[eb98f24] | 1 | """ |
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| 2 | NXcanSAS 1/2D data reader for writing HDF5 formatted NXcanSAS 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 | |
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| 10 | from sas.sascalc.dataloader.readers.cansas_reader_HDF5 import Reader as Cansas2Reader |
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| 11 | from sas.sascalc.dataloader.data_info import Data1D, Data2D |
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| 12 | |
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| 13 | class NXcanSASWriter(Cansas2Reader): |
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| 14 | """ |
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| 15 | A class for writing in NXcanSAS data files. Any number of data sets may be |
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| 16 | written to the file. Currently 1D and 2D SAS data sets are supported |
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| 17 | |
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| 18 | NXcanSAS spec: http://download.nexusformat.org/sphinx/classes/contributed_definitions/NXcanSAS.html |
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| 19 | |
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| 20 | :Dependencies: |
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| 21 | The NXcanSAS writer requires h5py => v2.5.0 or later. |
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| 22 | """ |
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| 23 | |
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[fe498b83] | 24 | def write(self, dataset, filename): |
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[eb98f24] | 25 | """ |
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| 26 | Write an array of Data1d or Data2D objects to an NXcanSAS file, as |
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| 27 | one SASEntry with multiple SASData elements. The metadata of the first |
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| 28 | elememt in the array will be written as the SASentry metadata |
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| 29 | (detector, instrument, sample, etc). |
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| 30 | |
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| 31 | :param dataset: A list of Data1D or Data2D objects to write |
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| 32 | :param filename: Where to write the NXcanSAS file |
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| 33 | """ |
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| 34 | |
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| 35 | def _h5_string(string): |
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| 36 | """ |
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| 37 | Convert a string to a numpy string in a numpy array. This way it is |
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| 38 | written to the HDF5 file as a fixed length ASCII string and is |
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| 39 | compatible with the Reader read() method. |
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| 40 | """ |
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| 41 | if not isinstance(string, str): |
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| 42 | string = str(string) |
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| 43 | |
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| 44 | return np.array([np.string_(string)]) |
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| 45 | |
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[ac3353d] | 46 | def _write_h5_string(entry, value, key): |
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| 47 | entry[key] = _h5_string(value) |
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| 48 | |
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| 49 | |
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[eb98f24] | 50 | def _h5_float(x): |
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| 51 | if not (isinstance(x, list)): |
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| 52 | x = [x] |
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| 53 | return np.array(x, dtype=np.float32) |
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| 54 | |
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[ac3353d] | 55 | def _write_h5_float(entry, value, key): |
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| 56 | entry.create_dataset(key, data=_h5_float(value)) |
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| 57 | |
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| 58 | def _write_h5_vector(entry, vector, names=['x_position', 'y_position'], |
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| 59 | units=None, write_fn=_write_h5_string): |
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| 60 | if len(names) < 2: |
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| 61 | raise ValueError("Length of names must be >= 2.") |
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| 62 | |
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| 63 | if vector.x is not None: |
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| 64 | write_fn(entry, vector.x, names[0]) |
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| 65 | if units is not None: |
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| 66 | entry[names[0]].attrs['units'] = units |
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| 67 | if vector.y is not None: |
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| 68 | write_fn(entry, vector.y, names[1]) |
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| 69 | if units is not None: |
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| 70 | entry[names[1]].attrs['units'] = units |
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| 71 | if len(names) == 3 and vector.z is not None: |
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| 72 | write_fn(entry, vector.z, names[2]) |
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| 73 | if units is not None: |
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| 74 | entry[names[2]].attrs['units'] = units |
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| 75 | |
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[eb98f24] | 76 | valid_data = all([issubclass(d.__class__, (Data1D, Data2D)) for d in dataset]) |
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| 77 | if not valid_data: |
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| 78 | raise ValueError("All entries of dataset must be Data1D or Data2D objects") |
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| 79 | |
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| 80 | # Get run name and number from first Data object |
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| 81 | data_info = dataset[0] |
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| 82 | run_number = '' |
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| 83 | run_name = '' |
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| 84 | if len(data_info.run) > 0: |
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| 85 | run_number = data_info.run[0] |
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| 86 | if len(data_info.run_name) > 0: |
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| 87 | run_name = data_info.run_name[run_number] |
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| 88 | |
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| 89 | f = h5py.File(filename, 'w') |
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| 90 | sasentry = f.create_group('sasentry01') |
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| 91 | sasentry['definition'] = _h5_string('NXcanSAS') |
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| 92 | sasentry['run'] = _h5_string(run_number) |
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| 93 | sasentry['run'].attrs['name'] = run_name |
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| 94 | sasentry['title'] = _h5_string(data_info.title) |
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| 95 | sasentry.attrs['canSAS_class'] = 'SASentry' |
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| 96 | sasentry.attrs['version'] = '1.0' |
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| 97 | |
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| 98 | i = 1 |
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| 99 | |
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| 100 | for data_obj in dataset: |
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| 101 | data_entry = sasentry.create_group("sasdata{0:0=2d}".format(i)) |
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| 102 | data_entry.attrs['canSAS_class'] = 'SASdata' |
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| 103 | if isinstance(data_obj, Data1D): |
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| 104 | self._write_1d_data(data_obj, data_entry) |
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| 105 | elif isinstance(data_obj, Data2D): |
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[fe498b83] | 106 | self._write_2d_data(data_obj, data_entry) |
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[eb98f24] | 107 | i += 1 |
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| 108 | |
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| 109 | data_info = dataset[0] |
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[ac3353d] | 110 | # Sample metadata |
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[eb98f24] | 111 | sample_entry = sasentry.create_group('sassample') |
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| 112 | sample_entry.attrs['canSAS_class'] = 'SASsample' |
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[ac3353d] | 113 | sample_entry['ID'] = _h5_string(data_info.sample.name) |
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| 114 | sample_attrs = ['thickness', 'temperature', 'transmission'] |
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[eb98f24] | 115 | for key in sample_attrs: |
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| 116 | if getattr(data_info.sample, key) is not None: |
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| 117 | sample_entry.create_dataset(key, |
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[346d56e] | 118 | data=_h5_float(getattr(data_info.sample, key))) |
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[ac3353d] | 119 | _write_h5_vector(sample_entry, data_info.sample.position) |
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[9ddffe0] | 120 | # NXcanSAS doesn't save information about pitch, only roll |
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| 121 | # and yaw. The _write_h5_vector method writes vector.y, but we |
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| 122 | # need to write vector.z for yaw |
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| 123 | data_info.sample.orientation.y = data_info.orientation.z |
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[ac3353d] | 124 | _write_h5_vector(sample_entry, data_info.sample.orientation, |
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| 125 | names=['polar_angle', 'azimuthal_angle']) |
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[eb98f24] | 126 | |
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[ac3353d] | 127 | # Instrumment metadata |
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[eb98f24] | 128 | instrument_entry = sasentry.create_group('sasinstrument') |
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| 129 | instrument_entry.attrs['canSAS_class'] = 'SASinstrument' |
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| 130 | instrument_entry['name'] = _h5_string(data_info.instrument) |
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| 131 | |
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[ac3353d] | 132 | # Source metadata |
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[eb98f24] | 133 | source_entry = instrument_entry.create_group('sassource') |
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| 134 | source_entry.attrs['canSAS_class'] = 'SASsource' |
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| 135 | if data_info.source.radiation is None: |
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| 136 | source_entry['radiation'] = _h5_string('neutron') |
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| 137 | else: |
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| 138 | source_entry['radiation'] = _h5_string(data_info.source.radiation) |
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| 139 | |
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[ac3353d] | 140 | # Collimation metadata |
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[eb98f24] | 141 | if len(data_info.collimation) > 0: |
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| 142 | i = 1 |
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| 143 | for coll_info in data_info.collimation: |
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| 144 | collimation_entry = instrument_entry.create_group( |
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| 145 | 'sascollimation{0:0=2d}'.format(i)) |
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| 146 | collimation_entry.attrs['canSAS_class'] = 'SAScollimation' |
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| 147 | if coll_info.length is not None: |
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[ac3353d] | 148 | _write_h5_float(collimation_entry, coll_info.length, 'SDD') |
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[eb98f24] | 149 | collimation_entry['SDD'].attrs['units'] = coll_info.length_unit |
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| 150 | if coll_info.name is not None: |
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| 151 | collimation_entry['name'] = _h5_string(coll_info.name) |
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| 152 | else: |
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[ac3353d] | 153 | # Create a blank one - at least 1 set of collimation metadata |
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| 154 | # required by format |
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[eb98f24] | 155 | collimation_entry = instrument_entry.create_group('sascollimation01') |
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| 156 | |
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[ac3353d] | 157 | # Detector metadata |
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[eb98f24] | 158 | if len(data_info.detector) > 0: |
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| 159 | i = 1 |
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| 160 | for det_info in data_info.detector: |
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| 161 | detector_entry = instrument_entry.create_group( |
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| 162 | 'sasdetector{0:0=2d}'.format(i)) |
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| 163 | detector_entry.attrs['canSAS_class'] = 'SASdetector' |
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| 164 | if det_info.distance is not None: |
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[ac3353d] | 165 | _write_h5_float(detector_entry, det_info.distance, 'SDD') |
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[eb98f24] | 166 | detector_entry['SDD'].attrs['units'] = det_info.distance_unit |
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| 167 | if det_info.name is not None: |
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| 168 | detector_entry['name'] = _h5_string(det_info.name) |
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| 169 | else: |
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| 170 | detector_entry['name'] = _h5_string('') |
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[ac3353d] | 171 | if det_info.slit_length is not None: |
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| 172 | _write_h5_float(detector_entry, det_info.slit_length, 'slit_length') |
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| 173 | detector_entry['slit_length'].attrs['units'] = det_info.slit_length_unit |
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| 174 | _write_h5_vector(detector_entry, det_info.offset) |
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[9ddffe0] | 175 | # NXcanSAS doesn't save information about pitch, only roll |
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| 176 | # and yaw. The _write_h5_vector method writes vector.y, but we |
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| 177 | # need to write vector.z for yaw |
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| 178 | det_info.orientation.y = det_info.orientation.z |
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[ac3353d] | 179 | _write_h5_vector(detector_entry, det_info.orientation, |
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| 180 | names=['polar_angle', 'azimuthal_angle']) |
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| 181 | _write_h5_vector(detector_entry, det_info.beam_center, |
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| 182 | names=['beam_center_x', 'beam_center_y'], |
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| 183 | write_fn=_write_h5_float, units=det_info.beam_center_unit) |
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| 184 | _write_h5_vector(detector_entry, det_info.pixel_size, |
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| 185 | names=['x_pixel_size', 'y_pixel_size'], |
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| 186 | write_fn=_write_h5_float, units=det_info.pixel_size_unit) |
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| 187 | |
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[eb98f24] | 188 | i += 1 |
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| 189 | else: |
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[ac3353d] | 190 | # Create a blank one - at least 1 detector required by format |
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[eb98f24] | 191 | detector_entry = instrument_entry.create_group('sasdetector01') |
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| 192 | detector_entry.attrs['canSAS_class'] = 'SASdetector' |
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| 193 | detector_entry.attrs['name'] = '' |
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| 194 | |
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| 195 | # TODO: implement writing SASnote |
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[afbd172] | 196 | i = 1 |
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[eb98f24] | 197 | note_entry = sasentry.create_group('sasnote{0:0=2d}'.format(i)) |
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| 198 | note_entry.attrs['canSAS_class'] = 'SASnote' |
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| 199 | |
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| 200 | f.close() |
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| 201 | |
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| 202 | def _write_1d_data(self, data_obj, data_entry): |
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| 203 | """ |
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| 204 | Writes the contents of a Data1D object to a SASdata h5py Group |
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| 205 | |
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| 206 | :param data_obj: A Data1D object to write to the file |
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| 207 | :param data_entry: A h5py Group object representing the SASdata |
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| 208 | """ |
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| 209 | data_entry.attrs['signal'] = 'I' |
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| 210 | data_entry.attrs['I_axes'] = 'Q' |
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| 211 | data_entry.attrs['I_uncertainties'] = 'Idev' |
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| 212 | data_entry.attrs['Q_indicies'] = 0 |
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[a14fa99] | 213 | |
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| 214 | dI = data_obj.dy |
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| 215 | if dI is None: |
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| 216 | dI = np.zeros((data_obj.y.shape)) |
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| 217 | |
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[eb98f24] | 218 | data_entry.create_dataset('Q', data=data_obj.x) |
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| 219 | data_entry.create_dataset('I', data=data_obj.y) |
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[a14fa99] | 220 | data_entry.create_dataset('Idev', data=dI) |
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[eb98f24] | 221 | |
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[fe498b83] | 222 | def _write_2d_data(self, data, data_entry): |
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[eb98f24] | 223 | """ |
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| 224 | Writes the contents of a Data2D object to a SASdata h5py Group |
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| 225 | |
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| 226 | :param data: A Data2D object to write to the file |
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| 227 | :param data_entry: A h5py Group object representing the SASdata |
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| 228 | """ |
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| 229 | data_entry.attrs['signal'] = 'I' |
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| 230 | data_entry.attrs['I_axes'] = 'Q,Q' |
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| 231 | data_entry.attrs['I_uncertainties'] = 'Idev' |
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| 232 | data_entry.attrs['Q_indicies'] = [0,1] |
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| 233 | |
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[fe498b83] | 234 | (n_rows, n_cols) = (len(data.y_bins), len(data.x_bins)) |
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[afbd172] | 235 | |
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[fe498b83] | 236 | if n_rows == 0 and n_cols == 0: |
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[afbd172] | 237 | # Calculate rows and columns, assuming detector is square |
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| 238 | # Same logic as used in PlotPanel.py _get_bins |
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| 239 | n_cols = int(np.floor(np.sqrt(len(data.qy_data)))) |
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| 240 | n_rows = int(np.floor(len(data.qy_data) / n_cols)) |
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[eb98f24] | 241 | |
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[afbd172] | 242 | if n_rows * n_cols != len(data.qy_data): |
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| 243 | raise ValueError("Unable to calculate dimensions of 2D data") |
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[eb98f24] | 244 | |
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| 245 | I = np.reshape(data.data, (n_rows, n_cols)) |
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[afbd172] | 246 | dI = np.zeros((n_rows, n_cols)) |
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| 247 | if not all(data.err_data == [None]): |
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| 248 | dI = np.reshape(data.err_data, (n_rows, n_cols)) |
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[eb98f24] | 249 | qx = np.reshape(data.qx_data, (n_rows, n_cols)) |
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| 250 | qy = np.reshape(data.qy_data, (n_rows, n_cols)) |
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[346d56e] | 251 | |
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[eb98f24] | 252 | I_entry = data_entry.create_dataset('I', data=I) |
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| 253 | I_entry.attrs['units'] = data.I_unit |
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| 254 | Qx_entry = data_entry.create_dataset('Qx', data=qx) |
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| 255 | Qx_entry.attrs['units'] = data.Q_unit |
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| 256 | Qy_entry = data_entry.create_dataset('Qy', data=qy) |
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| 257 | Qy_entry.attrs['units'] = data.Q_unit |
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[9f4d891] | 258 | Idev_entry = data_entry.create_dataset('Idev', data=dI) |
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| 259 | Idev_entry.attrs['units'] = data.I_unit |
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