ChessAnalysisPipeline 0.0.14__py3-none-any.whl → 0.0.16__py3-none-any.whl

CHAP/edd/processor.py

@@ -18,19 +18,17 @@ import numpy as np
 # Local modules
 from CHAP.processor import Processor
 
+# Current good detector channels for the 23 channel EDD detector:
+#    0, 2, 3, 5, 6, 7, 8, 10, 13, 14, 16, 17, 18, 19, 21, 22
 
 class DiffractionVolumeLengthProcessor(Processor):
     """A Processor using a steel foil raster scan to calculate the
     length of the diffraction volume for an EDD setup.
     """
 
-    def process(self,
-                data,
-                config=None,
-                save_figures=False,
-                inputdir='.',
-                outputdir='.',
-                interactive=False):
+    def process(
+            self, data, config=None, save_figures=False, inputdir='.',
+            outputdir='.', interactive=False):
         """Return the calculated value of the DV length.
 
         :param data: Input configuration for the raw scan data & DVL
@@ -41,17 +39,17 @@ class DiffractionVolumeLengthProcessor(Processor):
             `None`.
         :type config: dict, optional
         :param save_figures: Save .pngs of plots for checking inputs &
-            outputs of this Processor, defaults to False.
+            outputs of this Processor, defaults to `False`.
         :type save_figures: bool, optional
         :param outputdir: Directory to which any output figures will
-            be saved, defaults to '.'
+            be saved, defaults to `'.'`.
         :type outputdir: str, optional
         :param inputdir: Input directory, used only if files in the
             input configuration are not absolute paths,
-            defaults to '.'.
+            defaults to `'.'`.
         :type inputdir: str, optional
         :param interactive: Allows for user interactions, defaults to
-            False.
+            `False`.
         :type interactive: bool, optional
         :raises RuntimeError: Unable to get a valid DVL configuration.
         :return: Complete DVL configuraiton dictionary.
@@ -85,12 +83,9 @@ class DiffractionVolumeLengthProcessor(Processor):
 
         return dvl_config.dict()
 
-    def measure_dvl(self,
-                    dvl_config,
-                    detector,
-                    save_figures=False,
-                    outputdir='.',
-                    interactive=False):
+    def measure_dvl(
+            self, dvl_config, detector, save_figures=False, outputdir='.',
+            interactive=False):
         """Return a measured value for the length of the diffraction
         volume. Use the iron foil raster scan data provided in
         `dvl_config` and fit a gaussian to the sum of all MCA channel
@@ -105,13 +100,13 @@ class DiffractionVolumeLengthProcessor(Processor):
         :type detector:
             CHAP.edd.models.MCAElementDiffractionVolumeLengthConfig
         :param save_figures: Save .pngs of plots for checking inputs &
-            outputs of this Processor, defaults to False.
+            outputs of this Processor, defaults to `False`.
         :type save_figures: bool, optional
         :param outputdir: Directory to which any output figures will
-            be saved, defaults to '.'.
+            be saved, defaults to `'.'`.
         :type outputdir: str, optional
         :param interactive: Allows for user interactions, defaults to
-            False.
+            `False`.
         :type interactive: bool, optional
         :raises ValueError: No value provided for included bin ranges
             for the MCA detector element.
@@ -126,42 +121,46 @@ class DiffractionVolumeLengthProcessor(Processor):
         )
 
         # Get raw MCA data from raster scan
+        raise RuntimeError('DiffractionVolumeLengthProcessor not updated yet')
         mca_data = dvl_config.mca_data(detector)
 
-        # Interactively set mask, if needed & possible.
-        if interactive or save_figures:
-            # Third party modules
-            import matplotlib.pyplot as plt
+        # Blank out data below bin 500 (~25keV) as well as the last bin
+        # RV Not backward compatible with old detector
+        energy_mask = np.ones(detector.num_bins, dtype=np.int16)
+        energy_mask[:500] = 0
+        energy_mask[-1] = 0
+        mca_data = mca_data*energy_mask
 
-            self.logger.info(
-                'Interactively select a mask in the matplotlib figure')
-
-            fig, mask, include_bin_ranges = select_mask_1d(
+        # Interactively set or update mask, if needed & possible.
+        if interactive or save_figures:
+            if interactive:
+                self.logger.info(
+                    'Interactively select a mask in the matplotlib figure')
+            if save_figures:
+                filename = os.path.join(
+                    outputdir, f'{detector.detector_name}_dvl_mask.png')
+            else:
+                filename = None
+            _, detector.include_bin_ranges = select_mask_1d(
                 np.sum(mca_data, axis=0),
-                x=np.linspace(0, detector.max_energy_kev, detector.num_bins),
+                x=np.arange(detector.num_bins, dtype=np.int16),
                 label='Sum of MCA spectra over all scan points',
                 preselected_index_ranges=detector.include_bin_ranges,
                 title='Click and drag to select data range to include when '
                       'measuring diffraction volume length',
-                xlabel='Uncalibrated Energy (keV)',
+                xlabel='Uncalibrated energy (keV)',
                 ylabel='MCA intensity (counts)',
                 min_num_index_ranges=1,
-                interactive=interactive)
-            detector.include_energy_ranges = detector.get_energy_ranges(
-                include_bin_ranges)
+                interactive=interactive, filename=filename)
             self.logger.debug(
-                'Mask selected. Including detector energy ranges: '
-                + str(detector.include_energy_ranges))
-            if save_figures:
-                fig.savefig(os.path.join(
-                    outputdir, f'{detector.detector_name}_dvl_mask.png'))
-            plt.close()
-        if not detector.include_energy_ranges:
+                'Mask selected. Including detector bin ranges: '
+                + str(detector.include_bin_ranges))
+        if not detector.include_bin_ranges:
             raise ValueError(
-                'No value provided for include_energy_ranges. '
-                + 'Provide them in the Diffraction Volume Length '
-                + 'Measurement Configuration, or re-run the pipeline '
-                + 'with the --interactive flag.')
+                'No value provided for include_bin_ranges. '
+                'Provide them in the Diffraction Volume Length '
+                'Measurement Configuration, or re-run the pipeline '
+                'with the --interactive flag.')
 
         # Reduce the raw MCA data in 3 ways:
         # 1) sum of intensities in all detector bins
@@ -195,17 +194,18 @@ class DiffractionVolumeLengthProcessor(Processor):
         detector.fit_sigma = fit.best_values['sigma']
         if detector.measurement_mode == 'manual':
             if interactive:
-                _, _, dvl_bounds = select_mask_1d(
+                _, dvl_bounds = select_mask_1d(
                     masked_sum, x=x,
                     label='Total (masked & normalized)',
                     preselected_index_ranges=[
                         (index_nearest(x, -dvl/2), index_nearest(x, dvl/2))],
                     title=('Click and drag to indicate the boundary '
                            'of the diffraction volume'),
-                    xlabel=('Beam Direction (offset from scan "center")'),
+                    xlabel=('Beam direction (offset from scan "center")'),
                     ylabel='MCA intensity (normalized)',
                     min_num_index_ranges=1,
-                    max_num_index_ranges=1)
+                    max_num_index_ranges=1,
+                    interactive=interactive)
                 dvl_bounds = dvl_bounds[0]
                 dvl = abs(x[dvl_bounds[1]] - x[dvl_bounds[0]])
             else:
@@ -220,7 +220,7 @@ class DiffractionVolumeLengthProcessor(Processor):
 
             fig, ax = plt.subplots()
             ax.set_title(f'Diffraction Volume ({detector.detector_name})')
-            ax.set_xlabel('Beam Direction (offset from scan "center")')
+            ax.set_xlabel('Beam direction (offset from scan "center")')
             ax.set_ylabel('MCA intensity (normalized)')
             ax.plot(x, masked_sum, label='total (masked & normalized)')
             ax.plot(x, fit.best_fit, label='gaussian fit (to total)')
@@ -252,19 +252,27 @@ class DiffractionVolumeLengthProcessor(Processor):
 
 class LatticeParameterRefinementProcessor(Processor):
     """Processor to get a refined estimate for a sample's lattice
-    parameters"""
-    def process(self,
-                data,
-                config=None,
-                save_figures=False,
-                outputdir='.',
-                inputdir='.',
-                interactive=False):
+    parameters."""
+    def process(
+            self, data, config=None, save_figures=False, outputdir='.',
+            inputdir='.', interactive=False):
         """Given a strain analysis configuration, return a copy
         contining refined values for the materials' lattice
         parameters."""
-        ceria_calibration_config = self.get_config(
-            data, 'edd.models.MCACeriaCalibrationConfig', inputdir=inputdir)
+        # Third party modules
+        from nexusformat.nexus import (
+            NXdata,
+            NXentry,
+            NXsubentry,
+            NXprocess,
+            NXroot,
+        )
+
+        # Local modules
+        from CHAP.common import MapProcessor
+
+        calibration_config = self.get_config(
+            data, 'edd.models.MCATthCalibrationConfig', inputdir=inputdir)
         try:
             strain_analysis_config = self.get_config(
                 data, 'edd.models.StrainAnalysisConfig', inputdir=inputdir)
@@ -285,70 +293,295 @@ class LatticeParameterRefinementProcessor(Processor):
             self.logger.error('Not implemented for multiple materials')
             raise NotImplementedError(msg)
 
-        lattice_parameters = self.refine_lattice_parameters(
-            strain_analysis_config, ceria_calibration_config, 0,
-            interactive, save_figures, outputdir)
-        self.logger.debug(f'Refined lattice parameters: {lattice_parameters}')
+        # Collect the raw MCA data
+        raise RuntimeError(
+            'LatticeParameterRefinementProcessor not updated yet')
+        self.logger.debug(f'Reading data ...')
+        mca_data = strain_analysis_config.mca_data()
+        self.logger.debug(f'... done')
+        self.logger.debug(f'mca_data.shape: {mca_data.shape}')
+        if mca_data.ndim == 2:
+            mca_data_summed = mca_data
+        else:
+            mca_data_summed = np.mean(
+                mca_data, axis=tuple(np.arange(1, mca_data.ndim-1)))
+        self.logger.debug(f'mca_data_summed.shape: {mca_data_summed.shape}')
 
-        strain_analysis_config.materials[0].lattice_parameters = \
-            lattice_parameters
-        return strain_analysis_config.dict()
+        # Create the NXroot object
+        nxroot = NXroot()
+        nxentry = NXentry()
+        nxroot.entry = nxentry
+        nxentry.set_default()
+        nxsubentry = NXsubentry()
+        nxentry.nexus_output = nxsubentry
+        nxsubentry.attrs['schema'] = 'h5'
+        nxsubentry.attrs['filename'] = 'lattice_parameter_map.nxs'
+        map_config = strain_analysis_config.map_config
+        nxsubentry[map_config.title] = MapProcessor.get_nxentry(map_config)
+        nxsubentry[f'{map_config.title}_lat_par_refinement'] = NXprocess()
+        nxprocess = nxsubentry[f'{map_config.title}_lat_par_refinement']
+        nxprocess.strain_analysis_config = dumps(
+            strain_analysis_config.dict())
+        nxprocess.calibration_config = dumps(calibration_config.dict())
+
+        lattice_parameters = []
+        for i, detector in enumerate(strain_analysis_config.detectors):
+            lattice_parameters.append(self.refine_lattice_parameters(
+                strain_analysis_config, calibration_config, detector,
+                mca_data[i], mca_data_summed[i], nxsubentry, interactive,
+                save_figures, outputdir))
+        lattice_parameters_mean = np.asarray(lattice_parameters).mean(axis=0)
+        self.logger.debug(
+            'Lattice parameters refinement averaged over all detectors: '
+            f'{lattice_parameters_mean}')
+        strain_analysis_config.materials[0].lattice_parameters = [
+            float(v) for v in lattice_parameters_mean]
+        nxprocess.lattice_parameters = lattice_parameters_mean
+
+        nxentry.lat_par_output = NXsubentry()
+        nxentry.lat_par_output.attrs['schema'] = 'yaml'
+        nxentry.lat_par_output.attrs['filename'] = 'lattice_parameters.yaml'
+        nxentry.lat_par_output.data = dumps(
+            strain_analysis_config.dict())
+
+        return nxroot
 
     def refine_lattice_parameters(
-            self, strain_analysis_config, ceria_calibration_config,
-            detector_i, interactive, save_figures, outputdir):
+            self, strain_analysis_config, calibration_config, detector,
+            mca_data, mca_data_summed, nxsubentry, interactive, save_figures,
+            outputdir):
         """Return refined values for the lattice parameters of the
         materials indicated in `strain_analysis_config`. Method: given
-        a scan of a material, fit the peaks of each MCA
-        spectrum. Based on those fitted peak locations, calculate the
-        lattice parameters that would produce them. Return the
-        avearaged value of the calculated lattice parameters across
-        all spectra.
-
-        :param strain_analysis_config: Strain analysis configuration
-        :type strain_analysis_config: CHAP.edd.models.StrainAnalysisConfig
-        :param detector_i: Index of the detector in
-            `strain_analysis_config` whose data will be used for the
-            refinement
-        :type detector_i: int
+        a scan of a material, fit the peaks of each MCA spectrum for a
+        given detector. Based on those fitted peak locations,
+        calculate the lattice parameters that would produce them.
+        Return the averaged value of the calculated lattice parameters
+        across all spectra.
+
+        :param strain_analysis_config: Strain analysis configuration.
+        :type strain_analysis_config:
+            CHAP.edd.models.StrainAnalysisConfig
+        :param calibration_config: Energy calibration configuration.
+        :type calibration_config: edd.models.MCATthCalibrationConfig
+        :param detector: A single MCA detector element configuration.
+        :type detector: CHAP.edd.models.MCAElementStrainAnalysisConfig
+        :param mca_data: Raw specta for the current MCA detector.
+        :type mca_data: numpy.ndarray
+        :param mca_data_summed: Raw specta for the current MCA detector
+            summed over all data point.
+        :type mca_data_summed: numpy.ndarray
+        :param nxsubentry: NeXus subentry to store the detailed refined
+            lattice parameters for each detector.
+        :type nxsubentry: nexusformat.nexus.NXprocess
         :param interactive: Boolean to indicate whether interactive
-            matplotlib figures should be presented
+            matplotlib figures should be presented.
         :type interactive: bool
         :param save_figures: Boolean to indicate whether figures
-            indicating the selection should be saved
+            indicating the selection should be saved.
         :type save_figures: bool
         :param outputdir: Where to save figures (if `save_figures` is
-            `True`)
+            `True`).
         :type outputdir: str
         :returns: List of refined lattice parameters for materials in
             `strain_analysis_config`
         :rtype: list[numpy.ndarray]
         """
-        import numpy as np
-        from CHAP.edd.utils import get_unique_hkls_ds, get_spectra_fits
+        # Third party modules
+        from nexusformat.nexus import (
+            NXcollection,
+            NXdata,
+            NXdetector,
+            NXfield,
+        )
+        from scipy.constants import physical_constants
 
-        self.add_detector_calibrations(
-            strain_analysis_config, ceria_calibration_config)
+        # Local modules
+        from CHAP.edd.utils import (
+            get_peak_locations,
+            get_spectra_fits,
+            get_unique_hkls_ds,
+        )
 
-        detector = strain_analysis_config.detectors[detector_i]
-        mca_bin_energies = self.get_mca_bin_energies(strain_analysis_config)
-        mca_data = strain_analysis_config.mca_data()
+        def linkdims(nxgroup, field_dims=[]):
+            if isinstance(field_dims, dict):
+                field_dims = [field_dims]
+            if map_config.map_type == 'structured':
+                axes = deepcopy(map_config.dims)
+                for dims in field_dims:
+                    axes.append(dims['axes'])
+            else:
+                axes = ['map_index']
+                for dims in field_dims:
+                    axes.append(dims['axes'])
+                nxgroup.attrs[f'map_index_indices'] = 0
+            for dim in map_config.dims:
+                nxgroup.makelink(nxsubentry[map_config.title].data[dim])
+                if f'{dim}_indices' in nxsubentry[map_config.title].data.attrs:
+                    nxgroup.attrs[f'{dim}_indices'] = \
+                        nxsubentry[map_config.title].data.attrs[
+                            f'{dim}_indices']
+            nxgroup.attrs['axes'] = axes
+            for dims in field_dims:
+                nxgroup.attrs[f'{dims["axes"]}_indices'] = dims['index']
+
+        # Get and add the calibration info to the detector
+        calibration = [
+            d for d in calibration_config.detectors \
+            if d.detector_name == detector.detector_name][0]
+        detector.add_calibration(calibration)
+
+        # Get the MCA bin energies
+        mca_bin_energies = detector.energies
+
+        # Blank out data below 25 keV as well as the last bin
+        energy_mask = np.where(mca_bin_energies >= 25.0, 1, 0)
+        energy_mask[-1] = 0
+
+        # Subtract the baseline
+        if detector.baseline:
+            # Local modules
+            from CHAP.edd.models import BaselineConfig
+            from CHAP.common.processor import ConstructBaseline
+
+            if isinstance(detector.baseline, bool):
+                detector.baseline = BaselineConfig()
+            if save_figures:
+                filename = os.path.join(
+                    outputdir,
+                    f'{detector.detector_name}_lat_param_refinement_'
+                    'baseline.png')
+            else:
+                filename = None
+            baseline, baseline_config = \
+                ConstructBaseline.construct_baseline(
+                    mca_data_summed, mask=energy_mask,
+                    tol=detector.baseline.tol, lam=detector.baseline.lam,
+                    max_iter=detector.baseline.max_iter,
+                    title=
+                        f'Baseline for detector {detector.detector_name}',
+                    xlabel='Energy (keV)', ylabel='Intensity (counts)',
+                    interactive=interactive, filename=filename)
+
+            mca_data_summed -= baseline
+            detector.baseline.lam = baseline_config['lambda']
+            detector.baseline.attrs['num_iter'] = \
+                baseline_config['num_iter']
+            detector.baseline.attrs['error'] = baseline_config['error']
+
+        # Get the unique HKLs and lattice spacings for the strain
+        # analysis materials
         hkls, ds = get_unique_hkls_ds(
             strain_analysis_config.materials,
             tth_tol=detector.hkl_tth_tol,
             tth_max=detector.tth_max)
 
-        self.select_material_params(
-            strain_analysis_config, detector_i, mca_data, mca_bin_energies,
-            interactive, save_figures, outputdir)
-        self.logger.debug(
-            'Starting lattice parameters: '
-            + str(strain_analysis_config.materials[0].lattice_parameters))
-        self.select_fit_mask_hkls(
-            strain_analysis_config, detector_i, mca_data, mca_bin_energies,
-            hkls, ds,
-            interactive, save_figures, outputdir)
+        if interactive or save_figures:
+            # Local modules
+            from CHAP.edd.utils import (
+                select_material_params,
+                select_mask_and_hkls,
+            )
+
+            # Interactively adjust the initial material parameters
+            tth = detector.tth_calibrated
+            if save_figures:
+                filename = os.path.join(
+                    outputdir,
+                    f'{detector.detector_name}_lat_param_refinement_'
+                    'initial_material_config.png')
+            else:
+                filename = None
+            strain_analysis_config.materials = select_material_params(
+                mca_bin_energies, mca_data_summed*energy_mask, tth,
+                preselected_materials=strain_analysis_config.materials,
+                label='Sum of all spectra in the map',
+                interactive=interactive, filename=filename)
+            self.logger.debug(
+                f'materials: {strain_analysis_config.materials}')
+    
+            # Interactively adjust the mask and HKLs used in the
+            # lattice parameter refinement
+            if save_figures:
+                filename = os.path.join(
+                    outputdir,
+                    f'{detector.detector_name}_lat_param_refinement_'
+                    'fit_mask_hkls.png')
+            else:
+                filename = None
+            include_bin_ranges, hkl_indices = \
+                select_mask_and_hkls(
+                    mca_bin_energies, mca_data_summed*energy_mask,
+                    hkls, ds, detector.tth_calibrated,
+                    preselected_bin_ranges=detector.include_bin_ranges,
+                    preselected_hkl_indices=detector.hkl_indices,
+                    detector_name=detector.detector_name,
+                    ref_map=mca_data*energy_mask,
+                    calibration_bin_ranges=detector.calibration_bin_ranges,
+                    label='Sum of all spectra in the map',
+                    interactive=interactive, filename=filename)
+            detector.include_energy_ranges = \
+                detector.get_include_energy_ranges(include_bin_ranges)
+            detector.hkl_indices = hkl_indices
+            self.logger.debug(
+                f'include_energy_ranges for detector {detector.detector_name}:'
+                f' {detector.include_energy_ranges}')
+            self.logger.debug(
+                f'hkl_indices for detector {detector.detector_name}:'
+                f' {detector.hkl_indices}')
+            if not detector.include_energy_ranges:
+                raise ValueError(
+                    'No value provided for include_energy_ranges. '
+                    'Provide them in the MCA Tth Calibration Configuration, '
+                    'or re-run the pipeline with the --interactive flag.')
+            if not detector.hkl_indices:
+                raise ValueError(
+                    'No value provided for hkl_indices. Provide them in '
+                    'the detector\'s MCA Tth Calibration Configuration, or'
+                    ' re-run the pipeline with the --interactive flag.')
 
+        effective_map_shape = mca_data.shape[:-1]
+        mask = detector.mca_mask()
+        energies = mca_bin_energies[mask]
+        intensities = np.empty(
+            (*effective_map_shape, len(energies)), dtype=np.float64)
+        for map_index in np.ndindex(effective_map_shape):
+            if detector.baseline:
+                intensities[map_index] = \
+                    (mca_data[map_index]-baseline).astype(
+                        np.float64)[mask]
+            else:
+                intensities[map_index] = \
+                    mca_data[map_index].astype(np.float64)[mask]
+        mean_intensity = np.mean(
+            intensities, axis=tuple(range(len(effective_map_shape))))
+        hkls_fit = np.asarray([hkls[i] for i in detector.hkl_indices])
+        ds_fit = np.asarray([ds[i] for i in detector.hkl_indices])
+        Rs = np.sqrt(np.sum(hkls_fit**2, 1))
+        peak_locations = get_peak_locations(
+            ds_fit, detector.tth_calibrated)
+
+        map_config = strain_analysis_config.map_config
+        nxprocess = nxsubentry[f'{map_config.title}_lat_par_refinement']
+        nxprocess[detector.detector_name] = NXdetector()
+        nxdetector = nxprocess[detector.detector_name]
+        nxdetector.local_name = detector.detector_name
+        nxdetector.detector_config = dumps(detector.dict())
+        nxdetector.data = NXdata()
+        det_nxdata = nxdetector.data
+        linkdims(
+            det_nxdata,
+            {'axes': 'energy', 'index': len(effective_map_shape)})
+        det_nxdata.energy = NXfield(value=energies, attrs={'units': 'keV'})
+        det_nxdata.intensity = NXfield(
+            value=intensities,
+            shape=(*effective_map_shape, len(energies)),
+            dtype=np.float64,
+            attrs={'units': 'counts'})
+        det_nxdata.mean_intensity = mean_intensity
+
+        # Get the interplanar spacings measured for each fit HKL peak
+        # at every point in the map to get the refined estimate
+        # for the material's lattice parameter
         (uniform_fit_centers, uniform_fit_centers_errors,
          uniform_fit_amplitudes, uniform_fit_amplitudes_errors,
          uniform_fit_sigmas, uniform_fit_sigmas_errors,
@@ -359,311 +592,941 @@ class LatticeParameterRefinementProcessor(Processor):
          unconstrained_fit_sigmas, unconstrained_fit_sigmas_errors,
          unconstrained_best_fit, unconstrained_residuals,
          unconstrained_redchi, unconstrained_success) = \
-            self.get_spectra_fits(
-                strain_analysis_config, detector_i,
-                mca_data, mca_bin_energies, hkls, ds)
+            get_spectra_fits(
+                intensities, energies, peak_locations, detector)
+        Rs_map = Rs.repeat(np.prod(effective_map_shape))
+        d_uniform = get_peak_locations(
+            np.asarray(uniform_fit_centers), detector.tth_calibrated)
+        a_uniform = (Rs_map * d_uniform.flatten()).reshape(d_uniform.shape)
+        a_uniform = a_uniform.mean(axis=0)
+        a_uniform_mean = float(a_uniform.mean())
+        d_unconstrained = get_peak_locations(
+            unconstrained_fit_centers, detector.tth_calibrated)
+        a_unconstrained = (
+            Rs_map * d_unconstrained.flatten()).reshape(d_unconstrained.shape)
+        a_unconstrained = np.moveaxis(a_unconstrained, 0, -1)
+        a_unconstrained_mean = float(a_unconstrained.mean())
+        self.logger.warning(
+            'Lattice parameter refinement assumes cubic lattice')
+        self.logger.info(
+            f'Refined lattice parameter from uniform fit: {a_uniform_mean}')
+        self.logger.info(
+            'Refined lattice parameter from unconstrained fit: '
+            f'{a_unconstrained_mean}')
+        nxdetector.lat_pars = NXcollection()
+        nxdetector.lat_pars.uniform = NXdata()
+        nxdata = nxdetector.lat_pars.uniform
+        nxdata.nxsignal = NXfield(
+            value=a_uniform, name='a_uniform', attrs={'units': r'\AA'})
+        linkdims(nxdata)
+        nxdetector.lat_pars.a_uniform_mean = float(a_uniform.mean())
+        nxdetector.lat_pars.unconstrained = NXdata()
+        nxdata = nxdetector.lat_pars.unconstrained
+        nxdata.nxsignal = NXfield(
+            value=a_unconstrained, name='a_unconstrained',
+            attrs={'units': r'\AA'})
+        nxdata.hkl_index = detector.hkl_indices
+        linkdims(
+            nxdata,
+            {'axes': 'hkl_index', 'index': len(effective_map_shape)})
+        nxdetector.lat_pars.a_unconstrained_mean = a_unconstrained_mean
 
         # Get the interplanar spacings measured for each fit HKL peak
-        # at every point in the map.
-        from scipy.constants import physical_constants
-        hc = 1e7 * physical_constants['Planck constant in eV/Hz'][0] \
-             * physical_constants['speed of light in vacuum'][0]
-        d_measured = hc / \
-             (2.0 \
-              * unconstrained_fit_centers \
-              * np.sin(np.radians(detector.tth_calibrated / 2.0)))
-        # Convert interplanar spacings to lattice parameters
-        self.logger.warning('Implemented for cubic materials only!')
-        fit_hkls  = np.asarray([hkls[i] for i in detector.hkl_indices])
-        Rs = np.sqrt(np.sum(fit_hkls**2, 1))
-        a_measured = Rs[:, None] * d_measured
-        # Average all computed lattice parameters for every fit HKL
-        # peak at every point in the map to get the refined estimate
-        # for the material's lattice parameter
-        a_refined = float(np.mean(a_measured))
-        return [a_refined, a_refined, a_refined, 90.0, 90.0, 90.0]
+        # at the spectrum averaged over every point in the map to get
+        # the refined estimate for the material's lattice parameter
+        (uniform_fit_centers, uniform_fit_centers_errors,
+         uniform_fit_amplitudes, uniform_fit_amplitudes_errors,
+         uniform_fit_sigmas, uniform_fit_sigmas_errors,
+         uniform_best_fit, uniform_residuals,
+         uniform_redchi, uniform_success,
+         unconstrained_fit_centers, unconstrained_fit_centers_errors,
+         unconstrained_fit_amplitudes, unconstrained_fit_amplitudes_errors,
+         unconstrained_fit_sigmas, unconstrained_fit_sigmas_errors,
+         unconstrained_best_fit, unconstrained_residuals,
+         unconstrained_redchi, unconstrained_success) = \
+            get_spectra_fits(
+                mean_intensity, energies, peak_locations, detector)
+        d_uniform = get_peak_locations(
+            np.asarray(uniform_fit_centers), detector.tth_calibrated)
+        d_unconstrained = get_peak_locations(
+            np.asarray(unconstrained_fit_centers), detector.tth_calibrated)
+        a_uniform = float((Rs * d_uniform).mean())
+        a_unconstrained = (Rs * d_unconstrained)
+        self.logger.warning(
+            'Lattice parameter refinement assumes cubic lattice')
+        self.logger.info(
+            'Refined lattice parameter from uniform fit over averaged '
+            f'spectrum: {a_uniform}')
+        self.logger.info(
+            'Refined lattice parameter from unconstrained fit over averaged '
+            f'spectrum: {a_unconstrained}')
+        nxdetector.lat_pars_mean_intensity = NXcollection()
+        nxdetector.lat_pars_mean_intensity.a_uniform = a_uniform
+        nxdetector.lat_pars_mean_intensity.a_unconstrained = a_unconstrained
+        nxdetector.lat_pars_mean_intensity.a_unconstrained_mean = \
+            float(a_unconstrained.mean())
 
-    def get_mca_bin_energies(self, strain_analysis_config):
-        """Return a list of the MCA bin energies for each detector.
+        if interactive or save_figures:
+            # Third party modules
+            import matplotlib.pyplot as plt
 
-        :param strain_analysis_config: Strain analysis configuration
-            containing a list of detectors to return the bin energies
-            for.
-        :type strain_analysis_config: CHAP.edd.models.StrainAnalysisConfig
-        :returns: List of MCA bin energies
-        :rtype: list[numpy.ndarray]
+            fig, ax = plt.subplots(figsize=(11, 8.5))
+            ax.set_title(f'Detector {detector.detector_name}: '
+                         'Lattice Parameter Refinement')
+            ax.set_xlabel('Detector energy (keV)')
+            ax.set_ylabel('Mean intensity (a.u.)')
+            ax.plot(energies, mean_intensity, 'k.', label='MCA data')
+            ax.plot(energies, uniform_best_fit, 'r', label='Best uniform fit')
+            ax.plot(
+                energies, unconstrained_best_fit, 'b',
+                label='Best unconstrained fit')
+            ax.legend()
+            for i, loc in enumerate(peak_locations):
+                ax.axvline(loc, c='k', ls='--')
+                ax.text(loc, 1, str(hkls_fit[i])[1:-1],
+                              ha='right', va='top', rotation=90,
+                              transform=ax.get_xaxis_transform())
+            if save_figures:
+                fig.tight_layout()#rect=(0, 0, 1, 0.95))
+                figfile = os.path.join(
+                    outputdir, f'{detector.detector_name}_lat_param_fits.png')
+                plt.savefig(figfile)
+                self.logger.info(f'Saved figure to {figfile}')
+            if interactive:
+                plt.show()
+
+        return [
+            a_uniform, a_uniform, a_uniform, 90., 90., 90.]
+
+
+class MCAEnergyCalibrationProcessor(Processor):
+    """Processor to return parameters for linearly transforming MCA
+    channel indices to energies (in keV). Procedure: provide a
+    spectrum from the MCA element to be calibrated and the theoretical
+    location of at least one peak present in that spectrum (peak
+    locations must be given in keV). It is strongly recommended to use
+    the location of fluorescence peaks whenever possible, _not_
+    diffraction peaks, as this Processor does not account for
+    2&theta."""
+    def process(
+            self, data, config=None, centers_range=20, fwhm_min=None,
+            fwhm_max=None, max_energy_kev=200.0, background=None,
+            baseline=False, save_figures=False, interactive=False,
+            inputdir='.', outputdir='.'):
+        """For each detector in the `MCAEnergyCalibrationConfig`
+        provided with `data`, fit the specified peaks in the MCA
+        spectrum specified. Using the difference between the provided
+        peak locations and the fit centers of those peaks, compute
+        the correction coefficients to convert uncalibrated MCA
+        channel energies to calibrated channel energies. For each
+        detector, set `energy_calibration_coeffs` in the calibration
+        config provided to these values and return the updated
+        configuration.
+
+        :param data: An energy Calibration configuration.
+        :type data: PipelineData
+        :param config: Initialization parameters for an instance of
+            CHAP.edd.models.MCAEnergyCalibrationConfig, defaults to
+            `None`.
+        :type config: dict, optional
+        :param centers_range: Set boundaries on the peak centers in
+            MCA channels when performing the fit. The min/max
+            possible values for the peak centers will be the initial
+            values ± `centers_range`. Defaults to `20`.
+        :type centers_range: int, optional
+        :param fwhm_min: Lower bound on the peak FWHM in MCA channels
+            when performing the fit, defaults to `None`.
+        :type fwhm_min: float, optional
+        :param fwhm_max: Lower bound on the peak FWHM in MCA channels
+            when performing the fit, defaults to `None`.
+        :type fwhm_max: float, optional
+        :param max_energy_kev: Maximum channel energy of the MCA in
+            keV, defaults to `200.0`.
+        :type max_energy_kev: float, optional
+        :param background: Background model for peak fitting.
+        :type background: str, list[str], optional
+        :param baseline: Automated baseline subtraction configuration,
+            defaults to `False`.
+        :type baseline: bool, BaselineConfig, optional
+        :param save_figures: Save .pngs of plots for checking inputs &
+            outputs of this Processor, defaults to `False`.
+        :type save_figures: bool, optional
+        :param interactive: Allows for user interactions, defaults to
+            `False`.
+        :type interactive: bool, optional
+        :param inputdir: Input directory, used only if files in the
+            input configuration are not absolute paths,
+            defaults to `'.'`.
+        :type inputdir: str, optional
+        :param outputdir: Directory to which any output figures will
+            be saved, defaults to `'.'`.
+        :type outputdir: str, optional
+        :returns: Dictionary representing the energy-calibrated
+            version of the calibrated configuration.
+        :rtype: dict
         """
-        mca_bin_energies = []
-        for i, detector in enumerate(strain_analysis_config.detectors):
-            mca_bin_energies.append(
-                detector.slope_calibrated
-                * np.linspace(0, detector.max_energy_kev, detector.num_bins)
-                + detector.intercept_calibrated)
-        return mca_bin_energies
-
-    def add_detector_calibrations(
-            self, strain_analysis_config, ceria_calibration_config):
-        """Add calibrated quantities to the detectors configured in
-        `strain_analysis_config`, modifying `strain_analysis_config`
-        in place.
-
-        :param strain_analysis_config: Strain analysisi configuration
-            containing a list of detectors to add calibration values
-            to.
-        :type strain_analysis_config: CHAP.edd.models.StrainAnalysisConfig
-        :param ceria_calibration_config: Configuration of a completed
-            ceria calibration containing a list of detector swith the
-            same names as those in `strain_analysis_config`
-        :returns: None"""
-        for detector in strain_analysis_config.detectors:
-            calibration = [
-                d for d in ceria_calibration_config.detectors \
-                if d.detector_name == detector.detector_name][0]
-            detector.add_calibration(calibration)
-
-    def select_fit_mask_hkls(
-            self, strain_analysis_config, detector_i,
-            mca_data, mca_bin_energies, hkls, ds,
-            interactive, save_figures, outputdir):
-        """Select the maks & HKLs to use for fitting for each
-        detector. Update `strain_analysis_config` with new values for
-        `hkl_indices` and `include_bin_ranges` if needed.
-
-        :param strain_analysis_config: Strain analysis configuration
-        :type strain_analysis_config: CHAP.edd.models.StrainAnalysisConfig
-        :param detector_i: Index of the detector in
-            `strain_analysis_config` to select mask & HKLs for.
-        :type detector_i: int
-        :param mca_data: List of maps of MCA spectra for all detectors
-            in `strain_analysis_config`
-        :type mca_data: list[numpy.ndarray]
-        :param mca_bin_energies: List of MCA bin energies for all
-            detectors in `strain_analysis_config`
-        :type mca_bin_energies: list[numpy.ndarray]
-        :param hkls: Nominal HKL peak energy locations for the
-            material in `strain_analysis_config`
-        :type hkls: list[float]
-        :param ds: Nominal d-spacing for the material in
-            `strain_analysis_config`
-        :type ds: list[float]
-        :param interactive: Boolean to indicate whether interactive
-            matplotlib figures should be presented
-        :type interactive: bool
-        :param save_figures: Boolean to indicate whether figures
-            indicating the selection should be saved
+        # Third party modules
+        from nexusformat.nexus import (
+            NXentry,
+            NXroot,
+        )
+
+        # Local modules
+        from CHAP.edd.models import (
+            BaselineConfig,
+            MCAElementCalibrationConfig,
+        )
+        from CHAP.utils.general import (
+            is_int,
+            is_num,
+            is_str_series,
+        )
+
+        # Load the detector data
+        # FIX input a numpy and create/use NXobject to numpy proc
+        # FIX right now spec info is lost in output yaml, add to it?
+        nxroot = self.get_data(data, 'SpecReader')
+        if not isinstance(nxroot, NXroot):
+            raise RuntimeError('No valid NXroot data in input pipeline data')
+        nxentry = nxroot[nxroot.default]
+
+        # Load the validated energy calibration configuration
+        try:
+            calibration_config = self.get_config(
+                data, 'edd.models.MCAEnergyCalibrationConfig',
+                inputdir=inputdir)
+        except Exception as data_exc:
+            self.logger.info('No valid calibration config in input pipeline '
+                             'data, using config parameter instead.')
+            try:
+                # Local modules
+                from CHAP.edd.models import MCAEnergyCalibrationConfig
+
+                calibration_config = MCAEnergyCalibrationConfig(
+                    **config, inputdir=inputdir)
+            except Exception as dict_exc:
+                raise RuntimeError from dict_exc
+
+        # Validate the detector configuration
+        available_detector_indices = [
+            int(d) for d in nxentry.detector_names]
+        if calibration_config.detectors is None:
+            calibration_config.detectors = [
+                MCAElementCalibrationConfig(detector_name=d)
+                for d in nxentry.detector_names]
+        else:
+            for detector in deepcopy(calibration_config.detectors):
+                index = int(detector.detector_name)
+                if index not in available_detector_indices:
+                    self.logger.warning(
+                        f'Skipping detector {int} (no raw data)')
+                    calibration_config.detectors.remove(detector)
+
+        # Validate the fit index range
+        if calibration_config.fit_index_ranges is None and not interactive:
+            raise RuntimeError(
+                'If `fit_index_ranges` is not explicitly provided, '
+                + self.__class__.__name__
+                + ' must be run with `interactive=True`.')
+
+        # Validate the optional inputs
+        if not is_int(centers_range, gt=0, log=False):
+            raise RuntimeError(
+                f'Invalid centers_range parameter ({centers_range})')
+        if fwhm_min is not None and not is_int(fwhm_min, gt=0, log=False):
+            raise RuntimeError(f'Invalid fwhm_min parameter ({fwhm_min})')
+        if fwhm_max is not None and not is_int(fwhm_max, gt=0, log=False):
+            raise RuntimeError(f'Invalid fwhm_max parameter ({fwhm_max})')
+        if not is_num(max_energy_kev, gt=0, log=False):
+            raise RuntimeError(
+                f'Invalid max_energy_kev parameter ({max_energy_kev})')
+        if background is not None:
+            if isinstance(background, str):
+                background = [background]
+            elif not is_str_series(background, log=False):
+                raise RuntimeError(
+                    f'Invalid background parameter ({background})')
+        if isinstance(baseline, bool):
+            if baseline:
+                baseline = BaselineConfig()
+        else:
+            try:
+                baseline = BaselineConfig(**baseline)
+            except Exception as dict_exc:
+                raise RuntimeError from dict_exc
+
+        # Collect and sum the detector data
+        mca_data = []
+        for scan_name in nxentry.spec_scans:
+            for scan_number, scan_data in nxentry.spec_scans[scan_name].items():
+                mca_data.append(scan_data.data.data.nxdata)
+        summed_detector_data = np.asarray(mca_data).sum(axis=(0,1))
+
+        # Get the detectors' num_bins parameter
+        for detector in calibration_config.detectors:
+            if detector.num_bins is None:
+                detector.num_bins = summed_detector_data.shape[-1]
+
+        # Check each detector's include_energy_ranges field against the
+        # flux file, if available.
+        if calibration_config.flux_file is not None:
+            flux = np.loadtxt(flux_file)
+            flux_file_energies = flux[:,0]/1.e3
+            flux_e_min = flux_file_energies.min()
+            flux_e_max = flux_file_energies.max()
+            for detector in calibration_config.detectors:
+                for i, (det_e_min, det_e_max) in enumerate(
+                        deepcopy(detector.include_energy_ranges)):
+                    if det_e_min < flux_e_min or det_e_max > flux_e_max:
+                        energy_range = [float(max(det_e_min, flux_e_min)),
+                                        float(min(det_e_max, flux_e_max))]
+                        print(
+                            f'WARNING: include_energy_ranges[{i}] out of range'
+                            f' ({detector.include_energy_ranges[i]}): adjusted'
+                            f' to {energy_range}')
+                        detector.include_energy_ranges[i] = energy_range
+
+        # Calibrate detector channel energies based on fluorescence peaks
+        for detector in calibration_config.detectors:
+            index = available_detector_indices.index(
+                int(detector.detector_name))
+            if background is not None:
+                detector.background = background.copy()
+            if baseline:
+                detector.baseline = baseline.model_copy()
+            detector.energy_calibration_coeffs = self.calibrate(
+                calibration_config, detector, summed_detector_data[index],
+                centers_range, fwhm_min, fwhm_max, max_energy_kev,
+                save_figures, interactive, outputdir)
+
+        return calibration_config.dict()
+
+    def calibrate(
+            self, calibration_config, detector, spectrum, centers_range,
+            fwhm_min, fwhm_max, max_energy_kev, save_figures, interactive,
+            outputdir):
+        """Return energy_calibration_coeffs (a, b, and c) for
+        quadratically converting the current detector's MCA channels
+        to bin energies.
+
+        :param calibration_config: Energy calibration configuration.
+        :type calibration_config: MCAEnergyCalibrationConfig
+        :param detector: Configuration of the current detector.
+        :type detector: MCAElementCalibrationConfig
+        :param spectrum: Summed MCA spectrum for the current detector.
+        :type spectrum: numpy.ndarray
+        :param centers_range: Set boundaries on the peak centers in
+            MCA channels when performing the fit. The min/max
+            possible values for the peak centers will be the initial
+            values &pm; `centers_range`. Defaults to `20`.
+        :type centers_range: int, optional
+        :param fwhm_min: Lower bound on the peak FWHM in MCA channels
+            when performing the fit, defaults to `None`.
+        :type fwhm_min: float, optional
+        :param fwhm_max: Lower bound on the peak FWHM in MCA channels
+            when performing the fit, defaults to `None`.
+        :type fwhm_max: float, optional
+        :param max_energy_kev: Maximum channel energy of the MCA in
+            keV, defaults to `200.0`.
+        :type max_energy_kev: float
+        :param save_figures: Save .pngs of plots for checking inputs &
+            outputs of this Processor.
         :type save_figures: bool
-        :param outputdir: Where to save figures (if `save_figures` is
-            `True`)
+        :param interactive: Allows for user interactions.
+        :type interactive: bool
+        :param outputdir: Directory to which any output figures will
+            be saved.
         :type outputdir: str
-        :returns: None
+        :returns: Slope and intercept for linearly correcting the
+            detector's MCA channels to bin energies.
+        :rtype: tuple[float, float]
         """
-        if not interactive and not save_figures:
-            return
-        import matplotlib.pyplot as plt
-        import numpy as np
-        from CHAP.edd.utils import select_mask_and_hkls
-
-        detector = strain_analysis_config.detectors[detector_i]
-        fig, include_bin_ranges, hkl_indices = \
-            select_mask_and_hkls(
-                mca_bin_energies[detector_i],
-                np.sum(mca_data[detector_i], axis=0),
-                hkls, ds,
-                detector.tth_calibrated,
-                detector.include_bin_ranges, detector.hkl_indices,
-                detector.detector_name, mca_data[detector_i],
-                calibration_bin_ranges=detector.calibration_bin_ranges,
-                label='Sum of all spectra in the map',
-                interactive=interactive)
-        detector.include_energy_ranges = detector.get_energy_ranges(
-            include_bin_ranges)
-        detector.hkl_indices = hkl_indices
+        # Third party modules
+        from nexusformat.nexus import (
+            NXdata,
+            NXfield,
+        )
+
+        # Local modules
+        from CHAP.utils.fit import FitProcessor
+        from CHAP.utils.general import (
+            index_nearest,
+            index_nearest_down,
+            index_nearest_up,
+            select_mask_1d,
+        )
+
+        self.logger.info(f'Calibrating detector {detector.detector_name}')
+
+        # Get the MCA bin energies
+        uncalibrated_energies = np.linspace(
+            0, max_energy_kev, detector.num_bins)
+        bins = np.arange(detector.num_bins, dtype=np.int16)
+
+        # Blank out data below 25keV as well as the last bin
+        energy_mask = np.where(uncalibrated_energies >= 25.0, 1, 0)
+        energy_mask[-1] = 0
+        spectrum = spectrum*energy_mask
+
+        # Subtract the baseline
+        if detector.baseline:
+            # Local modules
+            from CHAP.common.processor import ConstructBaseline
+
+            if save_figures:
+                filename = os.path.join(outputdir,
+                                        f'{detector.detector_name}_energy_'
+                                        'calibration_baseline.png')
+            else:
+                filename = None
+            baseline, baseline_config = ConstructBaseline.construct_baseline(
+                spectrum, mask=energy_mask, tol=detector.baseline.tol,
+                lam=detector.baseline.lam, max_iter=detector.baseline.max_iter,
+                title=f'Baseline for detector {detector.detector_name}',
+                xlabel='Energy (keV)', ylabel='Intensity (counts)',
+                interactive=interactive, filename=filename)
+
+            spectrum -= baseline
+            detector.baseline.lam = baseline_config['lambda']
+            detector.baseline.attrs['num_iter'] = baseline_config['num_iter']
+            detector.baseline.attrs['error'] = baseline_config['error']
+
+        # Select the mask/detector channel ranges for fitting
         if save_figures:
-            fig.savefig(os.path.join(
+            filename = os.path.join(
                 outputdir,
-                f'{detector.detector_name}_strainanalysis_'
-                'fit_mask_hkls.png'))
-        plt.close()
-
-    def select_material_params(self, strain_analysis_config, detector_i,
-                               mca_data, mca_bin_energies,
-                               interactive, save_figures, outputdir):
-        """Select initial material parameters to use for determining
-        nominal HKL peak locations. Modify `strain_analysis_config` in
-        place if needed.
-
-        :param strain_analysis_config: Strain analysis configuration
-        :type strain_analysis_config: CHAP.edd.models.StrainAnalysisConfig
-        :param detector_i: Index of the detector in
-            `strain_analysis_config` to select mask & HKLs for.
-        :type detector_i: int
-        :param mca_data: List of maps of MCA spectra for all detectors
-            in `strain_analysis_config`
-        :type mca_data: list[numpy.ndarray]
-        :param mca_bin_energies: List of MCA bin energies for all
-            detectors in `strain_analysis_config`
-        :type mca_bin_energies: list[numpy.ndarray]
-        :param interactive: Boolean to indicate whether interactive
-            matplotlib figures should be presented
-        :type interactive: bool
-        :param save_figures: Boolean to indicate whether figures
-            indicating the selection should be saved
-        :type save_figures: bool
-        :param outputdir: Where to save figures (if `save_figures` is
-            `True`)
-        :type outputdir: str
-        :returns: None
-        """
-        if not interactive and not save_figures:
-            return
-        from CHAP.edd.utils import select_material_params
-        import matplotlib.pyplot as plt
-        import numpy as np
-        fig, strain_analysis_config.materials = select_material_params(
-            mca_bin_energies[detector_i], np.sum(mca_data[detector_i], axis=0),
-            strain_analysis_config.detectors[detector_i].tth_calibrated,
-            strain_analysis_config.materials,
-            label='Sum of all spectra in the map', interactive=interactive)
+                f'{detector.detector_name}_mca_energy_calibration_mask.png')
+        else:
+            filename = None
+        mask, fit_index_ranges = select_mask_1d(
+            spectrum, x=bins,
+            preselected_index_ranges=calibration_config.fit_index_ranges,
+            xlabel='Detector channel', ylabel='Intensity',
+            min_num_index_ranges=1, interactive=interactive,
+            filename=filename)
         self.logger.debug(
-                f'materials: {strain_analysis_config.materials}')
+            f'Selected index ranges to fit: {fit_index_ranges}')
+
+        # Get the intial peak positions for fitting
+        max_peak_energy = calibration_config.peak_energies[
+            calibration_config.max_peak_index]
+        peak_energies = list(np.sort(calibration_config.peak_energies))
+        max_peak_index = peak_energies.index(max_peak_energy)
         if save_figures:
-            detector_name = \
-                strain_analysis_config.detectors[detector_i].detector_name
-            fig.savefig(os.path.join(
+            filename = os.path.join(
                 outputdir,
-                f'{detector_name}_strainanalysis_'
-                'material_config.png'))
+                f'{detector.detector_name}'
+                    '_mca_energy_calibration_initial_peak_positions.png')
+        else:
+            filename = None
+        input_indices = [index_nearest(uncalibrated_energies, energy)
+                         for energy in peak_energies]
+        initial_peak_indices = self._get_initial_peak_positions(
+            spectrum*np.asarray(mask).astype(np.int32), fit_index_ranges,
+            input_indices, max_peak_index, interactive, filename,
+            detector.detector_name)
+
+        # Construct the fit model
+        models = []
+        if detector.background is not None:
+            if isinstance(detector.background, str):
+                models.append(
+                    {'model': detector.background, 'prefix': 'bkgd_'})
+            else:
+                for model in detector.background:
+                    models.append({'model': model, 'prefix': f'{model}_'})
+        models.append(
+            {'model': 'multipeak', 'centers': initial_peak_indices,
+             'centers_range': centers_range, 'fwhm_min': fwhm_min,
+             'fwhm_max': fwhm_max})
+        self.logger.debug('Fitting spectrum')
+        fit = FitProcessor()
+        spectrum_fit = fit.process(
+                NXdata(NXfield(spectrum[mask], 'y'), NXfield(bins[mask], 'x')),
+                {'models': models, 'method': 'trf'})
+
+        fit_peak_indices = sorted([
+            spectrum_fit.best_values[f'peak{i+1}_center']
+            for i in range(len(initial_peak_indices))])
+        self.logger.debug(f'Fit peak centers: {fit_peak_indices}')
+
+        #RV for now stick with a linear energy correction
+        fit = FitProcessor()
+        energy_fit = fit.process(
+                NXdata(
+                    NXfield(peak_energies, 'y'),
+                    NXfield(fit_peak_indices, 'x')),
+                {'models': [{'model': 'linear'}]})
+        a = 0.0
+        b = float(energy_fit.best_values['slope'])
+        c = float(energy_fit.best_values['intercept'])
+
+        # Reference plot to see fit results:
+        if interactive or save_figures:
+            # Third part modules
+            import matplotlib.pyplot as plt
+
+            fig, axs = plt.subplots(1, 2, figsize=(11, 4.25))
+            fig.suptitle(
+                f'Detector {detector.detector_name} Energy Calibration')
+            # Left plot: raw MCA data & best fit of peaks
+            axs[0].set_title(f'MCA Spectrum Peak Fit')
+            axs[0].set_xlabel('Detector channel')
+            axs[0].set_ylabel('Intensity (a.u)')
+            axs[0].plot(bins[mask], spectrum[mask], 'b.', label='MCA data')
+            axs[0].plot(
+                bins[mask], spectrum_fit.best_fit, 'r', label='Best fit')
+            axs[0].legend()
+            # Right plot: linear fit of theoretical peak energies vs
+            # fit peak locations
+            axs[1].set_title(
+                'Channel Energies vs. Channel Indices')
+            axs[1].set_xlabel('Detector channel')
+            axs[1].set_ylabel('Channel energy (keV)')
+            axs[1].plot(fit_peak_indices, peak_energies,
+                        c='b', marker='o', ms=6, mfc='none', ls='',
+                        label='Initial peak positions')
+            axs[1].plot(fit_peak_indices, energy_fit.best_fit,
+                        c='k', marker='+', ms=6, ls='',
+                        label='Fitted peak positions')
+            axs[1].plot(bins[mask], b*bins[mask] + c, 'r',
+                        label='Best linear fit')
+            axs[1].legend()
+            # Add text box showing computed values of linear E
+            # correction parameters
+            axs[1].text(
+                0.98, 0.02,
+                'Calibrated values:\n\n'
+                    f'Linear coefficient:\n    {b:.5f} $keV$/channel\n\n'
+                    f'Constant offset:\n    {c:.5f} $keV$',
+                ha='right', va='bottom', ma='left',
+                transform=axs[1].transAxes,
+                bbox=dict(boxstyle='round',
+                          ec=(1., 0.5, 0.5),
+                          fc=(1., 0.8, 0.8, 0.8)))
+
+            fig.tight_layout()
+
+            if save_figures:
+                figfile = os.path.join(
+                    outputdir,
+                    f'{detector.detector_name}_energy_calibration_fit.png')
+                plt.savefig(figfile)
+                self.logger.info(f'Saved figure to {figfile}')
+            if interactive:
+                plt.show()
+
+        return [a, b, c]
+
+    def _get_initial_peak_positions(
+            self, y, index_ranges, input_indices, input_max_peak_index,
+            interactive, filename, detector_name, reset_flag=0):
+        # Third party modules
+        import matplotlib.pyplot as plt
+        from matplotlib.widgets import TextBox, Button
+
+        def change_fig_title(title):
+            if fig_title:
+                fig_title[0].remove()
+                fig_title.pop()
+            fig_title.append(plt.figtext(*title_pos, title, **title_props))
+
+        def change_error_text(error=''):
+            if error_texts:
+                error_texts[0].remove()
+                error_texts.pop()
+            error_texts.append(plt.figtext(*error_pos, error, **error_props))
+
+        def reset(event):
+            """Callback function for the "Reset" button."""
+            peak_indices.clear()
+            plt.close()
+
+        def confirm(event):
+            """Callback function for the "Confirm" button."""
+            if error_texts:
+                error_texts[0].remove()
+                error_texts.pop()
+            plt.close()
+
+        def find_peaks(min_height=0.05, min_width=5, tolerance=0.05):
+            # Third party modules
+            from scipy.signal import find_peaks as find_peaks_scipy
+
+            # Find peaks
+            peaks = find_peaks_scipy(y, height=min_height,
+                prominence=0.05*y.max(), width=min_width)
+            available_peak_indices = list(peaks[0])
+            max_peak_index = np.asarray(peaks[1]).argmax()
+            ratio = (available_peak_indices[max_peak_index]
+                     / input_indices[input_max_peak_index])
+            peak_indices = [-1]*num_peak
+            peak_indices[input_max_peak_index] = \
+                    available_peak_indices[max_peak_index]
+            available_peak_indices.pop(max_peak_index)
+            for i, input_index in enumerate(input_indices):
+                if i != input_max_peak_index:
+                    index_guess = int(input_index * ratio)
+                    for index in available_peak_indices.copy():
+                        if abs(index_guess-index) < tolerance*index:
+                            index_guess = index
+                            available_peak_indices.remove(index)
+                            break
+                    peak_indices[i] = index_guess
+            return peak_indices
+
+        def select_peaks():
+            """Manually select initial peak indices."""
+            peak_indices = []
+            while len(set(peak_indices)) < num_peak:
+                change_fig_title(f'Select {num_peak} peak positions')
+                peak_indices = [
+                    int(pt[0]) for pt in plt.ginput(num_peak, timeout=15)]
+                if len(set(peak_indices)) < num_peak:
+                    error_text = f'Choose {num_peak} unique position'
+                    peak_indices.clear()
+                outside_indices = []
+                for index in peak_indices:
+                    if not any(True if low <= index <= upp else False
+                           for low, upp in index_ranges):
+                        outside_indices.append(index)
+                if len(outside_indices) == 1:
+                    error_text = \
+                        f'Index {outside_indices[0]} outside of selection ' \
+                        f'region ({index_ranges}), try again'
+                    peak_indices.clear()
+                elif outside_indices:
+                    error_text = \
+                        f'Indices {outside_indices} outside of selection ' \
+                        'region, try again'
+                    peak_indices.clear()
+                if not peak_indices:
+                    plt.close()
+                    fig, ax = plt.subplots(figsize=(11, 8.5))
+                    ax.set_xlabel('Detector channel', fontsize='x-large')
+                    ax.set_ylabel('Intensity', fontsize='x-large')
+                    ax.set_xlim(index_ranges[0][0], index_ranges[-1][1])
+                    fig.subplots_adjust(bottom=0.0, top=0.85)
+                    ax.plot(np.arange(y.size), y, color='k')
+                    fig.subplots_adjust(bottom=0.2)
+                    change_error_text(error_text)
+                plt.draw()
+            return peak_indices
+
+        peak_indices = []
+        fig_title = []
+        error_texts = []
+
+        y = np.asarray(y)
+        if detector_name is None:
+            detector_name = ''
+        elif not isinstance(detector_name, str):
+            raise ValueError(
+                f'Invalid parameter `detector_name`: {detector_name}')
+        elif not reset_flag:
+            detector_name = f' on detector {detector_name}'
+        num_peak = len(input_indices)
+
+        # Setup the Matplotlib figure
+        title_pos = (0.5, 0.95)
+        title_props = {'fontsize': 'xx-large', 'horizontalalignment': 'center',
+                       'verticalalignment': 'bottom'}
+        error_pos = (0.5, 0.90)
+        error_props = {'fontsize': 'x-large', 'horizontalalignment': 'center',
+                       'verticalalignment': 'bottom'}
+        selected_peak_props = {
+            'color': 'red', 'linestyle': '-', 'linewidth': 2,
+            'marker': 10, 'markersize': 10, 'fillstyle': 'full'}
+
+        fig, ax = plt.subplots(figsize=(11, 8.5))
+        ax.plot(np.arange(y.size), y, color='k')
+        ax.set_xlabel('Detector channel', fontsize='x-large')
+        ax.set_ylabel('Intensity', fontsize='x-large')
+        ax.set_xlim(index_ranges[0][0], index_ranges[-1][1])
+        fig.subplots_adjust(bottom=0.0, top=0.85)
+
+        if not interactive:
+
+            peak_indices += find_peaks()
+
+            for index in peak_indices:
+                ax.axvline(index, **selected_peak_props)
+            change_fig_title('Initial peak positions from peak finding '
+                             f'routine{detector_name}')
+
+        else:
+
+            fig.subplots_adjust(bottom=0.2)
+
+            # Get initial peak indices
+            if not reset_flag:
+                peak_indices += find_peaks()
+                change_fig_title('Initial peak positions from peak finding '
+                                 f'routine{detector_name}')
+            if peak_indices:
+                for index in peak_indices:
+                    if not any(True if low <= index <= upp else False
+                           for low, upp in index_ranges):
+                        peak_indices.clear
+                        break
+            if not peak_indices:
+                peak_indices += select_peaks()
+                change_fig_title(
+                    'Selected initial peak positions{detector_name}')
+
+            for index in peak_indices:
+                ax.axvline(index, **selected_peak_props)
+
+            # Setup "Reset" button
+            if not reset_flag:
+                reset_btn = Button(
+                    plt.axes([0.1, 0.05, 0.15, 0.075]), 'Manually select')
+            else:
+                reset_btn = Button(
+                    plt.axes([0.1, 0.05, 0.15, 0.075]), 'Reset')
+            reset_cid = reset_btn.on_clicked(reset)
+
+            # Setup "Confirm" button
+            confirm_btn = Button(
+                plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm')
+            confirm_cid = confirm_btn.on_clicked(confirm)
+
+            plt.show()
+
+            # Disconnect all widget callbacks when figure is closed
+            reset_btn.disconnect(reset_cid)
+            confirm_btn.disconnect(confirm_cid)
+
+            # ... and remove the buttons before returning the figure
+            reset_btn.ax.remove()
+            confirm_btn.ax.remove()
+
+        if filename is not None:
+            fig_title[0].set_in_layout(True)
+            fig.tight_layout(rect=(0, 0, 1, 0.95))
+            fig.savefig(filename)
         plt.close()
 
-    def get_spectra_fits(
-            self, strain_analysis_config, detector_i,
-            mca_data, mca_bin_energies, hkls, ds):
-        """Return uniform and unconstrained fit results for all
-        spectra from a single detector.
-
-        :param strain_analysis_config: Strain analysis configuration
-        :type strain_analysis_config: CHAP.edd.models.StrainAnalysisConfig
-        :param detector_i: Index of the detector in
-            `strain_analysis_config` to select mask & HKLs for.
-        :type detector_i: int
-        :param mca_data: List of maps of MCA spectra for all detectors
-            in `strain_analysis_config`
-        :type mca_data: list[numpy.ndarray]
-        :param mca_bin_energies: List of MCA bin energies for all
-            detectors in `strain_analysis_config`
-        :type mca_bin_energies: list[numpy.ndarray]
-        :param hkls: Nominal HKL peak energy locations for the
-            material in `strain_analysis_config`
-        :type hkls: list[float]
-        :param ds: Nominal d-spacing for the material in
-            `strain_analysis_config`
-        :type ds: list[float]
-        :returns: Uniform and unconstrained centers, amplitdues,
-            sigmas (and errors for all three), best fits, residuals
-            between the best fits and the input spectra, reduced chi,
-            and fit success statuses.
-        :rtype: tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray,
-            numpy.ndarray, numpy.ndarray, numpy.ndarray,
-            numpy.ndarray, numpy.ndarray, numpy.ndarray,
-            numpy.ndarray, numpy.ndarray, numpy.ndarray,
-            numpy.ndarray, numpy.ndarray, numpy.ndarray,
-            numpy.ndarray, numpy.ndarray, numpy.ndarray,
-            numpy.ndarray, numpy.ndarray]
-        """
-        from CHAP.edd.utils import get_peak_locations, get_spectra_fits
-        detector = strain_analysis_config.detectors[detector_i]
-        self.logger.debug(
-            f'Fitting spectra from detector {detector.detector_name}')
-        mask = detector.mca_mask()
-        energies = mca_bin_energies[detector_i][mask]
-        intensities = np.empty(
-            (*strain_analysis_config.map_config.shape, len(energies)),
-            dtype='uint16')
-        for j, map_index in \
-            enumerate(np.ndindex(strain_analysis_config.map_config.shape)):
-            intensities[map_index] = \
-                mca_data[detector_i][j].astype('uint16')[mask]
-        fit_hkls  = np.asarray([hkls[i] for i in detector.hkl_indices])
-        fit_ds  = np.asarray([ds[i] for i in detector.hkl_indices])
-        peak_locations = get_peak_locations(
-            fit_ds, detector.tth_calibrated)
-        return get_spectra_fits(
-            intensities, energies, peak_locations, detector)
+        if interactive and len(peak_indices) != num_peak:
+            reset_flag += 1
+            return self._get_initial_peak_positions(
+                y, index_ranges, input_indices, input_max_peak_index,
+                interactive, filename, detector_name, reset_flag=reset_flag)
+        return peak_indices
 
 
-class MCACeriaCalibrationProcessor(Processor):
-    """A Processor using a CeO2 scan to obtain tuned values for the
-    bragg diffraction angle and linear correction parameters for MCA
-    channel energies for an EDD experimental setup.
+class MCATthCalibrationProcessor(Processor):
+    """Processor to calibrate the 2&theta angle and fine tune the
+    energy calibration coefficients for an EDD experimental setup.
     """
 
-    def process(self,
-                data,
-                config=None,
-                save_figures=False,
-                inputdir='.',
-                outputdir='.',
-                interactive=False):
-        """Return tuned values for 2&theta and linear correction
-        parameters for the MCA channel energies.
+    def process(
+            self, data, config=None, tth_initial_guess=None,
+            include_energy_ranges=None, calibration_method='iterate_tth',
+            quadratic_energy_calibration=False, centers_range=20,
+            fwhm_min=None, fwhm_max=None, background=None, baseline=False,
+            save_figures=False, inputdir='.', outputdir='.',
+            interactive=False):
+        """Return the calibrated 2&theta value and the fine tuned
+        energy calibration coefficients to convert MCA channel
+        indices to MCA channel energies.
 
         :param data: Input configuration for the raw data & tuning
             procedure.
         :type data: list[PipelineData]
         :param config: Initialization parameters for an instance of
-            CHAP.edd.models.MCACeriaCalibrationConfig, defaults to
-            None.
+            CHAP.edd.models.MCATthCalibrationConfig,
+            defaults to `None`.
         :type config: dict, optional
+        :param tth_initial_guess: Initial guess for 2&theta to supercede
+            the values from the energy calibration detector cofiguration
+            on each of the detectors.
+        :type tth_initial_guess: float, optional
+        :param include_energy_ranges: List of MCA channel energy ranges
+            in keV whose data should be included after applying a mask
+            (bounds are inclusive). If specified, these supercede the
+            values from the energy calibration detector cofiguration on
+            each of the detectors.
+        :type include_energy_ranges: list[[float, float]], optional
+        :param calibration_method: Type of calibration method,
+            defaults to `'iterate_tth'`.
+        :type calibration_method:
+            Union['direct_fit_residual', 'direct_fit_peak_energies',
+                'direct_fit_combined', 'iterate_tth'], optional
+        :param quadratic_energy_calibration: Adds a quadratic term to
+            the detector channel index to energy conversion, defaults
+            to `False` (linear only).
+        :type quadratic_energy_calibration: bool, optional
+        :param centers_range: Set boundaries on the peak centers in
+            MCA channels when performing the fit. The min/max
+            possible values for the peak centers will be the initial
+            values &pm; `centers_range`. Defaults to `20`.
+        :type centers_range: int, optional
+        :param fwhm_min: Lower bound on the peak FWHM in MCA channels
+            when performing the fit, defaults to `None`.
+        :type fwhm_min: float, optional
+        :param fwhm_max: Lower bound on the peak FWHM in MCA channels
+            when performing the fit, defaults to `None`.
+        :type fwhm_max: float, optional
+        :param background: Background model for peak fitting.
+        :type background: str, list[str], optional
+        :param baseline: Automated baseline subtraction configuration,
+            defaults to `False`.
+        :type baseline: bool, BaselineConfig, optional
         :param save_figures: Save .pngs of plots for checking inputs &
-            outputs of this Processor, defaults to False.
+            outputs of this Processor, defaults to `False`.
         :type save_figures: bool, optional
         :param outputdir: Directory to which any output figures will
-            be saved, defaults to '.'.
+            be saved, defaults to `'.'`.
         :type outputdir: str, optional
         :param inputdir: Input directory, used only if files in the
             input configuration are not absolute paths,
-            defaults to '.'.
+            defaults to `'.'`.
         :type inputdir: str, optional
-        :param interactive: Allows for user interactions, defaults to
-            False.
+        :param interactive: Allows for user interactions,
+            defaults to `False`.
         :type interactive: bool, optional
         :raises RuntimeError: Invalid or missing input configuration.
         :return: Original configuration with the tuned values for
             2&theta and the linear correction parameters added.
         :rtype: dict[str,float]
         """
+        # Third party modules
+        from nexusformat.nexus import (
+            NXentry,
+            NXroot,
+        )
+
+        # Local modules
+        from CHAP.edd.models import BaselineConfig
+        from CHAP.utils.general import (
+            is_int,
+            is_str_series,
+        )
+
+        # Load the detector data
+        # FIX input a numpy and create/use NXobject to numpy proc
+        # FIX right now spec info is lost in output yaml, add to it?
+        nxroot = self.get_data(data, 'SpecReader')
+        if not isinstance(nxroot, NXroot):
+            raise RuntimeError('No valid NXroot data in input pipeline data')
+        nxentry = nxroot[nxroot.default]
+
+        # Load the validated 2&theta calibration configuration
         try:
             calibration_config = self.get_config(
-                data, 'edd.models.MCACeriaCalibrationConfig',
+                data, 'edd.models.MCATthCalibrationConfig',
+                calibration_method=calibration_method,
                 inputdir=inputdir)
         except Exception as data_exc:
             self.logger.info('No valid calibration config in input pipeline '
                              'data, using config parameter instead.')
             try:
                 # Local modules
-                from CHAP.edd.models import MCACeriaCalibrationConfig
+                from CHAP.edd.models import MCATthCalibrationConfig
 
-                calibration_config = MCACeriaCalibrationConfig(
-                    **config, inputdir=inputdir)
+                calibration_config = MCATthCalibrationConfig(
+                    **config, calibration_method=calibration_method,
+                    inputdir=inputdir)
             except Exception as dict_exc:
                 raise RuntimeError from dict_exc
 
+        # Validate the detector configuration
+        if calibration_config.detectors is None:
+            raise RuntimeError('No available calibrated detectors')
+        available_detector_indices = [int(d) for d in nxentry.detector_names]
+        detectors = []
         for detector in calibration_config.detectors:
-            tth, slope, intercept = self.calibrate(
-                calibration_config, detector, save_figures=save_figures,
-                interactive=interactive, outputdir=outputdir)
-            detector.tth_calibrated = tth
-            detector.slope_calibrated = slope
-            detector.intercept_calibrated = intercept
+            index = int(detector.detector_name)
+            if index in available_detector_indices:
+                detectors.append(detector)
+            else:
+                self.logger.warning(
+                    f'Skipping detector {name} (no energy calibration data)')
+
+        # Validate the fit index range
+        if calibration_config.fit_index_ranges is None and not interactive:
+            raise RuntimeError(
+                'If `fit_index_ranges` is not explicitly provided, '
+                + self.__class__.__name__
+                + ' must be run with `interactive=True`.')
+
+        # Validate the optional inputs
+        if not is_int(centers_range, gt=0, log=False):
+            RuntimeError(f'Invalid centers_range parameter ({centers_range})')
+        if fwhm_min is not None and not is_int(fwhm_min, gt=0, log=False):
+            RuntimeError(f'Invalid fwhm_min parameter ({fwhm_min})')
+        if fwhm_max is not None and not is_int(fwhm_max, gt=0, log=False):
+            RuntimeError(f'Invalid fwhm_max parameter ({fwhm_max})')
+        if background is not None:
+            if isinstance(background, str):
+                background = [background]
+            elif not is_str_series(background, log=False):
+                RuntimeError(f'Invalid background parameter ({background})')
+        if isinstance(baseline, bool):
+            if baseline:
+                baseline = BaselineConfig()
+        else:
+            try:
+                baseline = BaselineConfig(**baseline)
+            except Exception as dict_exc:
+                raise RuntimeError from dict_exc
+
+        # Collect and sum the detector data
+        mca_data = []
+        for scan_name in nxentry.spec_scans:
+            for scan_number, scan_data in nxentry.spec_scans[scan_name].items():
+                mca_data.append(scan_data.data.data.nxdata)
+        summed_detector_data = np.asarray(mca_data).sum(axis=(0,1))
+
+        # Get the detectors' num_bins parameter
+        for detector in detectors:
+            if detector.num_bins is None:
+                detector.num_bins = summed_detector_data.shape[-1]
+
+        # Check each detector's include_energy_ranges field against the
+        # flux file, if available.
+        if calibration_config.flux_file is not None:
+            flux = np.loadtxt(flux_file)
+            flux_file_energies = flux[:,0]/1.e3
+            flux_e_min = flux_file_energies.min()
+            flux_e_max = flux_file_energies.max()
+            for detector in detectors:
+                for i, (det_e_min, det_e_max) in enumerate(
+                        deepcopy(detector.include_energy_ranges)):
+                    if det_e_min < flux_e_min or det_e_max > flux_e_max:
+                        energy_range = [float(max(det_e_min, flux_e_min)),
+                                        float(min(det_e_max, flux_e_max))]
+                        print(
+                            f'WARNING: include_energy_ranges[{i}] out of range'
+                            f' ({detector.include_energy_ranges[i]}): adjusted'
+                            f' to {energy_range}')
+                        detector.include_energy_ranges[i] = energy_range
+
+        # Calibrate detector channel energies
+        for detector in detectors:
+            index = available_detector_indices.index(
+                int(detector.detector_name))
+            if tth_initial_guess is not None:
+                detector.tth_initial_guess = tth_initial_guess
+            if include_energy_ranges is not None:
+                detector.include_energy_ranges = include_energy_ranges
+            if background is not None:
+                detector.background = background.copy()
+            if baseline:
+                detector.baseline = baseline
+            self.calibrate(
+                calibration_config, detector, summed_detector_data[index],
+                quadratic_energy_calibration, centers_range, fwhm_min,
+                fwhm_max, save_figures, interactive, outputdir)
 
         return calibration_config.dict()
 
-    def calibrate(self,
-                  calibration_config,
-                  detector,
-                  save_figures=False,
-                  outputdir='.',
-                  interactive=False):
+    def calibrate(
+            self, calibration_config, detector, spectrum,
+            quadratic_energy_calibration=False, centers_range=20,
+            fwhm_min=None, fwhm_max=None, save_figures=False,
+            interactive=False, outputdir='.'):
         """Iteratively calibrate 2&theta by fitting selected peaks of
         an MCA spectrum until the computed strain is sufficiently
         small. Use the fitted peak locations to determine linear
@@ -672,247 +1535,810 @@ class MCACeriaCalibrationProcessor(Processor):
         :param calibration_config: Object configuring the CeO2
             calibration procedure for an MCA detector.
         :type calibration_config:
-            CHAP.edd.models.MCACeriaCalibrationConfig
+            CHAP.edd.models.MCATthCalibrationConfig
         :param detector: A single MCA detector element configuration.
         :type detector: CHAP.edd.models.MCAElementCalibrationConfig
+        :param spectrum: Summed MCA spectrum for the current detector.
+        :type spectrum: numpy.ndarray
+        :param quadratic_energy_calibration: Adds a quadratic term to
+            the detector channel index to energy conversion, defaults
+            to `False` (linear only).
+        :type quadratic_energy_calibration: bool, optional
+        :param centers_range: Set boundaries on the peak centers in
+            MCA channels when performing the fit. The min/max
+            possible values for the peak centers will be the initial
+            values &pm; `centers_range`. Defaults to `20`.
+        :type centers_range: int, optional
+        :param fwhm_min: Lower bound on the peak FWHM in MCA channels
+            when performing the fit, defaults to `None`.
+        :type fwhm_min: float, optional
+        :param fwhm_max: Lower bound on the peak FWHM in MCA channels
+            when performing the fit, defaults to `None`.
+        :type fwhm_max: float, optional
         :param save_figures: Save .pngs of plots for checking inputs &
-            outputs of this Processor, defaults to False.
+            outputs of this Processor, defaults to `False`.
         :type save_figures: bool, optional
-        :param outputdir: Directory to which any output figures will
-            be saved, defaults to '.'.
-        :type outputdir: str, optional
         :param interactive: Allows for user interactions, defaults to
-            False.
+            `False`.
         :type interactive: bool, optional
+        :param outputdir: Directory to which any output figures will
+            be saved, defaults to `'.'`.
+        :type outputdir: str, optional
         :raises ValueError: No value provided for included bin ranges
             or the fitted HKLs for the MCA detector element.
-        :return: Calibrated values of 2&theta and the linear correction
-            parameters for MCA channel energies: tth, slope, intercept.
-        :rtype: float, float, float
         """
-        # Local modules
-        from CHAP.edd.utils import get_peak_locations
-        from CHAP.utils.fit import Fit
+        # System modules
+        from sys import float_info
 
-        # Get the unique HKLs and lattice spacings for the calibration
-        # material
-        hkls, ds = calibration_config.material.unique_hkls_ds(
-            tth_tol=detector.hkl_tth_tol, tth_max=detector.tth_max)
+        # Third party modules
+        from nexusformat.nexus import NXdata, NXfield
+        from scipy.constants import physical_constants
 
-        # Collect raw MCA data of interest
-        mca_bin_energies = np.linspace(
-            0, detector.max_energy_kev, detector.num_bins)
-        mca_data = calibration_config.mca_data(detector)
+        # Local modules
         if interactive or save_figures:
-            # Third party modules
-            import matplotlib.pyplot as plt
-
-            # Local modules
             from CHAP.edd.utils import (
                 select_tth_initial_guess,
                 select_mask_and_hkls,
             )
+        from CHAP.edd.utils import get_peak_locations
+        from CHAP.utils.fit import FitProcessor
+        from CHAP.utils.general import index_nearest
+
+        self.logger.info(f'Calibrating detector {detector.detector_name}')
+
+        calibration_method = calibration_config.calibration_method
+
+        # Get the unique HKLs and lattice spacings for the calibration
+        # material
+        hkls, ds = calibration_config.material.unique_hkls_ds(
+            tth_tol=detector.hkl_tth_tol, tth_max=detector.tth_max)
 
-            # Adjust initial tth guess
-            fig, detector.tth_initial_guess = select_tth_initial_guess(
-                mca_bin_energies, mca_data, hkls, ds,
-                detector.tth_initial_guess, interactive)
-            if save_figures:
-                fig.savefig(os.path.join(
-                   outputdir,
-                   f'{detector.detector_name}_calibration_'
-                   'tth_initial_guess.png'))
-            plt.close()
+        # Get the MCA bin energies
+        mca_bin_energies = detector.energies
+
+        # Blank out data below 25 keV as well as the last bin
+        energy_mask = np.where(mca_bin_energies >= 25.0, 1, 0)
+        energy_mask[-1] = 0
+        spectrum = spectrum*energy_mask
+
+        # Subtract the baseline
+        if detector.baseline:
+            # Local modules
+            from CHAP.common.processor import ConstructBaseline
 
-            # Select mask & HKLs for fitting
-            fig, include_bin_ranges, hkl_indices = select_mask_and_hkls(
-                mca_bin_energies, mca_data, hkls, ds,
-                detector.tth_initial_guess, detector.include_bin_ranges,
-                detector.hkl_indices, detector.detector_name,
-                flux_energy_range=calibration_config.flux_file_energy_range,
-                label='MCA data',
-                interactive=interactive)
-            detector.include_energy_ranges = detector.get_energy_ranges(
-                include_bin_ranges)
-            detector.hkl_indices = hkl_indices
             if save_figures:
-                fig.savefig(os.path.join(
-                    outputdir,
-                    f'{detector.detector_name}_calibration_fit_mask_hkls.png'))
-            plt.close()
+                filename = os.path.join(outputdir,
+                                        f'{detector.detector_name}_tth_'
+                                        'calibration_baseline.png')
+            else:
+                filename = None
+            baseline, baseline_config = ConstructBaseline.construct_baseline(
+                spectrum, mask=energy_mask, tol=detector.baseline.tol,
+                lam=detector.baseline.lam, max_iter=detector.baseline.max_iter,
+                title=f'Baseline for detector {detector.detector_name}',
+                xlabel='Energy (keV)', ylabel='Intensity (counts)',
+                interactive=interactive, filename=filename)
+
+            spectrum -= baseline
+            detector.baseline.lam = baseline_config['lambda']
+            detector.baseline.attrs['num_iter'] = baseline_config['num_iter']
+            detector.baseline.attrs['error'] = baseline_config['error']
+
+        # Adjust initial tth guess
+        if save_figures:
+            filename = os.path.join(
+               outputdir,
+               f'{detector.detector_name}_calibration_tth_initial_guess.png')
+        else:
+            filename = None
+        tth_init = select_tth_initial_guess(
+            mca_bin_energies, spectrum, hkls, ds,
+            detector.tth_initial_guess, interactive, filename)
+        detector.tth_initial_guess = tth_init
         self.logger.debug(f'tth_initial_guess = {detector.tth_initial_guess}')
+
+        # Select the mask and HKLs for the Bragg peaks
+        if save_figures:
+            filename = os.path.join(
+                outputdir,
+                f'{detector.detector_name}_calibration_fit_mask_hkls.png')
+        if calibration_method == 'iterate_tth':
+            num_hkl_min = 2
+        else:
+            num_hkl_min = 1
+        include_bin_ranges, hkl_indices = select_mask_and_hkls(
+            mca_bin_energies, spectrum, hkls, ds,
+            detector.tth_initial_guess,
+            preselected_bin_ranges=detector.include_bin_ranges,
+            num_hkl_min=num_hkl_min, detector_name=detector.detector_name,
+            flux_energy_range=calibration_config.flux_file_energy_range(),
+            label='MCA data', interactive=interactive, filename=filename)
+
+        # Add the mask for the fluorescence peaks
+        if calibration_method != 'iterate_tth':
+            include_bin_ranges = (
+                calibration_config.fit_index_ranges + include_bin_ranges)
+
+        # Apply the mask
+        detector.include_energy_ranges = detector.get_include_energy_ranges(
+            include_bin_ranges)
+        detector.set_hkl_indices(hkl_indices)
         self.logger.debug(
             f'include_energy_ranges = {detector.include_energy_ranges}')
+        self.logger.debug(
+            f'hkl_indices = {detector.hkl_indices}')
         if not detector.include_energy_ranges:
             raise ValueError(
                 'No value provided for include_energy_ranges. '
-                'Provide them in the MCA Ceria Calibration Configuration '
+                'Provide them in the MCA Tth Calibration Configuration '
                 'or re-run the pipeline with the --interactive flag.')
         if not detector.hkl_indices:
             raise ValueError(
-                'No value provided for hkl_indices. Provide them in '
-                'the detector\'s MCA Ceria Calibration Configuration or '
+                'Unable to get values for hkl_indices for the provided '
+                'value of include_energy_ranges. Change its value in '
+                'the detector\'s MCA Tth Calibration Configuration or '
                 're-run the pipeline with the --interactive flag.')
         mca_mask = detector.mca_mask()
-        fit_mca_energies = mca_bin_energies[mca_mask]
-        fit_mca_intensities = mca_data[mca_mask]
+        spectrum_fit = spectrum[mca_mask]
 
         # Correct raw MCA data for variable flux at different energies
         flux_correct = \
             calibration_config.flux_correction_interpolation_function()
-        mca_intensity_weights = flux_correct(fit_mca_energies)
-        fit_mca_intensities = fit_mca_intensities / mca_intensity_weights
-
-        # Get the HKLs and lattice spacings that will be used for
-        # fitting
-        # Restrict the range for the centers with some margin to 
-        # prevent having centers near the edge of the fitting range
-        delta = 0.1 * (fit_mca_energies[-1]-fit_mca_energies[0])
-        centers_range = (
-            max(0.0, fit_mca_energies[0]-delta), fit_mca_energies[-1]+delta)
-        fit_hkls  = np.asarray([hkls[i] for i in detector.hkl_indices])
-        fit_ds  = np.asarray([ds[i] for i in detector.hkl_indices])
-        c_1 = fit_hkls[:,0]**2 + fit_hkls[:,1]**2 + fit_hkls[:,2]**2
-        tth = detector.tth_initial_guess
-        fit_E0 = get_peak_locations(fit_ds, tth)
-        for iter_i in range(calibration_config.max_iter):
-            self.logger.debug(
-                f'Tuning tth: iteration no. {iter_i}, starting value = {tth} ')
-
-            # Perform the uniform fit first
-
-            # Get expected peak energy locations for this iteration's
-            # starting value of tth
-            _fit_E0 = get_peak_locations(fit_ds, tth)
-
-            # Run the uniform fit
-            fit = Fit(fit_mca_intensities, x=fit_mca_energies)
-            fit.create_multipeak_model(
-                _fit_E0, fit_type='uniform', background=detector.background,
-                centers_range=centers_range)
-            fit.fit()
-
-            # Extract values of interest from the best values for the
-            # uniform fit parameters
-            uniform_best_fit = fit.best_fit
-            uniform_residual = fit.residual
-            uniform_fit_centers = [
-                fit.best_values[f'peak{i+1}_center']
-                for i in range(len(fit_hkls))]
-            uniform_a = fit.best_values['scale_factor']
-            uniform_strain = np.log(
-                (uniform_a
-                 / calibration_config.material.lattice_parameters)) # CeO2 is cubic, so this is fine here.
-
-            # Next, perform the unconstrained fit
-
-            # Use the peak parameters from the uniform fit as the
-            # initial guesses for peak locations in the unconstrained
-            # fit
-            fit.create_multipeak_model(fit_type='unconstrained')
-            fit.fit()
-
-            # Extract values of interest from the best values for the
-            # unconstrained fit parameters
-            unconstrained_best_fit = fit.best_fit
-            unconstrained_residual = fit.residual
-            unconstrained_fit_centers = np.array(
-                [fit.best_values[f'peak{i+1}_center']
-                 for i in range(len(fit_hkls))])
-            unconstrained_a = np.sqrt(c_1)*abs(get_peak_locations(
-                unconstrained_fit_centers, tth))
-            unconstrained_strains = np.log(
-                (unconstrained_a
+        if flux_correct is not None:
+            mca_intensity_weights = flux_correct(
+                 mca_bin_energies[mca_mask])
+            spectrum_fit = spectrum_fit / mca_intensity_weights
+
+        # Get the fluorescence peak info
+        e_xrf = calibration_config.peak_energies
+        num_xrf = len(e_xrf)
+
+        # Get the Bragg peak HKLs, lattice spacings and energies
+        hkls_fit  = np.asarray([hkls[i] for i in detector.hkl_indices])
+        ds_fit  = np.asarray([ds[i] for i in detector.hkl_indices])
+        c_1_fit = hkls_fit[:,0]**2 + hkls_fit[:,1]**2 + hkls_fit[:,2]**2
+        e_bragg_init = get_peak_locations(ds_fit, tth_init)
+        num_bragg = len(e_bragg_init)
+
+        # Perform the fit
+        if calibration_method == 'direct_fit_residual':
+
+            # Get the initial free fit parameters
+            tth_init = np.radians(tth_init)
+            a_init, b_init, c_init = detector.energy_calibration_coeffs
+
+            # For testing: hardwired limits:
+            if False:
+                min_value = None
+                tth_min = None
+                tth_max = None
+                b_min = None
+                b_max = None
+                sig_min = None
+                sig_max = None
+            else:
+                min_value = float_info.min
+                tth_min = 0.9*tth_init
+                tth_max = 1.1*tth_init
+                b_min = 0.1*b_init
+                b_max = 10.0*b_init
+                if isinstance(fwhm_min, (int,float)):
+                    sig_min = fwhm_min/2.35482
+                else:
+                    sig_min = None
+                if isinstance(fwhm_max, (int,float)):
+                    sig_max = fwhm_max/2.35482
+                else:
+                    sig_max = None
+
+            # Construct the free fit parameters
+            parameters = [
+                {'name': 'tth', 'value': tth_init, 'min': tth_min,
+                 'max': tth_max}]
+            if quadratic_energy_calibration:
+                parameters.append({'name': 'a', 'value': a_init})
+            parameters.append(
+                {'name': 'b', 'value': b_init, 'min': b_min, 'max': b_max})
+            parameters.append({'name': 'c', 'value': c_init})
+
+            # Construct the fit model
+            models = []
+
+            # Add the background
+            if detector.background is not None:
+                if isinstance(detector.background, str):
+                    models.append(
+                        {'model': detector.background, 'prefix': 'bkgd_'})
+                else:
+                    for model in detector.background:
+                        models.append({'model': model, 'prefix': f'{model}_'})
+
+            # Add the fluorescent peaks
+            for i, e_peak in enumerate(e_xrf):
+                expr = f'({e_peak}-c)/b'
+                if quadratic_energy_calibration:
+                    expr = '(' + expr + f')*(1.0-a*(({e_peak}-c)/(b*b)))'
+                models.append(
+                    {'model': 'gaussian', 'prefix': f'xrf{i+1}_',
+                     'parameters': [
+                        {'name': 'amplitude', 'min': min_value},
+                        {'name': 'center', 'expr': expr},
+                        {'name': 'sigma', 'min': sig_min, 'max': sig_max}]})
+
+            # Add the Bragg peaks
+            hc = 1.e7 * physical_constants['Planck constant in eV/Hz'][0] \
+                 * physical_constants['speed of light in vacuum'][0]
+            for i, (e_peak, ds) in enumerate(zip(e_bragg_init, ds_fit)):
+                norm = 0.5*hc/ds
+                expr = f'(({norm}/sin(0.5*tth))-c)/b'
+                if quadratic_energy_calibration:
+                    expr = '(' + expr \
+                           + f')*(1.0-a*((({norm}/sin(0.5*tth))-c)/(b*b)))'
+                models.append(
+                    {'model': 'gaussian', 'prefix': f'peak{i+1}_',
+                     'parameters': [
+                        {'name': 'amplitude', 'min': min_value},
+                        {'name': 'center', 'expr': expr},
+                        {'name': 'sigma', 'min': sig_min, 'max': sig_max}]})
+
+            # Perform the fit
+            fit = FitProcessor()
+            result = fit.process(
+                NXdata(NXfield(spectrum_fit, 'y'),
+                       NXfield(np.arange(detector.num_bins)[mca_mask], 'x')),
+                {'parameters': parameters, 'models': models, 'method': 'trf'})
+
+            # Extract values of interest from the best values
+            best_fit_uniform = result.best_fit
+            residual_uniform = result.residual
+            tth_fit = np.degrees(result.best_values['tth'])
+            if quadratic_energy_calibration:
+                a_fit = result.best_values['a']
+            else:
+                a_fit = 0.0
+            b_fit = result.best_values['b']
+            c_fit = result.best_values['c']
+            peak_indices_fit = np.asarray(
+                [result.best_values[f'xrf{i+1}_center'] for i in range(num_xrf)]
+                + [result.best_values[f'peak{i+1}_center']
+                   for i in range(num_bragg)])
+            peak_energies_fit = ((a_fit*peak_indices_fit + b_fit)
+                                * peak_indices_fit + c_fit)
+            e_bragg_uniform = peak_energies_fit[num_xrf:]
+            a_uniform = np.sqrt(c_1_fit) * abs(
+                get_peak_locations(e_bragg_uniform, tth_fit))
+            strains_uniform = np.log(
+                (a_uniform
                  / calibration_config.material.lattice_parameters))
-            unconstrained_strain = np.mean(unconstrained_strains)
-            unconstrained_tth = tth * (1.0 + unconstrained_strain)
+            strain_uniform = np.mean(strains_uniform)
 
-            # Update tth for the next iteration of tuning
-            prev_tth = tth
-            tth = unconstrained_tth
-
-            # Stop tuning tth at this iteration if differences are
-            # small enough
-            if abs(tth - prev_tth) < calibration_config.tune_tth_tol:
-                break
-
-        # Fit line to expected / computed peak locations from the last
-        # unconstrained fit.
-        fit = Fit.fit_data(
-            fit_E0, 'linear', x=unconstrained_fit_centers, nan_policy='omit')
-        slope = fit.best_values['slope']
-        intercept = fit.best_values['intercept']
+        elif calibration_method == 'direct_fit_peak_energies':
+            # Third party modules
+            from scipy.optimize import minimize
+
+            def cost_function(
+                    pars, quadratic_energy_calibration, ds_fit,
+                    indices_unconstrained, e_xrf):
+                tth = pars[0]
+                b = pars[1]
+                c = pars[2]
+                if quadratic_energy_calibration:
+                    a = pars[3]
+                else:
+                    a = 0.0
+                energies_unconstrained = (
+                    (a*indices_unconstrained + b) * indices_unconstrained + c)
+                target_energies = np.concatenate(
+                    (e_xrf, get_peak_locations(ds_fit, tth)))
+                return np.sqrt(np.sum(
+                    (energies_unconstrained-target_energies)**2))
+
+            # Get the initial free fit parameters
+            a_init, b_init, c_init = detector.energy_calibration_coeffs
+
+            # Perform an unconstrained fit in terms of MCA bin index
+            mca_bins_fit = np.arange(detector.num_bins)[mca_mask]
+            centers = [index_nearest(mca_bin_energies, e_peak)
+                       for e_peak in np.concatenate((e_xrf, e_bragg_init))]
+            models = []
+            if detector.background is not None:
+                if isinstance(detector.background, str):
+                    models.append(
+                        {'model': detector.background, 'prefix': 'bkgd_'})
+                else:
+                    for model in detector.background:
+                        models.append({'model': model, 'prefix': f'{model}_'})
+            models.append(
+                {'model': 'multipeak', 'centers': centers,
+                 'centers_range': centers_range,
+                 'fwhm_min': fwhm_min, 'fwhm_max': fwhm_max})
+            fit = FitProcessor()
+            result = fit.process(
+                NXdata(NXfield(spectrum_fit, 'y'),
+                       NXfield(mca_bins_fit, 'x')),
+                {'models': models, 'method': 'trf'})
+
+            # Extract the peak properties from the fit
+            indices_unconstrained = np.asarray(
+                [result.best_values[f'peak{i+1}_center']
+                 for i in range(num_xrf+num_bragg)])
+
+            # Perform a peak center fit using the theoretical values
+            # for the fluorescense peaks and Bragg's law for the Bragg
+            # peaks for given material properties and a freely
+            # adjustable 2&theta angle and MCA energy axis calibration
+            pars_init = [tth_init, b_init, c_init]
+            if quadratic_energy_calibration:
+                pars_init.append(a_init)
+            # For testing: hardwired limits:
+            if True:
+                bounds = [
+                    (0.9*tth_init, 1.1*tth_init),
+                    (0.1*b_init, 10.*b_init),
+                    (0.1*c_init, 10.*c_init)]
+                if quadratic_energy_calibration:
+                    if a_init:
+                        bounds.append((0.1*a_init, 10.0*a_init))
+                    else:
+                        bounds.append((None, None))
+            else:
+                bounds = None
+            result = minimize(
+                cost_function, pars_init,
+                args=(
+                    quadratic_energy_calibration, ds_fit,
+                    indices_unconstrained, e_xrf),
+                method='Nelder-Mead', bounds=bounds)
+
+            # Extract values of interest from the best values
+            best_fit_uniform = None
+            residual_uniform = None
+            tth_fit = float(result['x'][0])
+            b_fit = float(result['x'][1])
+            c_fit = float(result['x'][2])
+            if quadratic_energy_calibration:
+                a_fit = float(result['x'][3])
+            else:
+                a_fit = 0.0
+            e_bragg_fit = get_peak_locations(ds_fit, tth_fit)
+            peak_energies_fit = [
+                (a_fit*i + b_fit) * i + c_fit
+                for i in indices_unconstrained[:num_xrf]] \
+                + list(e_bragg_fit)
+
+            fit_uniform = None
+            residual_uniform = None
+            e_bragg_uniform = e_bragg_fit
+            strain_uniform = None
+
+        elif calibration_method == 'direct_fit_combined':
+            # Third party modules
+            from scipy.optimize import minimize
+
+            def gaussian(x, a, b, c, amp, sig, e_peak):
+                sig2 = 2.*sig**2
+                norm = sig*np.sqrt(2.0*np.pi)
+                cen = (e_peak-c) * (1.0 - a * (e_peak-c) / b**2) / b
+                return amp*np.exp(-(x-cen)**2/sig2)/norm
+
+            def cost_function_combined(
+                    pars, x, y, quadratic_energy_calibration, ds_fit,
+                    indices_unconstrained, e_xrf):
+                tth = pars[0]
+                b = pars[1]
+                c = pars[2]
+                amplitudes = pars[3::2]
+                sigmas = pars[4::2]
+                if quadratic_energy_calibration:
+                    a = pars[-1]
+                else:
+                    a = 0.0
+                energies_unconstrained = (
+                    (a*indices_unconstrained + b) * indices_unconstrained + c)
+                target_energies = np.concatenate(
+                    (e_xrf, get_peak_locations(ds_fit, tth)))
+                y_fit = np.zeros((x.size))
+                for i, e_peak in enumerate(target_energies):
+                    y_fit += gaussian(
+                        x, a, b, c, amplitudes[i], sigmas[i], e_peak)
+                target_energies_error = np.sqrt(
+                    np.sum(
+                        (energies_unconstrained
+                         - np.asarray(target_energies))**2)
+                    / len(target_energies))
+                residual_error = np.sqrt(
+                    np.sum((y-y_fit)**2)
+                    / (np.sum(y**2) * len(target_energies)))
+                return target_energies_error+residual_error
+
+            # Get the initial free fit parameters
+            a_init, b_init, c_init = detector.energy_calibration_coeffs
+
+            # Perform an unconstrained fit in terms of MCS bin index
+            mca_bins_fit = np.arange(detector.num_bins)[mca_mask]
+            centers = [index_nearest(mca_bin_energies, e_peak)
+                       for e_peak in np.concatenate((e_xrf, e_bragg_init))]
+            models = []
+            if detector.background is not None:
+                if isinstance(detector.background, str):
+                    models.append(
+                        {'model': detector.background, 'prefix': 'bkgd_'})
+                else:
+                    for model in detector.background:
+                        models.append({'model': model, 'prefix': f'{model}_'})
+            models.append(
+                {'model': 'multipeak', 'centers': centers,
+                 'centers_range': centers_range,
+                 'fwhm_min': fwhm_min, 'fwhm_max': fwhm_max})
+            fit = FitProcessor()
+            result = fit.process(
+                NXdata(NXfield(spectrum_fit, 'y'),
+                       NXfield(mca_bins_fit, 'x')),
+                {'models': models, 'method': 'trf'})
+
+            # Extract the peak properties from the fit
+            num_peak = num_xrf+num_bragg
+            indices_unconstrained = np.asarray(
+                [result.best_values[f'peak{i+1}_center']
+                 for i in range(num_peak)])
+            amplitudes_init = np.asarray(
+                [result.best_values[f'peak{i+1}_amplitude']
+                 for i in range(num_peak)])
+            sigmas_init = np.asarray(
+                [result.best_values[f'peak{i+1}_sigma']
+                 for i in range(num_peak)])
+
+            # Perform a peak center fit using the theoretical values
+            # for the fluorescense peaks and Bragg's law for the Bragg
+            # peaks for given material properties and a freely
+            # adjustable 2&theta angle and MCA energy axis calibration
+            norm = spectrum_fit.max()
+            pars_init = [tth_init, b_init, c_init]
+            for amp, sig in zip(amplitudes_init, sigmas_init):
+                pars_init += [amp/norm, sig]
+            if quadratic_energy_calibration:
+                pars_init += [a_init]
+            # For testing: hardwired limits:
+            if True:
+                bounds = [
+                    (0.9*tth_init, 1.1*tth_init),
+                    (0.1*b_init, 10.*b_init),
+                    (0.1*c_init, 10.*c_init)]
+                for amp, sig in zip(amplitudes_init, sigmas_init):
+                    bounds += [
+                        (0.9*amp/norm, 1.1*amp/norm), (0.9*sig, 1.1*sig)]
+                if quadratic_energy_calibration:
+                    if a_init:
+                        bounds += [(0.1*a_init, 10.*a_init)]
+                    else:
+                        bounds += [(None, None)]
+            else:
+                bounds = None
+            result = minimize(
+                cost_function_combined, pars_init,
+                args=(
+                    mca_bins_fit, spectrum_fit/norm,
+                    quadratic_energy_calibration, ds_fit,
+                    indices_unconstrained, e_xrf),
+                method='Nelder-Mead', bounds=bounds)
+
+            # Extract values of interest from the best values
+            tth_fit = float(result['x'][0])
+            b_fit = float(result['x'][1])
+            c_fit = float(result['x'][2])
+            amplitudes_fit = norm * result['x'][3::2]
+            sigmas_fit = result['x'][4::2]
+            if quadratic_energy_calibration:
+                a_fit = float(result['x'][-1])
+            else:
+                a_fit = 0.0
+            e_bragg_fit = get_peak_locations(ds_fit, tth_fit)
+            peak_energies_fit = [
+                (a_fit*i + b_fit) * i + c_fit
+                for i in indices_unconstrained[:num_xrf]] \
+                + list(e_bragg_fit)
+
+            best_fit_uniform = np.zeros((mca_bins_fit.size))
+            for i, e_peak in enumerate(peak_energies_fit):
+                best_fit_uniform += gaussian(
+                    mca_bins_fit, a_fit, b_fit, c_fit, amplitudes_fit[i],
+                    sigmas_fit[i], e_peak)
+            residual_uniform = spectrum_fit - best_fit_uniform
+            e_bragg_uniform = e_bragg_fit
+            strain_uniform = 0.0
+
+        elif calibration_method == 'iterate_tth':
+
+            tth_fit = tth_init
+            e_bragg_fit = e_bragg_init
+            mca_bin_energies_fit = mca_bin_energies[mca_mask]
+            a_init, b_init, c_init = detector.energy_calibration_coeffs
+            if isinstance(fwhm_min, (int, float)):
+                fwhm_min = fwhm_min*b_init
+            else:
+                fwhm_min = None
+            if isinstance(fwhm_max, (int, float)):
+                fwhm_max = fwhm_max*b_init
+            else:
+                fwhm_max = None
+            for iter_i in range(calibration_config.max_iter):
+                self.logger.debug(f'Tuning tth: iteration no. {iter_i}, '
+                                  f'starting value = {tth_fit} ')
+
+                # Construct the fit model
+                models = []
+                if detector.background is not None:
+                    if isinstance(detector.background, str):
+                        models.append(
+                            {'model': detector.background, 'prefix': 'bkgd_'})
+                    else:
+                        for model in detector.background:
+                            models.append(
+                                {'model': model, 'prefix': f'{model}_'})
+                models.append(
+                    {'model': 'multipeak', 'centers': list(e_bragg_fit),
+                     'fit_type': 'uniform',
+                     'centers_range': centers_range*b_init,
+                     'fwhm_min': fwhm_min, 'fwhm_max': fwhm_max})
+
+                # Perform the uniform
+                fit = FitProcessor()
+                uniform_fit = fit.process(
+                    NXdata(
+                        NXfield(spectrum_fit, 'y'),
+                        NXfield(mca_bin_energies_fit, 'x')),
+                    {'models': models, 'method': 'trf'})
+
+                # Extract values of interest from the best values for
+                # the uniform fit parameters
+                best_fit_uniform = uniform_fit.best_fit
+                residual_uniform = uniform_fit.residual
+                e_bragg_uniform = [
+                    uniform_fit.best_values[f'peak{i+1}_center']
+                    for i in range(num_bragg)]
+                strain_uniform = -np.log(
+                    uniform_fit.best_values['scale_factor'])
+
+                # Next, perform the unconstrained fit
+
+                # Use the peak parameters from the uniform fit as
+                # the initial guesses for peak locations in the
+                # unconstrained fit
+                models[-1]['fit_type'] = 'unconstrained'
+                unconstrained_fit = fit.process(
+                    uniform_fit, {'models': models, 'method': 'trf'})
+
+                # Extract values of interest from the best values for
+                # the unconstrained fit parameters
+                best_fit_unconstrained = unconstrained_fit.best_fit
+                residual_unconstrained = unconstrained_fit.residual
+                e_bragg_unconstrained = np.array(
+                    [unconstrained_fit.best_values[f'peak{i+1}_center']
+                     for i in range(num_bragg)])
+                a_unconstrained = np.sqrt(c_1_fit)*abs(get_peak_locations(
+                    e_bragg_unconstrained, tth_fit))
+                strains_unconstrained = np.log(
+                    (a_unconstrained
+                     / calibration_config.material.lattice_parameters))
+                strain_unconstrained = np.mean(strains_unconstrained)
+                tth_unconstrained = tth_fit * (1.0 + strain_unconstrained)
+
+                # Update tth for the next iteration of tuning
+                prev_tth = tth_fit
+                tth_fit = float(tth_unconstrained)
+
+                # Update the peak energy locations for this iteration
+                e_bragg_fit = get_peak_locations(ds_fit, tth_fit)
+
+                # Stop tuning tth at this iteration if differences are
+                # small enough
+                if abs(tth_fit - prev_tth) < calibration_config.tune_tth_tol:
+                    break
+
+            # Fit line to expected / computed peak locations from the
+            # last unconstrained fit.
+            if quadratic_energy_calibration:
+                fit = FitProcessor()
+                result = fit.process(
+                    NXdata(
+                        NXfield(e_bragg_fit, 'y'),
+                        NXfield(e_bragg_unconstrained, 'x')),
+                    {'models': [{'model': 'quadratic'}]})
+                a = result.best_values['a']
+                b = result.best_values['b']
+                c = result.best_values['c']
+            else:
+                fit = FitProcessor()
+                result = fit.process(
+                    NXdata(
+                        NXfield(e_bragg_fit, 'y'),
+                        NXfield(e_bragg_unconstrained, 'x')),
+                    {'models': [{'model': 'linear'}]})
+                a = 0.0
+                b = result.best_values['slope']
+                c = result.best_values['intercept']
+            # The following assumes that a_init = 0
+            if a_init:
+                raise NotImplemented(
+                    f'A linear energy calibration is required at this time')
+            a_fit = float(a*b_init**2)
+            b_fit = float(2*a*b_init*c_init + b*b_init)
+            c_fit = float(a*c_init**2 + b*c_init + c)
+            peak_energies_fit = ((a*e_bragg_unconstrained + b)
+                                * e_bragg_unconstrained + c)
+
+        # Store the results in the detector object
+        detector.tth_calibrated = float(tth_fit)
+        detector.energy_calibration_coeffs = [
+            float(a_fit), float(b_fit), float(c_fit)]
+
+        # Update the MCA channel energies with the newly calibrated
+        # coefficients
+        mca_bin_energies = detector.energies
 
         if interactive or save_figures:
             # Third party modules
             import matplotlib.pyplot as plt
 
+            # Update the peak energies and the MCA channel energies
+            e_bragg_fit = get_peak_locations(ds_fit, tth_fit)
+            mca_energies_fit = mca_bin_energies[mca_mask]
+
+            # Get an unconstrained fit
+            if calibration_method != 'iterate_tth':
+                if isinstance(fwhm_min, (int, float)):
+                    fwhm_min = fwhm_min*b_fit
+                else:
+                    fwhm_min = None
+                if isinstance(fwhm_max, (int, float)):
+                    fwhm_max = fwhm_max*b_fit
+                else:
+                    fwhm_max = None
+                models = []
+                if detector.background is not None:
+                    if isinstance(detector.background, str):
+                        models.append(
+                            {'model': detector.background, 'prefix': 'bkgd_'})
+                    else:
+                        for model in detector.background:
+                            models.append(
+                                {'model': model, 'prefix': f'{model}_'})
+                models.append(
+                    {'model': 'multipeak', 'centers': list(peak_energies_fit),
+                     'centers_range': centers_range*b_fit,
+                     'fwhm_min': fwhm_min, 'fwhm_max': fwhm_max})
+                fit = FitProcessor()
+                result = fit.process(
+                    NXdata(NXfield(spectrum_fit, 'y'),
+                           NXfield(mca_energies_fit, 'x')),
+                    {'models': models, 'method': 'trf'})
+                best_fit_unconstrained = result.best_fit
+                residual_unconstrained = result.residual
+                e_bragg_unconstrained = np.sort(
+                    [result.best_values[f'peak{i+1}_center']
+                     for i in range(num_xrf, num_xrf+num_bragg)])
+                a_unconstrained = np.sqrt(c_1_fit) * abs(
+                    get_peak_locations(e_bragg_unconstrained, tth_fit))
+                strains_unconstrained = np.log(
+                    (a_unconstrained
+                     / calibration_config.material.lattice_parameters))
+                strain_unconstrained = np.mean(strains_unconstrained)
+
+            # Create the figure
             fig, axs = plt.subplots(2, 2, sharex='all', figsize=(11, 8.5))
+            fig.suptitle(
+                f'Detector {detector.detector_name} '
+                r'2$\theta$ Calibration')
 
-            # Upper left axes: Input data & best fits
-            axs[0,0].set_title('Ceria Calibration Fits')
+            # Upper left axes: best fit with calibrated peak centers
+            axs[0,0].set_title(r'2$\theta$ Calibration Fits')
             axs[0,0].set_xlabel('Energy (keV)')
             axs[0,0].set_ylabel('Intensity (a.u)')
-            for i, hkl_E in enumerate(fit_E0):
-                # KLS: annotate indicated HKLs w millier indices
-                axs[0,0].axvline(hkl_E, color='k', linestyle='--')
-                axs[0,0].text(hkl_E, 1, str(fit_hkls[i])[1:-1],
+            for i, e_peak in enumerate(e_bragg_fit):
+                axs[0,0].axvline(e_peak, c='k', ls='--')
+                axs[0,0].text(e_peak, 1, str(hkls_fit[i])[1:-1],
                               ha='right', va='top', rotation=90,
                               transform=axs[0,0].get_xaxis_transform())
-            axs[0,0].plot(fit_mca_energies, uniform_best_fit,
-                          label='Single Strain')
-            axs[0,0].plot(fit_mca_energies, unconstrained_best_fit,
-                          label='Unconstrained')
-            #axs[0,0].plot(fit_mca_energies, MISSING?, label='least squares')
-            axs[0,0].plot(fit_mca_energies, fit_mca_intensities,
-                          label='Flux-Corrected & Masked MCA Data')
+            if flux_correct is None:
+                axs[0,0].plot(
+                    mca_energies_fit, spectrum_fit, marker='.', c='C2', ms=3,
+                    ls='', label='MCA data')
+            else:
+                axs[0,0].plot(
+                    mca_energies_fit, spectrum_fit, marker='.', c='C2', ms=3,
+                    ls='', label='Flux-corrected MCA data')
+            if calibration_method == 'iterate_tth':
+                label_unconstrained = 'Unconstrained'
+            else:
+                if quadratic_energy_calibration:
+                    label_unconstrained = \
+                        'Unconstrained fit using calibrated a, b, and c'
+                else:
+                    label_unconstrained = \
+                        'Unconstrained fit using calibrated b and c'
+            if best_fit_uniform is None:
+                axs[0,0].plot(
+                    mca_energies_fit, best_fit_unconstrained, c='C1',
+                    label=label_unconstrained)
+            else:
+                axs[0,0].plot(
+                    mca_energies_fit, best_fit_uniform, c='C0',
+                    label='Single strain')
+                axs[0,0].plot(
+                    mca_energies_fit, best_fit_unconstrained, c='C1', ls='--',
+                    label=label_unconstrained)
             axs[0,0].legend()
 
-            # Lower left axes: fit residuals
+            # Lower left axes: fit residual
             axs[1,0].set_title('Fit Residuals')
             axs[1,0].set_xlabel('Energy (keV)')
             axs[1,0].set_ylabel('Residual (a.u)')
-            axs[1,0].plot(fit_mca_energies,
-                          uniform_residual,
-                          label='Single Strain')
-            axs[1,0].plot(fit_mca_energies,
-                          unconstrained_residual,
-                          label='Unconstrained')
+            if residual_uniform is None:
+                axs[1,0].plot(
+                    mca_energies_fit, residual_unconstrained, c='C1',
+                    label=label_unconstrained)
+            else:
+                axs[1,0].plot(
+                    mca_energies_fit, residual_uniform, c='C0',
+                    label='Single strain')
+                axs[1,0].plot(
+                    mca_energies_fit, residual_unconstrained, c='C1', ls='--',
+                    label=label_unconstrained)
             axs[1,0].legend()
 
             # Upper right axes: E vs strain for each fit
             axs[0,1].set_title('HKL Energy vs. Microstrain')
             axs[0,1].set_xlabel('Energy (keV)')
             axs[0,1].set_ylabel('Strain (\u03BC\u03B5)')
-            axs[0,1].axhline(uniform_strain * 1e6,
-                             linestyle='--', label='Single Strain')
-            axs[0,1].plot(fit_E0, unconstrained_strains * 1e6,
-                          color='C1', marker='s', label='Unconstrained')
-            axs[0,1].axhline(unconstrained_strain * 1e6,
-                             color='C1', linestyle='--',
-                             label='Unconstrained: Unweighted Mean')
+            if strain_uniform is not None:
+                axs[0,1].axhline(strain_uniform * 1e6,
+                                 ls='--', label='Single strain')
+            axs[0,1].plot(e_bragg_fit, strains_unconstrained * 1e6,
+                          marker='o', mfc='none', c='C1',
+                          label='Unconstrained')
+            axs[0,1].axhline(strain_unconstrained* 1e6,
+                             ls='--', c='C1',
+                             label='Unconstrained: unweighted mean')
             axs[0,1].legend()
 
-            # Lower right axes: theoretical HKL E vs fit HKL E for
-            # each fit
-            axs[1,1].set_title('Theoretical vs. Fit HKL Energies')
+            # Lower right axes: theoretical E vs fitted E for all peaks
+            axs[1,1].set_title('Theoretical vs. Fitted Peak Energies')
             axs[1,1].set_xlabel('Energy (keV)')
             axs[1,1].set_ylabel('Energy (keV)')
-            axs[1,1].plot(fit_E0, uniform_fit_centers,
-                          marker='o', label='Single Strain')
-            axs[1,1].plot(fit_E0, unconstrained_fit_centers,
-                          linestyle='', marker='o', label='Unconstrained')
-            axs[1,1].plot(slope * unconstrained_fit_centers + intercept,fit_E0,
-                          color='C1', label='Unconstrained: Linear Fit')
+            if calibration_method == 'iterate_tth':
+                e_fit = e_bragg_fit
+                e_unconstrained = e_bragg_unconstrained
+                if quadratic_energy_calibration:
+                    label = 'Unconstrained: quadratic fit'
+                else:
+                    label = 'Unconstrained: linear fit'
+            else:
+                e_fit = np.concatenate((e_xrf, e_bragg_fit))
+                e_unconstrained = np.concatenate(
+                    (e_xrf, e_bragg_unconstrained))
+                if quadratic_energy_calibration:
+                    label = 'Quadratic fit'
+                else:
+                    label = 'Linear fit'
+            axs[1,1].plot(
+                e_bragg_fit, e_bragg_uniform, marker='x', ls='',
+                label='Single strain')
+            axs[1,1].plot(
+                e_fit, e_unconstrained, marker='o', mfc='none', ls='',
+                label='Unconstrained')
+            axs[1,1].plot(
+                e_fit, peak_energies_fit, c='C1', label=label)
             axs[1,1].legend()
-
-            # Add a text box showing final calibrated values
+            txt = 'Calibrated values:' \
+                  f'\nTakeoff angle:\n    {tth_fit:.5f}$^\circ$'
+            if quadratic_energy_calibration:
+                txt += '\nQuadratic coefficient (a):' \
+                       f'\n    {a_fit:.5e} $keV$/channel$^2$'
+            txt += '\nLinear coefficient (b):' \
+                   f'\n    {b_fit:.5f} $keV$/channel' \
+                   f'\nConstant offset (c):\n    {c_fit:.5f}'
             axs[1,1].text(
-                0.98, 0.02,
-                'Calibrated Values:\n\n'
-                + f'Takeoff Angle:\n    {tth:.5f}$^\circ$\n\n'
-                + f'Slope:\n    {slope:.5f}\n\n'
-                + f'Intercept:\n    {intercept:.5f} $keV$',
+                0.98, 0.02, txt,
                 ha='right', va='bottom', ma='left',
                 transform=axs[1,1].transAxes,
                 bbox=dict(boxstyle='round',
@@ -922,169 +2348,30 @@ class MCACeriaCalibrationProcessor(Processor):
             fig.tight_layout()
 
             if save_figures:
-                figfile = os.path.join(outputdir, 'ceria_calibration_fits.png')
+                figfile = os.path.join(
+                    outputdir,
+                    f'{detector.detector_name}_tth_calibration_fits.png')
                 plt.savefig(figfile)
                 self.logger.info(f'Saved figure to {figfile}')
             if interactive:
                 plt.show()
 
-        return float(tth), float(slope), float(intercept)
-
-
-class MCAEnergyCalibrationProcessor(Processor):
-    """Processor to return parameters for linearly transforming MCA
-    channel indices to energies (in keV). Procedure: provide a
-    spectrum from the MCA element to be calibrated and the theoretical
-    location of at least one peak present in that spectrum (peak
-    locations must be given in keV). It is strongly recommended to use
-    the location of fluorescence peaks whenever possible, _not_
-    diffraction peaks, as this Processor does not account for
-    2&theta."""
-    def process(self,
-                data,
-                max_energy,
-                peak_energies,
-                peak_initial_guesses=None,
-                peak_center_fit_delta=2.0,
-                fit_ranges=None,
-                save_figures=False,
-                interactive=False,
-                outputdir='.'):
-        """Fit the specified peaks in the MCA spectrum provided. Using
-        the difference between the provided peak locations and the fit
-        centers of those peaks, compute linear correction parameters
-        to convert MCA channel indices to energies in keV. Return
-        those parameters as a dictionary.
-
-        :param data: An MCA spectrum
-        :type data: PipelineData
-        :param max_energy: The (uncalibrated) maximum energy measured
-            by the MCA spectrum provided.
-        :type max_energy: float
-        :param peak_energies: Theoretical locations of peaks to use
-            for calibrating the MCA channel energies. It is _strongly_
-            recommended to use fluorescence peaks.
-        :type peak_energies: list[float]
-        :param peak_initial_guesses: A list of values to use for the
-            initial guesses for peak locations when performing the fit
-            of the spectrum. Providing good values to this parameter
-            can greatly improve the quality of the spectrum fit when
-            the uncalibrated detector channel energies are too far off
-            to use the values in `peak_energies` for the initial
-            guesses for peak centers. Defaults to None.
-        :type peak_inital_guesses: Optional[list[float]]
-        :param peak_center_fit_delta: Set boundaries on the fit peak
-            centers when performing the fit. The min/max possible
-            values for the peak centers will be the values provided in
-            `peak_energies` (or `peak_initial_guesses`, if used) &pm;
-            `peak_center_fit_delta`. Defaults to 2.0.
-        :type peak_center_fit_delta: float
-        :param fit_ranges: Explicit ranges of MCA channel indices
-            (_not_ energies) to include when performing a fit of the
-            given peaks to the provied MCA spectrum. Use this
-            parameter or select it interactively by running a pipeline
-            with `config.interactive: True`. Defaults to []
-        :type fit_ranges: Optional[list[tuple[int, int]]]
-        :param save_figures: Save .pngs of plots for checking inputs &
-            outputs of this Processor, defaults to False.
-        :type save_figures: bool, optional
-        :param interactive: Allows for user interactions, defaults to
-            False.
-        :type interactive: bool, optional
-        :param outputdir: Directory to which any output figures will
-            be saved, defaults to '.'.
-        :type outputdir: str, optional
-        :returns: Dictionary containing linear energy correction
-            parameters for the MCA element
-        :rtype: dict[str, float]
-        """
-        # Validate arguments: fit_ranges & interactive
-        if not (fit_ranges or interactive):
-            self.logger.exception(
-                RuntimeError(
-                    'If `fit_ranges` is not explicitly provided, '
-                    + self.__class__.__name__
-                    + ' must be run with `interactive=True`.'))
-        # Validate arguments: peak_energies & peak_initial_guesses
-        if peak_initial_guesses is None:
-            peak_initial_guesses = peak_energies
-        else:
-            from CHAP.utils.general import is_num_series
-            is_num_series(peak_initial_guesses, raise_error=True)
-            if len(peak_initial_guesses) != len(peak_energies):
-                self.logger.exception(
-                    ValueError(
-                        'peak_initial_guesses must have the same number of '
-                        + 'values as peak_energies'))
-
-        import matplotlib.pyplot as plt
-        import numpy as np
-        from CHAP.utils.fit import Fit
-        from CHAP.utils.general import select_mask_1d
-
-        spectrum = self.unwrap_pipelinedata(data)[0]
-        num_bins = len(spectrum)
-        uncalibrated_energies = np.linspace(0, max_energy, num_bins)
-
-        fig, mask, fit_ranges = select_mask_1d(
-            spectrum, x=uncalibrated_energies,
-            preselected_index_ranges=fit_ranges,
-            xlabel='Uncalibrated Energy', ylabel='Intensity',
-            min_num_index_ranges=1, interactive=interactive)
-        if save_figures:
-            fig.savefig(os.path.join(
-                outputdir, 'mca_energy_calibration_mask.png'))
-        plt.close()
-        self.logger.debug(f'Selected index ranges to fit: {fit_ranges}')
-
-        spectrum_fit = Fit(spectrum[mask], x=uncalibrated_energies[mask])
-        for i, (peak_energy, initial_guess) in enumerate(
-                zip(peak_energies, peak_initial_guesses)):
-            spectrum_fit.add_model(
-                'gaussian', prefix=f'peak{i+1}_', parameters=(
-                    {'name': 'amplitude', 'min': 0.0},
-                    {'name': 'center', 'value': initial_guess,
-                     'min': initial_guess - peak_center_fit_delta,
-                     'max': initial_guess + peak_center_fit_delta}
-                ))
-        self.logger.debug('Fitting spectrum')
-        spectrum_fit.fit()
-        fit_peak_energies = [
-            spectrum_fit.best_values[f'peak{i+1}_center']
-            for i in range(len(peak_energies))]
-        self.logger.debug(f'Fit peak centers: {fit_peak_energies}')
-
-        energy_fit = Fit.fit_data(
-            peak_energies, 'linear', x=fit_peak_energies, nan_policy='omit')
-        slope = energy_fit.best_values['slope']
-        intercept = energy_fit.best_values['intercept']
-
-        # Rescale slope so results are a linear correction from
-        # channel indices -> calibrated energies, not uncalibrated
-        # energies -> calibrated energies
-        slope = (max_energy / num_bins) * slope
-        return({'slope': slope, 'intercept': intercept})
-
 
 class MCADataProcessor(Processor):
     """A Processor to return data from an MCA, restuctured to
     incorporate the shape & metadata associated with a map
     configuration to which the MCA data belongs, and linearly
-    transformed according to the results of a ceria calibration.
+    transformed according to the results of a energy/tth calibration.
     """
 
-    def process(self,
-                data,
-                config=None,
-                save_figures=False,
-                inputdir='.',
-                outputdir='.',
-                interactive=False):
+    def process(
+            self, data, config=None, save_figures=False, inputdir='.',
+            outputdir='.', interactive=False):
         """Process configurations for a map and MCA detector(s), and
         return the calibrated MCA data collected over the map.
 
-        :param data: Input map configuration and results of ceria
-            calibration.
+        :param data: Input map configuration and results of
+            energy/tth calibration.
         :type data: list[dict[str,object]]
         :return: Calibrated and flux-corrected MCA data.
         :rtype: nexusformat.nexus.NXentry
@@ -1094,9 +2381,9 @@ class MCADataProcessor(Processor):
         exit('Done Here')
         map_config = self.get_config(
             data, 'common.models.map.MapConfig', inputdir=inputdir)
-        ceria_calibration_config = self.get_config(
-            data, 'edd.models.MCACeriaCalibrationConfig', inputdir=inputdir)
-        nxroot = self.get_nxroot(map_config, ceria_calibration_config)
+        calibration_config = self.get_config(
+            data, 'edd.models.MCATthCalibrationConfig', inputdir=inputdir)
+        nxroot = self.get_nxroot(map_config, calibration_config)
 
         return nxroot
 
@@ -1111,7 +2398,7 @@ class MCADataProcessor(Processor):
         :type map_config: CHAP.common.models.MapConfig.
         :param calibration_config: The calibration configuration.
         :type calibration_config:
-            CHAP.edd.models.MCACeriaCalibrationConfig
+            CHAP.edd.models.MCATthCalibrationConfig
         :return: A map of the calibrated and flux-corrected MCA data.
         :rtype: nexusformat.nexus.NXroot
         """
@@ -1171,39 +2458,137 @@ class MCADataProcessor(Processor):
         return nxroot
 
 
+class MCACalibratedDataPlotter(Processor):
+    """Convenience Processor for quickly visualizing calibrated MCA
+       data from a single scan. Returns None!"""
+    def process(
+            self, data, spec_file, scan_number, scan_step_index=None,
+            material=None, save_figures=False, interactive=False,
+            outputdir='.'):
+        """Show a maplotlib figure of the MCA data fom the scan
+        provided on a calibrated energy axis. If `scan_step_index` is
+        None, a plot of the sum of all spectra across the whole scan
+        will be shown.
+
+        :param data: PipelineData containing an MCA calibration.
+        :type data: list[PipelineData]
+        :param spec_file: SPEC file containing scan of interest.
+        :type spec_file: str
+        :param scan_number: Scan number of interest.
+        :type scan_number: int
+        :param scan_step_index: Scan step index of interest,
+            defaults to `None`.
+        :type scan_step_index: int, optional
+        :param material: Material parameters to plot HKLs for.
+        :type material: dict
+        :param save_figures: Save .pngs of plots for checking inputs &
+            outputs of this Processor.
+        :type save_figures: bool
+        :param interactive: Allows for user interactions.
+        :type interactive: bool
+        :param outputdir: Directory to which any output figures will
+            be saved.
+        :type outputdir: str
+        :returns: None
+        :rtype: None
+        """
+        # Third party modules
+        import matplotlib.pyplot as plt
+
+        # Local modules
+        from chess_scanparsers import SMBMCAScanParser as ScanParser
+
+        if material is not None:
+            self.logger.warning('Plotting HKL lines is not supported yet.')
+
+        if scan_step_index is not None:
+            if not isinstance(scan_step_index, int):
+                try:
+                    scan_step_index = int(scan_step_index)
+                except:
+                    msg = 'scan_step_index must be an int'
+                    self.logger.error(msg)
+                    raise TypeError(msg)
+
+        calibration_config = self.get_config(
+            data, 'edd.models.MCATthCalibrationConfig')
+        scanparser = ScanParser(spec_file, scan_number)
+
+        fig, ax = plt.subplots(1, 1, figsize=(11, 8.5))
+        title = f'{scanparser.scan_title} MCA Data'
+        if scan_step_index is None:
+            title += ' (sum of all spectra in the scan)'
+        ax.set_title(title)
+        ax.set_xlabel('Calibrated energy (keV)')
+        ax.set_ylabel('Intenstiy (a.u)')
+        for detector in calibration_config.detectors:
+            if scan_step_index is None:
+                spectrum = np.sum(
+                    scanparser.get_all_detector_data(detector.detector_name),
+                    axis=0)
+            else:
+                spectrum = scanparser.get_detector_data(
+                    detector.detector_name, scan_step_index=scan_step_index)
+            ax.plot(detector.energies, spectrum,
+                    label=f'Detector {detector.detector_name}')
+        ax.legend()
+        if interactive:
+            plt.show()
+        if save_figures:
+            fig.savefig(os.path.join(
+                outputdir, f'spectrum_{scanparser.scan_title}'))
+        plt.close()
+        return None
+
+
 class StrainAnalysisProcessor(Processor):
     """Processor that takes a map of MCA data and returns a map of
     sample strains
     """
-    def process(self,
-                data,
-                config=None,
-                save_figures=False,
-                inputdir='.',
-                outputdir='.',
-                interactive=False):
+    def __init__(self):
+        super().__init__()
+        self._save_figures = False
+        self._inputdir = '.'
+        self._outputdir = '.'
+        self._interactive = False
+        self._detectors = []
+        self._detector_indices = []
+        self._nxdata = None
+
+    def process(
+            self, data, config=None, find_peaks=False, skip_animation=False,
+            save_figures=False, inputdir='.', outputdir='.',
+            interactive=False):
         """Return strain analysis maps & associated metadata in an NXprocess.
 
         :param data: Input data containing configurations for a map,
-            completed ceria calibration, and parameters for strain
-            analysis
+            completed energy/tth calibration, and parameters for strain
+            analysis.
         :type data: list[PipelineData]
         :param config: Initialization parameters for an instance of
             CHAP.edd.models.StrainAnalysisConfig, defaults to
-            None.
+            `None`.
         :type config: dict, optional
+        :param find_peaks: Exclude peaks where the average spectrum
+            is below the `rel_height_cutoff` (in the detector
+            configuration) cutoff relative to the maximum value of the
+            average spectrum, defaults to `False`.
+        :type find_peaks: bool, optional
+        :param skip_animation: Skip the animation and plotting of
+            the strain analysis fits, defaults to `False`.
+        :type skip_animation: bool, optional
         :param save_figures: Save .pngs of plots for checking inputs &
-            outputs of this Processor, defaults to False.
+            outputs of this Processor, defaults to `False`.
         :type save_figures: bool, optional
-        :param outputdir: Directory to which any output figures will
-            be saved, defaults to '.'.
-        :type outputdir: str, optional
         :param inputdir: Input directory, used only if files in the
             input configuration are not absolute paths,
-            defaults to '.'.
+            defaults to `'.'`.
         :type inputdir: str, optional
+        :param outputdir: Directory to which any output figures will
+            be saved, defaults to `'.'`.
+        :type outputdir: str, optional
         :param interactive: Allows for user interactions, defaults to
-            False.
+            `False`.
         :type interactive: bool, optional
         :raises RuntimeError: Unable to get a valid strain analysis
             configuration.
@@ -1213,67 +2598,122 @@ class StrainAnalysisProcessor(Processor):
         :rtype: nexusformat.nexus.NXprocess
 
         """
-        # Get required configuration models from input data
-        ceria_calibration_config = self.get_config(
-            data, 'edd.models.MCACeriaCalibrationConfig', inputdir=inputdir)
+        # Third party modules
+        from nexusformat.nexus import (
+            NXentry,
+            NXroot,
+        )
+
+        self._save_figures = save_figures
+        self._outputdir = outputdir
+        self._interactive = interactive
+
+        # Load the detector data
+        try:
+            nxentry = self.get_data(data, 'MapProcessor')
+            if not isinstance(nxentry, NXentry):
+                raise RuntimeError(
+                    'No valid NXentry data in MapProcessor pipeline data')
+        except:
+            try:
+                try:
+                    nxroot = self.get_data(data, 'NexusReader')
+                except:
+                    nxroot = self.get_data(data, 'NexusWriter')
+                if not isinstance(nxroot, NXroot):
+                    raise RuntimeError(
+                        'No valid NXroot data in NexusWriter pipeline data')
+                nxentry = nxroot[nxroot.default]
+                if not isinstance(nxentry, NXentry):
+                    raise RuntimeError(
+                        'No valid NXentry data in NexusWriter pipeline data')
+            except:
+                raise RuntimeError(
+                    'No valid detector data in input pipeline data')
+
+        # Load the validated calibration and strain analysis configuration
         try:
             strain_analysis_config = self.get_config(
                 data, 'edd.models.StrainAnalysisConfig', inputdir=inputdir)
         except Exception as data_exc:
-            # Local modules
-            from CHAP.edd.models import StrainAnalysisConfig
-
             self.logger.info('No valid strain analysis config in input '
-                             + 'pipeline data, using config parameter instead')
+                             'pipeline data, using config parameter instead')
             try:
+                # Local modules
+                from CHAP.edd.models import StrainAnalysisConfig
+
                 strain_analysis_config = StrainAnalysisConfig(
                     **config, inputdir=inputdir)
             except Exception as dict_exc:
                 raise RuntimeError from dict_exc
 
-        nxroot = self.get_nxroot(
-            strain_analysis_config.map_config,
-            ceria_calibration_config,
-            strain_analysis_config,
-            save_figures=save_figures,
-            outputdir=outputdir,
-            interactive=interactive)
-        self.logger.debug(nxroot.tree)
-
-        return nxroot
-
-    def get_nxroot(self,
-                   map_config,
-                   ceria_calibration_config,
-                   strain_analysis_config,
-                   save_figures=False,
-                   outputdir='.',
-                   interactive=False):
-        """Return NXroot containing strain maps.
-
-
-        :param map_config: The map configuration.
-        :type map_config: CHAP.common.models.map.MapConfig
-        :param ceria_calibration_config: The calibration configuration.
-        :type ceria_calibration_config:
-            'CHAP.edd.models.MCACeriaCalibrationConfig'
+        # Validate the detector configuration and load, validate and
+        # add the calibration info to the detectors
+        calibration_config = self.get_config(
+            data, 'edd.models.MCATthCalibrationConfig', inputdir=inputdir)
+        calibration_detector_indices = [
+            int(d.detector_name) for d in calibration_config.detectors]
+        if 'detector_names' in nxentry:
+            available_detector_indices = [
+                int(d) for d in nxentry.detector_names]
+        else:
+            available_detector_indices = calibration_detector_indices
+        if strain_analysis_config.detectors is None:
+            # Local modules:
+            from CHAP.edd.models import MCAElementStrainAnalysisConfig
+
+            strain_analysis_config.detectors = [
+                MCAElementStrainAnalysisConfig(**dict(d))
+                for d in calibration_config.detectors
+                if int(d.detector_name) in available_detector_indices]
+        for detector in deepcopy(strain_analysis_config.detectors):
+            index = int(detector.detector_name)
+            if index not in available_detector_indices:
+                self.logger.warning(
+                    f'Skipping detector {index} (no raw data)')
+                strain_analysis_config.detectors.remove(detector)
+            elif index in calibration_detector_indices:
+                self._detectors.append(detector)
+                self._detector_indices.append(
+                    available_detector_indices.index(index))
+                calibration = [
+                    d for d in calibration_config.detectors
+                    if d.detector_name == detector.detector_name][0]
+                detector.add_calibration(calibration)
+            else:
+                self.logger.warning(f'Skipping detector {index} '
+                                    '(no energy/tth calibration data)')
+        if not self._detectors:
+            raise ValueError('Unable to match an available calibrated '
+                             'detector for the strain analysis')
+
+        return self.strain_analysis(
+            nxentry, strain_analysis_config, find_peaks, skip_animation)
+
+    def strain_analysis(
+            self, nxentry, strain_analysis_config, find_peaks, skip_animation):
+        """Return NXroot containing the strain maps.
+
+        :param nxentry: The strain analysis map, including the raw
+            detector data.
+        :type nxentry: nexusformat.nexus.NXentry
         :param strain_analysis_config: Strain analysis processing
             configuration.
         :type strain_analysis_config:
             CHAP.edd.models.StrainAnalysisConfig
-        :param save_figures: Save .pngs of plots for checking inputs &
-            outputs of this Processor, defaults to False.
-        :type save_figures: bool, optional
-        :param outputdir: Directory to which any output figures will
-            be saved, defaults to '.'.
-        :type outputdir: str, optional
-        :param interactive: Allows for user interactions, defaults to
-            False.
-        :type interactive: bool, optional
-        :return: NXroot containing strain maps.
+        :param find_peaks: Exclude peaks where the average spectrum
+            is below the `rel_height_cutoff` (in the detector
+            configuration) cutoff relative to the maximum value of the
+            average spectrum, defaults to `False`.
+        :type find_peaks: bool, optional
+        :param skip_animation: Skip the animation and plotting of
+            the strain analysis fits, defaults to `False`.
+        :type skip_animation: bool, optional
+        :return: The strain maps.
         :rtype: nexusformat.nexus.NXroot
         """
         # Third party modules
+        from json import loads
         from nexusformat.nexus import (
             NXcollection,
             NXdata,
@@ -1283,150 +2723,145 @@ class StrainAnalysisProcessor(Processor):
             NXprocess,
             NXroot,
         )
+        from nexusformat.nexus.tree import NXlinkfield
 
         # Local modules
         from CHAP.common import MapProcessor
+        from CHAP.common.models.map import MapConfig
         from CHAP.edd.utils import (
             get_peak_locations,
+            get_spectra_fits,
             get_unique_hkls_ds,
-            get_spectra_fits
         )
 
-        def linkdims(nxgroup, field_dims=[]):
-            if isinstance(field_dims, dict):
-                field_dims = [field_dims]
-            if map_config.map_type == 'structured':
-                axes = deepcopy(map_config.dims)
-                for dims in field_dims:
-                    axes.append(dims['axes'])
-                nxgroup.attrs['axes'] = axes
-            else:
-                axes = ['map_index']
-                for dims in field_dims:
-                    axes.append(dims['axes'])
-                nxgroup.attrs['axes'] = axes
-                nxgroup.attrs[f'map_index_indices'] = 0
-            for dim in map_config.dims:
-                nxgroup.makelink(nxentry.data[dim])
-                if f'{dim}_indices' in nxentry.data.attrs:
-                    nxgroup.attrs[f'{dim}_indices'] = \
-                        nxentry.data.attrs[f'{dim}_indices']
+        def linkdims(
+                nxgroup, nxdata_source, field_dims=[], oversampling_axis={}):
+            source_axes = nxdata_source.axes
+            if isinstance(source_axes, str):
+                source_axes = [source_axes]
+            axes = []
+            for dim in source_axes:
+                axes.append(dim)
+                if dim in oversampling_axis:
+                    bin_name = dim.replace('fly_', 'bin_')
+                    axes[axes.index(dim)] = bin_name
+                    nxgroup[bin_name] = NXfield(
+                        value=oversampling_axis[dim],
+                        units=nxdata_source[dim].units,
+                        attrs={
+                            'long_name':
+                                f'oversampled {nxdata_source[dim].long_name}',
+                            'data_type': nxdata_source[dim].data_type,
+                            'local_name':
+                                f'oversampled {nxdata_source[dim].local_name}'})
+                else:
+                    if isinstance(nxdata_source[dim], NXlinkfield):
+                        nxgroup[dim] = nxdata_source[dim]
+                    else:
+                        nxgroup.makelink(nxdata_source[dim])
+                    if f'{dim}_indices' in nxdata_source.attrs:
+                        nxgroup.attrs[f'{dim}_indices'] = \
+                            nxdata_source.attrs[f'{dim}_indices']
             for dims in field_dims:
-                nxgroup.attrs[f'{dims["axes"]}_indices'] = dims['index']
+                axes.append(dims['axis'])
+                nxgroup.attrs[f'{dims["axis"]}_indices'] = dims['index']
+            nxgroup.attrs['axes'] = axes
 
-        if len(strain_analysis_config.detectors) != 1:
-            raise RuntimeError('Multiple detectors not tested')
-        for detector in strain_analysis_config.detectors:
-            calibration = [
-                d for d in ceria_calibration_config.detectors \
-                if d.detector_name == detector.detector_name][0]
-            detector.add_calibration(calibration)
+        if not self._interactive and not strain_analysis_config.materials:
+            raise ValueError(
+                'No material provided. Provide a material in the '
+                'StrainAnalysis Configuration, or re-run the pipeline with '
+                'the --interactive flag.')
+
+        # Get the map configuration
+        map_config = MapConfig(**loads(str(nxentry.map_config)))
 
+        # Create the NXroot object
         nxroot = NXroot()
-        nxroot[map_config.title] = MapProcessor.get_nxentry(map_config)
-        nxentry = nxroot[map_config.title]
+        nxroot[map_config.title] = nxentry
         nxroot[f'{map_config.title}_strainanalysis'] = NXprocess()
         nxprocess = nxroot[f'{map_config.title}_strainanalysis']
-        nxprocess.strain_analysis_config = dumps(strain_analysis_config.dict())
+        nxprocess.strain_analysis_config = dumps(
+            strain_analysis_config.dict())
 
         # Setup plottable data group
-        nxprocess.data = NXdata()
-        nxprocess.default = 'data'
-        nxdata = nxprocess.data
-        linkdims(nxdata)
-
-        # Collect raw MCA data of interest
-        mca_bin_energies = []
-        for i, detector in enumerate(strain_analysis_config.detectors):
-            mca_bin_energies.append(
-                detector.slope_calibrated
-                * np.linspace(0, detector.max_energy_kev, detector.num_bins)
-                + detector.intercept_calibrated)
-        mca_data = strain_analysis_config.mca_data()
-
-        # Select interactive params / save figures
-        if interactive or save_figures:
-            # Third party modules
-            import matplotlib.pyplot as plt
 
+        # Collect the raw MCA data
+        if (strain_analysis_config.sum_axes
+                and map_config.attrs['scan_type'] > 2):
+            # FIX? Could make this a processor
+            mca_data = self._get_sum_axes_data(
+                nxentry[nxentry.default],
+                map_config.attrs.get('fly_axis_labels', [])).astype(np.float64)
+            nxprocess.data = self._nxdata
+            nxdata = nxprocess.data
+        else:
+            mca_data = np.asarray(
+                nxentry[nxentry.default].nxsignal[:,self._detector_indices,:],
+                dtype=np.float64)
+            nxprocess.data = NXdata()
+            self._nxdata = nxprocess.data
+            linkdims(self._nxdata, nxentry.data)
+            self._nxdata.makelink(nxentry.data['detector_data'])
+            self._nxdata.attrs['signal'] = 'detector_data'
+        nxprocess.default = 'data'
+        self.logger.debug(f'mca_data.shape: {mca_data.shape}')
+        mca_data_mean = np.mean(mca_data, axis=0)
+        self.logger.debug(f'mca_data_mean.shape: {mca_data_mean.shape}')
+
+        # Check for oversampling axis and create the binned coordinates
+        oversampling_axis = {}
+        if (map_config.attrs.get('scan_type') == 4
+                and strain_analysis_config.sum_fly_axes):
             # Local modules
-            from CHAP.edd.utils import (
-                select_material_params,
-                select_mask_and_hkls,
-            )
-
-            # Mask during calibration
-            if len(ceria_calibration_config.detectors) != 1:
-                raise RuntimeError('Multiple detectors not implemented')
-            for detector in ceria_calibration_config.detectors:
-#                calibration_mask = detector.mca_mask()
-                calibration_bin_ranges = detector.include_bin_ranges
-
-            tth = strain_analysis_config.detectors[0].tth_calibrated
-            fig, strain_analysis_config.materials = select_material_params(
-                mca_bin_energies[0], np.sum(mca_data, axis=1)[0], tth,
-                materials=strain_analysis_config.materials,
-                label='Sum of all spectra in the map',
-                interactive=interactive)
-            self.logger.debug(
-                f'materials: {strain_analysis_config.materials}')
-            if save_figures:
-                fig.savefig(os.path.join(
-                    outputdir,
-                    f'{detector.detector_name}_strainanalysis_'
-                    'material_config.png'))
-            plt.close()
+            from CHAP.utils.general import rolling_average
+
+            raise RuntimeError('oversampling needs testing')
+            fly_axis = map_config.attrs.get('fly_axis_labels')[0]
+            oversampling = strain_analysis_config.oversampling
+            oversampling_axis[fly_axis] = rolling_average(
+                    nxdata[fly_axis].nxdata,
+                    start=oversampling.get('start', 0),
+                    end=oversampling.get('end'),
+                    width=oversampling.get('width'),
+                    stride=oversampling.get('stride'),
+                    num=oversampling.get('num'),
+                    mode=oversampling.get('mode', 'valid'))
+
+        # Get the energy masks
+        energy_masks = self._get_energy_and_masks()
+
+        # Get and subtract the detector baselines
+        baselines = self._get_baselines(mca_data_mean, energy_masks)
+        if baselines:
+            baselines = np.asarray(baselines)
+            mca_data_mean -= baselines
+            mca_data -= baselines
+
+        # Adjust the material properties
+        self._adjust_material_props(
+            mca_data_mean, strain_analysis_config.materials, energy_masks)
+
+        # Get the mask and HKLs used in the strain analysis
+        self._get_mask_hkls(
+            mca_data, mca_data_mean, strain_analysis_config.materials,
+            energy_masks)
+
+        # Loop over the detectors to perform the strain analysis
+        for index, detector in enumerate(self._detectors):
+
+            self.logger.info(f'Analysing detector {detector.detector_name}')
+
+            # Get the MCA bin energies
+            mca_bin_energies = detector.energies
 
-            # ASK: can we assume same hkl_tth_tol and tth_max for
-            # every detector in this part?
-            hkls, ds = get_unique_hkls_ds(
-                strain_analysis_config.materials,
-                tth_tol=strain_analysis_config.detectors[0].hkl_tth_tol,
-                tth_max=strain_analysis_config.detectors[0].tth_max)
-            for i, detector in enumerate(strain_analysis_config.detectors):
-                fig, include_bin_ranges, hkl_indices = \
-                    select_mask_and_hkls(
-                        mca_bin_energies[i],
-                        np.sum(mca_data[i], axis=0),
-                        hkls, ds,
-                        detector.tth_calibrated,
-                        detector.include_bin_ranges, detector.hkl_indices,
-                        detector.detector_name, mca_data[i],
-#                        calibration_mask=calibration_mask,
-                        calibration_bin_ranges=calibration_bin_ranges,
-                        label='Sum of all spectra in the map',
-                        interactive=interactive)
-                detector.include_energy_ranges = detector.get_energy_ranges(
-                    include_bin_ranges)
-                detector.hkl_indices = hkl_indices
-                if save_figures:
-                    fig.savefig(os.path.join(
-                        outputdir,
-                        f'{detector.detector_name}_strainanalysis_'
-                        'fit_mask_hkls.png'))
-                plt.close()
-        else:
-            # ASK: can we assume same hkl_tth_tol and tth_max for
-            # every detector in this part?
             # Get the unique HKLs and lattice spacings for the strain
-            # analysis materials (assume hkl_tth_tol and tth_max are the
-            # same for each detector)
+            # analysis materials
             hkls, ds = get_unique_hkls_ds(
                 strain_analysis_config.materials,
-                tth_tol=strain_analysis_config.detectors[0].hkl_tth_tol,
-                tth_max=strain_analysis_config.detectors[0].tth_max)
+                tth_tol=detector.hkl_tth_tol,
+                tth_max=detector.tth_max)
 
-        for i, detector in enumerate(strain_analysis_config.detectors):
-            if not detector.include_energy_ranges:
-                raise ValueError(
-                    'No value provided for include_energy_ranges. '
-                    'Provide them in the MCA Ceria Calibration Configuration, '
-                    'or re-run the pipeline with the --interactive flag.')
-            if not detector.hkl_indices:
-                raise ValueError(
-                    'No value provided for hkl_indices. Provide them in '
-                    'the detector\'s MCA Ceria Calibration Configuration, or'
-                    ' re-run the pipeline with the --interactive flag.')
             # Setup NXdata group
             self.logger.debug(
                 f'Setting up NXdata group for {detector.detector_name}')
@@ -1437,32 +2872,32 @@ class StrainAnalysisProcessor(Processor):
             nxdetector.data = NXdata()
             det_nxdata = nxdetector.data
             linkdims(
-                det_nxdata, {'axes': 'energy', 'index': len(map_config.shape)})
+                det_nxdata, self._nxdata,
+                [{'axis': 'energy', 'index': mca_data.ndim-1}],
+                oversampling_axis=oversampling_axis)
             mask = detector.mca_mask()
-            energies = mca_bin_energies[i][mask]
-            det_nxdata.energy = NXfield(value=energies,
-                                        attrs={'units': 'keV'})
+            energies = mca_bin_energies[mask]
+            det_nxdata.energy = NXfield(value=energies, attrs={'units': 'keV'})
+            det_nxdata.tth = NXfield(
+                dtype=np.float64,
+                shape=(mca_data.shape[0]),
+                attrs={'units':'degrees', 'long_name': '2\u03B8 (degrees)'})
+            det_nxdata.uniform_microstrain = NXfield(
+                dtype=np.float64,
+                shape=(mca_data.shape[0]),
+                attrs={'long_name': 'Strain from uniform fit(\u03BC\u03B5)'})
+            det_nxdata.unconstrained_microstrain = NXfield(
+                dtype=np.float64,
+                shape=(mca_data.shape[0]),
+                attrs={'long_name':
+                           'Strain from unconstrained fit(\u03BC\u03B5)'})
+
+            # Add detector data
             det_nxdata.intensity = NXfield(
-                dtype='uint16',
-                shape=(*map_config.shape, len(energies)),
+                value=np.asarray([mca_data[i,index,:].astype(np.float64)[mask]
+                                  for i in range(mca_data.shape[0])]),
                 attrs={'units': 'counts'})
-            det_nxdata.tth = NXfield(
-                dtype='float64',
-                shape=map_config.shape,
-                attrs={'units':'degrees', 'long_name': '2\u03B8 (degrees)'}
-            )
-            det_nxdata.microstrain = NXfield(
-                dtype='float64',
-                shape=map_config.shape,
-                attrs={'long_name': 'Strain (\u03BC\u03B5)'})
-
-            # Gather detector data
-            self.logger.debug(
-                f'Gathering detector data for {detector.detector_name}')
-            for j, map_index in enumerate(np.ndindex(map_config.shape)):
-                det_nxdata.intensity[map_index] = \
-                    mca_data[i][j].astype('uint16')[mask]
-            det_nxdata.summed_intensity = det_nxdata.intensity.sum(axis=-1)
+            det_nxdata.summed_intensity = det_nxdata.intensity.sum(axis=0)
 
             # Perform strain analysis
             self.logger.debug(
@@ -1470,11 +2905,55 @@ class StrainAnalysisProcessor(Processor):
 
             # Get the HKLs and lattice spacings that will be used for
             # fitting
-            fit_hkls  = np.asarray([hkls[i] for i in detector.hkl_indices])
-            fit_ds  = np.asarray([ds[i] for i in detector.hkl_indices])
+            hkls_fit = np.asarray([hkls[i] for i in detector.hkl_indices])
+            ds_fit = np.asarray([ds[i] for i in detector.hkl_indices])
             peak_locations = get_peak_locations(
-                fit_ds, detector.tth_calibrated)
+                ds_fit, detector.tth_calibrated)
+
+            # Find peaks
+            if not find_peaks or detector.rel_height_cutoff is None:
+                use_peaks = np.ones((peak_locations.size)).astype(bool)
+            else:
+                # Third party modules
+                from scipy.signal import find_peaks as find_peaks_scipy
+
+                # Local modules
+                from CHAP.utils.general import index_nearest
+
+                peaks = find_peaks_scipy(
+                    mca_data_mean[index],
+                    height=(detector.rel_height_cutoff
+                        * mca_data_mean[index][mask].max()),
+                    width=5)
+                heights = peaks[1]['peak_heights']
+                widths = peaks[1]['widths']
+                centers = [mca_bin_energies[v] for v in peaks[0]]
+                use_peaks = np.zeros((peak_locations.size)).astype(bool)
+                # RV Potentially use peak_heights/widths as initial
+                # values in fit?
+                # peak_heights = np.zeros((peak_locations.size))
+                # peak_widths = np.zeros((peak_locations.size))
+                delta = mca_bin_energies[1]-mca_bin_energies[0]
+                for height, width, center in zip(heights, widths, centers):
+                    for n, loc in enumerate(peak_locations):
+                        # RV Hardwired range now, use detector.centers_range?
+                        if center-width*delta < loc < center+width*delta:
+                            use_peaks[n] = True
+                            # peak_heights[n] = height
+                            # peak_widths[n] = width*delta
+                            break
+
+            if any(use_peaks):
+                self.logger.debug(
+                    f'Using peaks with centers at {peak_locations[use_peaks]}')
+            else:
+                self.logger.warning(
+                    'No matching peaks with heights above the threshold, '
+                    f'skipping the fit for detector {detector.detector_name}')
+                continue
 
+            # Perform the fit
+            self.logger.debug(f'Fitting detector {detector.detector_name} ...')
             (uniform_fit_centers, uniform_fit_centers_errors,
              uniform_fit_amplitudes, uniform_fit_amplitudes_errors,
              uniform_fit_sigmas, uniform_fit_sigmas_errors,
@@ -1487,7 +2966,8 @@ class StrainAnalysisProcessor(Processor):
              unconstrained_redchi, unconstrained_success) = \
                 get_spectra_fits(
                     det_nxdata.intensity.nxdata, energies,
-                    peak_locations, detector)
+                    peak_locations[use_peaks], detector)
+            self.logger.debug(f'... done')
 
             # Add uniform fit results to the NeXus structure
             nxdetector.uniform_fit = NXcollection()
@@ -1497,9 +2977,11 @@ class StrainAnalysisProcessor(Processor):
             fit_nxgroup.results = NXdata()
             fit_nxdata = fit_nxgroup.results
             linkdims(
-                fit_nxdata, {'axes': 'energy', 'index': len(map_config.shape)})
+                fit_nxdata, self._nxdata,
+                [{'axis': 'energy', 'index': mca_data.ndim-1}],
+                oversampling_axis=oversampling_axis)
             fit_nxdata.makelink(det_nxdata.energy)
-            fit_nxdata.best_fit= uniform_best_fit
+            fit_nxdata.best_fit = uniform_best_fit
             fit_nxdata.residuals = uniform_residuals
             fit_nxdata.redchi = uniform_redchi
             fit_nxdata.success = uniform_success
@@ -1507,14 +2989,14 @@ class StrainAnalysisProcessor(Processor):
             # Peak-by-peak results
 #            fit_nxgroup.fit_hkl_centers = NXdata()
 #            fit_nxdata = fit_nxgroup.fit_hkl_centers
-#            linkdims(fit_nxdata)
+#            linkdims(fit_nxdata, self._nxdata)
             for (hkl, center_guess, centers_fit, centers_error,
-                amplitudes_fit, amplitudes_error, sigmas_fit,
-                sigmas_error) in zip(
-                    fit_hkls, peak_locations,
-                    uniform_fit_centers, uniform_fit_centers_errors,
-                    uniform_fit_amplitudes, uniform_fit_amplitudes_errors,
-                    uniform_fit_sigmas, uniform_fit_sigmas_errors):
+                    amplitudes_fit, amplitudes_error, sigmas_fit,
+                    sigmas_error) in zip(
+                        hkls_fit, peak_locations,
+                        uniform_fit_centers, uniform_fit_centers_errors,
+                        uniform_fit_amplitudes, uniform_fit_amplitudes_errors,
+                        uniform_fit_sigmas, uniform_fit_sigmas_errors):
                 hkl_name = '_'.join(str(hkl)[1:-1].split(' '))
                 fit_nxgroup[hkl_name] = NXparameters()
                 # Report initial HKL peak centers
@@ -1523,7 +3005,7 @@ class StrainAnalysisProcessor(Processor):
                     'keV'
                 # Report HKL peak centers
                 fit_nxgroup[hkl_name].centers = NXdata()
-                linkdims(fit_nxgroup[hkl_name].centers)
+                linkdims(fit_nxgroup[hkl_name].centers, self._nxdata)
                 fit_nxgroup[hkl_name].centers.values = NXfield(
                     value=centers_fit, attrs={'units': 'keV'})
                 fit_nxgroup[hkl_name].centers.errors = NXfield(
@@ -1533,7 +3015,7 @@ class StrainAnalysisProcessor(Processor):
 #                    fit_nxgroup[f'{hkl_name}/centers/values'], name=hkl_name)
                 # Report HKL peak amplitudes
                 fit_nxgroup[hkl_name].amplitudes = NXdata()
-                linkdims(fit_nxgroup[hkl_name].amplitudes)
+                linkdims(fit_nxgroup[hkl_name].amplitudes, self._nxdata)
                 fit_nxgroup[hkl_name].amplitudes.values = NXfield(
                     value=amplitudes_fit, attrs={'units': 'counts'})
                 fit_nxgroup[hkl_name].amplitudes.errors = NXfield(
@@ -1541,59 +3023,66 @@ class StrainAnalysisProcessor(Processor):
                 fit_nxgroup[hkl_name].amplitudes.attrs['signal'] = 'values'
                 # Report HKL peak FWHM
                 fit_nxgroup[hkl_name].sigmas = NXdata()
-                linkdims(fit_nxgroup[hkl_name].sigmas)
+                linkdims(fit_nxgroup[hkl_name].sigmas, self._nxdata)
                 fit_nxgroup[hkl_name].sigmas.values = NXfield(
                     value=sigmas_fit, attrs={'units': 'keV'})
                 fit_nxgroup[hkl_name].sigmas.errors = NXfield(
                     value=sigmas_error)
                 fit_nxgroup[hkl_name].sigmas.attrs['signal'] = 'values'
 
-            if interactive or save_figures:
+            if ((self._interactive or self._save_figures)
+                    and not skip_animation):
                 # Third party modules
                 import matplotlib.animation as animation
+                import matplotlib.pyplot as plt
 
-                if save_figures:
+                if self._save_figures:
                     path = os.path.join(
-                        outputdir, f'{detector.detector_name}_strainanalysis_'
-                        'unconstrained_fits')
+                        self._outputdir,
+                        f'{detector.detector_name}_strainanalysis_'
+                            'unconstrained_fits')
                     if not os.path.isdir(path):
                         os.mkdir(path)
 
                 def animate(i):
-                    map_index = np.unravel_index(i, map_config.shape)
-                    intensity.set_ydata(
-                        det_nxdata.intensity.nxdata[map_index]
-                        / det_nxdata.intensity.nxdata[map_index].max())
-                    best_fit.set_ydata(
-                        unconstrained_best_fit[map_index]
-                        / unconstrained_best_fit[map_index].max())
-                    # residual.set_ydata(unconstrained_residuals[map_index])
-                    index.set_text('\n'.join(f'{k}[{i}] = {v}'
-                        for k, v in map_config.get_coords(map_index).items()))
-                    if save_figures:
+                    norm = det_nxdata.intensity.nxdata[i].max()
+                    intensity.set_ydata(det_nxdata.intensity.nxdata[i] / norm)
+                    best_fit.set_ydata(unconstrained_best_fit[i] / norm)
+                    axes = self._nxdata.attrs['axes']
+                    if isinstance(axes, str):
+                        axes = [axes]
+                    index.set_text('\n'.join(
+                        [f'norm = {int(norm)}'] +
+                        ['relative norm = '
+                         f'{(norm / det_nxdata.intensity.max()):.5f}'] +
+                        [f'{dim}[{i}] = {self._nxdata[dim][i]}'
+                         for dim in axes]))
+                    if self._save_figures:
                         plt.savefig(os.path.join(
                             path, f'frame_{str(i).zfill(num_digit)}.png'))
-                    #return intensity, best_fit, residual, index
                     return intensity, best_fit, index
 
                 fig, ax = plt.subplots()
-                map_index = np.unravel_index(0, map_config.shape)
                 data_normalized = (
-                    det_nxdata.intensity.nxdata[map_index]
-                    / det_nxdata.intensity.nxdata[map_index].max())
+                    det_nxdata.intensity.nxdata[0]
+                    / det_nxdata.intensity.nxdata[0].max())
                 intensity, = ax.plot(
                     energies, data_normalized, 'b.', label='data')
-                fit_normalized = (unconstrained_best_fit[map_index]
-                                  / unconstrained_best_fit[map_index].max())
+                if unconstrained_best_fit[0].max():
+                    fit_normalized = (
+                        unconstrained_best_fit[0]
+                        / unconstrained_best_fit[0].max())
+                else:
+                    fit_normalized = unconstrained_best_fit[0]
                 best_fit, = ax.plot(
                     energies, fit_normalized, 'k-', label='fit')
                 # residual, = ax.plot(
-                #     energies, unconstrained_residuals[map_index], 'r-',
+                #     energies, unconstrained_residuals[0], 'r-',
                 #     label='residual')
                 ax.set(
                     title='Unconstrained fits',
                     xlabel='Energy (keV)',
-                    ylabel='Normalized Intensity (-)')
+                    ylabel='Normalized intensity (-)')
                 ax.legend(loc='upper right')
                 index = ax.text(
                     0.05, 0.95, '', transform=ax.transAxes, va='top')
@@ -1601,7 +3090,7 @@ class StrainAnalysisProcessor(Processor):
                 num_frame = int(det_nxdata.intensity.nxdata.size
                               / det_nxdata.intensity.nxdata.shape[-1])
                 num_digit = len(str(num_frame))
-                if not save_figures:
+                if not self._save_figures:
                     ani = animation.FuncAnimation(
                         fig, animate,
                         frames=int(det_nxdata.intensity.nxdata.size
@@ -1629,25 +3118,32 @@ class StrainAnalysisProcessor(Processor):
                          plt.gcf(), frames, interval=1000, blit=True,
                          repeat=False)
 
-                if interactive:
+                if self._interactive:
                     plt.show()
 
-                if save_figures:
+                if self._save_figures:
                     path = os.path.join(
-                        outputdir,
+                        self._outputdir,
                         f'{detector.detector_name}_strainanalysis_'
-                        'unconstrained_fits.gif')
+                            'unconstrained_fits.gif')
                     ani.save(path)
                 plt.close()
 
-            tth_map = detector.get_tth_map(map_config)
+            tth_map = detector.get_tth_map((mca_data.shape[0],))
             det_nxdata.tth.nxdata = tth_map
             nominal_centers = np.asarray(
-                [get_peak_locations(d0, tth_map) for d0 in fit_ds])
+                [get_peak_locations(d0, tth_map)
+                 for d0, use_peak in zip(ds_fit, use_peaks) if use_peak])
+            uniform_strains = np.log(
+                nominal_centers / uniform_fit_centers)
+            uniform_strain = np.mean(uniform_strains, axis=0)
+            det_nxdata.uniform_microstrain.nxdata = uniform_strain * 1e6
+
             unconstrained_strains = np.log(
                 nominal_centers / unconstrained_fit_centers)
             unconstrained_strain = np.mean(unconstrained_strains, axis=0)
-            det_nxdata.microstrain.nxdata = unconstrained_strain * 1e6
+            det_nxdata.unconstrained_microstrain.nxdata = \
+                unconstrained_strain * 1e6
 
             # Add unconstrained fit results to the NeXus structure
             nxdetector.unconstrained_fit = NXcollection()
@@ -1657,7 +3153,9 @@ class StrainAnalysisProcessor(Processor):
             fit_nxgroup.results = NXdata()
             fit_nxdata = fit_nxgroup.results
             linkdims(
-                fit_nxdata, {'axes': 'energy', 'index': len(map_config.shape)})
+                fit_nxdata, self._nxdata,
+                [{'axis': 'energy', 'index': mca_data.ndim-1}],
+                oversampling_axis=oversampling_axis)
             fit_nxdata.makelink(det_nxdata.energy)
             fit_nxdata.best_fit= unconstrained_best_fit
             fit_nxdata.residuals = unconstrained_residuals
@@ -1667,11 +3165,11 @@ class StrainAnalysisProcessor(Processor):
             # Peak-by-peak results
             fit_nxgroup.fit_hkl_centers = NXdata()
             fit_nxdata = fit_nxgroup.fit_hkl_centers
-            linkdims(fit_nxdata)
+            linkdims(fit_nxdata, self._nxdata)
             for (hkl, center_guesses, centers_fit, centers_error,
                 amplitudes_fit, amplitudes_error, sigmas_fit,
                 sigmas_error) in zip(
-                    fit_hkls, uniform_fit_centers,
+                    hkls_fit, uniform_fit_centers,
                     unconstrained_fit_centers,
                     unconstrained_fit_centers_errors,
                     unconstrained_fit_amplitudes,
@@ -1681,7 +3179,7 @@ class StrainAnalysisProcessor(Processor):
                 fit_nxgroup[hkl_name] = NXparameters()
                 # Report initial guesses HKL peak centers
                 fit_nxgroup[hkl_name].center_initial_guess = NXdata()
-                linkdims(fit_nxgroup[hkl_name].center_initial_guess)
+                linkdims(fit_nxgroup[hkl_name].center_initial_guess, self._nxdata)
                 fit_nxgroup[hkl_name].center_initial_guess.makelink(
                     nxdetector.uniform_fit[f'{hkl_name}/centers/values'],
                     name='values')
@@ -1689,7 +3187,7 @@ class StrainAnalysisProcessor(Processor):
                     'values'
                 # Report HKL peak centers
                 fit_nxgroup[hkl_name].centers = NXdata()
-                linkdims(fit_nxgroup[hkl_name].centers)
+                linkdims(fit_nxgroup[hkl_name].centers, self._nxdata)
                 fit_nxgroup[hkl_name].centers.values = NXfield(
                     value=centers_fit, attrs={'units': 'keV'})
                 fit_nxgroup[hkl_name].centers.errors = NXfield(
@@ -1699,7 +3197,7 @@ class StrainAnalysisProcessor(Processor):
                 fit_nxgroup[hkl_name].centers.attrs['signal'] = 'values'
                 # Report HKL peak amplitudes
                 fit_nxgroup[hkl_name].amplitudes = NXdata()
-                linkdims(fit_nxgroup[hkl_name].amplitudes)
+                linkdims(fit_nxgroup[hkl_name].amplitudes, self._nxdata)
                 fit_nxgroup[hkl_name].amplitudes.values = NXfield(
                     value=amplitudes_fit, attrs={'units': 'counts'})
                 fit_nxgroup[hkl_name].amplitudes.errors = NXfield(
@@ -1707,7 +3205,7 @@ class StrainAnalysisProcessor(Processor):
                 fit_nxgroup[hkl_name].amplitudes.attrs['signal'] = 'values'
                 # Report HKL peak sigmas
                 fit_nxgroup[hkl_name].sigmas = NXdata()
-                linkdims(fit_nxgroup[hkl_name].sigmas)
+                linkdims(fit_nxgroup[hkl_name].sigmas, self._nxdata)
                 fit_nxgroup[hkl_name].sigmas.values = NXfield(
                     value=sigmas_fit, attrs={'units': 'keV'})
                 fit_nxgroup[hkl_name].sigmas.errors = NXfield(
@@ -1716,6 +3214,164 @@ class StrainAnalysisProcessor(Processor):
 
         return nxroot
 
+    def _get_sum_axes_data(self, nxdata, sum_axes):
+        """Get the raw MCA data collected by the scan averaged over the
+        sum_axes.
+        """
+        # Third party modules
+        from nexusformat.nexus import (
+            NXdata,
+            NXfield,
+        )
+
+        mca_data = np.asarray(
+            nxdata.nxsignal[:,self._detector_indices,:])
+        axes = [nxdata[axis] for axis in nxdata.axes if axis not in sum_axes]
+        unique_points = []
+        sum_indices = []
+        for i in range(mca_data.shape[0]):
+            point = [float(nxdata[axis.nxname][i]) for axis in axes]
+            try:
+                sum_indices[unique_points.index(point)].append(i)
+            except:
+                unique_points.append(point)
+                sum_indices.append([i])
+        mean_mca_data = np.empty((len(unique_points), *mca_data.shape[1:]))
+        for i in range(len(unique_points)):
+            mean_mca_data[i] = np.mean(mca_data[sum_indices[i],:,:], axis=0)
+        self._nxdata = NXdata(
+            NXfield(mean_mca_data, 'detector_data'),
+            tuple([
+                NXfield(
+                    [p[i] for p in unique_points], axis.nxname,
+                    attrs=axis.attrs)
+                for i, axis in enumerate(axes)]))
+        return mean_mca_data
+
+    def _get_energy_and_masks(self):
+        """Get the energy mask by blanking out data below 25 keV as
+        well as that in the last bin.
+        """
+        energy_masks = []
+        for detector in self._detectors:
+            energy_mask = np.where(detector.energies >= 25.0, 1, 0)
+            energy_mask[-1] = 0
+            energy_masks.append(energy_mask)
+        return energy_masks
+
+    def _get_baselines(self, mca_data_mean, energy_masks):
+        """Get the detector baselines."""
+        # Local modules
+        from CHAP.edd.models import BaselineConfig
+        from CHAP.common.processor import ConstructBaseline
+
+        baselines = []
+        for index, detector in enumerate(self._detectors):
+            if detector.baseline:
+                if isinstance(detector.baseline, bool):
+                    detector.baseline = BaselineConfig()
+                if self._save_figures:
+                    filename = os.path.join(
+                        self._outputdir,
+                        f'{detector.detector_name}_strainanalysis_'
+                        'baseline.png')
+                else:
+                    filename = None
+                baseline, baseline_config = \
+                    ConstructBaseline.construct_baseline(
+                        mca_data_mean[index], mask=energy_masks[index],
+                        tol=detector.baseline.tol, lam=detector.baseline.lam,
+                        max_iter=detector.baseline.max_iter,
+                        title=
+                            f'Baseline for detector {detector.detector_name}',
+                        xlabel='Energy (keV)', ylabel='Intensity (counts)',
+                        interactive=self._interactive, filename=filename)
+
+                baselines.append(baseline)
+                detector.baseline.lam = baseline_config['lambda']
+                detector.baseline.attrs['num_iter'] = \
+                    baseline_config['num_iter']
+                detector.baseline.attrs['error'] = baseline_config['error']
+        return baselines
+
+    def _adjust_material_props(self, mca_data_mean, materials, energy_masks):
+        """Adjust the material properties."""
+        # Local modules
+        from CHAP.edd.utils import select_material_params
+
+        # ASK: extend to multiple detectors?
+        detector = self._detectors[0]
+        tth = detector.tth_calibrated
+        if self._save_figures:
+            filename = os.path.join(
+                self._outputdir,
+                f'{detector.detector_name}_strainanalysis_'
+                    'material_config.png')
+        else:
+            filename = None
+        materials = select_material_params(
+            detector.energies, mca_data_mean[0]*energy_masks[0],
+            tth, label='Sum of all spectra in the map',
+            preselected_materials=materials, interactive=self._interactive,
+            filename=filename)
+        self.logger.debug(f'materials: {materials}')
+
+    def _get_mask_hkls(self, mca_data, mca_data_mean, materials, energy_masks):
+        """Get the mask and HKLs used in the strain analysis."""
+        # Local modules
+        from CHAP.edd.utils import (
+            get_unique_hkls_ds,
+            select_mask_and_hkls,
+        )
+
+        for index, detector in enumerate(self._detectors):
+
+            # Get the unique HKLs and lattice spacings for the strain
+            # analysis materials
+            hkls, ds = get_unique_hkls_ds(
+                materials, tth_tol=detector.hkl_tth_tol,
+                tth_max=detector.tth_max)
+
+            # Interactively adjust the mask and HKLs used in the
+            # strain analysis
+            if self._save_figures:
+                filename = os.path.join(
+                    self._outputdir,
+                    f'{detector.detector_name}_strainanalysis_'
+                        'fit_mask_hkls.png')
+            else:
+                filename = None
+            include_bin_ranges, hkl_indices = \
+                select_mask_and_hkls(
+                    detector.energies,
+                    mca_data_mean[index]*energy_masks[index],
+                    hkls, ds, detector.tth_calibrated,
+                    preselected_bin_ranges=detector.include_bin_ranges,
+                    preselected_hkl_indices=detector.hkl_indices,
+                    detector_name=detector.detector_name,
+                    ref_map=mca_data[:,index,:]*energy_masks[index],
+                    calibration_bin_ranges=detector.calibration_bin_ranges,
+                    label='Sum of all spectra in the map',
+                    interactive=self._interactive, filename=filename)
+            detector.include_energy_ranges = \
+                detector.get_include_energy_ranges(include_bin_ranges)
+            detector.hkl_indices = hkl_indices
+            self.logger.debug(
+                f'include_energy_ranges for detector {detector.detector_name}:'
+                f' {detector.include_energy_ranges}')
+            self.logger.debug(
+                f'hkl_indices for detector {detector.detector_name}:'
+                f' {detector.hkl_indices}')
+            if not detector.include_energy_ranges:
+                raise ValueError(
+                    'No value provided for include_energy_ranges. '
+                    'Provide them in the MCA Tth Calibration Configuration, '
+                    'or re-run the pipeline with the --interactive flag.')
+            if not detector.hkl_indices:
+                raise ValueError(
+                    'No value provided for hkl_indices. Provide them in '
+                    'the detector\'s MCA Tth Calibration Configuration, or'
+                    ' re-run the pipeline with the --interactive flag.')
 
 if __name__ == '__main__':
     # Local modules