#
os.chdir(old_cwd)