Source code for sas.sascalc.dataloader.readers.anton_paar_saxs_reader
"""
CanSAS 2D data reader for reading HDF5 formatted CanSAS files.
"""
import numpy as np
import re
import os
import sys
from sas.sascalc.dataloader.readers.xml_reader import XMLreader
from sas.sascalc.dataloader.data_info import plottable_1D, Data1D, DataInfo, Sample, Source
from sas.sascalc.dataloader.data_info import Process, Aperture, Collimation, TransmissionSpectrum, Detector
from sas.sascalc.dataloader.loader_exceptions import FileContentsException, DataReaderException
[docs]class Reader(XMLreader):
"""
A class for reading in Anton Paar .pdh files
"""
## Logged warnings or messages
logging = None
## List of errors for the current data set
errors = None
## Raw file contents to be processed
raw_data = None
## For recursion and saving purposes, remember parent objects
parent_list = None
## Data type name
type_name = "Anton Paar SAXSess"
## Wildcards
type = ["Anton Paar SAXSess Files (*.pdh)|*.pdh"]
## List of allowed extensions
ext = ['.pdh', '.PDH']
## Flag to bypass extension check
allow_all = False
[docs] 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
[docs] def get_file_contents(self):
"""
This is the general read method that all SasView data_loaders must have.
:param filename: A path for an XML formatted Anton Paar SAXSess data file.
:return: List of Data1D objects or a list of errors.
"""
## Reinitialize the class when loading a new data file to reset all class variables
self.reset_state()
buff = self.readall()
self.raw_data = buff.splitlines()
self.read_data()
[docs] def read_data(self):
correctly_loaded = True
error_message = ""
q_unit = "1/nm"
i_unit = "1/um^2"
try:
self.current_datainfo.title = self.raw_data[0]
self.current_datainfo.meta_data["Keywords"] = self.raw_data[1]
line3 = self.raw_data[2].split()
line4 = self.raw_data[3].split()
line5 = self.raw_data[4].split()
self.data_points = int(line3[0])
self.lower = 5
self.upper = self.lower + self.data_points
self.source.radiation = 'x-ray'
self.current_datainfo.source.radiation = "x-ray"
self.current_datainfo.source.name = "Anton Paar SAXSess Instrument"
self.current_datainfo.source.wavelength = float(line4[4])
xvals = []
yvals = []
dyvals = []
for i in range(self.lower, self.upper):
index = i - self.lower
data = self.raw_data[i].split()
xvals.insert(index, float(data[0]))
yvals.insert(index, float(data[1]))
dyvals.insert(index, float(data[2]))
except Exception as e:
error_message = f"Couldn't load {self.f_open.name}.\n{e}"
raise FileContentsException(error_message)
self.current_dataset.x = np.append(self.current_dataset.x, xvals)
self.current_dataset.y = np.append(self.current_dataset.y, yvals)
self.current_dataset.dy = np.append(self.current_dataset.dy, dyvals)
if self.data_points != self.current_dataset.x.size:
error_message += "Not all data points could be loaded.\n"
correctly_loaded = False
if self.current_dataset.x.size != self.current_dataset.y.size:
error_message += "The x and y data sets are not the same size.\n"
correctly_loaded = False
if self.current_dataset.y.size != self.current_dataset.dy.size:
error_message += "The y and dy datasets are not the same size.\n"
correctly_loaded = False
self.current_dataset.xaxis("Q", q_unit)
self.current_dataset.yaxis("Intensity", i_unit)
xml_intermediate = self.raw_data[self.upper:]
xml = bytes(''.join(xml_intermediate), 'utf-8')
try:
self.set_xml_string(xml)
dom = self.xmlroot.xpath('/fileinfo')
self._parse_child(dom)
except Exception as e:
# Data loaded but XML metadata has an error
error_message += "Data points have been loaded but there was an "
error_message += f"error reading XML metadata: {e}"
correctly_loaded = False
self.send_to_output()
if not correctly_loaded:
raise DataReaderException(error_message)
def _parse_child(self, dom, parent=''):
"""
Recursive method for stepping through the embedded XML
:param dom: XML node with or without children
"""
for node in dom:
tagname = node.tag
value = node.text
attr = node.attrib
key = attr.get("key", '')
if len(node.getchildren()) > 1:
self._parse_child(node, key)
if key == "SampleDetector":
self.current_datainfo.detector.append(self.detector)
self.detector = Detector()
else:
if key == "value":
if parent == "Wavelength":
self.current_datainfo.source.wavelength = value
elif parent == "SampleDetector":
self.detector.distance = value
elif parent == "Temperature":
self.current_datainfo.sample.temperature = value
elif parent == "CounterSlitLength":
self.detector.slit_length = value
elif key == "unit":
value = value.replace("_", "")
if parent == "Wavelength":
self.current_datainfo.source.wavelength_unit = value
elif parent == "SampleDetector":
self.detector.distance_unit = value
elif parent == "X":
self.current_dataset.xaxis(self.current_dataset._xaxis, value)
elif parent == "Y":
self.current_dataset.yaxis(self.current_dataset._yaxis, value)
elif parent == "Temperature":
self.current_datainfo.sample.temperature_unit = value
elif parent == "CounterSlitLength":
self.detector.slit_length_unit = value
elif key == "quantity":
if parent == "X":
self.current_dataset.xaxis(value, self.current_dataset._xunit)
elif parent == "Y":
self.current_dataset.yaxis(value, self.current_dataset._yunit)