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' normal = float(line4[3]) 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, normal * float(data[0])) yvals.insert(index, normal * float(data[1])) dyvals.insert(index, normal * float(data[2])) except Exception as e: error_message = "Couldn't load {}.\n".format(self.f_open.name) error_message += e.message 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 = ''.join(xml_intermediate) 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 += "error reading XML metadata: " + e.message 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)