[68aa210] | 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 h5py |
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| 6 | import numpy as np |
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| 7 | import re |
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| 8 | import os |
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| 9 | import sys |
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| 10 | |
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[082239e] | 11 | from sas.sascalc.dataloader.data_info import plottable_1D, plottable_2D,\ |
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| 12 | Data1D, Data2D, DataInfo, Process, Aperture, Collimation, \ |
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| 13 | TransmissionSpectrum, Detector |
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[d72567e] | 14 | from sas.sascalc.dataloader.data_info import combine_data_info_with_plottable |
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| 15 | |
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[68aa210] | 16 | |
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| 17 | class Reader(): |
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| 18 | """ |
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[082239e] | 19 | A class for reading in CanSAS v2.0 data files. The existing iteration opens |
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| 20 | Mantid generated HDF5 formatted files with file extension .h5/.H5. Any |
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| 21 | number of data sets may be present within the file and any dimensionality |
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| 22 | of data may be used. Currently 1D and 2D SAS data sets are supported, but |
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| 23 | future implementations will include 1D and 2D SESANS data. |
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[d72567e] | 24 | |
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[082239e] | 25 | Any number of SASdata sets may be present in a SASentry and the data within |
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| 26 | can be either 1D I(Q) or 2D I(Qx, Qy). |
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[68aa210] | 27 | |
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[5e906207] | 28 | Also supports reading NXcanSAS formatted HDF5 files |
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| 29 | |
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[68aa210] | 30 | :Dependencies: |
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[d72567e] | 31 | The CanSAS HDF5 reader requires h5py => v2.5.0 or later. |
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[68aa210] | 32 | """ |
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| 33 | |
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[082239e] | 34 | # CanSAS version |
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[68aa210] | 35 | cansas_version = 2.0 |
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[082239e] | 36 | # Logged warnings or messages |
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[68aa210] | 37 | logging = None |
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[082239e] | 38 | # List of errors for the current data set |
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[68aa210] | 39 | errors = None |
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[082239e] | 40 | # Raw file contents to be processed |
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[68aa210] | 41 | raw_data = None |
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[082239e] | 42 | # Data info currently being read in |
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[d72567e] | 43 | current_datainfo = None |
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[082239e] | 44 | # SASdata set currently being read in |
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[68aa210] | 45 | current_dataset = None |
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[082239e] | 46 | # List of plottable1D objects that should be linked to the current_datainfo |
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[d72567e] | 47 | data1d = None |
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[082239e] | 48 | # List of plottable2D objects that should be linked to the current_datainfo |
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[d72567e] | 49 | data2d = None |
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[082239e] | 50 | # Data type name |
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[ad52d31] | 51 | type_name = "CanSAS 2.0" |
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[082239e] | 52 | # Wildcards |
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[ad52d31] | 53 | type = ["CanSAS 2.0 HDF5 Files (*.h5)|*.h5"] |
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[082239e] | 54 | # List of allowed extensions |
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[68aa210] | 55 | ext = ['.h5', '.H5'] |
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[082239e] | 56 | # Flag to bypass extension check |
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[54544637] | 57 | allow_all = True |
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[082239e] | 58 | # List of files to return |
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[68aa210] | 59 | output = None |
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| 60 | |
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| 61 | def read(self, filename): |
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| 62 | """ |
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[ad52d31] | 63 | This is the general read method that all SasView data_loaders must have. |
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[68aa210] | 64 | |
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| 65 | :param filename: A path for an HDF5 formatted CanSAS 2D data file. |
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[d72567e] | 66 | :return: List of Data1D/2D objects and/or a list of errors. |
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[68aa210] | 67 | """ |
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[082239e] | 68 | # Reinitialize when loading a new data file to reset all class variables |
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[d72567e] | 69 | self.reset_class_variables() |
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[082239e] | 70 | # Check that the file exists |
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[68aa210] | 71 | if os.path.isfile(filename): |
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| 72 | basename = os.path.basename(filename) |
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| 73 | _, extension = os.path.splitext(basename) |
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| 74 | # If the file type is not allowed, return empty list |
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| 75 | if extension in self.ext or self.allow_all: |
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[082239e] | 76 | # Load the data file |
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[68aa210] | 77 | self.raw_data = h5py.File(filename, 'r') |
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[082239e] | 78 | # Read in all child elements of top level SASroot |
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[d72567e] | 79 | self.read_children(self.raw_data, []) |
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[082239e] | 80 | # Add the last data set to the list of outputs |
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[68aa210] | 81 | self.add_data_set() |
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[082239e] | 82 | # Close the data file |
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[995f4eb] | 83 | self.raw_data.close() |
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[082239e] | 84 | # Return data set(s) |
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[68aa210] | 85 | return self.output |
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| 86 | |
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[d72567e] | 87 | def reset_class_variables(self): |
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| 88 | """ |
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| 89 | Create the reader object and define initial states for class variables |
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| 90 | """ |
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| 91 | self.current_datainfo = None |
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| 92 | self.current_dataset = None |
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| 93 | self.data1d = [] |
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| 94 | self.data2d = [] |
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| 95 | self.raw_data = None |
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| 96 | self.errors = set() |
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| 97 | self.logging = [] |
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| 98 | self.output = [] |
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| 99 | self.parent_class = u'' |
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| 100 | self.detector = Detector() |
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| 101 | self.collimation = Collimation() |
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| 102 | self.aperture = Aperture() |
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| 103 | self.process = Process() |
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| 104 | self.trans_spectrum = TransmissionSpectrum() |
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| 105 | |
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| 106 | def read_children(self, data, parent_list): |
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[68aa210] | 107 | """ |
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[ad52d31] | 108 | A recursive method for stepping through the hierarchical data file. |
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[68aa210] | 109 | |
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| 110 | :param data: h5py Group object of any kind |
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| 111 | :param parent: h5py Group parent name |
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| 112 | """ |
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| 113 | |
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[082239e] | 114 | # Loop through each element of the parent and process accordingly |
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[68aa210] | 115 | for key in data.keys(): |
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[082239e] | 116 | # Get all information for the current key |
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[68aa210] | 117 | value = data.get(key) |
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[d398285] | 118 | if value.attrs.get(u'canSAS_class') is not None: |
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| 119 | class_name = value.attrs.get(u'canSAS_class') |
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| 120 | else: |
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| 121 | class_name = value.attrs.get(u'NX_class') |
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[68aa210] | 122 | if class_name is not None: |
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| 123 | class_prog = re.compile(class_name) |
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| 124 | else: |
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| 125 | class_prog = re.compile(value.name) |
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| 126 | |
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| 127 | if isinstance(value, h5py.Group): |
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[7c24685] | 128 | parent_class = class_name |
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[d72567e] | 129 | self.parent_class = class_name |
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| 130 | parent_list.append(key) |
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[082239e] | 131 | # If a new sasentry, store the current data sets and create |
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| 132 | # a fresh Data1D/2D object |
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[68aa210] | 133 | if class_prog.match(u'SASentry'): |
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| 134 | self.add_data_set(key) |
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[d72567e] | 135 | elif class_prog.match(u'SASdata'): |
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| 136 | self._initialize_new_data_set(parent_list) |
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[082239e] | 137 | # Recursion step to access data within the group |
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[d72567e] | 138 | self.read_children(value, parent_list) |
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[7c24685] | 139 | self.parent_class = parent_class |
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[d72567e] | 140 | self.add_intermediate() |
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| 141 | parent_list.remove(key) |
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[68aa210] | 142 | |
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| 143 | elif isinstance(value, h5py.Dataset): |
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[082239e] | 144 | # If this is a dataset, store the data appropriately |
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[68aa210] | 145 | data_set = data[key][:] |
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[7bd6860a] | 146 | unit = self._get_unit(value) |
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[ac370c5] | 147 | |
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[082239e] | 148 | # I and Q Data |
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[7bd6860a] | 149 | if key == u'I': |
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[082239e] | 150 | if isinstance(self.current_dataset, plottable_2D): |
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[ac370c5] | 151 | self.current_dataset.data = data_set |
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[7bd6860a] | 152 | self.current_dataset.zaxis("Intensity", unit) |
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| 153 | else: |
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| 154 | self.current_dataset.y = data_set.flatten() |
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| 155 | self.current_dataset.yaxis("Intensity", unit) |
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| 156 | continue |
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| 157 | elif key == u'Idev': |
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[082239e] | 158 | if isinstance(self.current_dataset, plottable_2D): |
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[7bd6860a] | 159 | self.current_dataset.err_data = data_set.flatten() |
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| 160 | else: |
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| 161 | self.current_dataset.dy = data_set.flatten() |
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| 162 | continue |
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| 163 | elif key == u'Q': |
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| 164 | self.current_dataset.xaxis("Q", unit) |
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[082239e] | 165 | if isinstance(self.current_dataset, plottable_2D): |
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[7bd6860a] | 166 | self.current_dataset.q = data_set.flatten() |
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| 167 | else: |
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| 168 | self.current_dataset.x = data_set.flatten() |
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| 169 | continue |
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[bbd0f37] | 170 | elif key == u'Qdev': |
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| 171 | self.current_dataset.dx = data_set.flatten() |
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| 172 | continue |
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[082239e] | 173 | elif key == u'dQw': |
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| 174 | self.current_dataset.dxw = data_set.flatten() |
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| 175 | continue |
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| 176 | elif key == u'dQl': |
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| 177 | self.current_dataset.dxl = data_set.flatten() |
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| 178 | continue |
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[7bd6860a] | 179 | elif key == u'Qy': |
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| 180 | self.current_dataset.yaxis("Q_y", unit) |
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| 181 | self.current_dataset.qy_data = data_set.flatten() |
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| 182 | continue |
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| 183 | elif key == u'Qydev': |
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| 184 | self.current_dataset.dqy_data = data_set.flatten() |
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| 185 | continue |
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| 186 | elif key == u'Qx': |
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| 187 | self.current_dataset.xaxis("Q_x", unit) |
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| 188 | self.current_dataset.qx_data = data_set.flatten() |
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| 189 | continue |
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| 190 | elif key == u'Qxdev': |
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| 191 | self.current_dataset.dqx_data = data_set.flatten() |
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| 192 | continue |
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| 193 | elif key == u'Mask': |
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| 194 | self.current_dataset.mask = data_set.flatten() |
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| 195 | continue |
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[082239e] | 196 | # Transmission Spectrum |
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[c94280c] | 197 | elif (key == u'T' |
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| 198 | and self.parent_class == u'SAStransmission_spectrum'): |
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[082239e] | 199 | self.trans_spectrum.transmission = data_set.flatten() |
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| 200 | continue |
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[c94280c] | 201 | elif (key == u'Tdev' |
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| 202 | and self.parent_class == u'SAStransmission_spectrum'): |
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[082239e] | 203 | self.trans_spectrum.transmission_deviation = \ |
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| 204 | data_set.flatten() |
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| 205 | continue |
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[c94280c] | 206 | elif (key == u'lambda' |
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| 207 | and self.parent_class == u'SAStransmission_spectrum'): |
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[082239e] | 208 | self.trans_spectrum.wavelength = data_set.flatten() |
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| 209 | continue |
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[68aa210] | 210 | |
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| 211 | for data_point in data_set: |
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[082239e] | 212 | # Top Level Meta Data |
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[68aa210] | 213 | if key == u'definition': |
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[d72567e] | 214 | self.current_datainfo.meta_data['reader'] = data_point |
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[68aa210] | 215 | elif key == u'run': |
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[d72567e] | 216 | self.current_datainfo.run.append(data_point) |
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[be88076] | 217 | try: |
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| 218 | run_name = value.attrs['name'] |
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| 219 | run_dict = {data_point: run_name} |
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| 220 | self.current_datainfo.run_name = run_dict |
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| 221 | except: |
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| 222 | pass |
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[68aa210] | 223 | elif key == u'title': |
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[d72567e] | 224 | self.current_datainfo.title = data_point |
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[68aa210] | 225 | elif key == u'SASnote': |
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[d72567e] | 226 | self.current_datainfo.notes.append(data_point) |
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[68aa210] | 227 | |
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[082239e] | 228 | # Sample Information |
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| 229 | # CanSAS 2.0 format |
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| 230 | elif key == u'Title' and self.parent_class == u'SASsample': |
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[d72567e] | 231 | self.current_datainfo.sample.name = data_point |
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[082239e] | 232 | # NXcanSAS format |
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| 233 | elif key == u'name' and self.parent_class == u'SASsample': |
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[88d85c6] | 234 | self.current_datainfo.sample.name = data_point |
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[082239e] | 235 | # NXcanSAS format |
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| 236 | elif key == u'ID' and self.parent_class == u'SASsample': |
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| 237 | self.current_datainfo.sample.name = data_point |
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[c94280c] | 238 | elif (key == u'thickness' |
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| 239 | and self.parent_class == u'SASsample'): |
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[d72567e] | 240 | self.current_datainfo.sample.thickness = data_point |
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[c94280c] | 241 | elif (key == u'temperature' |
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| 242 | and self.parent_class == u'SASsample'): |
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[d72567e] | 243 | self.current_datainfo.sample.temperature = data_point |
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[c94280c] | 244 | elif (key == u'transmission' |
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| 245 | and self.parent_class == u'SASsample'): |
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[5e906207] | 246 | self.current_datainfo.sample.transmission = data_point |
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[c94280c] | 247 | elif (key == u'x_position' |
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| 248 | and self.parent_class == u'SASsample'): |
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[5e906207] | 249 | self.current_datainfo.sample.position.x = data_point |
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[c94280c] | 250 | elif (key == u'y_position' |
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| 251 | and self.parent_class == u'SASsample'): |
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[5e906207] | 252 | self.current_datainfo.sample.position.y = data_point |
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[082239e] | 253 | elif key == u'pitch' and self.parent_class == u'SASsample': |
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[5e906207] | 254 | self.current_datainfo.sample.orientation.x = data_point |
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[082239e] | 255 | elif key == u'yaw' and self.parent_class == u'SASsample': |
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| 256 | self.current_datainfo.sample.orientation.y = data_point |
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| 257 | elif key == u'roll' and self.parent_class == u'SASsample': |
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[5e906207] | 258 | self.current_datainfo.sample.orientation.z = data_point |
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[c94280c] | 259 | elif (key == u'details' |
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| 260 | and self.parent_class == u'SASsample'): |
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[5e906207] | 261 | self.current_datainfo.sample.details.append(data_point) |
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[68aa210] | 262 | |
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[082239e] | 263 | # Instrumental Information |
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[c94280c] | 264 | elif (key == u'name' |
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| 265 | and self.parent_class == u'SASinstrument'): |
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[d72567e] | 266 | self.current_datainfo.instrument = data_point |
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| 267 | elif key == u'name' and self.parent_class == u'SASdetector': |
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[ad52d31] | 268 | self.detector.name = data_point |
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[d72567e] | 269 | elif key == u'SDD' and self.parent_class == u'SASdetector': |
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| 270 | self.detector.distance = float(data_point) |
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[d398285] | 271 | self.detector.distance_unit = unit |
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[c94280c] | 272 | elif (key == u'slit_length' |
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| 273 | and self.parent_class == u'SASdetector'): |
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[5e906207] | 274 | self.detector.slit_length = float(data_point) |
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| 275 | self.detector.slit_length_unit = unit |
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[c94280c] | 276 | elif (key == u'x_position' |
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| 277 | and self.parent_class == u'SASdetector'): |
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[5e906207] | 278 | self.detector.offset.x = float(data_point) |
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| 279 | self.detector.offset_unit = unit |
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[c94280c] | 280 | elif (key == u'y_position' |
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| 281 | and self.parent_class == u'SASdetector'): |
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[5e906207] | 282 | self.detector.offset.y = float(data_point) |
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| 283 | self.detector.offset_unit = unit |
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[c94280c] | 284 | elif (key == u'pitch' |
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| 285 | and self.parent_class == u'SASdetector'): |
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[5e906207] | 286 | self.detector.orientation.x = float(data_point) |
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| 287 | self.detector.orientation_unit = unit |
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[082239e] | 288 | elif key == u'roll' and self.parent_class == u'SASdetector': |
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[5e906207] | 289 | self.detector.orientation.z = float(data_point) |
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| 290 | self.detector.orientation_unit = unit |
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[082239e] | 291 | elif key == u'yaw' and self.parent_class == u'SASdetector': |
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| 292 | self.detector.orientation.y = float(data_point) |
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| 293 | self.detector.orientation_unit = unit |
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[c94280c] | 294 | elif (key == u'beam_center_x' |
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| 295 | and self.parent_class == u'SASdetector'): |
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[5e906207] | 296 | self.detector.beam_center.x = float(data_point) |
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| 297 | self.detector.beam_center_unit = unit |
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[c94280c] | 298 | elif (key == u'beam_center_y' |
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| 299 | and self.parent_class == u'SASdetector'): |
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[5e906207] | 300 | self.detector.beam_center.y = float(data_point) |
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| 301 | self.detector.beam_center_unit = unit |
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[c94280c] | 302 | elif (key == u'x_pixel_size' |
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| 303 | and self.parent_class == u'SASdetector'): |
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[5e906207] | 304 | self.detector.pixel_size.x = float(data_point) |
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| 305 | self.detector.pixel_size_unit = unit |
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[c94280c] | 306 | elif (key == u'y_pixel_size' |
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| 307 | and self.parent_class == u'SASdetector'): |
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[5e906207] | 308 | self.detector.pixel_size.y = float(data_point) |
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| 309 | self.detector.pixel_size_unit = unit |
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[c94280c] | 310 | elif (key == u'distance' |
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| 311 | and self.parent_class == u'SAScollimation'): |
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[ad52d31] | 312 | self.collimation.length = data_point |
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[d398285] | 313 | self.collimation.length_unit = unit |
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[c94280c] | 314 | elif (key == u'name' |
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| 315 | and self.parent_class == u'SAScollimation'): |
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[ad52d31] | 316 | self.collimation.name = data_point |
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[c94280c] | 317 | elif (key == u'shape' |
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| 318 | and self.parent_class == u'SASaperture'): |
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[082239e] | 319 | self.aperture.shape = data_point |
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[c94280c] | 320 | elif (key == u'x_gap' |
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| 321 | and self.parent_class == u'SASaperture'): |
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[082239e] | 322 | self.aperture.size.x = data_point |
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[c94280c] | 323 | elif (key == u'y_gap' |
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| 324 | and self.parent_class == u'SASaperture'): |
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[082239e] | 325 | self.aperture.size.y = data_point |
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| 326 | |
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| 327 | # Process Information |
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[c94280c] | 328 | elif (key == u'Title' |
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| 329 | and self.parent_class == u'SASprocess'): # CanSAS 2.0 |
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[68aa210] | 330 | self.process.name = data_point |
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[c94280c] | 331 | elif (key == u'name' |
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| 332 | and self.parent_class == u'SASprocess'): # NXcanSAS |
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[68aa210] | 333 | self.process.name = data_point |
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[c94280c] | 334 | elif (key == u'description' |
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| 335 | and self.parent_class == u'SASprocess'): |
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[68aa210] | 336 | self.process.description = data_point |
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[d72567e] | 337 | elif key == u'date' and self.parent_class == u'SASprocess': |
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[68aa210] | 338 | self.process.date = data_point |
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[082239e] | 339 | elif key == u'term' and self.parent_class == u'SASprocess': |
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| 340 | self.process.term = data_point |
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[d72567e] | 341 | elif self.parent_class == u'SASprocess': |
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[ad52d31] | 342 | self.process.notes.append(data_point) |
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| 343 | |
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[082239e] | 344 | # Source |
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[c94280c] | 345 | elif (key == u'wavelength' |
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| 346 | and self.parent_class == u'SASdata'): |
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[d72567e] | 347 | self.current_datainfo.source.wavelength = data_point |
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[5e906207] | 348 | self.current_datainfo.source.wavelength_unit = unit |
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[c94280c] | 349 | elif (key == u'incident_wavelength' |
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| 350 | and self.parent_class == 'SASsource'): |
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[5e906207] | 351 | self.current_datainfo.source.wavelength = data_point |
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| 352 | self.current_datainfo.source.wavelength_unit = unit |
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[c94280c] | 353 | elif (key == u'wavelength_max' |
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| 354 | and self.parent_class == u'SASsource'): |
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[5e906207] | 355 | self.current_datainfo.source.wavelength_max = data_point |
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| 356 | self.current_datainfo.source.wavelength_max_unit = unit |
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[c94280c] | 357 | elif (key == u'wavelength_min' |
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| 358 | and self.parent_class == u'SASsource'): |
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[5e906207] | 359 | self.current_datainfo.source.wavelength_min = data_point |
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| 360 | self.current_datainfo.source.wavelength_min_unit = unit |
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[c94280c] | 361 | elif (key == u'incident_wavelength_spread' |
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| 362 | and self.parent_class == u'SASsource'): |
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[082239e] | 363 | self.current_datainfo.source.wavelength_spread = \ |
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| 364 | data_point |
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| 365 | self.current_datainfo.source.wavelength_spread_unit = \ |
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| 366 | unit |
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[c94280c] | 367 | elif (key == u'beam_size_x' |
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| 368 | and self.parent_class == u'SASsource'): |
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[5e906207] | 369 | self.current_datainfo.source.beam_size.x = data_point |
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| 370 | self.current_datainfo.source.beam_size_unit = unit |
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[c94280c] | 371 | elif (key == u'beam_size_y' |
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| 372 | and self.parent_class == u'SASsource'): |
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[5e906207] | 373 | self.current_datainfo.source.beam_size.y = data_point |
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| 374 | self.current_datainfo.source.beam_size_unit = unit |
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[c94280c] | 375 | elif (key == u'beam_shape' |
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| 376 | and self.parent_class == u'SASsource'): |
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[5e906207] | 377 | self.current_datainfo.source.beam_shape = data_point |
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[c94280c] | 378 | elif (key == u'radiation' |
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| 379 | and self.parent_class == u'SASsource'): |
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[d72567e] | 380 | self.current_datainfo.source.radiation = data_point |
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[c94280c] | 381 | elif (key == u'transmission' |
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| 382 | and self.parent_class == u'SASdata'): |
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[d72567e] | 383 | self.current_datainfo.sample.transmission = data_point |
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[68aa210] | 384 | |
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[082239e] | 385 | # Everything else goes in meta_data |
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[68aa210] | 386 | else: |
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[082239e] | 387 | new_key = self._create_unique_key( |
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| 388 | self.current_datainfo.meta_data, key) |
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[d72567e] | 389 | self.current_datainfo.meta_data[new_key] = data_point |
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[68aa210] | 390 | |
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| 391 | else: |
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[082239e] | 392 | # I don't know if this reachable code |
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[68aa210] | 393 | self.errors.add("ShouldNeverHappenException") |
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| 394 | |
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[d72567e] | 395 | def add_intermediate(self): |
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[ad52d31] | 396 | """ |
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[082239e] | 397 | This method stores any intermediate objects within the final data set |
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| 398 | after fully reading the set. |
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[ad52d31] | 399 | |
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[082239e] | 400 | :param parent: The NXclass name for the h5py Group object that just |
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| 401 | finished being processed |
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[ad52d31] | 402 | """ |
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| 403 | |
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[d72567e] | 404 | if self.parent_class == u'SASprocess': |
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| 405 | self.current_datainfo.process.append(self.process) |
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[ad52d31] | 406 | self.process = Process() |
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[d72567e] | 407 | elif self.parent_class == u'SASdetector': |
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| 408 | self.current_datainfo.detector.append(self.detector) |
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[ad52d31] | 409 | self.detector = Detector() |
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[d72567e] | 410 | elif self.parent_class == u'SAStransmission_spectrum': |
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| 411 | self.current_datainfo.trans_spectrum.append(self.trans_spectrum) |
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[ad52d31] | 412 | self.trans_spectrum = TransmissionSpectrum() |
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[d72567e] | 413 | elif self.parent_class == u'SAScollimation': |
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| 414 | self.current_datainfo.collimation.append(self.collimation) |
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[ad52d31] | 415 | self.collimation = Collimation() |
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[d72567e] | 416 | elif self.parent_class == u'SASaperture': |
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[ad52d31] | 417 | self.collimation.aperture.append(self.aperture) |
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| 418 | self.aperture = Aperture() |
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[d72567e] | 419 | elif self.parent_class == u'SASdata': |
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[082239e] | 420 | if isinstance(self.current_dataset, plottable_2D): |
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[d72567e] | 421 | self.data2d.append(self.current_dataset) |
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[082239e] | 422 | elif isinstance(self.current_dataset, plottable_1D): |
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[d72567e] | 423 | self.data1d.append(self.current_dataset) |
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[68aa210] | 424 | |
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| 425 | def final_data_cleanup(self): |
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| 426 | """ |
---|
[082239e] | 427 | Does some final cleanup and formatting on self.current_datainfo and |
---|
| 428 | all data1D and data2D objects and then combines the data and info into |
---|
| 429 | Data1D and Data2D objects |
---|
[68aa210] | 430 | """ |
---|
| 431 | |
---|
[082239e] | 432 | # Type cast data arrays to float64 |
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[d72567e] | 433 | if len(self.current_datainfo.trans_spectrum) > 0: |
---|
[ad52d31] | 434 | spectrum_list = [] |
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[d72567e] | 435 | for spectrum in self.current_datainfo.trans_spectrum: |
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[ad52d31] | 436 | spectrum.transmission = np.delete(spectrum.transmission, [0]) |
---|
| 437 | spectrum.transmission = spectrum.transmission.astype(np.float64) |
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[082239e] | 438 | spectrum.transmission_deviation = np.delete( |
---|
| 439 | spectrum.transmission_deviation, [0]) |
---|
| 440 | spectrum.transmission_deviation = \ |
---|
| 441 | spectrum.transmission_deviation.astype(np.float64) |
---|
[ad52d31] | 442 | spectrum.wavelength = np.delete(spectrum.wavelength, [0]) |
---|
| 443 | spectrum.wavelength = spectrum.wavelength.astype(np.float64) |
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[d72567e] | 444 | if len(spectrum.transmission) > 0: |
---|
| 445 | spectrum_list.append(spectrum) |
---|
| 446 | self.current_datainfo.trans_spectrum = spectrum_list |
---|
[68aa210] | 447 | |
---|
[082239e] | 448 | # Append errors to dataset and reset class errors |
---|
[d72567e] | 449 | self.current_datainfo.errors = self.errors |
---|
[68aa210] | 450 | self.errors.clear() |
---|
| 451 | |
---|
[082239e] | 452 | # Combine all plottables with datainfo and append each to output |
---|
| 453 | # Type cast data arrays to float64 and find min/max as appropriate |
---|
[d72567e] | 454 | for dataset in self.data2d: |
---|
| 455 | dataset.data = dataset.data.astype(np.float64) |
---|
| 456 | dataset.err_data = dataset.err_data.astype(np.float64) |
---|
| 457 | if dataset.qx_data is not None: |
---|
| 458 | dataset.xmin = np.min(dataset.qx_data) |
---|
| 459 | dataset.xmax = np.max(dataset.qx_data) |
---|
| 460 | dataset.qx_data = dataset.qx_data.astype(np.float64) |
---|
| 461 | if dataset.dqx_data is not None: |
---|
| 462 | dataset.dqx_data = dataset.dqx_data.astype(np.float64) |
---|
| 463 | if dataset.qy_data is not None: |
---|
| 464 | dataset.ymin = np.min(dataset.qy_data) |
---|
| 465 | dataset.ymax = np.max(dataset.qy_data) |
---|
| 466 | dataset.qy_data = dataset.qy_data.astype(np.float64) |
---|
| 467 | if dataset.dqy_data is not None: |
---|
| 468 | dataset.dqy_data = dataset.dqy_data.astype(np.float64) |
---|
| 469 | if dataset.q_data is not None: |
---|
| 470 | dataset.q_data = dataset.q_data.astype(np.float64) |
---|
| 471 | zeros = np.ones(dataset.data.size, dtype=bool) |
---|
| 472 | try: |
---|
[082239e] | 473 | for i in range(0, dataset.mask.size - 1): |
---|
[d72567e] | 474 | zeros[i] = dataset.mask[i] |
---|
| 475 | except: |
---|
| 476 | self.errors.add(sys.exc_value) |
---|
| 477 | dataset.mask = zeros |
---|
[082239e] | 478 | # Calculate the actual Q matrix |
---|
[d72567e] | 479 | try: |
---|
| 480 | if dataset.q_data.size <= 1: |
---|
[54544637] | 481 | dataset.q_data = np.sqrt(dataset.qx_data |
---|
| 482 | * dataset.qx_data |
---|
| 483 | + dataset.qy_data |
---|
| 484 | * dataset.qy_data) |
---|
[d72567e] | 485 | except: |
---|
| 486 | dataset.q_data = None |
---|
[ac370c5] | 487 | |
---|
| 488 | if dataset.data.ndim == 2: |
---|
| 489 | (n_rows, n_cols) = dataset.data.shape |
---|
[479799c] | 490 | dataset.y_bins = dataset.qy_data[0::n_cols] |
---|
[ac370c5] | 491 | dataset.x_bins = dataset.qx_data[:n_cols] |
---|
| 492 | dataset.data = dataset.data.flatten() |
---|
| 493 | |
---|
[082239e] | 494 | final_dataset = combine_data_info_with_plottable( |
---|
| 495 | dataset, self.current_datainfo) |
---|
[d72567e] | 496 | self.output.append(final_dataset) |
---|
| 497 | |
---|
| 498 | for dataset in self.data1d: |
---|
| 499 | if dataset.x is not None: |
---|
| 500 | dataset.x = dataset.x.astype(np.float64) |
---|
| 501 | dataset.xmin = np.min(dataset.x) |
---|
| 502 | dataset.xmax = np.max(dataset.x) |
---|
| 503 | if dataset.y is not None: |
---|
| 504 | dataset.y = dataset.y.astype(np.float64) |
---|
| 505 | dataset.ymin = np.min(dataset.y) |
---|
| 506 | dataset.ymax = np.max(dataset.y) |
---|
| 507 | if dataset.dx is not None: |
---|
| 508 | dataset.dx = dataset.dx.astype(np.float64) |
---|
| 509 | if dataset.dxl is not None: |
---|
| 510 | dataset.dxl = dataset.dxl.astype(np.float64) |
---|
| 511 | if dataset.dxw is not None: |
---|
| 512 | dataset.dxw = dataset.dxw.astype(np.float64) |
---|
| 513 | if dataset.dy is not None: |
---|
| 514 | dataset.dy = dataset.dy.astype(np.float64) |
---|
[082239e] | 515 | final_dataset = combine_data_info_with_plottable( |
---|
| 516 | dataset, self.current_datainfo) |
---|
[d72567e] | 517 | self.output.append(final_dataset) |
---|
| 518 | |
---|
[68aa210] | 519 | def add_data_set(self, key=""): |
---|
| 520 | """ |
---|
[082239e] | 521 | Adds the current_dataset to the list of outputs after preforming final |
---|
| 522 | processing on the data and then calls a private method to generate a |
---|
| 523 | new data set. |
---|
[68aa210] | 524 | |
---|
| 525 | :param key: NeXus group name for current tree level |
---|
| 526 | """ |
---|
[d72567e] | 527 | |
---|
| 528 | if self.current_datainfo and self.current_dataset: |
---|
[68aa210] | 529 | self.final_data_cleanup() |
---|
[d72567e] | 530 | self.data1d = [] |
---|
| 531 | self.data2d = [] |
---|
| 532 | self.current_datainfo = DataInfo() |
---|
[68aa210] | 533 | |
---|
[54ba66e] | 534 | |
---|
[082239e] | 535 | def _initialize_new_data_set(self, parent_list=None): |
---|
[68aa210] | 536 | """ |
---|
[082239e] | 537 | A private class method to generate a new 1D or 2D data object based on |
---|
| 538 | the type of data within the set. Outside methods should call |
---|
| 539 | add_data_set() to be sure any existing data is stored properly. |
---|
[68aa210] | 540 | |
---|
[d72567e] | 541 | :param parent_list: List of names of parent elements |
---|
[68aa210] | 542 | """ |
---|
[d72567e] | 543 | |
---|
| 544 | if parent_list is None: |
---|
| 545 | parent_list = [] |
---|
| 546 | if self._find_intermediate(parent_list, "Qx"): |
---|
| 547 | self.current_dataset = plottable_2D() |
---|
[68aa210] | 548 | else: |
---|
| 549 | x = np.array(0) |
---|
| 550 | y = np.array(0) |
---|
[d72567e] | 551 | self.current_dataset = plottable_1D(x, y) |
---|
| 552 | self.current_datainfo.filename = self.raw_data.filename |
---|
[68aa210] | 553 | |
---|
[d72567e] | 554 | def _find_intermediate(self, parent_list, basename=""): |
---|
[ad52d31] | 555 | """ |
---|
[082239e] | 556 | A private class used to find an entry by either using a direct key or |
---|
| 557 | knowing the approximate basename. |
---|
[ad52d31] | 558 | |
---|
[082239e] | 559 | :param parent_list: List of parents nodes in the HDF5 file |
---|
[d72567e] | 560 | :param basename: Approximate name of an entry to search for |
---|
[ad52d31] | 561 | :return: |
---|
| 562 | """ |
---|
[d72567e] | 563 | |
---|
| 564 | entry = False |
---|
| 565 | key_prog = re.compile(basename) |
---|
| 566 | top = self.raw_data |
---|
| 567 | for parent in parent_list: |
---|
| 568 | top = top.get(parent) |
---|
| 569 | for key in top.keys(): |
---|
[082239e] | 570 | if key_prog.match(key): |
---|
[d72567e] | 571 | entry = True |
---|
| 572 | break |
---|
[ad52d31] | 573 | return entry |
---|
| 574 | |
---|
[68aa210] | 575 | def _create_unique_key(self, dictionary, name, numb=0): |
---|
| 576 | """ |
---|
| 577 | Create a unique key value for any dictionary to prevent overwriting |
---|
| 578 | Recurses until a unique key value is found. |
---|
| 579 | |
---|
| 580 | :param dictionary: A dictionary with any number of entries |
---|
| 581 | :param name: The index of the item to be added to dictionary |
---|
| 582 | :param numb: The number to be appended to the name, starts at 0 |
---|
[d72567e] | 583 | :return: The new name for the dictionary entry |
---|
[68aa210] | 584 | """ |
---|
| 585 | if dictionary.get(name) is not None: |
---|
| 586 | numb += 1 |
---|
| 587 | name = name.split("_")[0] |
---|
| 588 | name += "_{0}".format(numb) |
---|
| 589 | name = self._create_unique_key(dictionary, name, numb) |
---|
[d398285] | 590 | return name |
---|
| 591 | |
---|
| 592 | def _get_unit(self, value): |
---|
| 593 | """ |
---|
| 594 | Find the unit for a particular value within the h5py dictionary |
---|
| 595 | |
---|
| 596 | :param value: attribute dictionary for a particular value set |
---|
[d72567e] | 597 | :return: unit for the value passed to the method |
---|
[d398285] | 598 | """ |
---|
| 599 | unit = value.attrs.get(u'units') |
---|
[54544637] | 600 | if unit is None: |
---|
[d398285] | 601 | unit = value.attrs.get(u'unit') |
---|
[082239e] | 602 | # Convert the unit formats |
---|
[d398285] | 603 | if unit == "1/A": |
---|
| 604 | unit = "A^{-1}" |
---|
| 605 | elif unit == "1/cm": |
---|
| 606 | unit = "cm^{-1}" |
---|
[54ba66e] | 607 | return unit |
---|