| 1 | """ |
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| 2 | SESANS reader (based on ASCII reader) |
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| 3 | |
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| 4 | Reader for .ses or .sesans file format |
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| 5 | |
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| 6 | Jurrian Bakker |
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| 7 | """ |
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| 8 | import os |
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| 9 | |
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| 10 | import numpy as np |
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| 11 | |
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| 12 | from ..file_reader_base_class import FileReader |
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| 13 | from ..data_info import plottable_1D, DataInfo |
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| 14 | from ..loader_exceptions import FileContentsException |
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| 15 | |
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| 16 | # Check whether we have a converter available |
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| 17 | has_converter = True |
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| 18 | try: |
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| 19 | from sas.sascalc.data_util.nxsunit import Converter |
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| 20 | except ImportError: |
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| 21 | has_converter = False |
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| 22 | _ZERO = 1e-16 |
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| 23 | |
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| 24 | class Reader(FileReader): |
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| 25 | """ |
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| 26 | Class to load sesans files (6 columns). |
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| 27 | """ |
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| 28 | # File type |
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| 29 | type_name = "SESANS" |
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| 30 | |
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| 31 | ## Wildcards |
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| 32 | type = ["SESANS files (*.ses)|*.ses", |
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| 33 | "SESANS files (*..sesans)|*.sesans"] |
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| 34 | # List of allowed extensions |
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| 35 | ext = ['.ses', '.SES', '.sesans', '.SESANS'] |
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| 36 | |
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| 37 | # Flag to bypass extension check |
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| 38 | allow_all = True |
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| 39 | |
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| 40 | def get_file_contents(self): |
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| 41 | self.current_datainfo = DataInfo() |
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| 42 | self.current_dataset = plottable_1D(np.array([]), np.array([])) |
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| 43 | self.current_datainfo.isSesans = True |
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| 44 | self.output = [] |
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| 45 | |
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| 46 | line = self.nextline() |
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| 47 | params = {} |
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| 48 | while line and not line.startswith("BEGIN_DATA"): |
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| 49 | terms = line.split() |
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| 50 | if len(terms) >= 2: |
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| 51 | params[terms[0]] = " ".join(terms[1:]) |
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| 52 | line = self.nextline() |
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| 53 | self.params = params |
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| 54 | |
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| 55 | if "FileFormatVersion" not in self.params: |
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| 56 | raise FileContentsException("SES file missing FileFormatVersion") |
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| 57 | if float(self.params["FileFormatVersion"]) >= 2.0: |
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| 58 | raise FileContentsException("SASView only supports SES version 1") |
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| 59 | |
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| 60 | if "SpinEchoLength_unit" not in self.params: |
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| 61 | raise FileContentsException("SpinEchoLength has no units") |
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| 62 | if "Wavelength_unit" not in self.params: |
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| 63 | raise FileContentsException("Wavelength has no units") |
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| 64 | if params["SpinEchoLength_unit"] != params["Wavelength_unit"]: |
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| 65 | raise FileContentsException( |
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| 66 | "The spin echo data has rudely used " |
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| 67 | "different units for the spin echo length " |
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| 68 | "and the wavelength. While sasview could " |
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| 69 | "handle this instance, it is a violation " |
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| 70 | "of the file format and will not be " |
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| 71 | "handled by other software.") |
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| 72 | |
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| 73 | headers = self.nextline().split() |
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| 74 | |
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| 75 | self._insist_header(headers, "SpinEchoLength") |
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| 76 | self._insist_header(headers, "Depolarisation") |
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| 77 | self._insist_header(headers, "Depolarisation_error") |
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| 78 | self._insist_header(headers, "Wavelength") |
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| 79 | |
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| 80 | data = np.loadtxt(self.f_open) |
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| 81 | |
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| 82 | if data.shape[1] != len(headers): |
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| 83 | raise FileContentsException( |
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| 84 | "File has {} headers, but {} columns".format( |
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| 85 | len(headers), |
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| 86 | data.shape[1])) |
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| 87 | |
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| 88 | if not data.size: |
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| 89 | raise FileContentsException("{} is empty".format(self.filepath)) |
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| 90 | x = data[:, headers.index("SpinEchoLength")] |
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| 91 | if "SpinEchoLength_error" in headers: |
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| 92 | dx = data[:, headers.index("SpinEchoLength_error")] |
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| 93 | else: |
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| 94 | dx = x * 0.05 |
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| 95 | lam = data[:, headers.index("Wavelength")] |
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| 96 | if "Wavelength_error" in headers: |
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| 97 | dlam = data[:, headers.index("Wavelength_error")] |
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| 98 | else: |
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| 99 | dlam = lam * 0.05 |
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| 100 | y = data[:, headers.index("Depolarisation")] |
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| 101 | dy = data[:, headers.index("Depolarisation_error")] |
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| 102 | |
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| 103 | lam_unit = self._unit_fetch("Wavelength") |
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| 104 | x, x_unit = self._unit_conversion(x, "A", |
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| 105 | self._unit_fetch( |
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| 106 | "SpinEchoLength")) |
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| 107 | dx, dx_unit = self._unit_conversion( |
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| 108 | dx, lam_unit, |
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| 109 | self._unit_fetch("SpinEchoLength")) |
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| 110 | dlam, dlam_unit = self._unit_conversion( |
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| 111 | dlam, lam_unit, |
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| 112 | self._unit_fetch("Wavelength")) |
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| 113 | y_unit = self._unit_fetch("Depolarisation") |
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| 114 | |
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| 115 | self.current_dataset.x = x |
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| 116 | self.current_dataset.y = y |
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| 117 | self.current_dataset.lam = lam |
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| 118 | self.current_dataset.dy = dy |
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| 119 | self.current_dataset.dx = dx |
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| 120 | self.current_dataset.dlam = dlam |
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| 121 | self.current_datainfo.isSesans = True |
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| 122 | |
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| 123 | self.current_datainfo._yunit = y_unit |
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| 124 | self.current_datainfo._xunit = x_unit |
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| 125 | self.current_datainfo.source.wavelength_unit = lam_unit |
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| 126 | self.current_datainfo.source.wavelength = lam |
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| 127 | self.current_datainfo.filename = os.path.basename(self.f_open.name) |
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| 128 | self.current_dataset.xaxis(r"\rm{z}", x_unit) |
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| 129 | # Adjust label to ln P/(lam^2 t), remove lam column refs |
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| 130 | self.current_dataset.yaxis(r"\rm{ln(P)/(t \lambda^2)}", y_unit) |
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| 131 | # Store loading process information |
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| 132 | self.current_datainfo.meta_data['loader'] = self.type_name |
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| 133 | self.current_datainfo.sample.name = params["Sample"] |
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| 134 | self.current_datainfo.sample.ID = params["DataFileTitle"] |
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| 135 | self.current_datainfo.sample.thickness = self._unit_conversion( |
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| 136 | float(params["Thickness"]), "cm", |
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| 137 | self._unit_fetch("Thickness"))[0] |
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| 138 | |
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| 139 | self.current_datainfo.sample.zacceptance = ( |
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| 140 | float(params["Theta_zmax"]), |
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| 141 | self._unit_fetch("Theta_zmax")) |
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| 142 | |
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| 143 | self.current_datainfo.sample.yacceptance = ( |
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| 144 | float(params["Theta_ymax"]), |
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| 145 | self._unit_fetch("Theta_ymax")) |
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| 146 | |
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| 147 | self.send_to_output() |
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| 148 | |
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| 149 | @staticmethod |
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| 150 | def _insist_header(headers, name): |
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| 151 | if name not in headers: |
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| 152 | raise FileContentsException( |
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| 153 | "Missing {} column in spin echo data".format(name)) |
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| 154 | |
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| 155 | @staticmethod |
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| 156 | def _unit_conversion(value, value_unit, default_unit): |
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| 157 | """ |
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| 158 | Performs unit conversion on a measurement. |
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| 159 | |
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| 160 | :param value: The magnitude of the measurement |
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| 161 | :param value_unit: a string containing the final desired unit |
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| 162 | :param default_unit: string with the units of the original measurement |
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| 163 | :return: The magnitude of the measurement in the new units |
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| 164 | """ |
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| 165 | # (float, string, string) -> float |
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| 166 | if has_converter and value_unit != default_unit: |
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| 167 | data_conv_q = Converter(default_unit) |
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| 168 | value = data_conv_q(value, units=value_unit) |
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| 169 | new_unit = default_unit |
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| 170 | else: |
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| 171 | new_unit = value_unit |
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| 172 | return value, new_unit |
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| 173 | |
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| 174 | def _unit_fetch(self, unit): |
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| 175 | return self.params[unit+"_unit"] |
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