[5e326a6] | 1 | """ |
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[edfc8ac] | 2 | SESANS reader (based on ASCII reader) |
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[ecc8d1a8] | 3 | |
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[edfc8ac] | 4 | Reader for .ses or .sesans file format |
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[ecc8d1a8] | 5 | |
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| 6 | Jurrian Bakker |
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[5e326a6] | 7 | """ |
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[0ac6e11] | 8 | import logging |
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[e935ddb1] | 9 | import numpy as np |
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[5e326a6] | 10 | import os |
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[b5db35d] | 11 | from sas.sascalc.dataloader.data_info import Data1D |
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[5e326a6] | 12 | |
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| 13 | # Check whether we have a converter available |
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| 14 | has_converter = True |
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| 15 | try: |
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[b699768] | 16 | from sas.sascalc.data_util.nxsunit import Converter |
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[5e326a6] | 17 | except: |
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| 18 | has_converter = False |
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| 19 | _ZERO = 1e-16 |
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| 20 | |
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[def97a0] | 21 | |
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[5e326a6] | 22 | class Reader: |
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| 23 | """ |
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| 24 | Class to load sesans files (6 columns). |
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| 25 | """ |
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[def97a0] | 26 | # File type |
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[5e326a6] | 27 | type_name = "SESANS" |
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[ecc8d1a8] | 28 | |
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[def97a0] | 29 | # Wildcards |
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[5e326a6] | 30 | type = ["SESANS files (*.ses)|*.ses", |
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| 31 | "SESANS files (*..sesans)|*.sesans"] |
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[def97a0] | 32 | # List of allowed extensions |
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[5e326a6] | 33 | ext = ['.ses', '.SES', '.sesans', '.SESANS'] |
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[ecc8d1a8] | 34 | |
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[def97a0] | 35 | # Flag to bypass extension check |
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[5e326a6] | 36 | allow_all = True |
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[ecc8d1a8] | 37 | |
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[5e326a6] | 38 | def read(self, path): |
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| 39 | """ |
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| 40 | Load data file |
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[ecc8d1a8] | 41 | |
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[5e326a6] | 42 | :param path: file path |
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[ecc8d1a8] | 43 | |
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[5e326a6] | 44 | :return: SESANSData1D object, or None |
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[ecc8d1a8] | 45 | |
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[5e326a6] | 46 | :raise RuntimeError: when the file can't be opened |
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| 47 | :raise ValueError: when the length of the data vectors are inconsistent |
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| 48 | """ |
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| 49 | if os.path.isfile(path): |
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| 50 | basename = os.path.basename(path) |
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| 51 | _, extension = os.path.splitext(basename) |
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[cb9feea8] | 52 | if not (self.allow_all or extension.lower() in self.ext): |
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[5ae40e7] | 53 | raise RuntimeError( |
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| 54 | "{} has an unrecognized file extension".format(path)) |
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[5e326a6] | 55 | else: |
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[5ae40e7] | 56 | raise RuntimeError("{} is not a file".format(path)) |
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[cb9feea8] | 57 | with open(path, 'r') as input_f: |
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| 58 | # Read in binary mode since GRASP frequently has no-ascii |
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| 59 | # characters that brakes the open operation |
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| 60 | line = input_f.readline() |
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| 61 | params = {} |
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[2b310602] | 62 | while not line.startswith("BEGIN_DATA"): |
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| 63 | terms = line.split() |
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| 64 | if len(terms) >= 2: |
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| 65 | params[terms[0]] = " ".join(terms[1:]) |
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[cb9feea8] | 66 | line = input_f.readline() |
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[2b310602] | 67 | self.params = params |
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[10ab40e] | 68 | |
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[f344f6c] | 69 | if "FileFormatVersion" not in self.params: |
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| 70 | raise RuntimeError("SES file missing FileFormatVersion") |
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[a81af92] | 71 | if float(self.params["FileFormatVersion"]) >= 2.0: |
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| 72 | raise RuntimeError("SASView only supports SES version 1") |
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[f344f6c] | 73 | |
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[10ab40e] | 74 | if "SpinEchoLength_unit" not in self.params: |
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| 75 | raise RuntimeError("SpinEchoLength has no units") |
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| 76 | if "Wavelength_unit" not in self.params: |
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| 77 | raise RuntimeError("Wavelength has no units") |
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[5ae40e7] | 78 | if params["SpinEchoLength_unit"] != params["Wavelength_unit"]: |
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| 79 | raise RuntimeError("The spin echo data has rudely used " |
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| 80 | "different units for the spin echo length " |
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| 81 | "and the wavelength. While sasview could " |
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| 82 | "handle this instance, it is a violation " |
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| 83 | "of the file format and will not be " |
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| 84 | "handled by other software.") |
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[10ab40e] | 85 | |
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[2b310602] | 86 | headers = input_f.readline().split() |
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| 87 | |
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[e801a4e] | 88 | self._insist_header(headers, "SpinEchoLength") |
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| 89 | self._insist_header(headers, "Depolarisation") |
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| 90 | self._insist_header(headers, "Depolarisation_error") |
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| 91 | self._insist_header(headers, "Wavelength") |
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| 92 | |
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[cb9feea8] | 93 | data = np.loadtxt(input_f) |
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| 94 | if data.size < 1: |
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| 95 | raise RuntimeError("{} is empty".format(path)) |
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[2b310602] | 96 | x = data[:, headers.index("SpinEchoLength")] |
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[8e0dcac] | 97 | if "SpinEchoLength_error" in headers: |
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| 98 | dx = data[:, headers.index("SpinEchoLength_error")] |
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| 99 | else: |
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| 100 | dx = x*0.05 |
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[2b310602] | 101 | lam = data[:, headers.index("Wavelength")] |
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[8e0dcac] | 102 | if "Wavelength_error" in headers: |
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| 103 | dlam = data[:, headers.index("Wavelength_error")] |
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| 104 | else: |
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| 105 | dlam = lam*0.05 |
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[2b310602] | 106 | y = data[:, headers.index("Depolarisation")] |
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| 107 | dy = data[:, headers.index("Depolarisation_error")] |
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| 108 | |
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| 109 | lam_unit = self._unit_fetch("Wavelength") |
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| 110 | x, x_unit = self._unit_conversion(x, "A", self._unit_fetch("SpinEchoLength")) |
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[cb9feea8] | 111 | dx, dx_unit = self._unit_conversion( |
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| 112 | dx, lam_unit, |
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[2b310602] | 113 | self._unit_fetch("SpinEchoLength")) |
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[cb9feea8] | 114 | dlam, dlam_unit = self._unit_conversion( |
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| 115 | dlam, lam_unit, |
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[2b310602] | 116 | self._unit_fetch("Wavelength")) |
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| 117 | y_unit = self._unit_fetch("Depolarisation") |
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[cb9feea8] | 118 | |
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| 119 | output = Data1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam, |
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| 120 | isSesans=True) |
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[2b310602] | 121 | |
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| 122 | output.y_unit = y_unit |
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| 123 | output.x_unit = x_unit |
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[0ac6e11] | 124 | output.source.wavelength_unit = lam_unit |
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| 125 | output.source.wavelength = lam |
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[cb9feea8] | 126 | self.filename = output.filename = basename |
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| 127 | output.xaxis(r"\rm{z}", x_unit) |
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| 128 | # Adjust label to ln P/(lam^2 t), remove lam column refs |
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| 129 | output.yaxis(r"\rm{ln(P)/(t \lambda^2)}", y_unit) |
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| 130 | # Store loading process information |
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| 131 | output.meta_data['loader'] = self.type_name |
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| 132 | output.sample.name = params["Sample"] |
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| 133 | output.sample.ID = params["DataFileTitle"] |
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[857cc58] | 134 | output.sample.thickness = self._unit_conversion( |
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| 135 | float(params["Thickness"]), "cm", |
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| 136 | self._unit_fetch("Thickness"))[0] |
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[cb9feea8] | 137 | |
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| 138 | output.sample.zacceptance = ( |
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[2b310602] | 139 | float(params["Theta_zmax"]), |
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| 140 | self._unit_fetch("Theta_zmax")) |
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[cb9feea8] | 141 | |
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| 142 | output.sample.yacceptance = ( |
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[2b310602] | 143 | float(params["Theta_ymax"]), |
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| 144 | self._unit_fetch("Theta_ymax")) |
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[cb9feea8] | 145 | return output |
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[26d4864] | 146 | |
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[2d866370] | 147 | @staticmethod |
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[e801a4e] | 148 | def _insist_header(headers, name): |
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| 149 | if name not in headers: |
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| 150 | raise RuntimeError( |
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| 151 | "Missing {} column in spin echo data".format(name)) |
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| 152 | |
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| 153 | @staticmethod |
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[2d866370] | 154 | def _unit_conversion(value, value_unit, default_unit): |
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[09a0be5] | 155 | """ |
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| 156 | Performs unit conversion on a measurement. |
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| 157 | |
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| 158 | :param value: The magnitude of the measurement |
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| 159 | :param value_unit: a string containing the final desired unit |
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| 160 | :param default_unit: a string containing the units of the original measurement |
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| 161 | :return: The magnitude of the measurement in the new units |
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| 162 | """ |
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[bc6532e] | 163 | # (float, string, string) -> float |
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[def97a0] | 164 | if has_converter and value_unit != default_unit: |
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[857cc58] | 165 | data_conv_q = Converter(default_unit) |
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| 166 | value = data_conv_q(value, units=value_unit) |
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[26d4864] | 167 | new_unit = default_unit |
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| 168 | else: |
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| 169 | new_unit = value_unit |
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[e935ddb1] | 170 | return value, new_unit |
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| 171 | |
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[2b310602] | 172 | def _unit_fetch(self, unit): |
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| 173 | return self.params[unit+"_unit"] |
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