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