[68aa210] | 1 | """ |
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| 2 | CanSAS 2D data reader for reading HDF5 formatted CanSAS files. |
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| 3 | """ |
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| 4 | |
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| 5 | import h5py |
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| 6 | import numpy as np |
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| 7 | import re |
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| 8 | import os |
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| 9 | import sys |
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| 10 | |
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[082239e] | 11 | from sas.sascalc.dataloader.data_info import plottable_1D, plottable_2D,\ |
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| 12 | Data1D, Data2D, DataInfo, Process, Aperture, Collimation, \ |
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| 13 | TransmissionSpectrum, Detector |
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[d72567e] | 14 | from sas.sascalc.dataloader.data_info import combine_data_info_with_plottable |
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| 15 | |
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[68aa210] | 16 | |
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| 17 | class Reader(): |
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| 18 | """ |
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[082239e] | 19 | A class for reading in CanSAS v2.0 data files. The existing iteration opens |
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| 20 | Mantid generated HDF5 formatted files with file extension .h5/.H5. Any |
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| 21 | number of data sets may be present within the file and any dimensionality |
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| 22 | of data may be used. Currently 1D and 2D SAS data sets are supported, but |
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| 23 | future implementations will include 1D and 2D SESANS data. |
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[d72567e] | 24 | |
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[082239e] | 25 | Any number of SASdata sets may be present in a SASentry and the data within |
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| 26 | can be either 1D I(Q) or 2D I(Qx, Qy). |
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[68aa210] | 27 | |
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[5e906207] | 28 | Also supports reading NXcanSAS formatted HDF5 files |
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| 29 | |
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[68aa210] | 30 | :Dependencies: |
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[d72567e] | 31 | The CanSAS HDF5 reader requires h5py => v2.5.0 or later. |
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[68aa210] | 32 | """ |
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| 33 | |
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[082239e] | 34 | # CanSAS version |
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[68aa210] | 35 | cansas_version = 2.0 |
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[082239e] | 36 | # Logged warnings or messages |
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[68aa210] | 37 | logging = None |
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[082239e] | 38 | # List of errors for the current data set |
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[68aa210] | 39 | errors = None |
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[082239e] | 40 | # Raw file contents to be processed |
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[68aa210] | 41 | raw_data = None |
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[082239e] | 42 | # Data info currently being read in |
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[d72567e] | 43 | current_datainfo = None |
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[082239e] | 44 | # SASdata set currently being read in |
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[68aa210] | 45 | current_dataset = None |
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[082239e] | 46 | # List of plottable1D objects that should be linked to the current_datainfo |
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[d72567e] | 47 | data1d = None |
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[082239e] | 48 | # List of plottable2D objects that should be linked to the current_datainfo |
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[d72567e] | 49 | data2d = None |
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[082239e] | 50 | # Data type name |
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[ad52d31] | 51 | type_name = "CanSAS 2.0" |
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[082239e] | 52 | # Wildcards |
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[ad52d31] | 53 | type = ["CanSAS 2.0 HDF5 Files (*.h5)|*.h5"] |
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[082239e] | 54 | # List of allowed extensions |
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[68aa210] | 55 | ext = ['.h5', '.H5'] |
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[082239e] | 56 | # Flag to bypass extension check |
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[54544637] | 57 | allow_all = True |
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[082239e] | 58 | # List of files to return |
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[68aa210] | 59 | output = None |
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| 60 | |
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| 61 | def read(self, filename): |
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| 62 | """ |
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[ad52d31] | 63 | This is the general read method that all SasView data_loaders must have. |
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[68aa210] | 64 | |
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| 65 | :param filename: A path for an HDF5 formatted CanSAS 2D data file. |
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[d72567e] | 66 | :return: List of Data1D/2D objects and/or a list of errors. |
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[68aa210] | 67 | """ |
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[082239e] | 68 | # Reinitialize when loading a new data file to reset all class variables |
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[d72567e] | 69 | self.reset_class_variables() |
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[082239e] | 70 | # Check that the file exists |
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[68aa210] | 71 | if os.path.isfile(filename): |
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| 72 | basename = os.path.basename(filename) |
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| 73 | _, extension = os.path.splitext(basename) |
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| 74 | # If the file type is not allowed, return empty list |
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| 75 | if extension in self.ext or self.allow_all: |
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[082239e] | 76 | # Load the data file |
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[68aa210] | 77 | self.raw_data = h5py.File(filename, 'r') |
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[082239e] | 78 | # Read in all child elements of top level SASroot |
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[d72567e] | 79 | self.read_children(self.raw_data, []) |
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[082239e] | 80 | # Add the last data set to the list of outputs |
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[68aa210] | 81 | self.add_data_set() |
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[082239e] | 82 | # Close the data file |
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[995f4eb] | 83 | self.raw_data.close() |
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[082239e] | 84 | # Return data set(s) |
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[68aa210] | 85 | return self.output |
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| 86 | |
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[d72567e] | 87 | def reset_class_variables(self): |
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| 88 | """ |
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| 89 | Create the reader object and define initial states for class variables |
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| 90 | """ |
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| 91 | self.current_datainfo = None |
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| 92 | self.current_dataset = None |
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| 93 | self.data1d = [] |
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| 94 | self.data2d = [] |
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| 95 | self.raw_data = None |
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| 96 | self.errors = set() |
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| 97 | self.logging = [] |
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| 98 | self.output = [] |
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| 99 | self.parent_class = u'' |
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| 100 | self.detector = Detector() |
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| 101 | self.collimation = Collimation() |
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| 102 | self.aperture = Aperture() |
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| 103 | self.process = Process() |
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| 104 | self.trans_spectrum = TransmissionSpectrum() |
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| 105 | |
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| 106 | def read_children(self, data, parent_list): |
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[68aa210] | 107 | """ |
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[ad52d31] | 108 | A recursive method for stepping through the hierarchical data file. |
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[68aa210] | 109 | |
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| 110 | :param data: h5py Group object of any kind |
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| 111 | :param parent: h5py Group parent name |
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| 112 | """ |
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| 113 | |
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[082239e] | 114 | # Loop through each element of the parent and process accordingly |
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[68aa210] | 115 | for key in data.keys(): |
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[082239e] | 116 | # Get all information for the current key |
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[68aa210] | 117 | value = data.get(key) |
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[d398285] | 118 | if value.attrs.get(u'canSAS_class') is not None: |
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| 119 | class_name = value.attrs.get(u'canSAS_class') |
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[0d93464] | 120 | elif value.attrs.get(u'NX_class') is not None: |
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[d398285] | 121 | class_name = value.attrs.get(u'NX_class') |
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[0d93464] | 122 | else: |
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| 123 | class_name = key |
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[68aa210] | 124 | if class_name is not None: |
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| 125 | class_prog = re.compile(class_name) |
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| 126 | else: |
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| 127 | class_prog = re.compile(value.name) |
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| 128 | |
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| 129 | if isinstance(value, h5py.Group): |
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[d72567e] | 130 | self.parent_class = class_name |
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| 131 | parent_list.append(key) |
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[082239e] | 132 | # If a new sasentry, store the current data sets and create |
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| 133 | # a fresh Data1D/2D object |
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[68aa210] | 134 | if class_prog.match(u'SASentry'): |
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| 135 | self.add_data_set(key) |
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[d72567e] | 136 | elif class_prog.match(u'SASdata'): |
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| 137 | self._initialize_new_data_set(parent_list) |
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[9e0dd49] | 138 | self._find_data_attributes(value) |
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[082239e] | 139 | # Recursion step to access data within the group |
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[d72567e] | 140 | self.read_children(value, parent_list) |
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| 141 | self.add_intermediate() |
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| 142 | parent_list.remove(key) |
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[68aa210] | 143 | |
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| 144 | elif isinstance(value, h5py.Dataset): |
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[082239e] | 145 | # If this is a dataset, store the data appropriately |
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[68aa210] | 146 | data_set = data[key][:] |
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[7bd6860a] | 147 | unit = self._get_unit(value) |
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[ac370c5] | 148 | |
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[68aa210] | 149 | for data_point in data_set: |
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[082239e] | 150 | # Top Level Meta Data |
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[68aa210] | 151 | if key == u'definition': |
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[d72567e] | 152 | self.current_datainfo.meta_data['reader'] = data_point |
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[0d93464] | 153 | # Run |
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[68aa210] | 154 | elif key == u'run': |
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[d72567e] | 155 | self.current_datainfo.run.append(data_point) |
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[be88076] | 156 | try: |
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| 157 | run_name = value.attrs['name'] |
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| 158 | run_dict = {data_point: run_name} |
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| 159 | self.current_datainfo.run_name = run_dict |
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| 160 | except: |
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| 161 | pass |
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[0d93464] | 162 | # Title |
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[68aa210] | 163 | elif key == u'title': |
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[d72567e] | 164 | self.current_datainfo.title = data_point |
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[0d93464] | 165 | # Note |
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[68aa210] | 166 | elif key == u'SASnote': |
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[d72567e] | 167 | self.current_datainfo.notes.append(data_point) |
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[082239e] | 168 | # Sample Information |
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[0d93464] | 169 | elif self.parent_class == u'SASsample': |
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| 170 | self.process_sample(data_point, key) |
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[082239e] | 171 | # Instrumental Information |
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[c94280c] | 172 | elif (key == u'name' |
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| 173 | and self.parent_class == u'SASinstrument'): |
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[d72567e] | 174 | self.current_datainfo.instrument = data_point |
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[0d93464] | 175 | # Detector |
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| 176 | elif self.parent_class == u'SASdetector': |
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| 177 | self.process_detector(data_point, key, unit) |
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| 178 | # Collimation |
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| 179 | elif self.parent_class == u'SAScollimation': |
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| 180 | self.process_collimation(data_point, key, unit) |
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| 181 | # Aperture |
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| 182 | elif self.parent_class == u'SASaperture': |
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| 183 | self.process_aperture(data_point, key) |
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[082239e] | 184 | # Process Information |
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[0d93464] | 185 | elif self.parent_class == u'SASprocess': # CanSAS 2.0 |
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| 186 | self.process_process(data_point, key) |
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[082239e] | 187 | # Source |
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[0d93464] | 188 | elif self.parent_class == u'SASsource': |
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| 189 | self.process_source(data_point, key, unit) |
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[082239e] | 190 | # Everything else goes in meta_data |
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[0d93464] | 191 | elif self.parent_class == u'SASdata': |
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| 192 | self.process_data_object(data_set, key, unit) |
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| 193 | break |
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| 194 | elif self.parent_class == u'SAStransmission_spectrum': |
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| 195 | self.process_trans_spectrum(data_set, key) |
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| 196 | break |
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[68aa210] | 197 | else: |
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[082239e] | 198 | new_key = self._create_unique_key( |
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| 199 | self.current_datainfo.meta_data, key) |
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[d72567e] | 200 | self.current_datainfo.meta_data[new_key] = data_point |
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[68aa210] | 201 | |
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| 202 | else: |
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[082239e] | 203 | # I don't know if this reachable code |
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[68aa210] | 204 | self.errors.add("ShouldNeverHappenException") |
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| 205 | |
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[0d93464] | 206 | def process_data_object(self, data_set, key, unit): |
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| 207 | """ |
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| 208 | SASdata processor method |
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| 209 | :param data_set: data from HDF5 file |
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| 210 | :param key: canSAS_class attribute |
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| 211 | :param unit: unit attribute |
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| 212 | """ |
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| 213 | # FIXME: check attributes of SASdata for Q, dQ, Mask, etc. |
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| 214 | if key == u'I': |
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| 215 | if isinstance(self.current_dataset, plottable_2D): |
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| 216 | self.current_dataset.data = data_set |
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| 217 | self.current_dataset.zaxis("Intensity", unit) |
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| 218 | else: |
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| 219 | self.current_dataset.y = data_set.flatten() |
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| 220 | self.current_dataset.yaxis("Intensity", unit) |
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| 221 | elif key == u'Idev': |
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| 222 | if isinstance(self.current_dataset, plottable_2D): |
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| 223 | self.current_dataset.err_data = data_set.flatten() |
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| 224 | else: |
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| 225 | self.current_dataset.dy = data_set.flatten() |
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| 226 | elif key == u'Q': |
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| 227 | self.current_dataset.xaxis("Q", unit) |
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| 228 | if isinstance(self.current_dataset, plottable_2D): |
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| 229 | self.current_dataset.q = data_set.flatten() |
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| 230 | else: |
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| 231 | self.current_dataset.x = data_set.flatten() |
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| 232 | elif key == u'Qdev': |
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| 233 | self.current_dataset.dx = data_set.flatten() |
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| 234 | elif key == u'dQw': |
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| 235 | self.current_dataset.dxw = data_set.flatten() |
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| 236 | elif key == u'dQl': |
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| 237 | self.current_dataset.dxl = data_set.flatten() |
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| 238 | elif key == u'Qy': |
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| 239 | self.current_dataset.yaxis("Q_y", unit) |
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| 240 | self.current_dataset.qy_data = data_set.flatten() |
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| 241 | elif key == u'Qydev': |
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| 242 | self.current_dataset.dqy_data = data_set.flatten() |
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| 243 | elif key == u'Qx': |
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| 244 | self.current_dataset.xaxis("Q_x", unit) |
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| 245 | self.current_dataset.qx_data = data_set.flatten() |
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| 246 | elif key == u'Qxdev': |
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| 247 | self.current_dataset.dqx_data = data_set.flatten() |
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| 248 | elif key == u'Mask': |
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| 249 | self.current_dataset.mask = data_set.flatten() |
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| 250 | elif key == u'wavelength': |
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| 251 | self.current_datainfo.source.wavelength = data_set[0] |
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| 252 | self.current_datainfo.source.wavelength_unit = unit |
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| 253 | |
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| 254 | def process_trans_spectrum(self, data_set, key): |
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| 255 | """ |
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| 256 | SAStransmission_spectrum processor |
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| 257 | :param data_set: data from HDF5 file |
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| 258 | :param key: canSAS_class attribute |
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| 259 | """ |
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| 260 | if key == u'T': |
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| 261 | self.trans_spectrum.transmission = data_set.flatten() |
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| 262 | elif key == u'Tdev': |
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| 263 | self.trans_spectrum.transmission_deviation = data_set.flatten() |
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| 264 | elif key == u'lambda': |
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| 265 | self.trans_spectrum.wavelength = data_set.flatten() |
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| 266 | |
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| 267 | def process_sample(self, data_point, key): |
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| 268 | """ |
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| 269 | SASsample processor |
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| 270 | :param data_point: Single point from an HDF5 data file |
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| 271 | :param key: class name data_point was taken from |
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| 272 | """ |
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| 273 | if key == u'Title': |
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| 274 | self.current_datainfo.sample.name = data_point |
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| 275 | elif key == u'name': |
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| 276 | self.current_datainfo.sample.name = data_point |
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| 277 | elif key == u'ID': |
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| 278 | self.current_datainfo.sample.name = data_point |
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| 279 | elif key == u'thickness': |
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| 280 | self.current_datainfo.sample.thickness = data_point |
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| 281 | elif key == u'temperature': |
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| 282 | self.current_datainfo.sample.temperature = data_point |
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| 283 | elif key == u'transmission': |
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| 284 | self.current_datainfo.sample.transmission = data_point |
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| 285 | elif key == u'x_position': |
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| 286 | self.current_datainfo.sample.position.x = data_point |
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| 287 | elif key == u'y_position': |
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| 288 | self.current_datainfo.sample.position.y = data_point |
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| 289 | elif key == u'pitch': |
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| 290 | self.current_datainfo.sample.orientation.x = data_point |
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| 291 | elif key == u'yaw': |
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| 292 | self.current_datainfo.sample.orientation.y = data_point |
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| 293 | elif key == u'roll': |
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| 294 | self.current_datainfo.sample.orientation.z = data_point |
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| 295 | elif key == u'details': |
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| 296 | self.current_datainfo.sample.details.append(data_point) |
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| 297 | |
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| 298 | def process_detector(self, data_point, key, unit): |
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| 299 | """ |
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| 300 | SASdetector processor |
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| 301 | :param data_point: Single point from an HDF5 data file |
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| 302 | :param key: class name data_point was taken from |
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| 303 | :param unit: unit attribute from data set |
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| 304 | """ |
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| 305 | if key == u'name': |
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| 306 | self.detector.name = data_point |
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| 307 | elif key == u'SDD': |
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| 308 | self.detector.distance = float(data_point) |
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| 309 | self.detector.distance_unit = unit |
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| 310 | elif key == u'slit_length': |
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| 311 | self.detector.slit_length = float(data_point) |
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| 312 | self.detector.slit_length_unit = unit |
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| 313 | elif key == u'x_position': |
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| 314 | self.detector.offset.x = float(data_point) |
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| 315 | self.detector.offset_unit = unit |
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| 316 | elif key == u'y_position': |
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| 317 | self.detector.offset.y = float(data_point) |
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| 318 | self.detector.offset_unit = unit |
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| 319 | elif key == u'pitch': |
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| 320 | self.detector.orientation.x = float(data_point) |
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| 321 | self.detector.orientation_unit = unit |
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| 322 | elif key == u'roll': |
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| 323 | self.detector.orientation.z = float(data_point) |
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| 324 | self.detector.orientation_unit = unit |
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| 325 | elif key == u'yaw': |
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| 326 | self.detector.orientation.y = float(data_point) |
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| 327 | self.detector.orientation_unit = unit |
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| 328 | elif key == u'beam_center_x': |
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| 329 | self.detector.beam_center.x = float(data_point) |
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| 330 | self.detector.beam_center_unit = unit |
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| 331 | elif key == u'beam_center_y': |
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| 332 | self.detector.beam_center.y = float(data_point) |
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| 333 | self.detector.beam_center_unit = unit |
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| 334 | elif key == u'x_pixel_size': |
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| 335 | self.detector.pixel_size.x = float(data_point) |
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| 336 | self.detector.pixel_size_unit = unit |
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| 337 | elif key == u'y_pixel_size': |
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| 338 | self.detector.pixel_size.y = float(data_point) |
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| 339 | self.detector.pixel_size_unit = unit |
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| 340 | |
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| 341 | def process_collimation(self, data_point, key, unit): |
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| 342 | """ |
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| 343 | SAScollimation processor |
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| 344 | :param data_point: Single point from an HDF5 data file |
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| 345 | :param key: class name data_point was taken from |
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| 346 | :param unit: unit attribute from data set |
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| 347 | """ |
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| 348 | if key == u'distance': |
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| 349 | self.collimation.length = data_point |
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| 350 | self.collimation.length_unit = unit |
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| 351 | elif key == u'name': |
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| 352 | self.collimation.name = data_point |
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| 353 | |
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| 354 | def process_aperture(self, data_point, key): |
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| 355 | """ |
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| 356 | SASaperture processor |
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| 357 | :param data_point: Single point from an HDF5 data file |
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| 358 | :param key: class name data_point was taken from |
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| 359 | """ |
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| 360 | if key == u'shape': |
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| 361 | self.aperture.shape = data_point |
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| 362 | elif key == u'x_gap': |
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| 363 | self.aperture.size.x = data_point |
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| 364 | elif key == u'y_gap': |
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| 365 | self.aperture.size.y = data_point |
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| 366 | |
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| 367 | def process_source(self, data_point, key, unit): |
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| 368 | """ |
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| 369 | SASsource processor |
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| 370 | :param data_point: Single point from an HDF5 data file |
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| 371 | :param key: class name data_point was taken from |
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| 372 | :param unit: unit attribute from data set |
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| 373 | """ |
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| 374 | if key == u'incident_wavelength': |
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| 375 | self.current_datainfo.source.wavelength = data_point |
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| 376 | self.current_datainfo.source.wavelength_unit = unit |
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| 377 | elif key == u'wavelength_max': |
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| 378 | self.current_datainfo.source.wavelength_max = data_point |
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| 379 | self.current_datainfo.source.wavelength_max_unit = unit |
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| 380 | elif key == u'wavelength_min': |
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| 381 | self.current_datainfo.source.wavelength_min = data_point |
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| 382 | self.current_datainfo.source.wavelength_min_unit = unit |
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| 383 | elif key == u'incident_wavelength_spread': |
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| 384 | self.current_datainfo.source.wavelength_spread = data_point |
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| 385 | self.current_datainfo.source.wavelength_spread_unit = unit |
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| 386 | elif key == u'beam_size_x': |
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| 387 | self.current_datainfo.source.beam_size.x = data_point |
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| 388 | self.current_datainfo.source.beam_size_unit = unit |
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| 389 | elif key == u'beam_size_y': |
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| 390 | self.current_datainfo.source.beam_size.y = data_point |
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| 391 | self.current_datainfo.source.beam_size_unit = unit |
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| 392 | elif key == u'beam_shape': |
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| 393 | self.current_datainfo.source.beam_shape = data_point |
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| 394 | elif key == u'radiation': |
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| 395 | self.current_datainfo.source.radiation = data_point |
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| 396 | |
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| 397 | def process_process(self, data_point, key): |
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| 398 | """ |
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| 399 | SASprocess processor |
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| 400 | :param data_point: Single point from an HDF5 data file |
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| 401 | :param key: class name data_point was taken from |
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| 402 | """ |
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| 403 | if key == u'Title': # CanSAS 2.0 |
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| 404 | self.process.name = data_point |
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| 405 | elif key == u'name': # NXcanSAS |
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| 406 | self.process.name = data_point |
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| 407 | elif key == u'description': |
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| 408 | self.process.description = data_point |
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| 409 | elif key == u'date': |
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| 410 | self.process.date = data_point |
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| 411 | elif key == u'term': |
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| 412 | self.process.term = data_point |
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| 413 | else: |
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| 414 | self.process.notes.append(data_point) |
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| 415 | |
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[d72567e] | 416 | def add_intermediate(self): |
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[ad52d31] | 417 | """ |
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[082239e] | 418 | This method stores any intermediate objects within the final data set |
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| 419 | after fully reading the set. |
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[ad52d31] | 420 | |
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[082239e] | 421 | :param parent: The NXclass name for the h5py Group object that just |
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| 422 | finished being processed |
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[ad52d31] | 423 | """ |
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| 424 | |
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[d72567e] | 425 | if self.parent_class == u'SASprocess': |
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| 426 | self.current_datainfo.process.append(self.process) |
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[ad52d31] | 427 | self.process = Process() |
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[d72567e] | 428 | elif self.parent_class == u'SASdetector': |
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| 429 | self.current_datainfo.detector.append(self.detector) |
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[ad52d31] | 430 | self.detector = Detector() |
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[d72567e] | 431 | elif self.parent_class == u'SAStransmission_spectrum': |
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| 432 | self.current_datainfo.trans_spectrum.append(self.trans_spectrum) |
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[ad52d31] | 433 | self.trans_spectrum = TransmissionSpectrum() |
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[d72567e] | 434 | elif self.parent_class == u'SAScollimation': |
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| 435 | self.current_datainfo.collimation.append(self.collimation) |
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[ad52d31] | 436 | self.collimation = Collimation() |
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[d72567e] | 437 | elif self.parent_class == u'SASaperture': |
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[ad52d31] | 438 | self.collimation.aperture.append(self.aperture) |
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| 439 | self.aperture = Aperture() |
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[d72567e] | 440 | elif self.parent_class == u'SASdata': |
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[082239e] | 441 | if isinstance(self.current_dataset, plottable_2D): |
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[d72567e] | 442 | self.data2d.append(self.current_dataset) |
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[082239e] | 443 | elif isinstance(self.current_dataset, plottable_1D): |
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[d72567e] | 444 | self.data1d.append(self.current_dataset) |
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[68aa210] | 445 | |
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| 446 | def final_data_cleanup(self): |
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| 447 | """ |
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[082239e] | 448 | Does some final cleanup and formatting on self.current_datainfo and |
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| 449 | all data1D and data2D objects and then combines the data and info into |
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| 450 | Data1D and Data2D objects |
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[68aa210] | 451 | """ |
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| 452 | |
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[082239e] | 453 | # Type cast data arrays to float64 |
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[d72567e] | 454 | if len(self.current_datainfo.trans_spectrum) > 0: |
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[ad52d31] | 455 | spectrum_list = [] |
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[d72567e] | 456 | for spectrum in self.current_datainfo.trans_spectrum: |
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[ad52d31] | 457 | spectrum.transmission = np.delete(spectrum.transmission, [0]) |
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| 458 | spectrum.transmission = spectrum.transmission.astype(np.float64) |
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[082239e] | 459 | spectrum.transmission_deviation = np.delete( |
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| 460 | spectrum.transmission_deviation, [0]) |
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| 461 | spectrum.transmission_deviation = \ |
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| 462 | spectrum.transmission_deviation.astype(np.float64) |
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[ad52d31] | 463 | spectrum.wavelength = np.delete(spectrum.wavelength, [0]) |
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| 464 | spectrum.wavelength = spectrum.wavelength.astype(np.float64) |
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[d72567e] | 465 | if len(spectrum.transmission) > 0: |
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| 466 | spectrum_list.append(spectrum) |
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| 467 | self.current_datainfo.trans_spectrum = spectrum_list |
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[68aa210] | 468 | |
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[082239e] | 469 | # Append errors to dataset and reset class errors |
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[d72567e] | 470 | self.current_datainfo.errors = self.errors |
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[68aa210] | 471 | self.errors.clear() |
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| 472 | |
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[082239e] | 473 | # Combine all plottables with datainfo and append each to output |
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| 474 | # Type cast data arrays to float64 and find min/max as appropriate |
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[d72567e] | 475 | for dataset in self.data2d: |
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| 476 | dataset.data = dataset.data.astype(np.float64) |
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| 477 | dataset.err_data = dataset.err_data.astype(np.float64) |
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| 478 | if dataset.qx_data is not None: |
---|
| 479 | dataset.xmin = np.min(dataset.qx_data) |
---|
| 480 | dataset.xmax = np.max(dataset.qx_data) |
---|
| 481 | dataset.qx_data = dataset.qx_data.astype(np.float64) |
---|
| 482 | if dataset.dqx_data is not None: |
---|
| 483 | dataset.dqx_data = dataset.dqx_data.astype(np.float64) |
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| 484 | if dataset.qy_data is not None: |
---|
| 485 | dataset.ymin = np.min(dataset.qy_data) |
---|
| 486 | dataset.ymax = np.max(dataset.qy_data) |
---|
| 487 | dataset.qy_data = dataset.qy_data.astype(np.float64) |
---|
| 488 | if dataset.dqy_data is not None: |
---|
| 489 | dataset.dqy_data = dataset.dqy_data.astype(np.float64) |
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| 490 | if dataset.q_data is not None: |
---|
| 491 | dataset.q_data = dataset.q_data.astype(np.float64) |
---|
| 492 | zeros = np.ones(dataset.data.size, dtype=bool) |
---|
| 493 | try: |
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[082239e] | 494 | for i in range(0, dataset.mask.size - 1): |
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[d72567e] | 495 | zeros[i] = dataset.mask[i] |
---|
| 496 | except: |
---|
| 497 | self.errors.add(sys.exc_value) |
---|
| 498 | dataset.mask = zeros |
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[082239e] | 499 | # Calculate the actual Q matrix |
---|
[d72567e] | 500 | try: |
---|
| 501 | if dataset.q_data.size <= 1: |
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[54544637] | 502 | dataset.q_data = np.sqrt(dataset.qx_data |
---|
| 503 | * dataset.qx_data |
---|
| 504 | + dataset.qy_data |
---|
| 505 | * dataset.qy_data) |
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[d72567e] | 506 | except: |
---|
| 507 | dataset.q_data = None |
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[ac370c5] | 508 | |
---|
| 509 | if dataset.data.ndim == 2: |
---|
| 510 | (n_rows, n_cols) = dataset.data.shape |
---|
[479799c] | 511 | dataset.y_bins = dataset.qy_data[0::n_cols] |
---|
[ac370c5] | 512 | dataset.x_bins = dataset.qx_data[:n_cols] |
---|
| 513 | dataset.data = dataset.data.flatten() |
---|
| 514 | |
---|
[082239e] | 515 | final_dataset = combine_data_info_with_plottable( |
---|
| 516 | dataset, self.current_datainfo) |
---|
[d72567e] | 517 | self.output.append(final_dataset) |
---|
| 518 | |
---|
| 519 | for dataset in self.data1d: |
---|
| 520 | if dataset.x is not None: |
---|
| 521 | dataset.x = dataset.x.astype(np.float64) |
---|
| 522 | dataset.xmin = np.min(dataset.x) |
---|
| 523 | dataset.xmax = np.max(dataset.x) |
---|
| 524 | if dataset.y is not None: |
---|
| 525 | dataset.y = dataset.y.astype(np.float64) |
---|
| 526 | dataset.ymin = np.min(dataset.y) |
---|
| 527 | dataset.ymax = np.max(dataset.y) |
---|
| 528 | if dataset.dx is not None: |
---|
| 529 | dataset.dx = dataset.dx.astype(np.float64) |
---|
| 530 | if dataset.dxl is not None: |
---|
| 531 | dataset.dxl = dataset.dxl.astype(np.float64) |
---|
| 532 | if dataset.dxw is not None: |
---|
| 533 | dataset.dxw = dataset.dxw.astype(np.float64) |
---|
| 534 | if dataset.dy is not None: |
---|
| 535 | dataset.dy = dataset.dy.astype(np.float64) |
---|
[082239e] | 536 | final_dataset = combine_data_info_with_plottable( |
---|
| 537 | dataset, self.current_datainfo) |
---|
[d72567e] | 538 | self.output.append(final_dataset) |
---|
| 539 | |
---|
[68aa210] | 540 | def add_data_set(self, key=""): |
---|
| 541 | """ |
---|
[082239e] | 542 | Adds the current_dataset to the list of outputs after preforming final |
---|
| 543 | processing on the data and then calls a private method to generate a |
---|
| 544 | new data set. |
---|
[68aa210] | 545 | |
---|
| 546 | :param key: NeXus group name for current tree level |
---|
| 547 | """ |
---|
[d72567e] | 548 | |
---|
| 549 | if self.current_datainfo and self.current_dataset: |
---|
[68aa210] | 550 | self.final_data_cleanup() |
---|
[d72567e] | 551 | self.data1d = [] |
---|
| 552 | self.data2d = [] |
---|
| 553 | self.current_datainfo = DataInfo() |
---|
[68aa210] | 554 | |
---|
[54ba66e] | 555 | |
---|
[082239e] | 556 | def _initialize_new_data_set(self, parent_list=None): |
---|
[68aa210] | 557 | """ |
---|
[082239e] | 558 | A private class method to generate a new 1D or 2D data object based on |
---|
| 559 | the type of data within the set. Outside methods should call |
---|
| 560 | add_data_set() to be sure any existing data is stored properly. |
---|
[68aa210] | 561 | |
---|
[d72567e] | 562 | :param parent_list: List of names of parent elements |
---|
[68aa210] | 563 | """ |
---|
[d72567e] | 564 | |
---|
| 565 | if parent_list is None: |
---|
| 566 | parent_list = [] |
---|
| 567 | if self._find_intermediate(parent_list, "Qx"): |
---|
| 568 | self.current_dataset = plottable_2D() |
---|
[68aa210] | 569 | else: |
---|
| 570 | x = np.array(0) |
---|
| 571 | y = np.array(0) |
---|
[d72567e] | 572 | self.current_dataset = plottable_1D(x, y) |
---|
| 573 | self.current_datainfo.filename = self.raw_data.filename |
---|
[68aa210] | 574 | |
---|
[9e0dd49] | 575 | def _find_data_attributes(self, value): |
---|
| 576 | attrs = value.attrs |
---|
| 577 | signal = attrs.get("signal") |
---|
| 578 | i_axes = attrs.get("I_axes") |
---|
| 579 | q_indices = attrs.get("Q_indices") |
---|
| 580 | mask = attrs.get("mask") |
---|
| 581 | mask_indices = attrs.get("Mask_indices") |
---|
| 582 | keys = value.keys() |
---|
| 583 | self.q_name = i_axes[q_indices] |
---|
| 584 | self.mask_name = mask[mask_indices] |
---|
| 585 | self.i_name = signal |
---|
| 586 | if self.q_name in keys: |
---|
| 587 | q_vals = value.get(self.q_name) |
---|
| 588 | self.q_uncertainties = q_vals.attrs.get("uncertainties") |
---|
| 589 | self.q_resolutions = q_vals.attrs.get("resolutions") |
---|
| 590 | if self.i_name in keys: |
---|
| 591 | i_vals = value.get(self.i_name) |
---|
| 592 | self.i_uncertainties = i_vals.attrs.get("uncertainties") |
---|
| 593 | |
---|
[d72567e] | 594 | def _find_intermediate(self, parent_list, basename=""): |
---|
[ad52d31] | 595 | """ |
---|
[082239e] | 596 | A private class used to find an entry by either using a direct key or |
---|
| 597 | knowing the approximate basename. |
---|
[ad52d31] | 598 | |
---|
[082239e] | 599 | :param parent_list: List of parents nodes in the HDF5 file |
---|
[d72567e] | 600 | :param basename: Approximate name of an entry to search for |
---|
[ad52d31] | 601 | :return: |
---|
| 602 | """ |
---|
[d72567e] | 603 | |
---|
| 604 | entry = False |
---|
| 605 | key_prog = re.compile(basename) |
---|
| 606 | top = self.raw_data |
---|
| 607 | for parent in parent_list: |
---|
| 608 | top = top.get(parent) |
---|
| 609 | for key in top.keys(): |
---|
[082239e] | 610 | if key_prog.match(key): |
---|
[d72567e] | 611 | entry = True |
---|
| 612 | break |
---|
[ad52d31] | 613 | return entry |
---|
| 614 | |
---|
[68aa210] | 615 | def _create_unique_key(self, dictionary, name, numb=0): |
---|
| 616 | """ |
---|
| 617 | Create a unique key value for any dictionary to prevent overwriting |
---|
| 618 | Recurses until a unique key value is found. |
---|
| 619 | |
---|
| 620 | :param dictionary: A dictionary with any number of entries |
---|
| 621 | :param name: The index of the item to be added to dictionary |
---|
| 622 | :param numb: The number to be appended to the name, starts at 0 |
---|
[d72567e] | 623 | :return: The new name for the dictionary entry |
---|
[68aa210] | 624 | """ |
---|
| 625 | if dictionary.get(name) is not None: |
---|
| 626 | numb += 1 |
---|
| 627 | name = name.split("_")[0] |
---|
| 628 | name += "_{0}".format(numb) |
---|
| 629 | name = self._create_unique_key(dictionary, name, numb) |
---|
[d398285] | 630 | return name |
---|
| 631 | |
---|
| 632 | def _get_unit(self, value): |
---|
| 633 | """ |
---|
| 634 | Find the unit for a particular value within the h5py dictionary |
---|
| 635 | |
---|
| 636 | :param value: attribute dictionary for a particular value set |
---|
[d72567e] | 637 | :return: unit for the value passed to the method |
---|
[d398285] | 638 | """ |
---|
| 639 | unit = value.attrs.get(u'units') |
---|
[54544637] | 640 | if unit is None: |
---|
[d398285] | 641 | unit = value.attrs.get(u'unit') |
---|
[082239e] | 642 | # Convert the unit formats |
---|
[d398285] | 643 | if unit == "1/A": |
---|
| 644 | unit = "A^{-1}" |
---|
| 645 | elif unit == "1/cm": |
---|
| 646 | unit = "cm^{-1}" |
---|
[54ba66e] | 647 | return unit |
---|