Changeset 8cb1a07 in sasview for src/sas

Timestamp:

Aug 18, 2016 7:03:43 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:

eb98f24

Parents:

1f6d293

Message:

Implement writing 2D data to NXcanSAS

File:

• src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py (modified) (3 diffs)

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

@@ -390 +390 @@
         :param filename: Where to write the CanSAS 2.0 file
         """
-        is_1d = all([isinstance(d, Data1D) for d in dataset])
-        is_2d = all([isinstance(d, Data2D) for d in dataset])
-
-        if not (is_1d or is_2d):
-            msg = ("All elements of dataset must be of the same class "
-                "(Data1D or Data2D)")
-            raise ValueError(msg)
 
         def _h5_string(string):
@@ -414 +407 @@
             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]
@@ -434 +431 @@
         i = 1
 
-        if is_1d:
-            for data_obj in dataset:
-                data_entry = sasentry.create_group("sasdata{0:0=2d}".format(i))
-                data_entry.attrs['canSAS_class'] = 'SASdata'
-                data_entry.attrs['signal'] = 'I'
-                data_entry.attrs['I_axes'] = 'Q'
-                data_entry.attrs['I_uncertainties'] = 'Idev'
-                data_entry.attrs['Q_indicies'] = 0
-                Q_data = data_entry.create_dataset('Q', data=data_obj.x)
-                I_data = data_entry.create_dataset('I', data=data_obj.y)
-                dI_data = data_entry.create_dataset('Idev', data=data_obj.dy)
+        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
-
-            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'
-
-        elif is_2d:
-            f.close()
-            raise NotImplementedError("Saving 2D data as CanSAS 2.0 is not yet implemented")
+        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