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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24 | def write(self, dataset, filename): |
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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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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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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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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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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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106 | self._write_2d_data(data_obj, data_entry) |
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107 | i += 1 |
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108 | |
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109 | data_info = dataset[0] |
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110 | # Sample metadata |
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111 | sample_entry = sasentry.create_group('sassample') |
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112 | sample_entry.attrs['canSAS_class'] = 'SASsample' |
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113 | sample_entry['ID'] = _h5_string(data_info.sample.name) |
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114 | sample_attrs = ['thickness', 'temperature', 'transmission'] |
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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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118 | data=_h5_float(getattr(data_info.sample, key))) |
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119 | _write_h5_vector(sample_entry, data_info.sample.position) |
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120 | _write_h5_vector(sample_entry, data_info.sample.orientation, |
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121 | names=['polar_angle', 'azimuthal_angle']) |
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122 | |
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123 | # Instrumment metadata |
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124 | instrument_entry = sasentry.create_group('sasinstrument') |
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125 | instrument_entry.attrs['canSAS_class'] = 'SASinstrument' |
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126 | instrument_entry['name'] = _h5_string(data_info.instrument) |
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127 | |
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128 | # Source metadata |
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129 | source_entry = instrument_entry.create_group('sassource') |
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130 | source_entry.attrs['canSAS_class'] = 'SASsource' |
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131 | if data_info.source.radiation is None: |
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132 | source_entry['radiation'] = _h5_string('neutron') |
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133 | else: |
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134 | source_entry['radiation'] = _h5_string(data_info.source.radiation) |
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135 | |
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136 | # Collimation metadata |
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137 | if len(data_info.collimation) > 0: |
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138 | i = 1 |
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139 | for coll_info in data_info.collimation: |
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140 | collimation_entry = instrument_entry.create_group( |
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141 | 'sascollimation{0:0=2d}'.format(i)) |
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142 | collimation_entry.attrs['canSAS_class'] = 'SAScollimation' |
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143 | if coll_info.length is not None: |
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144 | _write_h5_float(collimation_entry, coll_info.length, 'SDD') |
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145 | collimation_entry['SDD'].attrs['units'] = coll_info.length_unit |
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146 | if coll_info.name is not None: |
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147 | collimation_entry['name'] = _h5_string(coll_info.name) |
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148 | else: |
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149 | # Create a blank one - at least 1 set of collimation metadata |
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150 | # required by format |
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151 | collimation_entry = instrument_entry.create_group('sascollimation01') |
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152 | |
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153 | # Detector metadata |
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154 | if len(data_info.detector) > 0: |
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155 | i = 1 |
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156 | for det_info in data_info.detector: |
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157 | detector_entry = instrument_entry.create_group( |
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158 | 'sasdetector{0:0=2d}'.format(i)) |
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159 | detector_entry.attrs['canSAS_class'] = 'SASdetector' |
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160 | if det_info.distance is not None: |
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161 | _write_h5_float(detector_entry, det_info.distance, 'SDD') |
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162 | detector_entry['SDD'].attrs['units'] = det_info.distance_unit |
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163 | if det_info.name is not None: |
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164 | detector_entry['name'] = _h5_string(det_info.name) |
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165 | else: |
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166 | detector_entry['name'] = _h5_string('') |
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167 | if det_info.slit_length is not None: |
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168 | _write_h5_float(detector_entry, det_info.slit_length, 'slit_length') |
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169 | detector_entry['slit_length'].attrs['units'] = det_info.slit_length_unit |
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170 | _write_h5_vector(detector_entry, det_info.offset) |
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171 | _write_h5_vector(detector_entry, det_info.orientation, |
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172 | names=['polar_angle', 'azimuthal_angle']) |
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173 | _write_h5_vector(detector_entry, det_info.beam_center, |
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174 | names=['beam_center_x', 'beam_center_y'], |
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175 | write_fn=_write_h5_float, units=det_info.beam_center_unit) |
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176 | _write_h5_vector(detector_entry, det_info.pixel_size, |
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177 | names=['x_pixel_size', 'y_pixel_size'], |
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178 | write_fn=_write_h5_float, units=det_info.pixel_size_unit) |
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179 | |
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180 | i += 1 |
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181 | else: |
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182 | # Create a blank one - at least 1 detector required by format |
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183 | detector_entry = instrument_entry.create_group('sasdetector01') |
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184 | detector_entry.attrs['canSAS_class'] = 'SASdetector' |
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185 | detector_entry.attrs['name'] = '' |
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186 | |
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187 | # TODO: implement writing SASnote |
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188 | i = 1 |
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189 | note_entry = sasentry.create_group('sasnote{0:0=2d}'.format(i)) |
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190 | note_entry.attrs['canSAS_class'] = 'SASnote' |
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191 | |
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192 | f.close() |
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193 | |
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194 | def _write_1d_data(self, data_obj, data_entry): |
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195 | """ |
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196 | Writes the contents of a Data1D object to a SASdata h5py Group |
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197 | |
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198 | :param data_obj: A Data1D object to write to the file |
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199 | :param data_entry: A h5py Group object representing the SASdata |
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200 | """ |
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201 | data_entry.attrs['signal'] = 'I' |
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202 | data_entry.attrs['I_axes'] = 'Q' |
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203 | data_entry.attrs['I_uncertainties'] = 'Idev' |
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204 | data_entry.attrs['Q_indicies'] = 0 |
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205 | |
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206 | dI = data_obj.dy |
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207 | if dI is None: |
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208 | dI = np.zeros((data_obj.y.shape)) |
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209 | |
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210 | data_entry.create_dataset('Q', data=data_obj.x) |
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211 | data_entry.create_dataset('I', data=data_obj.y) |
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212 | data_entry.create_dataset('Idev', data=dI) |
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213 | |
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214 | def _write_2d_data(self, data, data_entry): |
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215 | """ |
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216 | Writes the contents of a Data2D object to a SASdata h5py Group |
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217 | |
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218 | :param data: A Data2D object to write to the file |
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219 | :param data_entry: A h5py Group object representing the SASdata |
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220 | """ |
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221 | data_entry.attrs['signal'] = 'I' |
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222 | data_entry.attrs['I_axes'] = 'Q,Q' |
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223 | data_entry.attrs['I_uncertainties'] = 'Idev' |
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224 | data_entry.attrs['Q_indicies'] = [0,1] |
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225 | |
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226 | (n_rows, n_cols) = (len(data.y_bins), len(data.x_bins)) |
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227 | |
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228 | if n_rows == 0 and n_cols == 0: |
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229 | # Calculate rows and columns, assuming detector is square |
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230 | # Same logic as used in PlotPanel.py _get_bins |
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231 | n_cols = int(np.floor(np.sqrt(len(data.qy_data)))) |
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232 | n_rows = int(np.floor(len(data.qy_data) / n_cols)) |
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233 | |
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234 | if n_rows * n_cols != len(data.qy_data): |
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235 | raise ValueError("Unable to calculate dimensions of 2D data") |
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236 | |
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237 | I = np.reshape(data.data, (n_rows, n_cols)) |
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238 | dI = np.zeros((n_rows, n_cols)) |
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239 | if not all(data.err_data == [None]): |
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240 | dI = np.reshape(data.err_data, (n_rows, n_cols)) |
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241 | qx = np.reshape(data.qx_data, (n_rows, n_cols)) |
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242 | qy = np.reshape(data.qy_data, (n_rows, n_cols)) |
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243 | |
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244 | I_entry = data_entry.create_dataset('I', data=I) |
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245 | I_entry.attrs['units'] = data.I_unit |
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246 | Qx_entry = data_entry.create_dataset('Qx', data=qx) |
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247 | Qx_entry.attrs['units'] = data.Q_unit |
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248 | Qy_entry = data_entry.create_dataset('Qy', data=qy) |
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249 | Qy_entry.attrs['units'] = data.Q_unit |
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250 | Idev_entry = data_entry.create_dataset('Idev', data=dI) |
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251 | Idev_entry.attrs['units'] = data.I_unit |
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