def test_McStasMetaData_add_info_title(self):
"""
Test that title can be set
"""
meta_data = McStasMetaData()
meta_data.set_title("title_test")
self.assertEqual(meta_data.title, "title_test")
def set_dummy_MetaData_2d(name):
meta_data = McStasMetaData()
meta_data.component_name = name
meta_data.dimension = [50, 100]
meta_data.filename = name + ".dat"
return meta_data
def test_McStasMetaData_add_info_ylabel(self):
"""
Test that ylabel can be set
"""
meta_data = McStasMetaData()
meta_data.set_ylabel("ylabel test")
self.assertEqual(meta_data.ylabel, "ylabel test")
def test_McStasMetaData_add_info_len(self):
"""
Test that info can be added to McStasMetaData
"""
meta_data = McStasMetaData()
meta_data.add_info("test", 3)
self.assertEqual(len(meta_data.info), 1)
def test_McStasMetaData_add_info(self):
"""
Test that info can be read from McStasMetaData
"""
meta_data = McStasMetaData()
meta_data.add_info("test", 3)
self.assertEqual(meta_data.info["test"], 3)
def set_dummy_MetaDataBinned_1d():
"""
Sets up simple McStasMetaData object with dimension, 1d case
"""
meta_data = McStasMetaData()
meta_data.component_name = "component for 1d"
meta_data.dimension = 50
return meta_data
def set_dummy_MetaDataBinned_2d():
"""
Sets up simple McStasMetaData object with dimensions, 2d case
"""
meta_data = McStasMetaData()
meta_data.component_name = "test a component"
meta_data.dimension = [50, 100]
return meta_data
def set_dummy_MetaData_2d(name):
"""
Sets up a dummy MetaData object for a 2d dataset
Parameters
----------
name : str
base for filename, .dat will be appended
"""
meta_data = McStasMetaData()
meta_data.component_name = name
meta_data.dimension = [50, 100]
meta_data.filename = name + ".dat"
return meta_data
def get_dummy_MetaData_2d():
meta_data = McStasMetaData()
meta_data.component_name = "test a component"
meta_data.dimension = [5, 4]
meta_data.limits = [0.1, 1.1, 2.0, 4.0]
meta_data.title = "test"
meta_data.xlabel = "test x"
meta_data.ylabel = "test y"
return meta_data
def get_dummy_MetaData_1d():
meta_data = McStasMetaData()
meta_data.component_name = "component for 1d"
meta_data.dimension = 50
meta_data.limits = [0.1, 1.1]
meta_data.title = "test"
meta_data.xlabel = "test x"
meta_data.ylabel = "test y"
return meta_data
def set_dummy_MetaDataBinned_1d():
"""
Sets up simple McStasMetaData object with dimension, 1d case
"""
meta_data = McStasMetaData()
meta_data.component_name = "component for 1d"
meta_data.dimension = 50
meta_data.limits = [0, 1]
meta_data.xlabel = ""
meta_data.ylabel = ""
meta_data.title = ""
meta_data.filename = "dummy"
return meta_data
def set_dummy_MetaDataBinned_2d():
"""
Sets up simple McStasMetaData object with dimensions, 2d case
"""
meta_data = McStasMetaData()
meta_data.component_name = "test a component"
meta_data.dimension = [5, 4]
meta_data.limits = [0, 1, 0, 1]
meta_data.xlabel = ""
meta_data.ylabel = ""
meta_data.title = ""
meta_data.filename = "dummy"
return meta_data
def set_dummy_MetaDataBinned_1d():
"""
Sets up simple McStasMetaData object with dimension, 1d case
"""
meta_data = McStasMetaData()
meta_data.component_name = "component for 1d"
meta_data.filename = "data.dat"
meta_data.dimension = 50
meta_data.info = {"Ncount": 40}
return meta_data
def load_metadata(data_folder_name):
"""
Function that loads metadata from a mcstas simulation
Returns list of metadata objects corresponding to each monitor, all
information is taken from mccode.sim file.
Parameters
----------
first argument : str
path to folder from which metadata should be loaded
"""
if not os.path.isdir(data_folder_name):
raise NameError("Given data directory does not exist.")
# Find all data files in generated folder
files_in_folder = os.listdir(data_folder_name)
# Raise an error if mccode.sim is not available
if "mccode.sim" not in files_in_folder:
raise NameError("No mccode.sim in data folder.")
instrument_parameters = {}
# Open mccode to read metadata for all datasets written to disk
with open(os.path.join(data_folder_name, "mccode.sim"), "r") as f:
# Loop that reads mccode.sim sections
metadata_list = []
current_object = None
in_data = False
in_sim = False
for lines in f:
# Could read other details about run
if lines == "end data\n":
# No more data for this metadata object
# Add parameter information
current_object.add_info("Parameters", instrument_parameters)
# Extract the information
current_object.extract_info()
# Add to metadata list
if current_object.filename != "":
metadata_list.append(current_object)
# Stop reading data
in_data = False
if in_sim:
if "Param" in lines:
parm_lst = lines.split(':')[1].split('=')
try:
value = float(parm_lst[1].strip())
except ValueError:
value = parm_lst[1].strip()
instrument_parameters[parm_lst[0].strip()] = value
if in_data:
# This line contains info to be added to metadata
colon_index = lines.index(":")
key = lines[2:colon_index]
value = lines[colon_index + 2:].strip()
current_object.add_info(key, value)
if lines == "begin data\n":
# Found data section, create new metadata object
current_object = McStasMetaData()
# Start recording data to metadata object
in_data = True
if 'begin simulation:' in lines:
in_sim = True
if 'end simulation:' in lines:
in_sim = False
# Close mccode.sim
f.close()
# Create a list for McStasData instances to return
results = []
# Load datasets described in metadata list individually
for metadata in metadata_list:
# Load data with numpy
data = np.loadtxt(data_folder_name + "/" +
metadata.filename.rstrip())
# Split data into intensity, error and ncount
if type(metadata.dimension) == int:
xaxis = data.T[0, :]
Intensity = data.T[1, :]
Error = data.T[2, :]
Ncount = data.T[3, :]
elif len(metadata.dimension) == 2:
xaxis = [] # Assume evenly binned in 2d
data_lines = metadata.dimension[1]
Intensity = data.T[:, 0:data_lines - 1]
Error = data.T[:, data_lines:2 * data_lines - 1]
Ncount = data.T[:, 2 * data_lines:3 * data_lines - 1]
return metadata_list
def set_dummy_MetaData_1d():
meta_data = McStasMetaData()
meta_data.component_name = "component for 1d"
meta_data.dimension = 50
return meta_data
def set_dummy_MetaData_2d():
meta_data = McStasMetaData()
meta_data.component_name = "test a component"
meta_data.dimension = [50, 100]
return meta_data
def load_results(data_folder_name):
"""
Function for loading data from a mcstas simulation
Loads data on all monitors in a McStas data folder, and returns these
as a list of McStasData objects.
Parameters
----------
first argument : str
path to folder from which data should be loaded
"""
if not os.path.isdir(data_folder_name):
raise NameError("Given data directory does not exist.")
# Find all data files in generated folder
files_in_folder = os.listdir(data_folder_name)
# Raise an error if mccode.sim is not available
if "mccode.sim" not in files_in_folder:
raise NameError("No mccode.sim in data folder.")
# Open mccode to read metadata for all datasets written to disk
with open(os.path.join(data_folder_name, "mccode.sim"), "r") as f:
# Loop that reads mccode.sim sections
metadata_list = []
current_object = None
in_data = False
for lines in f:
# Could read other details about run
if lines == "end data\n":
# No more data for this metadata object
# Extract the information
current_object.extract_info()
# Add to metadata list
if current_object.filename != "":
metadata_list.append(current_object)
# Stop reading data
in_data = False
if in_data:
# This line contains info to be added to metadata
colon_index = lines.index(":")
key = lines[2:colon_index]
value = lines[colon_index + 2:]
current_object.add_info(key, value)
if lines == "begin data\n":
# Found data section, create new metadata object
current_object = McStasMetaData()
# Start recording data to metadata object
in_data = True
# Create a list for McStasData instances to return
results = []
# Load datasets described in metadata list individually
for metadata in metadata_list:
# Load data with numpy
data = np.loadtxt(
os.path.join(data_folder_name, metadata.filename.rstrip()))
# Split data into intensity, error and ncount
if type(metadata.dimension) == int:
xaxis = data.T[0, :]
Intensity = data.T[1, :]
Error = data.T[2, :]
Ncount = data.T[3, :]
elif len(metadata.dimension) == 2:
xaxis = [] # Assume evenly binned in 2d
data_lines = metadata.dimension[1]
Intensity = data[0:data_lines, :]
Error = data[data_lines:2 * data_lines, :]
Ncount = data[2 * data_lines:3 * data_lines, :]
else:
raise NameError("Dimension not read correctly in data set " +
"connected to monitor named " +
metadata.component_name)
# The data is saved as a McStasData object
result = McStasData(metadata, Intensity, Error, Ncount, xaxis=xaxis)
# Add this result to the results list
results.append(result)
# Return list of McStasData objects
return results
def test_McStasMetaData_return_type(self):
"""
Test that newly created McStasMetaData has correct type
"""
meta_data = McStasMetaData()
self.assertIsInstance(meta_data, McStasMetaData)
def test_McStasMetaData_long_read_2d(self):
"""
Test that extract_info can read appropriate info, 2d case
"""
meta_data = McStasMetaData()
meta_data.add_info("type", "array_2d(500, 12)")
meta_data.add_info("component", "test_A_COMP")
meta_data.add_info("filename", "test_A_name")
meta_data.add_info("xlimits", "-2.4 5.99 0.92 3.68")
meta_data.add_info("xlabel", "test A xlabel")
meta_data.add_info("ylabel", "test A ylabel")
meta_data.add_info("title", "test A title")
meta_data.extract_info() # Converts info to attributes
self.assertEqual(len(meta_data.dimension), 2)
self.assertEqual(meta_data.dimension[0], 500)
self.assertEqual(meta_data.dimension[1], 12)
self.assertIs(meta_data.component_name, "test_A_COMP")
self.assertIs(meta_data.filename, "test_A_name")
self.assertEqual(len(meta_data.limits), 4)
self.assertEqual(meta_data.limits[0], -2.4)
self.assertEqual(meta_data.limits[1], 5.99)
self.assertEqual(meta_data.limits[2], 0.92)
self.assertEqual(meta_data.limits[3], 3.68)
self.assertIs(meta_data.xlabel, "test A xlabel")
self.assertIs(meta_data.ylabel, "test A ylabel")
self.assertIs(meta_data.title, "test A title")
def test_McStasMetaData_long_read_1d(self):
"""
Test that extract_info can read appropriate info, 1d case
"""
meta_data = McStasMetaData()
meta_data.add_info("type", "array_1d(500)")
meta_data.add_info("component", "test_A COMP")
meta_data.add_info("filename", "test_A name")
meta_data.add_info("xlimits", " 0.92 3.68")
meta_data.add_info("xlabel", "test A xlabel")
meta_data.add_info("ylabel", "test A ylabel")
meta_data.add_info("title", "test A title")
meta_data.extract_info() # Converts info to attributes
self.assertIsInstance(meta_data.dimension, int)
self.assertEqual(meta_data.dimension, 500)
self.assertIs(meta_data.component_name, "test_A COMP")
self.assertIs(meta_data.filename, "test_A name")
self.assertEqual(len(meta_data.limits), 2)
self.assertEqual(meta_data.limits[0], 0.92)
self.assertEqual(meta_data.limits[1], 3.68)
self.assertIs(meta_data.xlabel, "test A xlabel")
self.assertIs(meta_data.ylabel, "test A ylabel")
self.assertIs(meta_data.title, "test A title")
def test_McStasMetaData_init(self):
"""
Test that newly created McStasMetaData has no content
"""
meta_data = McStasMetaData()
self.assertEqual(len(meta_data.info), 0)