def get_file_contents(self):
"""
Reader specific class to access the contents of the file
All reader classes that inherit from FileReader must implement
"""
x = np.zeros(0)
y = np.zeros(0)
self.current_dataset = plottable_1D(x, y)
self.current_datainfo = DataInfo()
self.current_datainfo.meta_data["blah"] = self.nextline()
self.send_to_output()
def add_data_set(self, key=""):
"""
Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a
private method to generate a new data set.
:param key: NeXus group name for current tree level
"""
if self.current_datainfo and self.current_dataset:
self.final_data_cleanup()
self.data1d = []
self.data2d = []
self.current_datainfo = DataInfo()
def reset_state(self):
self.current_dataset = plottable_1D(np.empty(0), np.empty(0), np.empty(0), np.empty(0))
self.current_datainfo = DataInfo()
self.datasets = []
self.raw_data = None
self.errors = set()
self.logging = []
self.output = []
self.detector = Detector()
self.collimation = Collimation()
self.aperture = Aperture()
self.process = Process()
self.source = Source()
self.sample = Sample()
self.trans_spectrum = TransmissionSpectrum()
self.upper = 5
self.lower = 5
def get_file_contents(self):
"""
Get the contents of the file
"""
buff = self.readall()
filepath = self.f_open.name
lines = buff.splitlines()
self.output = []
self.current_datainfo = DataInfo()
self.current_datainfo.filename = filepath
self.reset_data_list(len(lines))
# The first good line of data will define whether
# we have 2-column or 3-column ascii
has_error_dx = None
has_error_dy = None
# Initialize counters for data lines and header lines.
is_data = False
# More than "5" lines of data is considered as actual
# To count # of current data candidate lines
candidate_lines = 0
# To count total # of previous data candidate lines
candidate_lines_previous = 0
# Current line number
line_no = 0
# minimum required number of columns of data
lentoks = 2
for line in lines:
toks = self.splitline(line.strip())
# To remember the number of columns in the current line of data
new_lentoks = len(toks)
try:
if new_lentoks == 0:
# If the line is blank, skip and continue on
# In case of breaks within data sets.
continue
elif new_lentoks != lentoks and is_data:
# If a footer is found, break the loop and save the data
break
elif new_lentoks != lentoks and not is_data:
# If header lines are numerical
candidate_lines = 0
self.reset_data_list(len(lines) - line_no)
self.current_dataset.x[candidate_lines] = float(toks[0])
if new_lentoks > 1:
self.current_dataset.y[candidate_lines] = float(toks[1])
# If a 3rd row is present, consider it dy
if new_lentoks > 2:
self.current_dataset.dy[candidate_lines] = \
float(toks[2])
has_error_dy = True
# If a 4th row is present, consider it dx
if new_lentoks > 3:
self.current_dataset.dx[candidate_lines] = \
float(toks[3])
has_error_dx = True
candidate_lines += 1
# If 5 or more lines, this is considering the set data
if candidate_lines >= self.min_data_pts:
is_data = True
if is_data and new_lentoks >= 8:
msg = "This data looks like 2D ASCII data. Use the file "
msg += "converter tool to convert it to NXcanSAS."
raise FileContentsException(msg)
# To remember the # of columns on the current line
# for the next line of data
lentoks = new_lentoks
line_no += 1
except ValueError:
# ValueError is raised when non numeric strings conv. to float
# It is data and meet non - number, then stop reading
if is_data:
break
# Delete the previously stored lines of data candidates if
# the list is not data
self.reset_data_list(len(lines) - line_no)
lentoks = 2
has_error_dx = None
has_error_dy = None
# Reset # of lines of data candidates
candidate_lines = 0
if not is_data:
self.set_all_to_none()
if self.extension in self.ext:
msg = "ASCII Reader error: Fewer than five Q data points found "
msg += "in {}.".format(filepath)
raise FileContentsException(msg)
else:
msg = "ASCII Reader could not load the file {}".format(
filepath)
raise DefaultReaderException(msg)
# Sanity check
if has_error_dy and not len(self.current_dataset.y) == \
len(self.current_dataset.dy):
msg = "ASCII Reader error: Number of I and dI data points are"
msg += " different in {}.".format(filepath)
# TODO: Add error to self.current_datainfo.errors instead?
self.set_all_to_none()
raise FileContentsException(msg)
if has_error_dx and not len(self.current_dataset.x) == \
len(self.current_dataset.dx):
msg = "ASCII Reader error: Number of Q and dQ data points are"
msg += " different in {}.".format(filepath)
# TODO: Add error to self.current_datainfo.errors instead?
self.set_all_to_none()
raise FileContentsException(msg)
self.remove_empty_q_values()
self.current_dataset = self.set_default_1d_units(self.current_dataset)
# Store loading process information
self.current_datainfo.meta_data['loader'] = self.type_name
self.send_to_output()