[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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[7b50f14] | 11 | from ..data_info import plottable_1D, plottable_2D,\ |
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[082239e] | 12 | Data1D, Data2D, DataInfo, Process, Aperture, Collimation, \ |
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| 13 | TransmissionSpectrum, Detector |
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[7b50f14] | 14 | from ..data_info import combine_data_info_with_plottable |
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| 15 | from ..loader_exceptions import FileContentsException, DefaultReaderException |
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| 16 | from ..file_reader_base_class import FileReader, decode |
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[d72567e] | 17 | |
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[5c5e7fd] | 18 | def h5attr(node, key, default=None): |
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| 19 | return decode(node.attrs.get(key, default)) |
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[68aa210] | 20 | |
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[9d786e5] | 21 | class Reader(FileReader): |
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[68aa210] | 22 | """ |
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[082239e] | 23 | A class for reading in CanSAS v2.0 data files. The existing iteration opens |
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| 24 | Mantid generated HDF5 formatted files with file extension .h5/.H5. Any |
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| 25 | number of data sets may be present within the file and any dimensionality |
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| 26 | of data may be used. Currently 1D and 2D SAS data sets are supported, but |
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| 27 | future implementations will include 1D and 2D SESANS data. |
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[d72567e] | 28 | |
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[082239e] | 29 | Any number of SASdata sets may be present in a SASentry and the data within |
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| 30 | can be either 1D I(Q) or 2D I(Qx, Qy). |
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[68aa210] | 31 | |
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[5e906207] | 32 | Also supports reading NXcanSAS formatted HDF5 files |
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| 33 | |
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[68aa210] | 34 | :Dependencies: |
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[d72567e] | 35 | The CanSAS HDF5 reader requires h5py => v2.5.0 or later. |
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[68aa210] | 36 | """ |
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| 37 | |
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[082239e] | 38 | # CanSAS version |
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[68aa210] | 39 | cansas_version = 2.0 |
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[082239e] | 40 | # Data type name |
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[ad52d31] | 41 | type_name = "CanSAS 2.0" |
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[082239e] | 42 | # Wildcards |
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[ad52d31] | 43 | type = ["CanSAS 2.0 HDF5 Files (*.h5)|*.h5"] |
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[082239e] | 44 | # List of allowed extensions |
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[68aa210] | 45 | ext = ['.h5', '.H5'] |
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[082239e] | 46 | # Flag to bypass extension check |
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[54544637] | 47 | allow_all = True |
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[68aa210] | 48 | |
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[9d786e5] | 49 | def get_file_contents(self): |
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[68aa210] | 50 | """ |
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[ad52d31] | 51 | This is the general read method that all SasView data_loaders must have. |
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[68aa210] | 52 | |
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| 53 | :param filename: A path for an HDF5 formatted CanSAS 2D data file. |
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[d72567e] | 54 | :return: List of Data1D/2D objects and/or a list of errors. |
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[68aa210] | 55 | """ |
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[082239e] | 56 | # Reinitialize when loading a new data file to reset all class variables |
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[61f329f0] | 57 | self.reset_state() |
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[9d786e5] | 58 | |
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| 59 | filename = self.f_open.name |
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| 60 | self.f_open.close() # IO handled by h5py |
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| 61 | |
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[082239e] | 62 | # Check that the file exists |
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[68aa210] | 63 | if os.path.isfile(filename): |
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| 64 | basename = os.path.basename(filename) |
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| 65 | _, extension = os.path.splitext(basename) |
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| 66 | # If the file type is not allowed, return empty list |
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| 67 | if extension in self.ext or self.allow_all: |
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[082239e] | 68 | # Load the data file |
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[7f75a3f] | 69 | try: |
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| 70 | self.raw_data = h5py.File(filename, 'r') |
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| 71 | except Exception as e: |
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[8dec7e7] | 72 | if extension not in self.ext: |
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| 73 | msg = "CanSAS2.0 HDF5 Reader could not load file {}".format(basename + extension) |
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| 74 | raise DefaultReaderException(msg) |
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| 75 | raise FileContentsException(e.message) |
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[dcb91cf] | 76 | try: |
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| 77 | # Read in all child elements of top level SASroot |
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| 78 | self.read_children(self.raw_data, []) |
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| 79 | # Add the last data set to the list of outputs |
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| 80 | self.add_data_set() |
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| 81 | except Exception as exc: |
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| 82 | raise FileContentsException(exc.message) |
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| 83 | finally: |
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| 84 | # Close the data file |
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| 85 | self.raw_data.close() |
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| 86 | |
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| 87 | for dataset in self.output: |
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| 88 | if isinstance(dataset, Data1D): |
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| 89 | if dataset.x.size < 5: |
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| 90 | self.output = [] |
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| 91 | raise FileContentsException("Fewer than 5 data points found.") |
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[68aa210] | 92 | |
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[61f329f0] | 93 | def reset_state(self): |
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[d72567e] | 94 | """ |
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| 95 | Create the reader object and define initial states for class variables |
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| 96 | """ |
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[61f329f0] | 97 | super(Reader, self).reset_state() |
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[d72567e] | 98 | self.data1d = [] |
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| 99 | self.data2d = [] |
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| 100 | self.raw_data = None |
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| 101 | self.errors = set() |
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| 102 | self.logging = [] |
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[2651724] | 103 | self.q_name = [] |
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| 104 | self.mask_name = u'' |
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| 105 | self.i_name = u'' |
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| 106 | self.i_node = u'' |
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| 107 | self.q_uncertainties = u'' |
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| 108 | self.q_resolutions = u'' |
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| 109 | self.i_uncertainties = u'' |
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[d72567e] | 110 | self.parent_class = u'' |
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| 111 | self.detector = Detector() |
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| 112 | self.collimation = Collimation() |
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| 113 | self.aperture = Aperture() |
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| 114 | self.process = Process() |
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| 115 | self.trans_spectrum = TransmissionSpectrum() |
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| 116 | |
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| 117 | def read_children(self, data, parent_list): |
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[68aa210] | 118 | """ |
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[ad52d31] | 119 | A recursive method for stepping through the hierarchical data file. |
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[68aa210] | 120 | |
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| 121 | :param data: h5py Group object of any kind |
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| 122 | :param parent: h5py Group parent name |
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| 123 | """ |
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| 124 | |
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[082239e] | 125 | # Loop through each element of the parent and process accordingly |
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[68aa210] | 126 | for key in data.keys(): |
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[082239e] | 127 | # Get all information for the current key |
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[68aa210] | 128 | value = data.get(key) |
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[7b50f14] | 129 | class_name = h5attr(value, u'canSAS_class') |
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| 130 | if class_name is None: |
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[5c5e7fd] | 131 | class_name = h5attr(value, u'NX_class') |
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[68aa210] | 132 | if class_name is not None: |
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| 133 | class_prog = re.compile(class_name) |
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| 134 | else: |
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| 135 | class_prog = re.compile(value.name) |
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| 136 | |
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| 137 | if isinstance(value, h5py.Group): |
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[c9ecd1b] | 138 | # Set parent class before recursion |
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[d72567e] | 139 | self.parent_class = class_name |
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| 140 | parent_list.append(key) |
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[082239e] | 141 | # If a new sasentry, store the current data sets and create |
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| 142 | # a fresh Data1D/2D object |
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[68aa210] | 143 | if class_prog.match(u'SASentry'): |
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| 144 | self.add_data_set(key) |
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[d72567e] | 145 | elif class_prog.match(u'SASdata'): |
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[9e0dd49] | 146 | self._find_data_attributes(value) |
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[2651724] | 147 | self._initialize_new_data_set(parent_list) |
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[082239e] | 148 | # Recursion step to access data within the group |
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[d72567e] | 149 | self.read_children(value, parent_list) |
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[c9ecd1b] | 150 | # Reset parent class when returning from recursive method |
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| 151 | self.parent_class = class_name |
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[d72567e] | 152 | self.add_intermediate() |
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| 153 | parent_list.remove(key) |
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[68aa210] | 154 | |
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| 155 | elif isinstance(value, h5py.Dataset): |
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[082239e] | 156 | # If this is a dataset, store the data appropriately |
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[68aa210] | 157 | data_set = data[key][:] |
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[7bd6860a] | 158 | unit = self._get_unit(value) |
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[ac370c5] | 159 | |
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[68aa210] | 160 | for data_point in data_set: |
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[2b538cd] | 161 | if isinstance(data_point, np.ndarray): |
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| 162 | if data_point.dtype.char == 'S': |
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| 163 | data_point = decode(bytes(data_point)) |
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| 164 | else: |
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| 165 | data_point = decode(data_point) |
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[082239e] | 166 | # Top Level Meta Data |
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[68aa210] | 167 | if key == u'definition': |
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[d72567e] | 168 | self.current_datainfo.meta_data['reader'] = data_point |
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[0d93464] | 169 | # Run |
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[68aa210] | 170 | elif key == u'run': |
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[d72567e] | 171 | self.current_datainfo.run.append(data_point) |
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[be88076] | 172 | try: |
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[5c5e7fd] | 173 | run_name = h5attr(value, 'name') |
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[be88076] | 174 | run_dict = {data_point: run_name} |
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| 175 | self.current_datainfo.run_name = run_dict |
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[7b50f14] | 176 | except Exception: |
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[be88076] | 177 | pass |
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[0d93464] | 178 | # Title |
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[68aa210] | 179 | elif key == u'title': |
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[d72567e] | 180 | self.current_datainfo.title = data_point |
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[0d93464] | 181 | # Note |
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[68aa210] | 182 | elif key == u'SASnote': |
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[d72567e] | 183 | self.current_datainfo.notes.append(data_point) |
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[082239e] | 184 | # Sample Information |
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[0d93464] | 185 | elif self.parent_class == u'SASsample': |
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| 186 | self.process_sample(data_point, key) |
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[082239e] | 187 | # Instrumental Information |
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[c94280c] | 188 | elif (key == u'name' |
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| 189 | and self.parent_class == u'SASinstrument'): |
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[d72567e] | 190 | self.current_datainfo.instrument = data_point |
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[0d93464] | 191 | # Detector |
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| 192 | elif self.parent_class == u'SASdetector': |
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| 193 | self.process_detector(data_point, key, unit) |
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| 194 | # Collimation |
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| 195 | elif self.parent_class == u'SAScollimation': |
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| 196 | self.process_collimation(data_point, key, unit) |
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| 197 | # Aperture |
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| 198 | elif self.parent_class == u'SASaperture': |
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| 199 | self.process_aperture(data_point, key) |
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[082239e] | 200 | # Process Information |
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[0d93464] | 201 | elif self.parent_class == u'SASprocess': # CanSAS 2.0 |
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| 202 | self.process_process(data_point, key) |
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[082239e] | 203 | # Source |
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[0d93464] | 204 | elif self.parent_class == u'SASsource': |
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| 205 | self.process_source(data_point, key, unit) |
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[082239e] | 206 | # Everything else goes in meta_data |
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[0d93464] | 207 | elif self.parent_class == u'SASdata': |
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| 208 | self.process_data_object(data_set, key, unit) |
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| 209 | break |
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| 210 | elif self.parent_class == u'SAStransmission_spectrum': |
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| 211 | self.process_trans_spectrum(data_set, key) |
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| 212 | break |
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[68aa210] | 213 | else: |
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[082239e] | 214 | new_key = self._create_unique_key( |
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| 215 | self.current_datainfo.meta_data, key) |
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[d72567e] | 216 | self.current_datainfo.meta_data[new_key] = data_point |
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[68aa210] | 217 | |
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| 218 | else: |
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[082239e] | 219 | # I don't know if this reachable code |
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[68aa210] | 220 | self.errors.add("ShouldNeverHappenException") |
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| 221 | |
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[0d93464] | 222 | def process_data_object(self, data_set, key, unit): |
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| 223 | """ |
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| 224 | SASdata processor method |
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| 225 | :param data_set: data from HDF5 file |
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| 226 | :param key: canSAS_class attribute |
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| 227 | :param unit: unit attribute |
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| 228 | """ |
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[2651724] | 229 | if key == self.i_name: |
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[0d93464] | 230 | if isinstance(self.current_dataset, plottable_2D): |
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| 231 | self.current_dataset.data = data_set |
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| 232 | self.current_dataset.zaxis("Intensity", unit) |
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| 233 | else: |
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| 234 | self.current_dataset.y = data_set.flatten() |
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| 235 | self.current_dataset.yaxis("Intensity", unit) |
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[2651724] | 236 | elif key == self.i_uncertainties: |
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[0d93464] | 237 | if isinstance(self.current_dataset, plottable_2D): |
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| 238 | self.current_dataset.err_data = data_set.flatten() |
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| 239 | else: |
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| 240 | self.current_dataset.dy = data_set.flatten() |
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[2651724] | 241 | elif key in self.q_name: |
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[0d93464] | 242 | self.current_dataset.xaxis("Q", unit) |
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| 243 | if isinstance(self.current_dataset, plottable_2D): |
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| 244 | self.current_dataset.q = data_set.flatten() |
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| 245 | else: |
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| 246 | self.current_dataset.x = data_set.flatten() |
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[2651724] | 247 | elif key in self.q_resolutions: |
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| 248 | if key == u'dQw': |
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| 249 | self.current_dataset.dxw = data_set.flatten() |
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| 250 | elif key == u'dQl': |
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| 251 | self.current_dataset.dxl = data_set.flatten() |
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| 252 | else: |
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| 253 | self.current_dataset.dx = data_set.flatten() |
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[0d93464] | 254 | elif key == u'Qy': |
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| 255 | self.current_dataset.yaxis("Q_y", unit) |
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| 256 | self.current_dataset.qy_data = data_set.flatten() |
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| 257 | elif key == u'Qydev': |
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| 258 | self.current_dataset.dqy_data = data_set.flatten() |
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| 259 | elif key == u'Qx': |
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| 260 | self.current_dataset.xaxis("Q_x", unit) |
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| 261 | self.current_dataset.qx_data = data_set.flatten() |
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| 262 | elif key == u'Qxdev': |
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| 263 | self.current_dataset.dqx_data = data_set.flatten() |
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[2651724] | 264 | elif key == self.mask_name: |
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[0d93464] | 265 | self.current_dataset.mask = data_set.flatten() |
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| 266 | elif key == u'wavelength': |
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| 267 | self.current_datainfo.source.wavelength = data_set[0] |
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| 268 | self.current_datainfo.source.wavelength_unit = unit |
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| 269 | |
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| 270 | def process_trans_spectrum(self, data_set, key): |
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| 271 | """ |
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| 272 | SAStransmission_spectrum processor |
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| 273 | :param data_set: data from HDF5 file |
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| 274 | :param key: canSAS_class attribute |
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| 275 | """ |
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| 276 | if key == u'T': |
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| 277 | self.trans_spectrum.transmission = data_set.flatten() |
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| 278 | elif key == u'Tdev': |
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| 279 | self.trans_spectrum.transmission_deviation = data_set.flatten() |
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| 280 | elif key == u'lambda': |
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| 281 | self.trans_spectrum.wavelength = data_set.flatten() |
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| 282 | |
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| 283 | def process_sample(self, data_point, key): |
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| 284 | """ |
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| 285 | SASsample processor |
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| 286 | :param data_point: Single point from an HDF5 data file |
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| 287 | :param key: class name data_point was taken from |
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| 288 | """ |
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| 289 | if key == u'Title': |
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| 290 | self.current_datainfo.sample.name = data_point |
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| 291 | elif key == u'name': |
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| 292 | self.current_datainfo.sample.name = data_point |
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| 293 | elif key == u'ID': |
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| 294 | self.current_datainfo.sample.name = data_point |
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| 295 | elif key == u'thickness': |
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| 296 | self.current_datainfo.sample.thickness = data_point |
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| 297 | elif key == u'temperature': |
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| 298 | self.current_datainfo.sample.temperature = data_point |
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| 299 | elif key == u'transmission': |
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| 300 | self.current_datainfo.sample.transmission = data_point |
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| 301 | elif key == u'x_position': |
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| 302 | self.current_datainfo.sample.position.x = data_point |
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| 303 | elif key == u'y_position': |
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| 304 | self.current_datainfo.sample.position.y = data_point |
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| 305 | elif key == u'pitch': |
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| 306 | self.current_datainfo.sample.orientation.x = data_point |
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| 307 | elif key == u'yaw': |
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| 308 | self.current_datainfo.sample.orientation.y = data_point |
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| 309 | elif key == u'roll': |
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| 310 | self.current_datainfo.sample.orientation.z = data_point |
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| 311 | elif key == u'details': |
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| 312 | self.current_datainfo.sample.details.append(data_point) |
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| 313 | |
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| 314 | def process_detector(self, data_point, key, unit): |
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| 315 | """ |
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| 316 | SASdetector processor |
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| 317 | :param data_point: Single point from an HDF5 data file |
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| 318 | :param key: class name data_point was taken from |
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| 319 | :param unit: unit attribute from data set |
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| 320 | """ |
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| 321 | if key == u'name': |
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| 322 | self.detector.name = data_point |
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| 323 | elif key == u'SDD': |
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| 324 | self.detector.distance = float(data_point) |
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| 325 | self.detector.distance_unit = unit |
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| 326 | elif key == u'slit_length': |
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| 327 | self.detector.slit_length = float(data_point) |
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| 328 | self.detector.slit_length_unit = unit |
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| 329 | elif key == u'x_position': |
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| 330 | self.detector.offset.x = float(data_point) |
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| 331 | self.detector.offset_unit = unit |
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| 332 | elif key == u'y_position': |
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| 333 | self.detector.offset.y = float(data_point) |
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| 334 | self.detector.offset_unit = unit |
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| 335 | elif key == u'pitch': |
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| 336 | self.detector.orientation.x = float(data_point) |
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| 337 | self.detector.orientation_unit = unit |
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| 338 | elif key == u'roll': |
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| 339 | self.detector.orientation.z = float(data_point) |
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| 340 | self.detector.orientation_unit = unit |
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| 341 | elif key == u'yaw': |
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| 342 | self.detector.orientation.y = float(data_point) |
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| 343 | self.detector.orientation_unit = unit |
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| 344 | elif key == u'beam_center_x': |
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| 345 | self.detector.beam_center.x = float(data_point) |
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| 346 | self.detector.beam_center_unit = unit |
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| 347 | elif key == u'beam_center_y': |
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| 348 | self.detector.beam_center.y = float(data_point) |
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| 349 | self.detector.beam_center_unit = unit |
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| 350 | elif key == u'x_pixel_size': |
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| 351 | self.detector.pixel_size.x = float(data_point) |
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| 352 | self.detector.pixel_size_unit = unit |
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| 353 | elif key == u'y_pixel_size': |
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| 354 | self.detector.pixel_size.y = float(data_point) |
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| 355 | self.detector.pixel_size_unit = unit |
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| 356 | |
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| 357 | def process_collimation(self, data_point, key, unit): |
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| 358 | """ |
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| 359 | SAScollimation processor |
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| 360 | :param data_point: Single point from an HDF5 data file |
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| 361 | :param key: class name data_point was taken from |
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| 362 | :param unit: unit attribute from data set |
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| 363 | """ |
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| 364 | if key == u'distance': |
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| 365 | self.collimation.length = data_point |
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| 366 | self.collimation.length_unit = unit |
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| 367 | elif key == u'name': |
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| 368 | self.collimation.name = data_point |
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| 369 | |
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| 370 | def process_aperture(self, data_point, key): |
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| 371 | """ |
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| 372 | SASaperture processor |
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| 373 | :param data_point: Single point from an HDF5 data file |
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| 374 | :param key: class name data_point was taken from |
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| 375 | """ |
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| 376 | if key == u'shape': |
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| 377 | self.aperture.shape = data_point |
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| 378 | elif key == u'x_gap': |
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| 379 | self.aperture.size.x = data_point |
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| 380 | elif key == u'y_gap': |
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| 381 | self.aperture.size.y = data_point |
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| 382 | |
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| 383 | def process_source(self, data_point, key, unit): |
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| 384 | """ |
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| 385 | SASsource processor |
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| 386 | :param data_point: Single point from an HDF5 data file |
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| 387 | :param key: class name data_point was taken from |
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| 388 | :param unit: unit attribute from data set |
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| 389 | """ |
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| 390 | if key == u'incident_wavelength': |
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| 391 | self.current_datainfo.source.wavelength = data_point |
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| 392 | self.current_datainfo.source.wavelength_unit = unit |
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| 393 | elif key == u'wavelength_max': |
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| 394 | self.current_datainfo.source.wavelength_max = data_point |
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| 395 | self.current_datainfo.source.wavelength_max_unit = unit |
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| 396 | elif key == u'wavelength_min': |
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| 397 | self.current_datainfo.source.wavelength_min = data_point |
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| 398 | self.current_datainfo.source.wavelength_min_unit = unit |
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| 399 | elif key == u'incident_wavelength_spread': |
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| 400 | self.current_datainfo.source.wavelength_spread = data_point |
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| 401 | self.current_datainfo.source.wavelength_spread_unit = unit |
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| 402 | elif key == u'beam_size_x': |
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| 403 | self.current_datainfo.source.beam_size.x = data_point |
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| 404 | self.current_datainfo.source.beam_size_unit = unit |
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| 405 | elif key == u'beam_size_y': |
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| 406 | self.current_datainfo.source.beam_size.y = data_point |
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| 407 | self.current_datainfo.source.beam_size_unit = unit |
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| 408 | elif key == u'beam_shape': |
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| 409 | self.current_datainfo.source.beam_shape = data_point |
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| 410 | elif key == u'radiation': |
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| 411 | self.current_datainfo.source.radiation = data_point |
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| 412 | |
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| 413 | def process_process(self, data_point, key): |
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| 414 | """ |
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| 415 | SASprocess processor |
---|
| 416 | :param data_point: Single point from an HDF5 data file |
---|
| 417 | :param key: class name data_point was taken from |
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| 418 | """ |
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| 419 | if key == u'Title': # CanSAS 2.0 |
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| 420 | self.process.name = data_point |
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| 421 | elif key == u'name': # NXcanSAS |
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| 422 | self.process.name = data_point |
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| 423 | elif key == u'description': |
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| 424 | self.process.description = data_point |
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| 425 | elif key == u'date': |
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| 426 | self.process.date = data_point |
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| 427 | elif key == u'term': |
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| 428 | self.process.term = data_point |
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| 429 | else: |
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| 430 | self.process.notes.append(data_point) |
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| 431 | |
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[d72567e] | 432 | def add_intermediate(self): |
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[ad52d31] | 433 | """ |
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[082239e] | 434 | This method stores any intermediate objects within the final data set |
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| 435 | after fully reading the set. |
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[ad52d31] | 436 | |
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[082239e] | 437 | :param parent: The NXclass name for the h5py Group object that just |
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| 438 | finished being processed |
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[ad52d31] | 439 | """ |
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| 440 | |
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[d72567e] | 441 | if self.parent_class == u'SASprocess': |
---|
| 442 | self.current_datainfo.process.append(self.process) |
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[ad52d31] | 443 | self.process = Process() |
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[d72567e] | 444 | elif self.parent_class == u'SASdetector': |
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| 445 | self.current_datainfo.detector.append(self.detector) |
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[ad52d31] | 446 | self.detector = Detector() |
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[d72567e] | 447 | elif self.parent_class == u'SAStransmission_spectrum': |
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| 448 | self.current_datainfo.trans_spectrum.append(self.trans_spectrum) |
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[ad52d31] | 449 | self.trans_spectrum = TransmissionSpectrum() |
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[d72567e] | 450 | elif self.parent_class == u'SAScollimation': |
---|
| 451 | self.current_datainfo.collimation.append(self.collimation) |
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[ad52d31] | 452 | self.collimation = Collimation() |
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[d72567e] | 453 | elif self.parent_class == u'SASaperture': |
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[ad52d31] | 454 | self.collimation.aperture.append(self.aperture) |
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| 455 | self.aperture = Aperture() |
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[d72567e] | 456 | elif self.parent_class == u'SASdata': |
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[082239e] | 457 | if isinstance(self.current_dataset, plottable_2D): |
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[d72567e] | 458 | self.data2d.append(self.current_dataset) |
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[082239e] | 459 | elif isinstance(self.current_dataset, plottable_1D): |
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[d72567e] | 460 | self.data1d.append(self.current_dataset) |
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[68aa210] | 461 | |
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| 462 | def final_data_cleanup(self): |
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| 463 | """ |
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[082239e] | 464 | Does some final cleanup and formatting on self.current_datainfo and |
---|
| 465 | all data1D and data2D objects and then combines the data and info into |
---|
| 466 | Data1D and Data2D objects |
---|
[68aa210] | 467 | """ |
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[082239e] | 468 | # Type cast data arrays to float64 |
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[d72567e] | 469 | if len(self.current_datainfo.trans_spectrum) > 0: |
---|
[ad52d31] | 470 | spectrum_list = [] |
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[d72567e] | 471 | for spectrum in self.current_datainfo.trans_spectrum: |
---|
[ad52d31] | 472 | spectrum.transmission = np.delete(spectrum.transmission, [0]) |
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| 473 | spectrum.transmission = spectrum.transmission.astype(np.float64) |
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[082239e] | 474 | spectrum.transmission_deviation = np.delete( |
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| 475 | spectrum.transmission_deviation, [0]) |
---|
| 476 | spectrum.transmission_deviation = \ |
---|
| 477 | spectrum.transmission_deviation.astype(np.float64) |
---|
[ad52d31] | 478 | spectrum.wavelength = np.delete(spectrum.wavelength, [0]) |
---|
| 479 | spectrum.wavelength = spectrum.wavelength.astype(np.float64) |
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[d72567e] | 480 | if len(spectrum.transmission) > 0: |
---|
| 481 | spectrum_list.append(spectrum) |
---|
| 482 | self.current_datainfo.trans_spectrum = spectrum_list |
---|
[68aa210] | 483 | |
---|
[082239e] | 484 | # Append errors to dataset and reset class errors |
---|
[d72567e] | 485 | self.current_datainfo.errors = self.errors |
---|
[68aa210] | 486 | self.errors.clear() |
---|
| 487 | |
---|
[082239e] | 488 | # Combine all plottables with datainfo and append each to output |
---|
| 489 | # Type cast data arrays to float64 and find min/max as appropriate |
---|
[d72567e] | 490 | for dataset in self.data2d: |
---|
| 491 | zeros = np.ones(dataset.data.size, dtype=bool) |
---|
| 492 | try: |
---|
[082239e] | 493 | for i in range(0, dataset.mask.size - 1): |
---|
[d72567e] | 494 | zeros[i] = dataset.mask[i] |
---|
| 495 | except: |
---|
| 496 | self.errors.add(sys.exc_value) |
---|
| 497 | dataset.mask = zeros |
---|
[082239e] | 498 | # Calculate the actual Q matrix |
---|
[d72567e] | 499 | try: |
---|
| 500 | if dataset.q_data.size <= 1: |
---|
[54544637] | 501 | dataset.q_data = np.sqrt(dataset.qx_data |
---|
| 502 | * dataset.qx_data |
---|
| 503 | + dataset.qy_data |
---|
| 504 | * dataset.qy_data) |
---|
[d72567e] | 505 | except: |
---|
| 506 | dataset.q_data = None |
---|
[ac370c5] | 507 | |
---|
| 508 | if dataset.data.ndim == 2: |
---|
| 509 | (n_rows, n_cols) = dataset.data.shape |
---|
[479799c] | 510 | dataset.y_bins = dataset.qy_data[0::n_cols] |
---|
[ac370c5] | 511 | dataset.x_bins = dataset.qx_data[:n_cols] |
---|
| 512 | dataset.data = dataset.data.flatten() |
---|
[9d786e5] | 513 | self.current_dataset = dataset |
---|
| 514 | self.send_to_output() |
---|
[d72567e] | 515 | |
---|
| 516 | for dataset in self.data1d: |
---|
[9d786e5] | 517 | self.current_dataset = dataset |
---|
| 518 | self.send_to_output() |
---|
[d72567e] | 519 | |
---|
[68aa210] | 520 | def add_data_set(self, key=""): |
---|
| 521 | """ |
---|
[082239e] | 522 | Adds the current_dataset to the list of outputs after preforming final |
---|
| 523 | processing on the data and then calls a private method to generate a |
---|
| 524 | new data set. |
---|
[68aa210] | 525 | |
---|
| 526 | :param key: NeXus group name for current tree level |
---|
| 527 | """ |
---|
[d72567e] | 528 | |
---|
| 529 | if self.current_datainfo and self.current_dataset: |
---|
[68aa210] | 530 | self.final_data_cleanup() |
---|
[d72567e] | 531 | self.data1d = [] |
---|
| 532 | self.data2d = [] |
---|
| 533 | self.current_datainfo = DataInfo() |
---|
[68aa210] | 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 |
---|
[18af6d2] | 553 | self.mask_name = "" |
---|
| 554 | self.i_name = "" |
---|
| 555 | self.i_node = "" |
---|
| 556 | self.q_name = [] |
---|
| 557 | self.q_uncertainties = "" |
---|
| 558 | self.q_resolutions = "" |
---|
| 559 | self.i_uncertainties = "" |
---|
[68aa210] | 560 | |
---|
[9e0dd49] | 561 | def _find_data_attributes(self, value): |
---|
[2651724] | 562 | """ |
---|
| 563 | A class to find the indices for Q, the name of the Qdev and Idev, and |
---|
| 564 | the name of the mask. |
---|
| 565 | :param value: SASdata/NXdata HDF5 Group |
---|
| 566 | """ |
---|
[9e0dd49] | 567 | attrs = value.attrs |
---|
| 568 | signal = attrs.get("signal") |
---|
[18af6d2] | 569 | i_axes = np.array(str(attrs.get("I_axes")).split(",")) |
---|
| 570 | q_indices = np.int_(attrs.get("Q_indices").split(",")) |
---|
[9e0dd49] | 571 | keys = value.keys() |
---|
[18af6d2] | 572 | self.mask_name = attrs.get("mask") |
---|
[2651724] | 573 | for val in q_indices: |
---|
| 574 | self.q_name.append(i_axes[val]) |
---|
[9e0dd49] | 575 | self.i_name = signal |
---|
[2651724] | 576 | self.i_node = value.get(self.i_name) |
---|
| 577 | for item in self.q_name: |
---|
| 578 | if item in keys: |
---|
| 579 | q_vals = value.get(item) |
---|
| 580 | self.q_uncertainties = q_vals.attrs.get("uncertainty") |
---|
| 581 | self.q_resolutions = q_vals.attrs.get("resolution") |
---|
[9e0dd49] | 582 | if self.i_name in keys: |
---|
| 583 | i_vals = value.get(self.i_name) |
---|
[2651724] | 584 | self.i_uncertainties = i_vals.attrs.get("uncertainty") |
---|
[9e0dd49] | 585 | |
---|
[d72567e] | 586 | def _find_intermediate(self, parent_list, basename=""): |
---|
[ad52d31] | 587 | """ |
---|
[082239e] | 588 | A private class used to find an entry by either using a direct key or |
---|
| 589 | knowing the approximate basename. |
---|
[ad52d31] | 590 | |
---|
[082239e] | 591 | :param parent_list: List of parents nodes in the HDF5 file |
---|
[d72567e] | 592 | :param basename: Approximate name of an entry to search for |
---|
[ad52d31] | 593 | :return: |
---|
| 594 | """ |
---|
[d72567e] | 595 | |
---|
| 596 | entry = False |
---|
| 597 | key_prog = re.compile(basename) |
---|
| 598 | top = self.raw_data |
---|
| 599 | for parent in parent_list: |
---|
| 600 | top = top.get(parent) |
---|
| 601 | for key in top.keys(): |
---|
[082239e] | 602 | if key_prog.match(key): |
---|
[d72567e] | 603 | entry = True |
---|
| 604 | break |
---|
[ad52d31] | 605 | return entry |
---|
| 606 | |
---|
[68aa210] | 607 | def _create_unique_key(self, dictionary, name, numb=0): |
---|
| 608 | """ |
---|
| 609 | Create a unique key value for any dictionary to prevent overwriting |
---|
| 610 | Recurses until a unique key value is found. |
---|
| 611 | |
---|
| 612 | :param dictionary: A dictionary with any number of entries |
---|
| 613 | :param name: The index of the item to be added to dictionary |
---|
| 614 | :param numb: The number to be appended to the name, starts at 0 |
---|
[d72567e] | 615 | :return: The new name for the dictionary entry |
---|
[68aa210] | 616 | """ |
---|
| 617 | if dictionary.get(name) is not None: |
---|
| 618 | numb += 1 |
---|
| 619 | name = name.split("_")[0] |
---|
| 620 | name += "_{0}".format(numb) |
---|
| 621 | name = self._create_unique_key(dictionary, name, numb) |
---|
[d398285] | 622 | return name |
---|
| 623 | |
---|
| 624 | def _get_unit(self, value): |
---|
| 625 | """ |
---|
| 626 | Find the unit for a particular value within the h5py dictionary |
---|
| 627 | |
---|
| 628 | :param value: attribute dictionary for a particular value set |
---|
[d72567e] | 629 | :return: unit for the value passed to the method |
---|
[d398285] | 630 | """ |
---|
[5c5e7fd] | 631 | unit = h5attr(value, u'units') |
---|
[54544637] | 632 | if unit is None: |
---|
[5c5e7fd] | 633 | unit = h5attr(value, u'unit') |
---|
[082239e] | 634 | # Convert the unit formats |
---|
[d398285] | 635 | if unit == "1/A": |
---|
| 636 | unit = "A^{-1}" |
---|
| 637 | elif unit == "1/cm": |
---|
| 638 | unit = "cm^{-1}" |
---|
[54ba66e] | 639 | return unit |
---|