Changeset eb98f24 in sasview for src/sas/sascalc

Timestamp:

Aug 18, 2016 8:35:43 AM (8 years ago)

Author:

lewis

Branches:

master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.1.1, release-4.1.2, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload

Children:

afbd172

Parents:

8cb1a07

Message:

Refactor write method to its own class

The cansas_reader_HDF5 read method is designed for reading CanSAS 2.0 HDF5
formatted files, but will also read NXcanSAS files. The write method was
following the NXcanSAS spec, so has been moved to its own class to avoid
confusion between then two (very simillar) formats.

Location:

src/sas/sascalc

Files:

• dataloader/readers/cansas_reader_HDF5.py (modified) (3 diffs)
• file_converter/nxcansas_writer.py (added)

src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py

@@ -182 +182 @@
 
                     ## Sample Information
-                    elif key == u'Title' and self.parent_class == u'SASsample':
+                    elif key == u'Title' and self.parent_class == u'SASsample': # CanSAS 2.0 format
                         self.current_datainfo.sample.name = data_point
-                    elif key == u'name' and self.parent_class == u'SASsample':
+                    elif key == u'name' and self.parent_class == u'SASsample': # NXcanSAS format
                         self.current_datainfo.sample.name = data_point
                     elif key == u'thickness' and self.parent_class == u'SASsample':
@@ -208 +208 @@
                     elif key == u'name' and self.parent_class == u'SASprocess':
                         self.process.name = data_point
-                    elif key == u'Title' and self.parent_class == u'SASprocess':
+                    elif key == u'Title' and self.parent_class == u'SASprocess': # CanSAS 2.0 format
                         self.process.name = data_point
-                    elif key == u'name' and self.parent_class == u'SASprocess':
+                    elif key == u'name' and self.parent_class == u'SASprocess': # NXcanSAS format
                         self.process.name = data_point
                     elif key == u'description' and self.parent_class == u'SASprocess':
@@ -380 +380 @@
         self.current_datainfo = DataInfo()
 
-    def write(self, dataset, filename):
-        """
-        Write an array of Data1d or Data2D objects to a CanSAS 2.0 file, as
-        one SASEntry with multiple SASData elements. The metadata of the first
-        elememt in the array will be written as the SASentry metadata
-        (detector, instrument, sample, etc)
-
-        :param dataset: A list of Data1D or Data2D objects to write
-        :param filename: Where to write the CanSAS 2.0 file
-        """
-
-        def _h5_string(string):
-            """
-            Convert a string to a numpy string in a numpy array. This way it is
-            written to the HDF5 file as a fixed length ASCII string and is
-            compatible with the Reader read() method.
-            """
-            if not isinstance(string, str):
-                raise ValueError("String should be of type str")
-
-            return np.array([np.string_(string)])
-
-        def _h5_float(x):
-            if not (isinstance(x, list)):
-                x = [x]
-            return np.array(x, dtype=np.float32)
-
-        valid_data = all([issubclass(d.__class__, (Data1D, Data2D)) for d in dataset])
-        if not valid_data:
-            raise ValueError("All entries of dataset must be Data1D or Data2D objects")
-
-        # Get run name and number from first Data object
-        data_info = dataset[0]
-        run_number = ''
-        run_name = ''
-        if len(data_info.run) > 0:
-            run_number = data_info.run[0]
-            if len(data_info.run_name) > 0:
-                run_name = data_info.run_name[run_number]
-
-        f = h5py.File(filename, 'w')
-        sasentry = f.create_group('sasentry01')
-        sasentry['definition'] = _h5_string('NXcanSAS')
-        sasentry['run'] = _h5_string(run_number)
-        sasentry['run'].attrs['name'] = run_name
-        sasentry['title'] = _h5_string(data_info.title)
-        sasentry.attrs['canSAS_class'] = 'SASentry'
-        sasentry.attrs['version'] = '1.0'
-
-        i = 1
-
-        for data_obj in dataset:
-            data_entry = sasentry.create_group("sasdata{0:0=2d}".format(i))
-            data_entry.attrs['canSAS_class'] = 'SASdata'
-            if isinstance(data_obj, Data1D):
-                self._write_1d_data(data_obj, data_entry)
-            elif isinstance(data_obj, Data2D):
-                self._write_2d_data(data_obj, data_entry)
-            i += 1
-
-        data_info = dataset[0]
-        sample_entry = sasentry.create_group('sassample')
-        sample_entry.attrs['canSAS_class'] = 'SASsample'
-        sample_entry['name'] = _h5_string(data_info.sample.name)
-        sample_attrs = ['thickness', 'temperature']
-        for key in sample_attrs:
-            if getattr(data_info.sample, key) is not None:
-                sample_entry.create_dataset(key, data=np.array([getattr(data_info.sample, key)]))
-
-        instrument_entry = sasentry.create_group('sasinstrument')
-        instrument_entry.attrs['canSAS_class'] = 'SASinstrument'
-        instrument_entry['name'] = _h5_string(data_info.instrument)
-
-        source_entry = instrument_entry.create_group('sassource')
-        source_entry.attrs['canSAS_class'] = 'SASsource'
-        if data_info.source.radiation is None:
-            source_entry['radiation'] = _h5_string('neutron')
-        else:
-            source_entry['radiation'] = _h5_string(data_info.source.radiation)
-
-        if len(data_info.collimation) > 0:
-            i = 1
-            for coll_info in data_info.collimation:
-                collimation_entry = instrument_entry.create_group(
-                    'sascollimation{0:0=2d}'.format(i))
-                collimation_entry.attrs['canSAS_class'] = 'SAScollimation'
-                if coll_info.length is not None:
-                    collimation_entry['SDD'] = _h5_float(coll_info.length)
-                    collimation_entry['SDD'].attrs['units'] = coll_info.length_unit
-                if coll_info.name is not None:
-                    collimation_entry['name'] = _h5_string(coll_info.name)
-        else:
-            collimation_entry = instrument_entry.create_group('sascollimation01')
-
-        if len(data_info.detector) > 0:
-            i = 1
-            for det_info in data_info.detector:
-                detector_entry = instrument_entry.create_group(
-                    'sasdetector{0:0=2d}'.format(i))
-                detector_entry.attrs['canSAS_class'] = 'SASdetector'
-                if det_info.distance is not None:
-                    detector_entry['SDD'] = _h5_float(det_info.distance)
-                    detector_entry['SDD'].attrs['units'] = det_info.distance_unit
-                if det_info.name is not None:
-                    detector_entry['name'] = _h5_string(det_info.name)
-                else:
-                    detector_entry['name'] = _h5_string('')
-                i += 1
-        else:
-            detector_entry = instrument_entry.create_group('sasdetector01')
-            detector_entry.attrs['canSAS_class'] = 'SASdetector'
-            detector_entry.attrs['name'] = ''
-
-        # TODO: implement writing SASnote
-        note_entry = sasentry.create_group('sasnote{0:0=2d}'.format(i))
-        note_entry.attrs['canSAS_class'] = 'SASnote'
-
-        f.close()
-
-    def _write_1d_data(self, data_obj, data_entry):
-        """
-        Writes the contents of a Data1D object to a SASdata h5py Group
-
-        :param data_obj: A Data1D object to write to the file
-        :param data_entry: A h5py Group object representing the SASdata
-        """
-        data_entry.attrs['signal'] = 'I'
-        data_entry.attrs['I_axes'] = 'Q'
-        data_entry.attrs['I_uncertainties'] = 'Idev'
-        data_entry.attrs['Q_indicies'] = 0
-        data_entry.create_dataset('Q', data=data_obj.x)
-        data_entry.create_dataset('I', data=data_obj.y)
-        data_entry.create_dataset('Idev', data=data_obj.dy)
-
-    def _write_2d_data(self, data, data_entry):
-        """
-        Writes the contents of a Data2D object to a SASdata h5py Group
-
-        :param data: A Data2D object to write to the file
-        :param data_entry: A h5py Group object representing the SASdata
-        """
-        data_entry.attrs['signal'] = 'I'
-        data_entry.attrs['I_axes'] = 'Q,Q'
-        data_entry.attrs['I_uncertainties'] = 'Idev'
-        data_entry.attrs['Q_indicies'] = [0,1]
-
-        # Calculate rows and columns, assuming detector is square
-        # Same logic as used in PlotPanel.py _get_bins
-        n_cols = int(np.floor(np.sqrt(len(data.qy_data))))
-        n_rows = int(np.floor(len(data.qy_data) / n_cols))
-
-        if n_rows * n_cols != len(data.qy_data):
-            raise ValueError("Unable to calculate dimensions of data")
-
-        I = np.reshape(data.data, (n_rows, n_cols))
-        dI = np.reshape(data.err_data, (n_rows, n_cols))
-        qx =  np.reshape(data.qx_data, (n_rows, n_cols))
-        qy = np.reshape(data.qy_data, (n_rows, n_cols))
-        I_entry = data_entry.create_dataset('I', data=I)
-        I_entry.attrs['units'] = data.I_unit
-        Qx_entry = data_entry.create_dataset('Qx', data=qx)
-        Qx_entry.attrs['units'] = data.Q_unit
-        Qy_entry = data_entry.create_dataset('Qy', data=qy)
-        Qy_entry.attrs['units'] = data.Q_unit
-
 
     def _initialize_new_data_set(self, parent_list = None):