def convert_solution_to_common_h5(self, filename):
root = filename.rsplit('.', 1)[0]
solution_filename = '{}_tough3.h5'.format(root)
solution = QASolutionWriter(solution_filename)
tough_obs = []
for root, dire, files in os.walk('.'):
for name in files:
if (name.startswith('FOFT')) \
and (name.endswith('.csv')):
tough_obs.append(name)
self._process_output_time_slice('OUTPUT_ELEME.csv', solution)
if len(tough_obs) > 0:
self._process_output_observation_file(solution, tough_obs)
solution.destroy()
return solution_filename
def convert_solution_to_common_h5(self, filename):
root = filename.rsplit('.', 1)[0]
solution_filename = '{}_tdycore.h5'.format(root)
solution = QASolutionWriter(solution_filename)
#--------------------------------------------------
# Assumptions:
# The results are on a 2D unit square. Calculate the descretization
# accordingly.
# fin = open('{}.sol'.format(root), 'r')
fin = open('{}.vtk'.format(root), 'r')
all_values = []
found = False
for line in fin:
if (found):
try:
f = float(line)
all_values.append(f)
except ValueError:
break
if line.startswith("LOOKUP_TABLE"):
found = True
n = int(math.sqrt(len(all_values)))
all_values = np.asarray(all_values, dtype=np.float64)
all_values = np.reshape(all_values, (n, n))
x = np.linspace(0.5 / n, 1. - 0.5 / n, n, dtype=np.float64)
z = np.zeros(1)
z[0] = 0.5
solution.write_coordinates(x, x, z)
time = 0.
# time = 1.e6
solution.set_time_unit('y')
solution.write_dataset(time, all_values, 'Liquid Pressure',
'Time Slice')
fin.close()
solution.destroy()
return solution_filename
def convert_solution_to_common_h5(self,root):
debug_push('QASimulatorPFLOTRAN convert_solution_to_common_h5')
solution_filename = \
'{}_pflotran.h5'.format(root)
solution = QASolutionWriter(solution_filename)
h5_filename = '{}_pft.h5'.format(root)
tec_filename = '{}_pft-obs-0.tec'.format(root)
time_slice = False
observation_file = False
try:
f = File(h5_filename,'r')
time_slice = True
except:
print ('No time slice file found, checking for observation file')
if time_slice:
x, y, z = self.get_cell_centered_coordinates_h5(h5_filename)
solution.write_coordinates(x,y,z)
first = True
group_name = 'Time Slice'
for tkey in list(f.keys()):
if tkey.startswith('Time'):
w = tkey.split()
time_string = float(w[1])
if first:
first = False
if len(w) < 3:
print('Time without unit in {}.'.format(h5_filename))
raise
solution.set_time_unit(w[2])
for dkey in list(f[tkey].keys()):
if dkey in h5_mapping:
new_key = h5_mapping[dkey]
else:
new_key = dkey
solution.write_dataset(time_string,
np.array(f[tkey+'/'+dkey]),new_key,group_name)
f.close()
try:
fin = open(tec_filename,'r')
observation_file = True
except:
print('No observation file found')
if observation_file:
group_name = 'Observation'
header = []
all_values = []
for line in fin:
if ('Time' in line):
header = [x.strip('"').strip().strip(' "') for x in line.split(',')]
else:
values = line.strip().split()
all_values.append(values)
all_values = np.asarray(all_values, dtype=np.float64).transpose()
solution.set_time_unit(header[0].split()[1].strip('[').strip(']'))
solution.write_time(all_values[0])
for i in range(1,len(header)):
s = [x.strip(')').strip('(') for x in header[i].split()]
location_string = s[-3:]
location_floats = [float(i) for i in location_string]
variable = all_values[i]
dkey = header[i].split(' obs_pt')[0]
if dkey in obs_mapping:
new_key = obs_mapping[dkey]
else:
new_key = dkey
solution.write_dataset(location_floats,
variable,new_key,group_name)
debug_pop()
return solution_filename
def convert_solution_to_common_h5(self, filename):
root = filename.rsplit('.', 1)[0]
solution_filename = '{}_crunchflow.h5'.format(root)
solution = QASolutionWriter(solution_filename)
c_out = []
obs_out = []
for root, dire, files in os.walk('.'):
for name in files:
if (name.startswith('conc') or
name.startswith('saturation')) \
and (name.endswith('.out') or ###not gonna work
name.endswith('.tec')):
c_out.append(name)
if (name.startswith('crunch_observation')
and name.endswith('.out')):
obs_out.append(name)
first = True
for i in range(len(c_out)):
fin = open(c_out[i], 'r')
log = False
time = None
variables = None
all_values = []
for line in fin:
words = line.strip().split()
if words == []:
continue
if ('Time' in words):
time = float(words[-1].strip())
if ('Distance' in words):
variables = words
if ('VARIABLES' in words):
variables = [x.strip('"') for x in words]
variables = variables[2:]
if ('Log10' in words):
log = True
if words[0][0].isdigit():
values = words
all_values.append(values)
all_values = np.asarray(all_values, dtype=np.float64).transpose()
if not variables:
print('ERROR: headers could not be found in %s.opt file' %
c_out[i])
sys.exit(0)
if not time:
num = re.findall(r'\d+', c_out[i])
time, time_unit = self._find_time_tecplot(
filename, int(num[0])) ##return time unit
else:
time_unit = self._find_time_unit_outfile(filename)
solution.set_time_unit(time_unit)
if variables[0] == 'Distance':
#write_coordinates
if first == True:
x = all_values[0]
y = np.ones(len(all_values[0]))
z = np.ones(len(all_values[0]))
solution.write_coordinates(x, y, z)
first = False
for n in range(1, len(all_values)):
if variables[n] in time_mapping:
new_key = time_mapping[variables[n]]
else:
new_key = variables[n]
if log == True: #####TECPLOT DOESN'T RECORD IF ITS LOG OR NOT?????
solution.write_dataset(time, 10**all_values[n],
new_key, 'Time Slice')
else:
solution.write_dataset(time, all_values[n], new_key,
'Time Slice')
else:
if first == True:
x = all_values[0]
y = all_values[1]
z = all_values[2]
first = False
solution.write_coordinates(x, y, z)
for n in range(3, len(all_values)):
if variables[n] in time_mapping:
new_key = time_mapping[variables[n]]
else:
new_key = variables[n]
if log == True:
all_values[n] == 10**all_values
solution.write_dataset(time, all_values[n], new_key,
'Time Slice')
first = True
for i in range(len(obs_out)):
counter = 0
fin = open(obs_out[i], 'r')
all_values = []
for line in fin:
words = line.strip().split()
if counter == 0:
location = words[-3:]
location = self._convert_location(filename, location)
if counter == 1:
if ('VARIABLES' in words):
variables = [
x.strip('"').strip('(').strip(')') for x in words
]
variables = [val for val in variables if val.isalnum()]
variables = variables[1:]
solution.set_time_unit(variables[1])
variables.pop(1)
else:
variables = words
solution.set_time_unit(
variables[0].strip(')').split('(')[1])
if words[0][0].isdigit():
values = words
all_values.append(values)
counter = counter + 1
all_values = np.asarray(all_values, dtype=np.float64).transpose()
if first == True:
solution.write_time(all_values[0])
first = False
for n in range(1, len(all_values)):
if variables[n] in obs_mapping:
new_key = time_mapping[variables[n]]
else:
new_key = variables[n]
solution.write_dataset(location, all_values[n], new_key,
'Observation')
solution.destroy()
return solution_filename
def convert_to_h5_file(filename, x, y, z, values):
solution = QASolutionWriter(filename)
solution.write_coordinates(x, y, z)
solution.write_dataset(0.0, values, 'Pressure', 'Time Slice')
solution.write_time(x)
solution.write_dataset((0.0, 0.0, 0.0), values, 'Pressure', 'Observation')
solution.destroy()
def convert_solution_to_common_h5(self, filename):
debug_push('QASimulatorSTOMP convert_solution_to_common_h5')
solution_filename = '{}_stomp.h5'.format(filename)
solution = QASolutionWriter(solution_filename)
tslice_out = []
x = []
y = []
z = []
dim = [''] * 3
first_file = True
for r, dirct, files in os.walk('.'):
for name in files:
if name.startswith('plot') and not name.endswith('.dat'):
tslice_out.append(name)
for i in range(len(tslice_out)):
if first_file:
fin = open(tslice_out[i], 'r')
for line in fin:
line = line.strip()
if line == []:
continue
#get dimensions
if ('Number of X' in line):
words = line.split('=')
n = words[1].split()
dim[0] = int(n[0])
if ('Number of Y' in line):
words = line.split('=')
n = words[1].split()
dim[1] = int(n[0])
if ('Number of Z' in line):
words = line.split('=')
n = words[1].split()
dim[2] = int(n[0])
#get coordinates
if ('X-Direction Nodal Vertices, m' in line):
for line in fin:
line = line.strip()
words = line.split()
if not words:
break
# get x-centroid
x_centroid = (float(words[0]) +
float(words[1])) * 0.5
x.append(x_centroid)
x = x[:dim[0]]
if ('Y-Direction Nodal Vertices, m' in line):
for line in fin:
line = line.strip()
words = line.split()
if not words:
break
# get y-centroid
y_centroid = (float(words[0]) +
float(words[2])) * 0.5
y.append(y_centroid)
start = 0
stop = dim[0] * dim[1]
step = dim[0]
keep_ind = np.arange(start, stop, step)
y = [y[ind] for ind in keep_ind]
if ('Z-Direction Nodal Vertices, m' in line):
for line in fin:
line = line.strip()
words = line.split()
if not words:
break
# get z-centroid
z_centroid = (float(words[0]) +
float(words[3])) * 0.5
z.append(z_centroid)
start = 0
stop = dim[0] * dim[1] * dim[2]
step = dim[0] * dim[1]
keep_ind = np.arange(start, stop, step)
z = [z[ind] for ind in keep_ind]
fin.close()
#check if one of the coordinates is empty and if so, populate with a (0.5 value)
#Note: For 2D problems, Stomp only output 2 of the 3 dimensions
if not x:
x = [0.5]
if not y:
y = [0.5]
if not z:
z = [0.5]
solution.write_coordinates(x, y, z)
first_file = False
# read file
fin = open(tslice_out[i], 'r')
time = None
all_values = []
for line in fin:
line = line.strip()
if line == []:
continue
# get time
if ('Time = ' in line):
words = line.split()
time_units = words[5].split(',')
time = float(time_units[0])
t_units = time_units[1]
solution.set_time_unit(t_units)
for j, (key, v_name) in enumerate(time_slice_mapping.items()):
all_values = []
if (key in line):
for line in fin:
line = line.strip()
words = line.split()
if not words:
break
for var_values in words:
all_values.append(float(var_values))
all_values_np = np.asarray(
all_values, dtype=np.float64).transpose()
all_values_np = np.reshape(all_values_np,
(dim[0], dim[1], dim[2]),
order='F')
solution.write_dataset(time, all_values_np, v_name,
'Time Slice')
fin.close()
debug_pop()
return solution_filename