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 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)*******#
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)*******#
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):
#**************** 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)