[68aa210] | 1 | """ |
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[802fc18] | 2 | NXcanSAS data reader for reading HDF5 formatted CanSAS files. |
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[68aa210] | 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 ..loader_exceptions import FileContentsException, DefaultReaderException |
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| 15 | from ..file_reader_base_class import FileReader, decode |
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[d72567e] | 16 | |
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[4fdcc65] | 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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[4fdcc65] | 21 | |
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[9d786e5] | 22 | class Reader(FileReader): |
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[68aa210] | 23 | """ |
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[802fc18] | 24 | A class for reading in NXcanSAS data files. The current implementation has |
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| 25 | been tested to load data generated by multiple facilities, all of which are |
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| 26 | known to produce NXcanSAS standards compliant data. Any number of data sets |
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| 27 | may be present within the file and any dimensionality of data may be used. |
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| 28 | Currently 1D and 2D SAS data sets are supported, but should be immediately |
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| 29 | extensible to SESANS data. |
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[d72567e] | 30 | |
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[802fc18] | 31 | Any number of SASdata groups may be present in a SASentry and the data |
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| 32 | within each SASdata group can be a single 1D I(Q), multi-framed 1D I(Q), |
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| 33 | 2D I(Qx, Qy) or multi-framed 2D I(Qx, Qy). |
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[5e906207] | 34 | |
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[68aa210] | 35 | :Dependencies: |
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[802fc18] | 36 | The NXcanSAS HDF5 reader requires h5py => v2.5.0 or later. |
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[68aa210] | 37 | """ |
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| 38 | |
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[082239e] | 39 | # CanSAS version |
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[68aa210] | 40 | cansas_version = 2.0 |
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[082239e] | 41 | # Data type name |
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[cf820f5] | 42 | type_name = "NXcanSAS" |
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[082239e] | 43 | # Wildcards |
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[cf820f5] | 44 | type = ["NXcanSAS HDF5 Files (*.h5)|*.h5|"] |
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[082239e] | 45 | # List of allowed extensions |
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[68aa210] | 46 | ext = ['.h5', '.H5'] |
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[082239e] | 47 | # Flag to bypass extension check |
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[54544637] | 48 | allow_all = True |
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[68aa210] | 49 | |
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[9d786e5] | 50 | def get_file_contents(self): |
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[68aa210] | 51 | """ |
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[ad52d31] | 52 | This is the general read method that all SasView data_loaders must have. |
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[68aa210] | 53 | |
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| 54 | :param filename: A path for an HDF5 formatted CanSAS 2D data file. |
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[d72567e] | 55 | :return: List of Data1D/2D objects and/or a list of errors. |
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[68aa210] | 56 | """ |
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[082239e] | 57 | # Reinitialize when loading a new data file to reset all class variables |
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[61f329f0] | 58 | self.reset_state() |
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[9d786e5] | 59 | |
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| 60 | filename = self.f_open.name |
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| 61 | self.f_open.close() # IO handled by h5py |
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| 62 | |
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[082239e] | 63 | # Check that the file exists |
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[68aa210] | 64 | if os.path.isfile(filename): |
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| 65 | basename = os.path.basename(filename) |
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| 66 | _, extension = os.path.splitext(basename) |
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| 67 | # If the file type is not allowed, return empty list |
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| 68 | if extension in self.ext or self.allow_all: |
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[082239e] | 69 | # Load the data file |
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[7f75a3f] | 70 | try: |
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| 71 | self.raw_data = h5py.File(filename, 'r') |
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| 72 | except Exception as e: |
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[8dec7e7] | 73 | if extension not in self.ext: |
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[4fdcc65] | 74 | msg = "NXcanSAS Reader could not load file {}".format( |
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| 75 | basename + extension) |
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[8dec7e7] | 76 | raise DefaultReaderException(msg) |
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| 77 | raise FileContentsException(e.message) |
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[dcb91cf] | 78 | try: |
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| 79 | # Read in all child elements of top level SASroot |
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| 80 | self.read_children(self.raw_data, []) |
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| 81 | # Add the last data set to the list of outputs |
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| 82 | self.add_data_set() |
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| 83 | except Exception as exc: |
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| 84 | raise FileContentsException(exc.message) |
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| 85 | finally: |
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| 86 | # Close the data file |
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| 87 | self.raw_data.close() |
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| 88 | |
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[4fdcc65] | 89 | for data_set in self.output: |
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| 90 | if isinstance(data_set, Data1D): |
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| 91 | if data_set.x.size < 5: |
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| 92 | exception = FileContentsException( |
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| 93 | "Fewer than 5 data points found.") |
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| 94 | data_set.errors.append(exception) |
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[68aa210] | 95 | |
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[61f329f0] | 96 | def reset_state(self): |
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[d72567e] | 97 | """ |
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| 98 | Create the reader object and define initial states for class variables |
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| 99 | """ |
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[61f329f0] | 100 | super(Reader, self).reset_state() |
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[d72567e] | 101 | self.data1d = [] |
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| 102 | self.data2d = [] |
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| 103 | self.raw_data = None |
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[802fc18] | 104 | self.multi_frame = False |
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| 105 | self.data_frames = [] |
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| 106 | self.data_uncertainty_frames = [] |
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[282bc3f] | 107 | self.errors = [] |
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[d72567e] | 108 | self.logging = [] |
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[b204004] | 109 | self.q_names = [] |
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[2651724] | 110 | self.mask_name = u'' |
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| 111 | self.i_name = u'' |
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| 112 | self.i_node = u'' |
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[b204004] | 113 | self.i_uncertainties_name = u'' |
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| 114 | self.q_uncertainty_names = [] |
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| 115 | self.q_resolution_names = [] |
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[d72567e] | 116 | self.parent_class = u'' |
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| 117 | self.detector = Detector() |
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| 118 | self.collimation = Collimation() |
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| 119 | self.aperture = Aperture() |
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| 120 | self.process = Process() |
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| 121 | self.trans_spectrum = TransmissionSpectrum() |
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| 122 | |
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| 123 | def read_children(self, data, parent_list): |
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[68aa210] | 124 | """ |
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[ad52d31] | 125 | A recursive method for stepping through the hierarchical data file. |
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[68aa210] | 126 | |
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| 127 | :param data: h5py Group object of any kind |
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| 128 | :param parent: h5py Group parent name |
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| 129 | """ |
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| 130 | |
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[082239e] | 131 | # Loop through each element of the parent and process accordingly |
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[68aa210] | 132 | for key in data.keys(): |
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[082239e] | 133 | # Get all information for the current key |
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[68aa210] | 134 | value = data.get(key) |
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[7b50f14] | 135 | class_name = h5attr(value, u'canSAS_class') |
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[2ca5d57b] | 136 | if isinstance(class_name, (list, tuple, np.ndarray)): |
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| 137 | class_name = class_name[0] |
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[7b50f14] | 138 | if class_name is None: |
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[5c5e7fd] | 139 | class_name = h5attr(value, u'NX_class') |
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[68aa210] | 140 | if class_name is not None: |
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| 141 | class_prog = re.compile(class_name) |
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| 142 | else: |
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| 143 | class_prog = re.compile(value.name) |
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| 144 | |
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| 145 | if isinstance(value, h5py.Group): |
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[c9ecd1b] | 146 | # Set parent class before recursion |
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[8f882fe] | 147 | last_parent_class = self.parent_class |
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[d72567e] | 148 | self.parent_class = class_name |
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| 149 | parent_list.append(key) |
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[082239e] | 150 | # If a new sasentry, store the current data sets and create |
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| 151 | # a fresh Data1D/2D object |
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[68aa210] | 152 | if class_prog.match(u'SASentry'): |
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| 153 | self.add_data_set(key) |
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[d72567e] | 154 | elif class_prog.match(u'SASdata'): |
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[9e0dd49] | 155 | self._find_data_attributes(value) |
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[802fc18] | 156 | self._initialize_new_data_set(value) |
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[082239e] | 157 | # Recursion step to access data within the group |
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[d72567e] | 158 | self.read_children(value, parent_list) |
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| 159 | self.add_intermediate() |
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[8f882fe] | 160 | # Reset parent class when returning from recursive method |
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| 161 | self.parent_class = last_parent_class |
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[d72567e] | 162 | parent_list.remove(key) |
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[68aa210] | 163 | |
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| 164 | elif isinstance(value, h5py.Dataset): |
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[082239e] | 165 | # If this is a dataset, store the data appropriately |
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[9dc1500] | 166 | data_set = value.value |
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[7bd6860a] | 167 | unit = self._get_unit(value) |
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[ac370c5] | 168 | |
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[68aa210] | 169 | for data_point in data_set: |
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[2b538cd] | 170 | if isinstance(data_point, np.ndarray): |
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| 171 | if data_point.dtype.char == 'S': |
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| 172 | data_point = decode(bytes(data_point)) |
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| 173 | else: |
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| 174 | data_point = decode(data_point) |
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[082239e] | 175 | # Top Level Meta Data |
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[68aa210] | 176 | if key == u'definition': |
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[c1dc994] | 177 | if isinstance(data_set, basestring): |
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| 178 | self.current_datainfo.meta_data['reader'] = data_set |
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| 179 | break |
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| 180 | else: |
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| 181 | self.current_datainfo.meta_data[ |
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| 182 | 'reader'] = data_point |
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[0d93464] | 183 | # Run |
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[68aa210] | 184 | elif key == u'run': |
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[be88076] | 185 | try: |
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[5c5e7fd] | 186 | run_name = h5attr(value, 'name') |
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[dfcdbf8] | 187 | run_dict = {data_set: run_name} |
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[be88076] | 188 | self.current_datainfo.run_name = run_dict |
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[7b50f14] | 189 | except Exception: |
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[be88076] | 190 | pass |
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[c1dc994] | 191 | if isinstance(data_set, basestring): |
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| 192 | self.current_datainfo.run.append(data_set) |
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| 193 | break |
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| 194 | else: |
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| 195 | self.current_datainfo.run.append(data_point) |
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[0d93464] | 196 | # Title |
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[68aa210] | 197 | elif key == u'title': |
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[c1dc994] | 198 | if isinstance(data_set, basestring): |
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| 199 | self.current_datainfo.title = data_set |
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| 200 | break |
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| 201 | else: |
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| 202 | self.current_datainfo.title = data_point |
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[0d93464] | 203 | # Note |
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[68aa210] | 204 | elif key == u'SASnote': |
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[dfcdbf8] | 205 | self.current_datainfo.notes.append(data_set) |
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| 206 | break |
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[082239e] | 207 | # Sample Information |
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[0d93464] | 208 | elif self.parent_class == u'SASsample': |
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| 209 | self.process_sample(data_point, key) |
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[082239e] | 210 | # Instrumental Information |
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[c94280c] | 211 | elif (key == u'name' |
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| 212 | and self.parent_class == u'SASinstrument'): |
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[d72567e] | 213 | self.current_datainfo.instrument = data_point |
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[0d93464] | 214 | # Detector |
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| 215 | elif self.parent_class == u'SASdetector': |
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| 216 | self.process_detector(data_point, key, unit) |
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| 217 | # Collimation |
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| 218 | elif self.parent_class == u'SAScollimation': |
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| 219 | self.process_collimation(data_point, key, unit) |
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| 220 | # Aperture |
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| 221 | elif self.parent_class == u'SASaperture': |
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| 222 | self.process_aperture(data_point, key) |
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[082239e] | 223 | # Process Information |
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[0d93464] | 224 | elif self.parent_class == u'SASprocess': # CanSAS 2.0 |
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| 225 | self.process_process(data_point, key) |
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[082239e] | 226 | # Source |
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[0d93464] | 227 | elif self.parent_class == u'SASsource': |
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| 228 | self.process_source(data_point, key, unit) |
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[082239e] | 229 | # Everything else goes in meta_data |
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[0d93464] | 230 | elif self.parent_class == u'SASdata': |
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[96d06a4] | 231 | if isinstance(self.current_dataset, plottable_2D): |
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| 232 | self.process_2d_data_object(data_set, key, unit) |
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| 233 | else: |
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| 234 | self.process_1d_data_object(data_set, key, unit) |
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| 235 | |
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[0d93464] | 236 | break |
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| 237 | elif self.parent_class == u'SAStransmission_spectrum': |
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| 238 | self.process_trans_spectrum(data_set, key) |
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| 239 | break |
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[68aa210] | 240 | else: |
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[082239e] | 241 | new_key = self._create_unique_key( |
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| 242 | self.current_datainfo.meta_data, key) |
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[d72567e] | 243 | self.current_datainfo.meta_data[new_key] = data_point |
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[68aa210] | 244 | |
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| 245 | else: |
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[082239e] | 246 | # I don't know if this reachable code |
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[282bc3f] | 247 | self.errors.append("ShouldNeverHappenException") |
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[68aa210] | 248 | |
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[96d06a4] | 249 | def process_1d_data_object(self, data_set, key, unit): |
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[0d93464] | 250 | """ |
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[96d06a4] | 251 | SASdata processor method for 1d data items |
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[0d93464] | 252 | :param data_set: data from HDF5 file |
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| 253 | :param key: canSAS_class attribute |
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| 254 | :param unit: unit attribute |
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| 255 | """ |
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[2651724] | 256 | if key == self.i_name: |
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[802fc18] | 257 | if self.multi_frame: |
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| 258 | for x in range(0, data_set.shape[0]): |
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| 259 | self.data_frames.append(data_set[x].flatten()) |
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| 260 | else: |
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| 261 | self.current_dataset.y = data_set.flatten() |
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| 262 | self.current_dataset.yaxis("Intensity", unit) |
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[b204004] | 263 | elif key == self.i_uncertainties_name: |
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[802fc18] | 264 | if self.multi_frame: |
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| 265 | for x in range(0, data_set.shape[0]): |
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| 266 | self.data_uncertainty_frames.append(data_set[x].flatten()) |
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[96d06a4] | 267 | self.current_dataset.dy = data_set.flatten() |
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[b204004] | 268 | elif key in self.q_names: |
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[0d93464] | 269 | self.current_dataset.xaxis("Q", unit) |
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[96d06a4] | 270 | self.current_dataset.x = data_set.flatten() |
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[b204004] | 271 | elif key in self.q_resolution_names: |
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| 272 | if (len(self.q_resolution_names) > 1 |
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| 273 | and np.where(self.q_resolution_names == key)[0] == 0): |
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[2651724] | 274 | self.current_dataset.dxw = data_set.flatten() |
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[b204004] | 275 | elif (len(self.q_resolution_names) > 1 |
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| 276 | and np.where(self.q_resolution_names == key)[0] == 1): |
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| 277 | self.current_dataset.dxl = data_set.flatten() |
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| 278 | else: |
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| 279 | self.current_dataset.dx = data_set.flatten() |
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| 280 | elif key in self.q_uncertainty_names: |
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| 281 | if (len(self.q_uncertainty_names) > 1 |
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| 282 | and np.where(self.q_uncertainty_names == key)[0] == 0): |
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| 283 | self.current_dataset.dxw = data_set.flatten() |
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| 284 | elif (len(self.q_uncertainty_names) > 1 |
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| 285 | and np.where(self.q_uncertainty_names == key)[0] == 1): |
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[2651724] | 286 | self.current_dataset.dxl = data_set.flatten() |
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| 287 | else: |
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| 288 | self.current_dataset.dx = data_set.flatten() |
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[96d06a4] | 289 | elif key == self.mask_name: |
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| 290 | self.current_dataset.mask = data_set.flatten() |
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| 291 | elif key == u'wavelength': |
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| 292 | self.current_datainfo.source.wavelength = data_set[0] |
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| 293 | self.current_datainfo.source.wavelength_unit = unit |
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| 294 | |
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| 295 | def process_2d_data_object(self, data_set, key, unit): |
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| 296 | if key == self.i_name: |
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[4fdcc65] | 297 | self.current_dataset.data = data_set |
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[96d06a4] | 298 | self.current_dataset.zaxis("Intensity", unit) |
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[b204004] | 299 | elif key == self.i_uncertainties_name: |
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[96d06a4] | 300 | self.current_dataset.err_data = data_set.flatten() |
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[b204004] | 301 | elif key in self.q_names: |
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[c2525bf] | 302 | self.current_dataset.xaxis("Q_x", unit) |
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| 303 | self.current_dataset.yaxis("Q_y", unit) |
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[b204004] | 304 | if self.q_names[0] == self.q_names[1]: |
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[c2525bf] | 305 | # All q data in a single array |
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[4fdcc65] | 306 | self.current_dataset.qx_data = data_set[0] |
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| 307 | self.current_dataset.qy_data = data_set[1] |
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[b204004] | 308 | elif self.q_names.index(key) == 0: |
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[4fdcc65] | 309 | self.current_dataset.qx_data = data_set |
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[b204004] | 310 | elif self.q_names.index(key) == 1: |
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[4fdcc65] | 311 | self.current_dataset.qy_data = data_set |
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[b204004] | 312 | elif key in self.q_uncertainty_names or key in self.q_resolution_names: |
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| 313 | if ((self.q_uncertainty_names[0] == self.q_uncertainty_names[1]) or |
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| 314 | (self.q_resolution_names[0] == self.q_resolution_names[1])): |
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[c2525bf] | 315 | # All q data in a single array |
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| 316 | self.current_dataset.dqx_data = data_set[0].flatten() |
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| 317 | self.current_dataset.dqy_data = data_set[1].flatten() |
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[b204004] | 318 | elif (self.q_uncertainty_names.index(key) == 0 or |
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| 319 | self.q_resolution_names.index(key) == 0): |
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[c2525bf] | 320 | self.current_dataset.dqx_data = data_set.flatten() |
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[b204004] | 321 | elif (self.q_uncertainty_names.index(key) == 1 or |
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| 322 | self.q_resolution_names.index(key) == 1): |
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[c2525bf] | 323 | self.current_dataset.dqy_data = data_set.flatten() |
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| 324 | self.current_dataset.yaxis("Q_y", unit) |
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| 325 | elif key == self.mask_name: |
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| 326 | self.current_dataset.mask = data_set.flatten() |
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[0d93464] | 327 | elif key == u'Qy': |
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| 328 | self.current_dataset.yaxis("Q_y", unit) |
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| 329 | self.current_dataset.qy_data = data_set.flatten() |
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| 330 | elif key == u'Qydev': |
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| 331 | self.current_dataset.dqy_data = data_set.flatten() |
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| 332 | elif key == u'Qx': |
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| 333 | self.current_dataset.xaxis("Q_x", unit) |
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| 334 | self.current_dataset.qx_data = data_set.flatten() |
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| 335 | elif key == u'Qxdev': |
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| 336 | self.current_dataset.dqx_data = data_set.flatten() |
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| 337 | |
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| 338 | def process_trans_spectrum(self, data_set, key): |
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| 339 | """ |
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| 340 | SAStransmission_spectrum processor |
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| 341 | :param data_set: data from HDF5 file |
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| 342 | :param key: canSAS_class attribute |
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| 343 | """ |
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| 344 | if key == u'T': |
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| 345 | self.trans_spectrum.transmission = data_set.flatten() |
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| 346 | elif key == u'Tdev': |
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| 347 | self.trans_spectrum.transmission_deviation = data_set.flatten() |
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| 348 | elif key == u'lambda': |
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| 349 | self.trans_spectrum.wavelength = data_set.flatten() |
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| 350 | |
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| 351 | def process_sample(self, data_point, key): |
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| 352 | """ |
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| 353 | SASsample processor |
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| 354 | :param data_point: Single point from an HDF5 data file |
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| 355 | :param key: class name data_point was taken from |
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| 356 | """ |
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| 357 | if key == u'Title': |
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| 358 | self.current_datainfo.sample.name = data_point |
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| 359 | elif key == u'name': |
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| 360 | self.current_datainfo.sample.name = data_point |
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| 361 | elif key == u'ID': |
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| 362 | self.current_datainfo.sample.name = data_point |
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| 363 | elif key == u'thickness': |
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| 364 | self.current_datainfo.sample.thickness = data_point |
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| 365 | elif key == u'temperature': |
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| 366 | self.current_datainfo.sample.temperature = data_point |
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| 367 | elif key == u'transmission': |
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| 368 | self.current_datainfo.sample.transmission = data_point |
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| 369 | elif key == u'x_position': |
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| 370 | self.current_datainfo.sample.position.x = data_point |
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| 371 | elif key == u'y_position': |
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| 372 | self.current_datainfo.sample.position.y = data_point |
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| 373 | elif key == u'pitch': |
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| 374 | self.current_datainfo.sample.orientation.x = data_point |
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| 375 | elif key == u'yaw': |
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| 376 | self.current_datainfo.sample.orientation.y = data_point |
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| 377 | elif key == u'roll': |
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| 378 | self.current_datainfo.sample.orientation.z = data_point |
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| 379 | elif key == u'details': |
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| 380 | self.current_datainfo.sample.details.append(data_point) |
---|
| 381 | |
---|
| 382 | def process_detector(self, data_point, key, unit): |
---|
| 383 | """ |
---|
| 384 | SASdetector processor |
---|
| 385 | :param data_point: Single point from an HDF5 data file |
---|
| 386 | :param key: class name data_point was taken from |
---|
| 387 | :param unit: unit attribute from data set |
---|
| 388 | """ |
---|
| 389 | if key == u'name': |
---|
| 390 | self.detector.name = data_point |
---|
| 391 | elif key == u'SDD': |
---|
| 392 | self.detector.distance = float(data_point) |
---|
| 393 | self.detector.distance_unit = unit |
---|
| 394 | elif key == u'slit_length': |
---|
| 395 | self.detector.slit_length = float(data_point) |
---|
| 396 | self.detector.slit_length_unit = unit |
---|
| 397 | elif key == u'x_position': |
---|
| 398 | self.detector.offset.x = float(data_point) |
---|
| 399 | self.detector.offset_unit = unit |
---|
| 400 | elif key == u'y_position': |
---|
| 401 | self.detector.offset.y = float(data_point) |
---|
| 402 | self.detector.offset_unit = unit |
---|
| 403 | elif key == u'pitch': |
---|
| 404 | self.detector.orientation.x = float(data_point) |
---|
| 405 | self.detector.orientation_unit = unit |
---|
| 406 | elif key == u'roll': |
---|
| 407 | self.detector.orientation.z = float(data_point) |
---|
| 408 | self.detector.orientation_unit = unit |
---|
| 409 | elif key == u'yaw': |
---|
| 410 | self.detector.orientation.y = float(data_point) |
---|
| 411 | self.detector.orientation_unit = unit |
---|
| 412 | elif key == u'beam_center_x': |
---|
| 413 | self.detector.beam_center.x = float(data_point) |
---|
| 414 | self.detector.beam_center_unit = unit |
---|
| 415 | elif key == u'beam_center_y': |
---|
| 416 | self.detector.beam_center.y = float(data_point) |
---|
| 417 | self.detector.beam_center_unit = unit |
---|
| 418 | elif key == u'x_pixel_size': |
---|
| 419 | self.detector.pixel_size.x = float(data_point) |
---|
| 420 | self.detector.pixel_size_unit = unit |
---|
| 421 | elif key == u'y_pixel_size': |
---|
| 422 | self.detector.pixel_size.y = float(data_point) |
---|
| 423 | self.detector.pixel_size_unit = unit |
---|
| 424 | |
---|
| 425 | def process_collimation(self, data_point, key, unit): |
---|
| 426 | """ |
---|
| 427 | SAScollimation processor |
---|
| 428 | :param data_point: Single point from an HDF5 data file |
---|
| 429 | :param key: class name data_point was taken from |
---|
| 430 | :param unit: unit attribute from data set |
---|
| 431 | """ |
---|
| 432 | if key == u'distance': |
---|
| 433 | self.collimation.length = data_point |
---|
| 434 | self.collimation.length_unit = unit |
---|
| 435 | elif key == u'name': |
---|
| 436 | self.collimation.name = data_point |
---|
| 437 | |
---|
| 438 | def process_aperture(self, data_point, key): |
---|
| 439 | """ |
---|
| 440 | SASaperture processor |
---|
| 441 | :param data_point: Single point from an HDF5 data file |
---|
| 442 | :param key: class name data_point was taken from |
---|
| 443 | """ |
---|
| 444 | if key == u'shape': |
---|
| 445 | self.aperture.shape = data_point |
---|
| 446 | elif key == u'x_gap': |
---|
| 447 | self.aperture.size.x = data_point |
---|
| 448 | elif key == u'y_gap': |
---|
| 449 | self.aperture.size.y = data_point |
---|
| 450 | |
---|
| 451 | def process_source(self, data_point, key, unit): |
---|
| 452 | """ |
---|
| 453 | SASsource processor |
---|
| 454 | :param data_point: Single point from an HDF5 data file |
---|
| 455 | :param key: class name data_point was taken from |
---|
| 456 | :param unit: unit attribute from data set |
---|
| 457 | """ |
---|
| 458 | if key == u'incident_wavelength': |
---|
| 459 | self.current_datainfo.source.wavelength = data_point |
---|
| 460 | self.current_datainfo.source.wavelength_unit = unit |
---|
| 461 | elif key == u'wavelength_max': |
---|
| 462 | self.current_datainfo.source.wavelength_max = data_point |
---|
| 463 | self.current_datainfo.source.wavelength_max_unit = unit |
---|
| 464 | elif key == u'wavelength_min': |
---|
| 465 | self.current_datainfo.source.wavelength_min = data_point |
---|
| 466 | self.current_datainfo.source.wavelength_min_unit = unit |
---|
| 467 | elif key == u'incident_wavelength_spread': |
---|
| 468 | self.current_datainfo.source.wavelength_spread = data_point |
---|
| 469 | self.current_datainfo.source.wavelength_spread_unit = unit |
---|
| 470 | elif key == u'beam_size_x': |
---|
| 471 | self.current_datainfo.source.beam_size.x = data_point |
---|
| 472 | self.current_datainfo.source.beam_size_unit = unit |
---|
| 473 | elif key == u'beam_size_y': |
---|
| 474 | self.current_datainfo.source.beam_size.y = data_point |
---|
| 475 | self.current_datainfo.source.beam_size_unit = unit |
---|
| 476 | elif key == u'beam_shape': |
---|
| 477 | self.current_datainfo.source.beam_shape = data_point |
---|
| 478 | elif key == u'radiation': |
---|
| 479 | self.current_datainfo.source.radiation = data_point |
---|
| 480 | |
---|
| 481 | def process_process(self, data_point, key): |
---|
| 482 | """ |
---|
| 483 | SASprocess processor |
---|
| 484 | :param data_point: Single point from an HDF5 data file |
---|
| 485 | :param key: class name data_point was taken from |
---|
| 486 | """ |
---|
[ac38ab4] | 487 | term_match = re.compile(u'^term[0-9]+$') |
---|
[0d93464] | 488 | if key == u'Title': # CanSAS 2.0 |
---|
| 489 | self.process.name = data_point |
---|
| 490 | elif key == u'name': # NXcanSAS |
---|
| 491 | self.process.name = data_point |
---|
| 492 | elif key == u'description': |
---|
| 493 | self.process.description = data_point |
---|
| 494 | elif key == u'date': |
---|
| 495 | self.process.date = data_point |
---|
[ac38ab4] | 496 | elif term_match.match(key): |
---|
| 497 | self.process.term.append(data_point) |
---|
[0d93464] | 498 | else: |
---|
| 499 | self.process.notes.append(data_point) |
---|
| 500 | |
---|
[d72567e] | 501 | def add_intermediate(self): |
---|
[ad52d31] | 502 | """ |
---|
[082239e] | 503 | This method stores any intermediate objects within the final data set |
---|
| 504 | after fully reading the set. |
---|
[ad52d31] | 505 | |
---|
[082239e] | 506 | :param parent: The NXclass name for the h5py Group object that just |
---|
| 507 | finished being processed |
---|
[ad52d31] | 508 | """ |
---|
| 509 | |
---|
[d72567e] | 510 | if self.parent_class == u'SASprocess': |
---|
| 511 | self.current_datainfo.process.append(self.process) |
---|
[ad52d31] | 512 | self.process = Process() |
---|
[d72567e] | 513 | elif self.parent_class == u'SASdetector': |
---|
| 514 | self.current_datainfo.detector.append(self.detector) |
---|
[ad52d31] | 515 | self.detector = Detector() |
---|
[d72567e] | 516 | elif self.parent_class == u'SAStransmission_spectrum': |
---|
| 517 | self.current_datainfo.trans_spectrum.append(self.trans_spectrum) |
---|
[ad52d31] | 518 | self.trans_spectrum = TransmissionSpectrum() |
---|
[d72567e] | 519 | elif self.parent_class == u'SAScollimation': |
---|
| 520 | self.current_datainfo.collimation.append(self.collimation) |
---|
[ad52d31] | 521 | self.collimation = Collimation() |
---|
[d72567e] | 522 | elif self.parent_class == u'SASaperture': |
---|
[ad52d31] | 523 | self.collimation.aperture.append(self.aperture) |
---|
| 524 | self.aperture = Aperture() |
---|
[d72567e] | 525 | elif self.parent_class == u'SASdata': |
---|
[082239e] | 526 | if isinstance(self.current_dataset, plottable_2D): |
---|
[d72567e] | 527 | self.data2d.append(self.current_dataset) |
---|
[082239e] | 528 | elif isinstance(self.current_dataset, plottable_1D): |
---|
[802fc18] | 529 | if self.multi_frame: |
---|
[a165bee] | 530 | for x in range(0, len(self.data_frames)): |
---|
[802fc18] | 531 | self.current_dataset.y = self.data_frames[x] |
---|
| 532 | if len(self.data_uncertainty_frames) > x: |
---|
| 533 | self.current_dataset.dy = \ |
---|
| 534 | self.data_uncertainty_frames[x] |
---|
| 535 | self.data1d.append(self.current_dataset) |
---|
| 536 | else: |
---|
| 537 | self.data1d.append(self.current_dataset) |
---|
[68aa210] | 538 | |
---|
| 539 | def final_data_cleanup(self): |
---|
| 540 | """ |
---|
[082239e] | 541 | Does some final cleanup and formatting on self.current_datainfo and |
---|
| 542 | all data1D and data2D objects and then combines the data and info into |
---|
| 543 | Data1D and Data2D objects |
---|
[68aa210] | 544 | """ |
---|
[082239e] | 545 | # Type cast data arrays to float64 |
---|
[d72567e] | 546 | if len(self.current_datainfo.trans_spectrum) > 0: |
---|
[ad52d31] | 547 | spectrum_list = [] |
---|
[d72567e] | 548 | for spectrum in self.current_datainfo.trans_spectrum: |
---|
[ad52d31] | 549 | spectrum.transmission = spectrum.transmission.astype(np.float64) |
---|
[082239e] | 550 | spectrum.transmission_deviation = \ |
---|
| 551 | spectrum.transmission_deviation.astype(np.float64) |
---|
[ad52d31] | 552 | spectrum.wavelength = spectrum.wavelength.astype(np.float64) |
---|
[d72567e] | 553 | if len(spectrum.transmission) > 0: |
---|
| 554 | spectrum_list.append(spectrum) |
---|
| 555 | self.current_datainfo.trans_spectrum = spectrum_list |
---|
[68aa210] | 556 | |
---|
[082239e] | 557 | # Append errors to dataset and reset class errors |
---|
[d72567e] | 558 | self.current_datainfo.errors = self.errors |
---|
[282bc3f] | 559 | self.errors = [] |
---|
[68aa210] | 560 | |
---|
[082239e] | 561 | # Combine all plottables with datainfo and append each to output |
---|
| 562 | # Type cast data arrays to float64 and find min/max as appropriate |
---|
[d72567e] | 563 | for dataset in self.data2d: |
---|
| 564 | zeros = np.ones(dataset.data.size, dtype=bool) |
---|
| 565 | try: |
---|
[082239e] | 566 | for i in range(0, dataset.mask.size - 1): |
---|
[d72567e] | 567 | zeros[i] = dataset.mask[i] |
---|
| 568 | except: |
---|
[282bc3f] | 569 | self.errors.append(sys.exc_value) |
---|
[d72567e] | 570 | dataset.mask = zeros |
---|
[082239e] | 571 | # Calculate the actual Q matrix |
---|
[d72567e] | 572 | try: |
---|
| 573 | if dataset.q_data.size <= 1: |
---|
[54544637] | 574 | dataset.q_data = np.sqrt(dataset.qx_data |
---|
| 575 | * dataset.qx_data |
---|
| 576 | + dataset.qy_data |
---|
| 577 | * dataset.qy_data) |
---|
[d72567e] | 578 | except: |
---|
| 579 | dataset.q_data = None |
---|
[ac370c5] | 580 | |
---|
| 581 | if dataset.data.ndim == 2: |
---|
| 582 | (n_rows, n_cols) = dataset.data.shape |
---|
[4fdcc65] | 583 | flat_qy = dataset.qy_data[0::n_cols].flatten() |
---|
[b204004] | 584 | # For 2D arrays of Qx and Qy, the Q value should be constant |
---|
| 585 | # along each row -OR- each column. The direction is not |
---|
| 586 | # specified in the NXcanSAS standard. |
---|
[4fdcc65] | 587 | if flat_qy[0] == flat_qy[1]: |
---|
| 588 | flat_qy = np.transpose(dataset.qy_data)[0::n_cols].flatten() |
---|
| 589 | dataset.y_bins = np.unique(flat_qy) |
---|
| 590 | flat_qx = dataset.qx_data[0::n_rows].flatten() |
---|
[b204004] | 591 | # For 2D arrays of Qx and Qy, the Q value should be constant |
---|
| 592 | # along each row -OR- each column. The direction is not |
---|
| 593 | # specified in the NXcanSAS standard. |
---|
[4fdcc65] | 594 | if flat_qx[0] == flat_qx[1]: |
---|
| 595 | flat_qx = np.transpose(dataset.qx_data)[0::n_rows].flatten() |
---|
| 596 | dataset.x_bins = np.unique(flat_qx) |
---|
[ac370c5] | 597 | dataset.data = dataset.data.flatten() |
---|
[4fdcc65] | 598 | dataset.qx_data = dataset.qx_data.flatten() |
---|
| 599 | dataset.qy_data = dataset.qy_data.flatten() |
---|
[9d786e5] | 600 | self.current_dataset = dataset |
---|
| 601 | self.send_to_output() |
---|
[d72567e] | 602 | |
---|
| 603 | for dataset in self.data1d: |
---|
[9d786e5] | 604 | self.current_dataset = dataset |
---|
| 605 | self.send_to_output() |
---|
[d72567e] | 606 | |
---|
[68aa210] | 607 | def add_data_set(self, key=""): |
---|
| 608 | """ |
---|
[082239e] | 609 | Adds the current_dataset to the list of outputs after preforming final |
---|
| 610 | processing on the data and then calls a private method to generate a |
---|
| 611 | new data set. |
---|
[68aa210] | 612 | |
---|
| 613 | :param key: NeXus group name for current tree level |
---|
| 614 | """ |
---|
[d72567e] | 615 | |
---|
| 616 | if self.current_datainfo and self.current_dataset: |
---|
[68aa210] | 617 | self.final_data_cleanup() |
---|
[802fc18] | 618 | self.data_frames = [] |
---|
| 619 | self.data_uncertainty_frames = [] |
---|
[d72567e] | 620 | self.data1d = [] |
---|
| 621 | self.data2d = [] |
---|
| 622 | self.current_datainfo = DataInfo() |
---|
[68aa210] | 623 | |
---|
[8f882fe] | 624 | def _initialize_new_data_set(self, value=None): |
---|
[68aa210] | 625 | """ |
---|
[082239e] | 626 | A private class method to generate a new 1D or 2D data object based on |
---|
| 627 | the type of data within the set. Outside methods should call |
---|
| 628 | add_data_set() to be sure any existing data is stored properly. |
---|
[68aa210] | 629 | |
---|
[d72567e] | 630 | :param parent_list: List of names of parent elements |
---|
[68aa210] | 631 | """ |
---|
[8f882fe] | 632 | if self._is2d(value): |
---|
[d72567e] | 633 | self.current_dataset = plottable_2D() |
---|
[68aa210] | 634 | else: |
---|
| 635 | x = np.array(0) |
---|
| 636 | y = np.array(0) |
---|
[d72567e] | 637 | self.current_dataset = plottable_1D(x, y) |
---|
| 638 | self.current_datainfo.filename = self.raw_data.filename |
---|
[68aa210] | 639 | |
---|
[cf29187] | 640 | @staticmethod |
---|
| 641 | def check_is_list_or_array(iterable): |
---|
| 642 | try: |
---|
| 643 | iter(iterable) |
---|
[4fdcc65] | 644 | if (not isinstance(iterable, np.ndarray) and not isinstance( |
---|
[926ece5] | 645 | iterable, list)) or (isinstance(iterable, basestring)): |
---|
[cf29187] | 646 | raise TypeError |
---|
| 647 | except TypeError: |
---|
[dfcdbf8] | 648 | if isinstance(iterable, basestring): |
---|
| 649 | iterable = iterable.split(",") |
---|
| 650 | else: |
---|
| 651 | iterable = [iterable] |
---|
[cf29187] | 652 | return iterable |
---|
| 653 | |
---|
[9e0dd49] | 654 | def _find_data_attributes(self, value): |
---|
[2651724] | 655 | """ |
---|
| 656 | A class to find the indices for Q, the name of the Qdev and Idev, and |
---|
| 657 | the name of the mask. |
---|
| 658 | :param value: SASdata/NXdata HDF5 Group |
---|
| 659 | """ |
---|
[802fc18] | 660 | # Initialize values to base types |
---|
| 661 | self.mask_name = u'' |
---|
| 662 | self.i_name = u'' |
---|
| 663 | self.i_node = u'' |
---|
| 664 | self.i_uncertainties_name = u'' |
---|
| 665 | self.q_names = [] |
---|
| 666 | self.q_uncertainty_names = [] |
---|
| 667 | self.q_resolution_names = [] |
---|
| 668 | # Get attributes |
---|
[9e0dd49] | 669 | attrs = value.attrs |
---|
[0bd8fac] | 670 | signal = attrs.get("signal", "I") |
---|
| 671 | i_axes = attrs.get("I_axes", ["Q"]) |
---|
| 672 | q_indices = attrs.get("Q_indices", [0]) |
---|
[cf29187] | 673 | q_indices = map(int, self.check_is_list_or_array(q_indices)) |
---|
| 674 | i_axes = self.check_is_list_or_array(i_axes) |
---|
[9e0dd49] | 675 | keys = value.keys() |
---|
[802fc18] | 676 | # Assign attributes to appropriate class variables |
---|
[18af6d2] | 677 | self.mask_name = attrs.get("mask") |
---|
[2651724] | 678 | for val in q_indices: |
---|
[b204004] | 679 | self.q_names.append(i_axes[val]) |
---|
[9e0dd49] | 680 | self.i_name = signal |
---|
[2651724] | 681 | self.i_node = value.get(self.i_name) |
---|
[b204004] | 682 | for item in self.q_names: |
---|
[2651724] | 683 | if item in keys: |
---|
| 684 | q_vals = value.get(item) |
---|
[0bd8fac] | 685 | if q_vals.attrs.get("uncertainties") is not None: |
---|
[b204004] | 686 | self.q_uncertainty_names = q_vals.attrs.get("uncertainties") |
---|
[0bd8fac] | 687 | elif q_vals.attrs.get("uncertainty") is not None: |
---|
[b204004] | 688 | self.q_uncertainty_names = q_vals.attrs.get("uncertainty") |
---|
| 689 | if isinstance(self.q_uncertainty_names, basestring): |
---|
| 690 | self.q_uncertainty_names = self.q_uncertainty_names.split(",") |
---|
[0bd8fac] | 691 | if q_vals.attrs.get("resolutions") is not None: |
---|
[b204004] | 692 | self.q_resolution_names = q_vals.attrs.get("resolutions") |
---|
| 693 | if isinstance(self.q_resolution_names, basestring): |
---|
| 694 | self.q_resolution_names = self.q_resolution_names.split(",") |
---|
[9e0dd49] | 695 | if self.i_name in keys: |
---|
| 696 | i_vals = value.get(self.i_name) |
---|
[b204004] | 697 | self.i_uncertainties_name = i_vals.attrs.get("uncertainties") |
---|
| 698 | if self.i_uncertainties_name is None: |
---|
| 699 | self.i_uncertainties_name = i_vals.attrs.get("uncertainty") |
---|
[9e0dd49] | 700 | |
---|
[802fc18] | 701 | def _is2d(self, value, i_base="", q_base=[]): |
---|
[ad52d31] | 702 | """ |
---|
[8f882fe] | 703 | A private class to determine if the data set is 1d or 2d. |
---|
[ad52d31] | 704 | |
---|
[802fc18] | 705 | :param value: Nexus/NXcanSAS data group |
---|
[d72567e] | 706 | :param basename: Approximate name of an entry to search for |
---|
[8f882fe] | 707 | :return: True if 2D, otherwise false |
---|
| 708 | """ |
---|
[802fc18] | 709 | i_basename = i_base if i_base != "" else self.i_name |
---|
| 710 | i_vals = value.get(i_basename) |
---|
| 711 | q_basename = q_base if q_base != [] else self.q_names |
---|
| 712 | q_vals = value.get(q_basename[0]) |
---|
| 713 | self.multi_frame = True if (i_vals is not None and q_vals is not None |
---|
| 714 | and len(i_vals.shape) != 1 |
---|
| 715 | and len(q_vals.shape) == 1) else False |
---|
| 716 | return (i_vals is not None and i_vals.shape is not None |
---|
| 717 | and len(i_vals.shape) != 1 and not self.multi_frame) |
---|
[ad52d31] | 718 | |
---|
[68aa210] | 719 | def _create_unique_key(self, dictionary, name, numb=0): |
---|
| 720 | """ |
---|
| 721 | Create a unique key value for any dictionary to prevent overwriting |
---|
| 722 | Recurses until a unique key value is found. |
---|
| 723 | |
---|
| 724 | :param dictionary: A dictionary with any number of entries |
---|
| 725 | :param name: The index of the item to be added to dictionary |
---|
| 726 | :param numb: The number to be appended to the name, starts at 0 |
---|
[d72567e] | 727 | :return: The new name for the dictionary entry |
---|
[68aa210] | 728 | """ |
---|
| 729 | if dictionary.get(name) is not None: |
---|
| 730 | numb += 1 |
---|
| 731 | name = name.split("_")[0] |
---|
| 732 | name += "_{0}".format(numb) |
---|
| 733 | name = self._create_unique_key(dictionary, name, numb) |
---|
[d398285] | 734 | return name |
---|
| 735 | |
---|
| 736 | def _get_unit(self, value): |
---|
| 737 | """ |
---|
| 738 | Find the unit for a particular value within the h5py dictionary |
---|
| 739 | |
---|
| 740 | :param value: attribute dictionary for a particular value set |
---|
[d72567e] | 741 | :return: unit for the value passed to the method |
---|
[d398285] | 742 | """ |
---|
[5c5e7fd] | 743 | unit = h5attr(value, u'units') |
---|
[54544637] | 744 | if unit is None: |
---|
[5c5e7fd] | 745 | unit = h5attr(value, u'unit') |
---|
[54ba66e] | 746 | return unit |
---|