[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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[e935ddb1] | 8 | import numpy as np |
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[5e326a6] | 9 | import os |
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[b5db35d] | 10 | from sas.sascalc.dataloader.data_info import Data1D |
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[5e326a6] | 11 | |
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| 12 | # Check whether we have a converter available |
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| 13 | has_converter = True |
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| 14 | try: |
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[b699768] | 15 | from sas.sascalc.data_util.nxsunit import Converter |
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[5e326a6] | 16 | except: |
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| 17 | has_converter = False |
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| 18 | _ZERO = 1e-16 |
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| 19 | |
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[def97a0] | 20 | |
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[5e326a6] | 21 | class Reader: |
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| 22 | """ |
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| 23 | Class to load sesans files (6 columns). |
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| 24 | """ |
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[def97a0] | 25 | # File type |
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[5e326a6] | 26 | type_name = "SESANS" |
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[ecc8d1a8] | 27 | |
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[def97a0] | 28 | # Wildcards |
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[5e326a6] | 29 | type = ["SESANS files (*.ses)|*.ses", |
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| 30 | "SESANS files (*..sesans)|*.sesans"] |
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[def97a0] | 31 | # List of allowed extensions |
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[5e326a6] | 32 | ext = ['.ses', '.SES', '.sesans', '.SESANS'] |
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[ecc8d1a8] | 33 | |
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[def97a0] | 34 | # Flag to bypass extension check |
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[5e326a6] | 35 | allow_all = True |
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[ecc8d1a8] | 36 | |
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[5e326a6] | 37 | def read(self, path): |
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| 38 | """ |
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| 39 | Load data file |
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[ecc8d1a8] | 40 | |
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[5e326a6] | 41 | :param path: file path |
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[ecc8d1a8] | 42 | |
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[5e326a6] | 43 | :return: SESANSData1D object, or None |
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[ecc8d1a8] | 44 | |
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[5e326a6] | 45 | :raise RuntimeError: when the file can't be opened |
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| 46 | :raise ValueError: when the length of the data vectors are inconsistent |
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| 47 | """ |
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| 48 | if os.path.isfile(path): |
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| 49 | basename = os.path.basename(path) |
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| 50 | _, extension = os.path.splitext(basename) |
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[cb9feea8] | 51 | if not (self.allow_all or extension.lower() in self.ext): |
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| 52 | raise RuntimeError("{} has an unrecognized file extension".format(path)) |
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[5e326a6] | 53 | else: |
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[cb9feea8] | 54 | raise RunetimeError("{} is not a file".format(path)) |
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| 55 | with open(path, 'r') as input_f: |
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| 56 | # Read in binary mode since GRASP frequently has no-ascii |
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| 57 | # characters that brakes the open operation |
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| 58 | line = input_f.readline() |
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| 59 | params = {} |
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| 60 | while line.strip() != "": |
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| 61 | terms = line.strip().split("\t") |
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| 62 | params[terms[0].strip()] = " ".join(terms[1:]).strip() |
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| 63 | line = input_f.readline() |
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| 64 | headers_temp = input_f.readline().strip().split("\t") |
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| 65 | headers = {} |
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| 66 | for h in headers_temp: |
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| 67 | temp = h.strip().split() |
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| 68 | headers[h[:-1].strip()] = temp[-1][1:-1] |
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| 69 | data = np.loadtxt(input_f) |
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| 70 | if data.size < 1: |
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| 71 | raise RuntimeError("{} is empty".format(path)) |
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| 72 | x = data[:, 0] |
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| 73 | dx = data[:, 3] |
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| 74 | lam = data[:, 4] |
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| 75 | dlam = data[:, 5] |
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| 76 | y = data[:, 1] |
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| 77 | dy = data[:, 2] |
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| 78 | |
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| 79 | lam_unit = self._header_fetch(headers, "wavelength") |
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| 80 | if lam_unit == "AA": |
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| 81 | lam_unit = "A" |
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| 82 | |
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| 83 | x, x_unit = self._unit_conversion( |
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| 84 | x, lam_unit, |
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| 85 | self._fetch_unit(headers, "spin echo length")) |
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| 86 | dx, dx_unit = self._unit_conversion( |
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| 87 | dx, lam_unit, |
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| 88 | self._fetch_unit(headers, "error SEL")) |
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| 89 | dlam, dlam_unit = self._unit_conversion( |
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| 90 | dlam, lam_unit, |
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| 91 | self._fetch_unit(headers, "error wavelength")) |
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| 92 | y_unit = r'\AA^{-2} cm^{-1}' |
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| 93 | |
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| 94 | output = Data1D(x=x, y=y, lam=lam, dy=dy, dx=dx, dlam=dlam, |
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| 95 | isSesans=True) |
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| 96 | self.filename = output.filename = basename |
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| 97 | output.xaxis(r"\rm{z}", x_unit) |
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| 98 | # Adjust label to ln P/(lam^2 t), remove lam column refs |
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| 99 | output.yaxis(r"\rm{ln(P)/(t \lambda^2)}", y_unit) |
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| 100 | # Store loading process information |
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| 101 | output.meta_data['loader'] = self.type_name |
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| 102 | output.sample.name = params["Sample"] |
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| 103 | output.sample.ID = params["DataFileTitle"] |
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| 104 | |
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| 105 | output.sample.zacceptance = ( |
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| 106 | float(self._header_fetch(params, "Q_zmax")), |
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| 107 | self._fetch_unit(params, "Q_zmax")) |
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| 108 | |
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| 109 | output.sample.yacceptance = ( |
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| 110 | float(self._header_fetch(params, "Q_ymax")), |
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| 111 | self._fetch_unit(params, "Q_ymax")) |
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| 112 | return output |
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[26d4864] | 113 | |
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[2d866370] | 114 | @staticmethod |
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| 115 | def _unit_conversion(value, value_unit, default_unit): |
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[09a0be5] | 116 | """ |
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| 117 | Performs unit conversion on a measurement. |
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| 118 | |
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| 119 | :param value: The magnitude of the measurement |
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| 120 | :param value_unit: a string containing the final desired unit |
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| 121 | :param default_unit: a string containing the units of the original measurement |
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| 122 | :return: The magnitude of the measurement in the new units |
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| 123 | """ |
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[bc6532e] | 124 | # (float, string, string) -> float |
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[def97a0] | 125 | if has_converter and value_unit != default_unit: |
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[26d4864] | 126 | data_conv_q = Converter(value_unit) |
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| 127 | value = data_conv_q(value, units=default_unit) |
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| 128 | new_unit = default_unit |
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| 129 | else: |
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| 130 | new_unit = value_unit |
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[e935ddb1] | 131 | return value, new_unit |
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| 132 | |
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[2d866370] | 133 | @staticmethod |
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| 134 | def _header_fetch(headers, key): |
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[09a0be5] | 135 | """ |
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| 136 | Pull the value of a unit defined header from a dict. Example:: |
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| 137 | |
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| 138 | d = {"Length [m]": 17} |
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| 139 | self._header_fetch(d, "Length") == 17 |
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| 140 | |
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| 141 | :param header: A dictionary of values |
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| 142 | :param key: A string which is a prefix for one of the keys in the dict |
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| 143 | :return: The value of the dictionary for the specified key |
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| 144 | """ |
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[bc6532e] | 145 | # (dict<string, x>, string) -> x |
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[388bd51] | 146 | index = [k for k in headers.keys() |
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| 147 | if k.startswith(key)][0] |
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| 148 | return headers[index] |
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| 149 | |
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[2d866370] | 150 | @staticmethod |
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| 151 | def _fetch_unit(params, key): |
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[09a0be5] | 152 | """ |
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| 153 | Pull the unit off of a dictionary header. Example:: |
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| 154 | |
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| 155 | d = {"Length [m]": 17} |
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| 156 | self._fetch_unit(d, "Length") == "m" |
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| 157 | |
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| 158 | :param header: A dictionary of values, where the keys are strings |
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| 159 | with the units for the values appended onto the string within square |
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| 160 | brackets (See the example above) |
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| 161 | :param key: A string with the prefix of the dictionary key whose unit |
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| 162 | is being fetched |
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| 163 | :return: A string containing the unit specifed in the header |
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| 164 | """ |
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[bc6532e] | 165 | # (dict<string, _>, string) -> string |
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[388bd51] | 166 | index = [k for k in params.keys() |
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| 167 | if k.startswith(key)][0] |
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| 168 | unit = index.strip().split()[-1][1:-1] |
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| 169 | if unit.startswith(r"\A"): |
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| 170 | unit = "1/A" |
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| 171 | return unit |
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