[80c5d46] | 1 | """ |
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| 2 | CanSAS 2D data reader for reading HDF5 formatted CanSAS files. |
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| 3 | """ |
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| 4 | |
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| 5 | import numpy as np |
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| 6 | import re |
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| 7 | import os |
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| 8 | import sys |
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| 9 | |
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| 10 | from sas.sascalc.dataloader.readers.xml_reader import XMLreader |
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| 11 | from sas.sascalc.dataloader.data_info import plottable_1D, Data1D, Sample, Source |
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| 12 | from sas.sascalc.dataloader.data_info import Process, Aperture, Collimation, TransmissionSpectrum, Detector |
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| 13 | |
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| 14 | |
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| 15 | class Reader(XMLreader): |
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| 16 | """ |
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| 17 | A class for reading in CanSAS v2.0 data files. The existing iteration opens Mantid generated HDF5 formatted files |
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| 18 | with file extension .h5/.H5. Any number of data sets may be present within the file and any dimensionality of data |
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| 19 | may be used. Currently 1D and 2D SAS data sets are supported, but future implementations will include 1D and 2D |
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| 20 | SESANS data. This class assumes a single data set for each sasentry. |
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| 21 | |
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| 22 | :Dependencies: |
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| 23 | The CanSAS HDF5 reader requires h5py v2.5.0 or later. |
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| 24 | """ |
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| 25 | |
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| 26 | ## Logged warnings or messages |
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| 27 | logging = None |
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| 28 | ## List of errors for the current data set |
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| 29 | errors = None |
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| 30 | ## Raw file contents to be processed |
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| 31 | raw_data = None |
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| 32 | ## Data set being modified |
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| 33 | current_dataset = None |
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| 34 | ## For recursion and saving purposes, remember parent objects |
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| 35 | parent_list = None |
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| 36 | ## Data type name |
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| 37 | type_name = "Anton Paar SAXSess" |
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| 38 | ## Wildcards |
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| 39 | type = ["Anton Paar SAXSess Files (*.pdh)|*.pdh"] |
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| 40 | ## List of allowed extensions |
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| 41 | ext = ['.pdh', '.PDH'] |
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| 42 | ## Flag to bypass extension check |
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| 43 | allow_all = False |
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| 44 | ## List of files to return |
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| 45 | output = None |
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| 46 | |
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[a235f715] | 47 | def reset_state(self): |
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[80c5d46] | 48 | self.current_dataset = Data1D(np.empty(0), np.empty(0), |
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| 49 | np.empty(0), np.empty(0)) |
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| 50 | self.datasets = [] |
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| 51 | self.raw_data = None |
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| 52 | self.errors = set() |
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| 53 | self.logging = [] |
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| 54 | self.output = [] |
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| 55 | self.detector = Detector() |
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| 56 | self.collimation = Collimation() |
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| 57 | self.aperture = Aperture() |
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| 58 | self.process = Process() |
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| 59 | self.source = Source() |
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| 60 | self.sample = Sample() |
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| 61 | self.trans_spectrum = TransmissionSpectrum() |
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| 62 | self.upper = 5 |
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| 63 | self.lower = 5 |
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| 64 | |
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| 65 | def read(self, filename): |
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| 66 | """ |
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| 67 | This is the general read method that all SasView data_loaders must have. |
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| 68 | |
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| 69 | :param filename: A path for an XML formatted Anton Paar SAXSess data file. |
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| 70 | :return: List of Data1D objects or a list of errors. |
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| 71 | """ |
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| 72 | |
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| 73 | ## Reinitialize the class when loading a new data file to reset all class variables |
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[a235f715] | 74 | self.reset_state() |
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[80c5d46] | 75 | ## Check that the file exists |
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| 76 | if os.path.isfile(filename): |
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| 77 | basename = os.path.basename(filename) |
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| 78 | _, extension = os.path.splitext(basename) |
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| 79 | # If the file type is not allowed, return empty list |
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| 80 | if extension in self.ext or self.allow_all: |
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| 81 | ## Load the data file |
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| 82 | input_f = open(filename, 'r') |
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| 83 | buff = input_f.read() |
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| 84 | self.raw_data = buff.splitlines() |
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| 85 | self.read_data() |
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| 86 | return self.output |
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| 87 | |
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| 88 | def read_data(self): |
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| 89 | q_unit = "1/nm" |
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| 90 | i_unit = "1/um^2" |
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| 91 | self.current_dataset.title = self.raw_data[0] |
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| 92 | self.current_dataset.meta_data["Keywords"] = self.raw_data[1] |
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| 93 | line3 = self.raw_data[2].split() |
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| 94 | line4 = self.raw_data[3].split() |
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| 95 | line5 = self.raw_data[4].split() |
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| 96 | self.data_points = int(line3[0]) |
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| 97 | self.lower = 5 |
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| 98 | self.upper = self.lower + self.data_points |
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[a235f715] | 99 | self.source.radiation = 'x-ray' |
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| 100 | normal = float(line4[3]) |
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[80c5d46] | 101 | self.current_dataset.source.radiation = "x-ray" |
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| 102 | self.current_dataset.source.name = "Anton Paar SAXSess Instrument" |
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| 103 | self.current_dataset.source.wavelength = float(line4[4]) |
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[a235f715] | 104 | xvals = [] |
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| 105 | yvals = [] |
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| 106 | dyvals = [] |
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[80c5d46] | 107 | for i in range(self.lower, self.upper): |
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[a235f715] | 108 | index = i - self.lower |
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[80c5d46] | 109 | data = self.raw_data[i].split() |
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[a235f715] | 110 | xvals.insert(index, normal * float(data[0])) |
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| 111 | yvals.insert(index, normal * float(data[1])) |
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| 112 | dyvals.insert(index, normal * float(data[2])) |
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| 113 | self.current_dataset.x = np.append(self.current_dataset.x, xvals) |
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| 114 | self.current_dataset.y = np.append(self.current_dataset.y, yvals) |
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| 115 | self.current_dataset.dy = np.append(self.current_dataset.dy, dyvals) |
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| 116 | if self.data_points != self.current_dataset.x.size: |
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| 117 | self.errors.add("Not all data was loaded properly.") |
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| 118 | if self.current_dataset.dx.size != self.current_dataset.x.size: |
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| 119 | dxvals = np.zeros(self.current_dataset.x.size) |
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| 120 | self.current_dataset.dx = dxvals |
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| 121 | if self.current_dataset.x.size != self.current_dataset.y.size: |
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| 122 | self.errors.add("The x and y data sets are not the same size.") |
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| 123 | if self.current_dataset.y.size != self.current_dataset.dy.size: |
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| 124 | self.errors.add("The y and dy datasets are not the same size.") |
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| 125 | self.current_dataset.errors = self.errors |
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| 126 | self.current_dataset.xaxis("Q", q_unit) |
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| 127 | self.current_dataset.yaxis("Intensity", i_unit) |
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| 128 | xml_intermediate = self.raw_data[self.upper:] |
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| 129 | xml = ''.join(xml_intermediate) |
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| 130 | self.set_xml_string(xml) |
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| 131 | dom = self.xmlroot.xpath('/fileinfo') |
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| 132 | self._parse_child(dom) |
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| 133 | self.output.append(self.current_dataset) |
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| 134 | |
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| 135 | def _parse_child(self, dom, parent=''): |
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| 136 | """ |
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| 137 | Recursive method for stepping through the embedded XML |
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| 138 | :param dom: XML node with or without children |
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| 139 | """ |
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| 140 | for node in dom: |
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| 141 | tagname = node.tag |
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| 142 | value = node.text |
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| 143 | attr = node.attrib |
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| 144 | key = attr.get("key", '') |
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| 145 | if len(node.getchildren()) > 1: |
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| 146 | self._parse_child(node, key) |
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| 147 | if key == "SampleDetector": |
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| 148 | self.current_dataset.detector.append(self.detector) |
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| 149 | self.detector = Detector() |
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| 150 | else: |
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| 151 | if key == "value": |
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| 152 | if parent == "Wavelength": |
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| 153 | self.current_dataset.source.wavelength = value |
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| 154 | elif parent == "SampleDetector": |
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| 155 | self.detector.distance = value |
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| 156 | elif parent == "Temperature": |
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| 157 | self.current_dataset.sample.temperature = value |
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| 158 | elif parent == "CounterSlitLength": |
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| 159 | self.detector.slit_length = value |
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| 160 | elif key == "unit": |
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| 161 | value = value.replace("_", "") |
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| 162 | if parent == "Wavelength": |
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| 163 | self.current_dataset.source.wavelength_unit = value |
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| 164 | elif parent == "SampleDetector": |
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| 165 | self.detector.distance_unit = value |
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| 166 | elif parent == "X": |
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| 167 | self.current_dataset.xaxis(self.current_dataset._xaxis, value) |
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| 168 | elif parent == "Y": |
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| 169 | self.current_dataset.yaxis(self.current_dataset._yaxis, value) |
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| 170 | elif parent == "Temperature": |
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| 171 | self.current_dataset.sample.temperature_unit = value |
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| 172 | elif parent == "CounterSlitLength": |
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| 173 | self.detector.slit_length_unit = value |
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| 174 | elif key == "quantity": |
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| 175 | if parent == "X": |
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| 176 | self.current_dataset.xaxis(value, self.current_dataset._xunit) |
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| 177 | elif parent == "Y": |
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| 178 | self.current_dataset.yaxis(value, self.current_dataset._yunit) |
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