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")
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):
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
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)