def check_files(base_filename, serial_filename, parallel_filenames):
global all_tests_successful
#print("{}: check_files {} {}".format(base_filename, serial_filename, parallel_filenames))
if serial_filename is None:
print("{}: Serial file not found!".format(base_filename))
return
if len(parallel_filenames) == 0:
print("{}: Parallel files not found!".format(base_filename))
return
data_parallel = py_reader.load_data(parallel_filenames)[0]
data_serial = py_reader.load_data([serial_filename])[0]
# check that non-data fields match
field_names = [
'dimension', 'nElements', 'timeStepNo', 'currentTime', 'basisFunction',
'meshType', 'basisOrder', 'onlyNodalValues'
]
files_are_equal = True
for field_name in field_names:
if data_parallel[field_name] != data_serial[field_name]:
print("{}: mismatch in '{}': serial={} != parallel={}".format(
base_filename, field_name, data_serial[field_name],
data_parallel[field_name]))
files_are_equal = False
# check that data is the same
for field_variable_serial, field_variable_parallel in zip(
data_serial['data'], data_parallel['data']):
if field_variable_serial['name'] != field_variable_parallel['name']:
print("{}: mismatch in field variable name: serial={} != parallel={}".\
format(base_filename, field_variable_serial['name'], field_variable_parallel['name']))
files_are_equal = False
for component_serial, component_parallel in zip(
field_variable_serial['components'],
field_variable_parallel['components']):
if component_serial['name'] != component_parallel['name']:
print("{}: mismatch in component name for field variable {}: serial={} != parallel={}".\
format(base_filename, field_variable_serial['name'], component_serial['name'], component_parallel['name']))
files_are_equal = False
for i, (value_serial, value_parallel) in enumerate(
zip(component_serial['values'],
component_parallel['values'])):
diff = abs(value_serial - value_parallel)
tolerance = 1e-2
if diff > tolerance:
print("{}: mismatch in \"{}\".{}[{}]: serial={} != parallel={} (|diff|={})".\
format(base_filename, field_variable_serial['name'], component_serial['name'], i, value_serial, value_parallel, diff))
files_are_equal = False
if files_are_equal:
print("{} ({} parallel files): match".format(base_filename,
len(parallel_filenames)))
else:
all_tests_successful = False
def compare_result(data):
import sys, os
import py_reader
import numpy as np
#print(os.getcwd())
# load data
data1 = py_reader.load_data(["out/febio_0000001.py"])
data2 = py_reader.load_data(["out/opendihu_0000001.py"])
# if files do not exist
if data1 == [] or data2 == []:
return
component_name = "0"
total_error = 0
values1 = py_reader.get_values(data1[0], "geometry", component_name)
values2 = py_reader.get_values(data2[0], "geometry", component_name)
# values2 contains entries for quadratic elements
# extract the corner values
n_elements = data2[0]['nElements']
nx = n_elements[0]
ny = n_elements[1]
nz = n_elements[2]
mx = nx * 2 + 1
my = ny * 2 + 1
mz = nz * 2 + 1
values2_linear = []
for k in range(nz + 1):
for j in range(ny + 1):
for i in range(nx + 1):
values2_linear.append(values2[2 * k * mx * my + 2 * j * mx +
2 * i])
#print("values1 (febio): ",list(values1))
#print("values2 (opendihu): ",values2_linear)
error_rms = np.sqrt(np.mean((values1 - values2_linear)**2))
print("rms: {}".format(error_rms))
with open("rms", "w") as f:
f.write(str(error_rms))
def compute_error_filenames(reference_filenames, filenames_to_test, field_variable_name="solution"):
if reference_filenames is None or len(reference_filenames) == 0:
print("No reference files given")
return None
if filenames_to_test is None or len(filenames_to_test) == 0:
print("No files to test given")
return None
data_reference = py_reader.load_data(reference_filenames)[0]
data_test = py_reader.load_data(filenames_to_test)[0]
# parse field variables and extract values
values_reference = None
values_test = None
# parse reference field variable
for field_variable in data_reference["data"]:
if field_variable["name"] == field_variable_name:
values_reference = field_variable["components"][0]["values"]
# parse test field variable
for field_variable in data_test["data"]:
if field_variable["name"] == field_variable_name:
values_test = field_variable["components"][0]["values"]
if values_reference is None or values_test is None:
return None
# compute error
absolute_error = np.linalg.norm(values_reference - values_test)
try:
relative_error = np.linalg.norm((values_reference - values_test) / values_reference)
except:
relative_error = np.linalg.norm((values_reference - values_test) / values_test)
relative_error /= len(values_reference)
return relative_error
def extract4(file):
if file.endswith('.py'):
data = py_reader.load_data([file])
data = data[0]['data']
solution = next(filter(lambda d: d['name'] == 'solution', data))
componentX = lambda x: next(
filter(lambda d: d['name'] == str(x), solution['components']))
channel_names = [
'membrane/V', 'sodium_channel_m_gate/m',
'sodium_channel_h_gate/h', 'potassium_channel_n_gate/n'
]
return np.vstack([componentX(i)['values']
for i in channel_names]).T
raise "FileType not understood: " + file
] # the traction force is specified in the reference configuration
#traction_vector = [0.2*variables.force, 0.4*variables.force, 0.5*variables.force] # the traction force in specified in the reference configuration
face = "2+"
variables.elasticity_neumann_bc = [{
"element": k * nx * ny + j * nx + i,
"constantVector": traction_vector,
"face": face
} for j in range(ny) for i in range(nx)]
#variables.elasticity_dirichlet_bc = {}
print("nRanks: ", variables.meshes["3Dmesh_quadratic"]["nRanks"])
# load initial values from file
initial_values_filename = "initial_values.py"
import py_reader
initial_data = py_reader.load_data([initial_values_filename])
field_variables = initial_data[0]["data"]
x_positions = field_variables[1]["components"][0]["values"]
y_positions = field_variables[1]["components"][1]["values"]
z_positions = field_variables[1]["components"][2]["values"]
config = {
"scenarioName": variables.scenario_name, # scenario name to identify the simulation runs in the log file
"logFormat": "csv", # "csv" or "json", format of the lines in the log file, csv gives smaller files
"solverStructureDiagramFile": "out/solver_structure.txt", # output file of a diagram that shows data connection between solvers
"mappingsBetweenMeshesLogFile": "out/mappings_between_meshes_log.txt", # log file for mappings
"Meshes": variables.meshes,
"PreciceAdapter": { # precice adapter for bottom tendon
"timeStepOutputInterval": 100, # interval in which to display current timestep and time in console
"timestepWidth": 1, # coupling time step width, must match the value in the precice config
solution_py_files = list(np.extract(np.array(list(map(solution_py_condition, files))), files))
# sort files by number in file name
solution_py_files = sorted(solution_py_files)
# output file names
if len(solution_py_files) == 1:
print("1 file: {}".format(solution_py_files[0]))
elif len(solution_py_files) <= 4:
print("{} files: {}".format(len(solution_py_files),solution_py_files))
else:
print("{} files: {}, {}, {}, ..., {}".format(len(solution_py_files), solution_py_files[0],solution_py_files[1],solution_py_files[2],solution_py_files[-1]))
# load data
data = py_reader.load_data(solution_py_files)
if len(data) == 0:
print( "no data found.")
sys.exit(0)
# set global parameters for font sizes
plt.rcParams.update({'font.size': 20})
plt.rcParams['lines.linewidth'] = 3
plt.rcParams['lines.markersize'] = 8
dimension = data[0]['dimension']
####################
# 1D
if dimension == 1:
files1 = []
for filename in os.listdir(directory1):
if filename.endswith(".py"):
files1.append(os.path.join(directory1, filename))
files1 = sorted(files1)
files2 = []
for filename in os.listdir(directory2):
if filename.endswith(".py"):
files2.append(os.path.join(directory2, filename))
files2 = sorted(files2)
print("files: ", files1, files2)
# load data
data1 = py_reader.load_data(files1)
data2 = py_reader.load_data(files2)
n_values = min(len(data1), len(data2))
if len(data1) != len(data2):
print(
"Warning: Directory {} contains {} files, directory {} contains {} files."
.format(directory1, len(data1), directory2, len(data2)))
component_name = "0"
total_error = 0
for i in range(n_values):
values1 = py_reader.get_values(data1[i], "solution", component_name)
values2 = py_reader.get_values(data2[i], "solution", component_name)
#node_positions = [[79.88196548528718, 138.44230490662775, 72.0], [84.1096260871754, 138.31655743349813, 72.0], [88.33728668906363, 138.19080996036848, 72.0], [89.598002133421, 139.96951371685657, 72.0], [90.85871757777839, 141.74821747334462, 72.0], [76.10149783100812, 143.16321149777914, 72.0], [80.27591827937458, 143.9465554749207, 72.0], [84.45033872774106, 144.72989945206223, 72.0], [86.5697220643283, 145.8000948322888, 72.0], [88.68910540091555, 146.87029021251539, 72.0], [72.32103017672904, 147.88411808893053, 72.0], [76.44221047157376, 149.57655351634324, 72.0], [80.56339076641848, 151.26898894375594, 72.0], [83.5414419952356, 151.63067594772104, 72.0], [86.51949322405271, 151.99236295168615, 72.0], [71.23271784225128, 150.78925110166716, 72.0], [74.85866336055606, 152.6577237501053, 72.0], [78.48460887886085, 154.52619639854342, 72.0], [81.43059188883157, 154.50720050492959, 72.0], [84.37657489880226, 154.48820461131572, 72.0], [70.1444055077735, 153.6943841144038, 72.0], [73.27511624953837, 155.73889398386734, 72.0], [76.40582699130324, 157.7834038533309, 72.0], [79.31974178242754, 157.38372506213807, 72.0], [82.23365657355183, 156.98404627094527, 72.0], [80.84363734642932, 136.53655485714376, 97.01690331304937], [86.73556883901792, 136.53695725848277, 97.01690331304937], [92.62750033160651, 136.5373596598218, 97.01690331304937], [94.55139199406882, 139.28174878330836, 97.01690331304937], [96.47528365653113, 142.02613790679493, 97.01690331304937], [74.78524747100565, 143.85646972154393, 97.01690331304937], [80.90002885669234, 144.9965358079074, 97.01690331304935], [87.01481024237904, 146.13660189427088, 97.01690331304937], [90.15936401210571, 147.9277813177691, 97.01690331304935], [93.30391778183241, 149.7189607412673, 97.01690331304937], [68.72685759558195, 151.17638458594408, 97.01690331304937], [75.06448887436676, 153.456114357332, 97.01690331304937], [81.40212015315156, 155.73584412871992, 97.01690331304937], [85.76733603014262, 156.57381385222982, 97.01690331304937], [90.13255190713367, 157.4117835757397, 97.01690331304937], [66.63137423780316, 155.5051701182433, 97.01690331304937], [72.57124988131899, 158.16285605471842, 97.01690331304935], [78.51112552483482, 160.8205419911935, 97.01690331304937], [82.84569431214274, 160.88758200727403, 97.01690331304935], [87.18026309945067, 160.95462202335457, 97.01690331304937], [64.53589088002435, 159.83395565054255, 97.01690331304937], [70.07801088827122, 162.8695977521048, 97.01690331304937], [75.6201308965181, 165.90523985366704, 97.01690331304937], [79.92405259414289, 165.20135016231825, 97.01690331304937], [84.22797429176767, 164.49746047096946, 97.01690331304937], [81.80530920757147, 134.63080480765976, 122.03380662609872], [89.36151159086043, 134.75735708346744, 122.03380662609872], [96.91771397414941, 134.88390935927512, 122.03380662609872], [99.50478185471664, 138.59398384976015, 122.03380662609872], [102.09184973528387, 142.3040583402452, 122.03380662609872], [73.46899711100318, 144.5497279453087, 122.03380662609872], [81.5241394340101, 146.04651614089408, 122.03380662609872], [89.57928175701701, 147.54330433647954, 122.03380662609872], [93.74900595988315, 150.05546780324937, 122.03380662609872], [97.91873016274926, 152.5676312700192, 122.03380662609872], [65.13268501443487, 154.46865108295762, 122.03380662609872], [73.68676727715976, 157.33567519832076, 122.03380662609872], [82.24084953988464, 160.20269931368392, 122.03380662609872], [87.99323006504963, 161.5169517567386, 122.03380662609872], [93.74561059021464, 162.83120419979323, 122.03380662609872], [62.03003063335504, 160.22108913481947, 122.03380662609872], [70.28383640208193, 163.6679883593315, 122.03380662609872], [78.5376421708088, 167.11488758384354, 122.03380662609872], [84.26079673545394, 167.2679635096185, 122.03380662609872], [89.98395130009908, 167.42103943539342, 122.03380662609872], [58.92737625227521, 165.9735271866813, 122.03380662609872], [66.88090552700407, 170.00030152034225, 122.03380662609872], [74.83443480173295, 174.0270758540032, 122.03380662609872], [80.52836340585823, 173.01897526249843, 122.03380662609872], [86.2222920099835, 172.01087467099364, 122.03380662609872], [81.37354014493069, 141.79567982331662, 147.05070993914808], [89.40590509478392, 141.9231018606853, 147.05070993914808], [97.43827004463714, 142.05052389805402, 147.05070993914808], [99.74245928673088, 145.98862102408094, 147.05070993914808], [102.04664852882463, 149.92671815010786, 147.05070993914808], [72.98931071812208, 151.536997634973, 147.05070993914808], [81.56829622615707, 153.29668067855795, 147.05070993914805], [90.14728173419206, 155.05636372214286, 147.05070993914808], [94.24073708709727, 157.85647235139828, 147.05070993914805], [98.33419244000247, 160.6565809806537, 147.05070993914808], [64.60508129131347, 161.2783154466294, 147.05070993914808], [73.73068735753023, 164.67025949643056, 147.05070993914808], [82.856293423747, 168.06220354623173, 147.05070993914808], [88.73901488746365, 169.72432367871562, 147.05070993914808], [94.62173635118032, 171.3864438111995, 147.05070993914808], [61.74810805854179, 166.92530483169884, 147.05070993914808], [70.65408215617077, 171.07873743206488, 147.05070993914808], [79.56005625379973, 175.23217003243093, 147.05070993914808], [85.37074274276061, 175.71304511796703, 147.05070993914808], [91.1814292317215, 176.1939202035031, 147.05070993914808], [58.89113482577012, 172.57229421676828, 147.05070993914808], [67.57747695481129, 177.48721536769918, 147.05070993914808], [76.26381908385247, 182.40213651863013, 147.05070993914808], [82.00247059805757, 181.7017665572184, 147.05070993914808], [87.74112211226267, 181.00139659580668, 147.05070993914808], [80.9417710822899, 148.96055483897348, 172.06761325219742], [89.45029859870739, 149.0888466379032, 172.06761325219742], [97.95882611512488, 149.21713843683293, 172.06761325219742], [99.98013671874514, 153.38325819840173, 172.06761325219742], [102.0014473223654, 157.5493779599705, 172.06761325219742], [72.50962432524098, 158.52426732463732, 172.06761325219742], [81.61245301830405, 160.54684521622175, 172.06761325219742], [90.71528171136713, 162.56942310780624, 172.06761325219742], [94.73246821431141, 165.6574768995472, 172.06761325219745], [98.74965471725568, 168.74553069128817, 172.06761325219742], [64.07747756819205, 168.08797981030116, 172.06761325219742], [73.77460743790071, 172.00484379454036, 172.06761325219742], [83.47173730760937, 175.92170777877953, 172.06761325219742], [89.48479970987768, 177.93169560069268, 172.06761325219742], [95.49786211214598, 179.94168342260582, 172.06761325219745], [61.46618548372854, 173.6295205285782, 172.06761325219742], [71.02432791025961, 178.48948650479824, 172.06761325219742], [80.58247033679068, 183.3494524810183, 172.06761325219742], [86.48068875006729, 184.15812672631552, 172.06761325219742], [92.37890716334391, 184.96680097161277, 172.06761325219742], [58.85489339926503, 179.17106124685523, 172.06761325219745], [68.2740483826185, 184.97412921505614, 172.06761325219742], [77.69320336597198, 190.77719718325704, 172.06761325219742], [83.47657779025691, 190.38455785193838, 172.06761325219742], [89.25995221454184, 189.99191852061975, 172.06761325219742], [83.58576782758489, 156.5780271037519, 196.0338066260987], [91.90427231291838, 157.41954937192602, 196.0338066260987], [100.22277679825189, 158.2610716401001, 196.0338066260987], [102.20869054780991, 161.60766324637603, 196.0338066260987], [104.19460429736793, 164.95425485265196, 196.0338066260987], [77.11405531960727, 164.92008447974362, 196.0338066260987], [85.56331247045148, 167.12438193438476, 196.0338066260987], [94.01256962129568, 169.3286793890259, 196.0338066260987], [97.7754830075483, 171.8308042034405, 196.03380662609874], [101.53839639380091, 174.33292901785512, 196.0338066260987], [70.64234281162965, 173.26214185573534, 196.0338066260987], [79.22235262798458, 176.8292144968435, 196.0338066260987], [87.8023624443395, 180.39628713795167, 196.0338066260987], [93.3422754672867, 182.05394516050498, 196.0338066260987], [98.88218849023389, 183.7116031830583, 196.03380662609874], [68.81682990712241, 178.21201297585026, 196.0338066260987], [77.12000478916683, 182.5803103631989, 196.0338066260987], [85.42317967121124, 186.94860775054755, 196.0338066260987], [90.73095357484405, 187.4768208671029, 196.0338066260987], [96.03872747847687, 188.00503398365834, 196.0338066260987], [66.99131700261518, 183.16188409596515, 196.03380662609874], [75.01765695034908, 188.3314062295543, 196.0338066260987], [83.04399689808301, 193.50092836314343, 196.0338066260987], [88.11963168240143, 192.8996965737009, 196.0338066260987], [93.19526646671986, 192.2984647842584, 196.0338066260987], [86.22976457287987, 164.19549936853034, 220.0], [94.35824602712938, 165.75025210594885, 220.0], [102.48672748137888, 167.30500484336733, 220.0], [104.43724437687467, 169.83206829435034, 220.0], [106.38776127237048, 172.35913174533337, 220.0], [81.71848631397356, 171.31590163484992, 220.0], [89.5141719225989, 173.70191865254773, 220.0], [97.30985753122425, 176.08793567024554, 220.0], [100.8184978007852, 178.0041315073338, 220.0], [104.32713807034614, 179.92032734442205, 220.0], [77.20720805506724, 178.4363039011695, 220.0], [84.67009781806843, 181.65358519914665, 220.0], [92.13298758106961, 184.87086649712379, 220.0], [97.1997512246957, 186.17619472031726, 220.0], [102.26651486832179, 187.48152294351073, 220.0], [76.16747433051628, 182.7945054231223, 220.0], [83.21568166807404, 186.67113422159954, 220.0], [90.26388900563182, 190.5477630200768, 220.0], [94.98121839962083, 190.79551500789034, 220.0], [99.69854779360983, 191.0432669957039, 220.0], [75.12774060596531, 187.1527069450751, 220.0], [81.76126551807967, 191.68868324405244, 220.0], [88.39479043019402, 196.2246595430298, 220.0], [92.76268557454594, 195.41483529546343, 220.0], [97.13058071889787, 194.60501104789708, 220.0]]
# artifical node positions
belly_width = 0.02
width = 1.0
height = 1.0
#node_positions = [[79.88196548528718, 138.44230490662775, 72.0], [84.1096260871754, 138.31655743349813, 72.0], [88.33728668906363, 138.19080996036848, 72.0], [89.598002133421, 139.96951371685657, 72.0], [90.85871757777839, 141.74821747334462, 72.0], [76.10149783100812, 143.16321149777914, 72.0], [80.27591827937458, 143.9465554749207, 72.0], [84.45033872774106, 144.72989945206223, 72.0], [86.5697220643283, 145.8000948322888, 72.0], [88.68910540091555, 146.87029021251539, 72.0], [72.32103017672904, 147.88411808893053, 72.0], [76.44221047157376, 149.57655351634324, 72.0], [80.56339076641848, 151.26898894375594, 72.0], [83.5414419952356, 151.63067594772104, 72.0], [86.51949322405271, 151.99236295168615, 72.0], [71.23271784225128, 150.78925110166716, 72.0], [74.85866336055606, 152.6577237501053, 72.0], [78.48460887886085, 154.52619639854342, 72.0], [81.43059188883157, 154.50720050492959, 72.0], [84.37657489880226, 154.48820461131572, 72.0], [70.1444055077735, 153.6943841144038, 72.0], 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192.08113590263687], [89.82840813796435, 156.6190243582219, 192.0811359026369], [98.70281973143355, 157.51492061485618, 192.0811359026369], [100.51663717157089, 161.18610494430408, 192.0811359026369], [102.33045461170825, 164.85728927375195, 192.08113590263687], [73.50321637926825, 164.23108235247912, 192.08113590263687], [82.89472687923299, 166.79351207300482, 192.0811359026369], [92.2862373791977, 169.35594179353055, 192.0811359026369], [96.1504290974148, 172.15043960153082, 192.0811359026369], [100.0146208156319, 174.94493740953106, 192.08113590263687], [66.05243621404139, 172.73903660337055, 192.08113590263687], [75.96104562050164, 176.96799978778773, 192.0811359026369], [85.86965502696187, 181.19696297220491, 192.0811359026369], [91.78422102325871, 183.11477425875754, 192.0811359026369], [97.69878701955555, 185.03258554531016, 192.08113590263687], [63.873585903932536, 178.14983250575574, 192.08113590263687], [73.64435655661144, 183.24053365373098, 192.0811359026369], [83.41512720929035, 188.33123480170622, 192.0811359026369], [89.15283451801699, 189.02995950040523, 192.0811359026369], [94.89054182674363, 189.72868419910426, 192.08113590263687], [61.69473559382369, 183.5606284081409, 192.08113590263687], [71.32766749272125, 189.5130675196742, 192.08113590263687], [80.96059939161881, 195.4655066312075, 192.08113590263687], [86.52144801277527, 194.94514474205295, 192.08113590263687], [92.0822966339317, 194.42478285289837, 192.08113590263687], [82.53820485826736, 158.58704454018255, 202.08789722785664], [91.22974340154617, 159.87551218275814, 202.08789722785667], [99.92128194482495, 161.1639798253338, 202.08789722785667], [101.71690466175029, 164.45697460374916, 202.08789722785667], [103.51252737867563, 167.74996938216455, 202.08789722785664], [76.13666913174268, 166.707992531156, 202.08789722785662], [85.06863759922922, 169.31988803530692, 202.08789722785667], [94.00060606671576, 171.93178353945788, 202.08789722785667], [97.70079242255639, 174.42749158066567, 202.08789722785667], [101.40097877839703, 176.9231996218735, 202.08789722785664], [69.735133405218, 174.82894052212947, 202.08789722785662], [78.90753179691228, 178.76426388785572, 202.08789722785667], [88.07993018860657, 182.69958725358197, 202.08789722785667], [93.6846801833625, 184.39800855758222, 202.08789722785667], [99.28943017811844, 186.09642986158246, 202.08789722785664], [67.85432607073284, 180.00441029941265, 202.08789722785664], [76.86161171488715, 184.71758032465138, 202.08789722785667], [85.86889735904145, 189.43075034989016, 202.08789722785667], [91.2240048714093, 189.9150071937429, 202.08789722785667], [96.57911238377717, 190.39926403759569, 202.08789722785664], [65.97351873624767, 185.1798800766958, 202.08789722785664], [74.81569163286201, 190.67089676144707, 202.08789722785664], [83.65786452947634, 196.16191344619835, 202.08789722785664], [88.76332955945612, 195.43200582990363, 202.08789722785664], [93.8687945894359, 194.7020982136089, 202.08789722785664], [84.1224131720396, 161.45096097877743, 212.0946585530764], [92.63107866512799, 163.1320000072944, 212.0946585530764], [101.13974415821637, 164.81303903581139, 212.0946585530764], [102.91717215192969, 167.72784426319427, 212.0946585530764], [104.69460014564301, 170.64264949057716, 212.0946585530764], [78.7701218842171, 169.18490270983293, 212.09465855307639], [87.24254831922546, 171.84626399760907, 212.0946585530764], [95.71497475423382, 174.5076252853852, 212.0946585530764], [99.251155747698, 176.70454355980058, 212.0946585530764], [102.78733674116216, 178.90146183421595, 212.0946585530764], [73.41783059639461, 176.91884444088842, 212.09465855307639], [81.85401797332293, 180.5605279879237, 212.09465855307639], [90.29020535025126, 184.20221153495902, 212.0946585530764], [95.5851393434663, 185.68124285640687, 212.0946585530764], [100.88007333668132, 187.16027417785475, 212.0946585530764], [71.83506623753314, 181.85898809306957, 212.09465855307639], [80.07886687316284, 186.19462699557184, 212.0946585530764], [88.32266750879256, 190.5302658980741, 212.0946585530764], [93.29517522480164, 190.8000548870806, 212.0946585530764], [98.2676829408107, 191.06984387608708, 212.0946585530764], [70.25230187867166, 186.79913174525072, 212.0946585530764], [78.30371577300276, 191.82872600321997, 212.0946585530764], [86.35512966733387, 196.85832026118922, 212.0946585530764], [91.00521110613698, 195.91886691775431, 212.0946585530764], [95.65529254494008, 194.97941357431944, 212.0946585530764], [85.17608887245973, 162.82323017365388, 216.04732927653822], [93.49466234612868, 164.4411260566216, 216.04732927653822], [101.81323581979763, 166.05902193958934, 216.04732927653822], [103.67720826440218, 168.77995627877232, 216.04732927653822], [105.54118070900674, 171.50089061795526, 216.04732927653822], [80.24430409909533, 170.2504021723414, 216.0473292765382], [88.37836012091219, 172.77409132507842, 216.04732927653822], [96.51241614272902, 175.29778047781537, 216.04732927653822], [100.0348267742416, 177.35433753356722, 216.04732927653822], [103.55723740575415, 179.410894589319, 216.04732927653822], [75.31251932573093, 177.67757417102897, 216.0473292765382], [83.26205789569568, 181.10705659353516, 216.0473292765382], [91.21159646566043, 184.5365390160414, 216.04732927653822], [96.39244528408099, 185.92871878836206, 216.04732927653822], [101.57329410250156, 187.32089856068274, 216.04732927653822], [74.00127028402471, 182.32674675809594, 216.0473292765382], [81.64727427061844, 186.4328806085857, 216.04732927653822], [89.2932782572122, 190.53901445907545, 216.04732927653822], [94.13819681221122, 190.79778494748544, 216.04732927653822], [98.98311536721026, 191.0565554358955, 216.04732927653822], [72.6900212423185, 186.9759193451629, 216.04732927653822], [80.03249064554122, 191.75870462363622, 216.04732927653822], [87.37496004876394, 196.5414899021095, 216.04732927653822], [91.88394834034146, 195.66685110660887, 216.04732927653822], [96.39293663191899, 194.79221231110824, 216.04732927653822], [86.22976457287987, 164.19549936853034, 220.0], [94.35824602712938, 165.75025210594885, 220.0], [102.48672748137888, 167.30500484336733, 220.0], [104.43724437687467, 169.83206829435034, 220.0], [106.38776127237048, 172.35913174533337, 220.0], [81.71848631397356, 171.31590163484992, 220.0], [89.5141719225989, 173.70191865254773, 220.0], [97.30985753122425, 176.08793567024554, 220.0], [100.8184978007852, 178.0041315073338, 220.0], [104.32713807034614, 179.92032734442205, 220.0], [77.20720805506724, 178.4363039011695, 220.0], [84.67009781806843, 181.65358519914665, 220.0], [92.13298758106961, 184.87086649712379, 220.0], [97.1997512246957, 186.17619472031726, 220.0], [102.26651486832179, 187.48152294351073, 220.0], [76.16747433051628, 182.7945054231223, 220.0], [83.21568166807404, 186.67113422159954, 220.0], [90.26388900563182, 190.5477630200768, 220.0], [94.98121839962083, 190.79551500789034, 220.0], 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# load mesh
import py_reader # reader utility for opendihu *.py files
# load data from file
input_files = ["static_result.py"]
static_data = py_reader.load_data(input_files)
# extract values
initial_displacements = []
geometry = []
u = []
for dataset in static_data:
print("field variables: {}".format(
py_reader.get_field_variable_names(dataset)))
# parse geometry (node positions)
x_values = py_reader.get_values(dataset, "geometry", "x")
y_values = py_reader.get_values(dataset, "geometry", "y")
z_values = py_reader.get_values(dataset, "geometry", "z")
def compute_error_filenames(reference_filenames,
filenames_to_test,
field_variable_name="solution"):
if reference_filenames is None or len(reference_filenames) == 0:
print("No reference files given")
return None
if filenames_to_test is None or len(filenames_to_test) == 0:
print("No files to test given")
return None
data_sets_reference = py_reader.load_data(reference_filenames)
data_sets_to_test = py_reader.load_data(filenames_to_test)
if len(data_sets_reference) != len(data_sets_to_test):
print(
"Number of timesteps does not match! Reference data set: {}, Test data set: {}"
.format(data_sets_reference, data_sets_to_test))
data_reference = data_sets_reference[-1]
data_test = data_sets_to_test[-1]
# parse field variables and extract values
values_reference = None
values_test = None
data_reference
# parse reference field variable
for field_variable in data_reference["data"]:
if field_variable["name"] == field_variable_name:
values_reference = field_variable["components"][0]["values"]
# parse test field variable
for field_variable in data_test["data"]:
if field_variable["name"] == field_variable_name:
values_test = field_variable["components"][0]["values"]
if values_reference is None or values_test is None:
return None
# compute error
absolute_error = np.linalg.norm(values_reference - values_test)
print("values_reference: ", values_reference)
print("values_test: ", values_test)
print("difference: ", values_reference - values_test)
try:
relative_error = np.linalg.norm(
(values_reference - values_test) / values_reference)
except:
relative_error = np.linalg.norm(
(values_reference - values_test) / values_test)
print("Absoluter Fehler: ", absolute_error)
relative_error /= len(values_reference)
print("Relativer Fehler: ", relative_error)
return relative_error
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Script that parses the output from the febio and opendihu scenarios and computes a total error
import sys, os
import py_reader
import numpy as np
#print(os.getcwd())
# load data
data1 = py_reader.load_data(["build_release/out/febio_0000001.py"])
data2 = py_reader.load_data(["build_release/out/opendihu_0000001.py"])
# if files do not exist
if data1 == [] or data2 == []:
quit()
component_name = "0"
total_error = 0
values1 = py_reader.get_values(data1[0], "geometry", component_name)
values2 = py_reader.get_values(data2[0], "geometry", component_name)
min_u1, max_u1 = py_reader.get_min_max(data1, "u", "2")
min_u2, max_u2 = py_reader.get_min_max(data2, "u", "z")
print("maximum z-displacement febio: {}".format(max_u1))
print("maximum z-displacement opendihu: {}".format(max_u2))
# values2 contains entries for quadratic elements
muscle_spindles_files = [
"out/{}".format(filename) for filename in sorted(
list(np.extract(np.array(list(map(condition, filenames))), filenames)))
]
condition = lambda filename: suffix in filename and "motoneurons" in filename
motoneurons_files = [
"out/{}".format(filename) for filename in sorted(
list(np.extract(np.array(list(map(condition, filenames))), filenames)))
]
print("Number of input files: muscle spindles: {}, motoneurons: {}".\
format(len(muscle_spindles_files), len(motoneurons_files)))
# load data
muscle_spindles_data = py_reader.load_data(muscle_spindles_files)
motoneurons_data = py_reader.load_data(motoneurons_files)
# create plots
fig, axes = plt.subplots(2, 1, figsize=(12, 6), sharex=True)
# ---------------------
# plot muscle spindles
component_name_input = "(P)modell/L"
component_name_output = "modell/primary_afferent"
t_values = None
values_output = None
values_input = None
# loop over datasets at different times
interneurons_files = [
"out/{}".format(filename) for filename in sorted(
list(np.extract(np.array(list(map(condition, filenames))), filenames)))
]
condition = lambda filename: ".py" in filename and "motoneurons" in filename
motoneurons_files = [
"out/{}".format(filename) for filename in sorted(
list(np.extract(np.array(list(map(condition, filenames))), filenames)))
]
print("Number of input files: muscle spindles: {}, golgi tendon organs: {}, interneurons: {}, motoneurons: {}".\
format(len(muscle_spindles_files), len(golgi_tendon_organs_files), len(interneurons_files), len(motoneurons_files)))
# load data
muscle_spindles_data = py_reader.load_data(muscle_spindles_files)
golgi_tendon_organs_data = py_reader.load_data(golgi_tendon_organs_files)
interneurons_data = py_reader.load_data(interneurons_files)
motoneurons_data = py_reader.load_data(motoneurons_files)
# create plots
fig, axes = plt.subplots(4, 1, figsize=(12, 8), sharex=True)
# ---------------------
# plot muscle spindles
component_name_input = "(P)membrane/i_Stim"
component_name_output = "membrane/V"
t_values = None
values_output = None
values_input = None
