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

CHAP/edd/utils.py

@@ -25,6 +25,7 @@ def get_peak_locations(ds, tth):
 
     return hc / (2. * ds * np.sin(0.5 * np.radians(tth)))
 
+
 def make_material(name, sgnum, lattice_parameters, dmin=0.6):
     """Return a hexrd.material.Material with the given properties.
 
@@ -59,6 +60,7 @@ def make_material(name, sgnum, lattice_parameters, dmin=0.6):
 
     return material
 
+
 def get_unique_hkls_ds(materials, tth_tol=None, tth_max=None, round_sig=8):
     """Return the unique HKLs and lattice spacings for the given list
     of materials.
@@ -107,8 +109,9 @@ def get_unique_hkls_ds(materials, tth_tol=None, tth_max=None, round_sig=8):
 
     return hkls_unique, ds_unique
 
+
 def select_tth_initial_guess(x, y, hkls, ds, tth_initial_guess=5.0,
-        interactive=False):
+        interactive=False, filename=None):
     """Show a matplotlib figure of a reference MCA spectrum on top of
     HKL locations. The figure includes an input field to adjust the
     initial 2&theta guess and responds by updating the HKL locations
@@ -127,13 +130,19 @@ def select_tth_initial_guess(x, y, hkls, ds, tth_initial_guess=5.0,
     :ivar tth_initial_guess: Initial guess for 2&theta,
         defaults to `5.0`.
     :type tth_initial_guess: float, optional
-    :param interactive: Allows for user interactions, defaults to
-        `False`.
+    :param interactive: Show the plot and allow user interactions with
+        the matplotlib figure, defaults to `True`.
+    :type interactive: bool, optional
+    :param filename: Save a .png of the plot to filename, defaults to
+        `None`, in which case the plot is not saved.
+    :type filename: str, optional
     :type interactive: bool, optional
-    :return: A saveable matplotlib figure and the selected initial
-        guess for 2&theta.
-    :type: matplotlib.figure.Figure, float
+    :return: The selected initial guess for 2&theta.
+    :type: float
     """
+    if not interactive and filename is None:
+        return tth_initial_guess
+
     # Third party modules
     import matplotlib.pyplot as plt
     from matplotlib.widgets import Button, TextBox
@@ -191,14 +200,15 @@ def select_tth_initial_guess(x, y, hkls, ds, tth_initial_guess=5.0,
     fig_title = []
     error_texts = []
 
+    assert np.asarray(hkls).shape[1] == 3
+    assert np.asarray(ds).size == np.asarray(hkls).shape[0]
+
+    # Setup the Matplotlib figure
     title_pos = (0.5, 0.95)
     title_props = {'fontsize': 'xx-large', 'ha': 'center', 'va': 'bottom'}
     error_pos = (0.5, 0.90)
     error_props = {'fontsize': 'x-large', 'ha': 'center', 'va': 'bottom'}
 
-    assert np.asarray(hkls).shape[1] == 3
-    assert np.asarray(ds).size == np.asarray(hkls).shape[0]
-
     fig, ax = plt.subplots(figsize=(11, 8.5))
     ax.plot(x, y)
     ax.set_xlabel('MCA channel energy (keV)')
@@ -244,8 +254,12 @@ def select_tth_initial_guess(x, y, hkls, ds, tth_initial_guess=5.0,
         tth_input.ax.remove()
         confirm_btn.ax.remove()
 
-    fig_title[0].set_in_layout(True)
-    fig.tight_layout(rect=(0, 0, 1, 0.95))
+    # Save the figures if requested and close
+    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()
 
     if not interactive:
         tth_new_guess = tth_initial_guess
@@ -253,13 +267,14 @@ def select_tth_initial_guess(x, y, hkls, ds, tth_initial_guess=5.0,
         try:
             tth_new_guess = float(tth_input.text)
         except:
-            fig, tth_new_guess = select_tth_initial_guess(
-                x, y, hkls, ds, tth_initial_guess, interactive)
+            tth_new_guess = select_tth_initial_guess(
+                x, y, hkls, ds, tth_initial_guess, interactive, filename)
+
+    return tth_new_guess
 
-    return fig, tth_new_guess
 
-def select_material_params(x, y, tth, materials=[], label='Reference Data',
-                           interactive=False):
+def select_material_params_old(x, y, tth, materials=[], label='Reference Data',
+                           interactive=False, filename=None):
     """Interactively select the lattice parameters and space group for
     a list of materials. A matplotlib figure will be shown with a plot
     of the reference data (`x` and `y`). The figure will contain
@@ -280,17 +295,19 @@ def select_material_params(x, y, tth, materials=[], label='Reference Data',
     :param label: Legend label for the 1D plot of reference MCA data
         from the parameters `x`, `y`, defaults to `"Reference Data"`
     :type label: str, optional
-    :param interactive: Allows for user interactions, defaults to
-        `False`.
+    :param interactive: Show the plot and allow user interactions with
+        the matplotlib figure, defaults to `False`.
     :type interactive: bool, optional
-    :return: A saveable matplotlib figure and the selected materials
-        for the strain analyses.
-    :rtype: matplotlib.figure.Figure,
-        list[CHAP.edd.models.MaterialConfig]
+    :param filename: Save a .png of the plot to filename, defaults to
+        `None`, in which case the plot is not saved.
+    :type filename: str, optional
+    :return: The selected materials for the strain analyses.
+    :rtype: list[CHAP.edd.models.MaterialConfig]
     """
     # Third party modules
-    import matplotlib.pyplot as plt
-    from matplotlib.widgets import Button, TextBox
+    if interactive or filename is not None:
+        import matplotlib.pyplot as plt
+        from matplotlib.widgets import Button, TextBox
 
     # Local modules
     from CHAP.edd.models import MaterialConfig
@@ -443,65 +460,323 @@ def select_material_params(x, y, tth, materials=[], label='Reference Data',
     widget_callbacks = []
     error_texts = []
 
-    error_pos = (0.5, 0.95)
-    error_props = {'fontsize': 'x-large', 'ha': 'center', 'va': 'bottom'}
-
     _materials = deepcopy(materials)
     for i, m in enumerate(_materials):
         if isinstance(m, MaterialConfig):
             _materials[i] = m._material
 
-    # Set up plot of reference data
+    # Create the Matplotlib figure
+    if interactive or filename is not None:
+        fig, ax = plt.subplots(figsize=(11, 8.5))
+
+        if not interactive:
+
+            draw_plot()
+
+        else:
+
+            error_pos = (0.5, 0.95)
+            error_props = {
+                'fontsize': 'x-large', 'ha': 'center', 'va': 'bottom'}
+
+            plt.subplots_adjust(bottom=0.1)
+
+            # Setup "Add material" button
+            add_material_btn = Button(
+                plt.axes([0.125, 0.015, 0.1, 0.05]), 'Add material')
+            add_material_cid = add_material_btn.on_clicked(add_material)
+            widget_callbacks.append([(add_material_btn, add_material_cid)])
+
+            # Setup "Confirm" button
+            confirm_btn = Button(plt.axes([0.75, 0.015, 0.1, 0.05]), 'Confirm')
+            confirm_cid = confirm_btn.on_clicked(confirm)
+            widget_callbacks.append([(confirm_btn, confirm_cid)])
+
+            # Setup material-property-editing buttons for each material
+            for material in _materials:
+                add_material(material=material)
+
+            # Show figure for user interaction
+            plt.show()
+
+            # Disconnect all widget callbacks when figure is closed
+            # and remove the buttons before returning the figure
+            for group in widget_callbacks:
+                for widget, callback in group:
+                    widget.disconnect(callback)
+                    widget.ax.remove()
+
+       # Save the figures if requested and close
+        fig.tight_layout()
+        if filename is not None:
+            fig.savefig(filename)
+        plt.close()
+
+    new_materials = [
+        MaterialConfig(
+            material_name=m.name, sgnum=m.sgnum,
+            lattice_parameters=[
+                m.latticeParameters[i].value for i in range(6)])
+        for m in _materials]
+
+    return new_materials
+
+
+def select_material_params(
+        x, y, tth, preselected_materials=[], label='Reference Data',
+        interactive=False, filename=None):
+    """Interactively select the lattice parameters and space group for
+    a list of materials. A matplotlib figure will be shown with a plot
+    of the reference data (`x` and `y`). The figure will contain
+    widgets to add / remove materials and update selections for space
+    group number and lattice parameters for each one. The HKLs for the
+    materials defined by the widgets' values will be shown over the
+    reference data and updated when the widgets' values are
+    updated.
+
+    :param x: MCA channel energies.
+    :type x: np.ndarray
+    :param y: MCA intensities.
+    :type y: np.ndarray
+    :param tth: The (calibrated) 2&theta angle.
+    :type tth: float
+    :param materials: Materials to get HKLs and lattice spacings for,
+        default to `[]`.
+    :type materials: list[hexrd.material.Material], optional
+    :param label: Legend label for the 1D plot of reference MCA data
+        from the parameters `x`, `y`, defaults to `"Reference Data"`
+    :type label: str, optional
+    :param interactive: Show the plot and allow user interactions with
+        the matplotlib figure, defaults to `False`.
+    :type interactive: bool, optional
+    :param filename: Save a .png of the plot to filename, defaults to
+        `None`, in which case the plot is not saved.
+    :type filename: str, optional
+    :return: The selected materials for the strain analyses.
+    :rtype: list[CHAP.edd.models.MaterialConfig]
+    """
+    # Third party modules
+    if interactive or filename is not None:
+        from hexrd.material import Material
+        import matplotlib.pyplot as plt
+        from matplotlib.widgets import Button, TextBox, RadioButtons
+
+    # Local modules
+    from CHAP.edd.models import MaterialConfig
+    from CHAP.utils.general import round_to_n
+
+    def add_material(new_material, add_buttons):
+        if isinstance(new_material, Material):
+            m = new_material
+        else:
+            if not isinstance(new_material, MaterialConfig):
+                new_material = MaterialConfig(**new_material)
+            m = new_material._material
+        materials.append(m)
+        lat_params = [round_to_n(m.latticeParameters[i].value, 6)
+                      for i in range(6)]
+        bottom = 0.05*len(materials)
+        if interactive:
+            bottom += 0.075
+        mat_texts.append(
+            plt.figtext(
+                0.15, bottom,
+                f'-  {m.name}:  sgnum = {m.sgnum},  lat params = {lat_params}',
+                fontsize='large', ha='left', va='center'))
+    def add(event):
+        """Callback function for the "Add" button."""
+        added_material.append(True)
+        plt.close()
+
+    def remove(event):
+        """Callback function for the "Remove" button."""
+        for mat_text in mat_texts:
+            mat_text.remove()
+        mat_texts.clear()
+        for button in buttons:
+            button[0].disconnect(button[1])
+            button[0].ax.remove()
+        buttons.clear()
+        if len(materials) == 1:
+            removed_material.clear()
+            removed_material.append(materials[0].name)
+            plt.close()
+        else:
+            def remove_material(label):
+                removed_material.clear()
+                removed_material.append(label)
+                radio_btn.disconnect(radio_cid)
+                radio_btn.ax.remove()
+                plt.close()
+
+            mat_texts.append(
+                plt.figtext(
+                    0.1, 0.1 + 0.05*len(materials),
+                    'Select a material to remove:',
+                    fontsize='x-large', ha='left', va='center'))
+            radio_btn = RadioButtons(
+                plt.axes([0.1, 0.05, 0.3, 0.05*len(materials)]),
+                labels = list(reversed([m.name for m in materials])),
+                activecolor='k')
+            removed_material.append(radio_btn.value_selected)
+            radio_cid = radio_btn.on_clicked(remove_material)
+            plt.draw()
+
+    def accept(event):
+        """Callback function for the "Accept" button."""
+        plt.close()
+
+    materials = []
+    added_material = []
+    removed_material = []
+    mat_texts = []
+    buttons = []
+
+    # Create figure
     fig, ax = plt.subplots(figsize=(11, 8.5))
+    ax.set_title(label, fontsize='x-large')
+    ax.set_xlabel('MCA channel energy (keV)', fontsize='large')
+    ax.set_ylabel('MCA intensity (counts)', fontsize='large')
+    ax.set_xlim(x[0], x[-1])
+    ax.plot(x, y)
 
-    if interactive:
+    # Add materials
+    for m in reversed(preselected_materials):
+        add_material(m, interactive)
+
+    # Add materials to figure
+    for i, material in enumerate(materials):
+        hkls, ds = get_unique_hkls_ds([material])
+        E0s = get_peak_locations(ds, tth)
+        for hkl, E0 in zip(hkls, E0s):
+            if x[0] <= E0 <= x[-1]:
+                ax.axvline(E0, c=f'C{i}', ls='--', lw=1)
+                ax.text(E0, 1, str(hkl)[1:-1], c=f'C{i}',
+                        ha='right', va='top', rotation=90,
+                        transform=ax.get_xaxis_transform())
 
-        plt.subplots_adjust(bottom=0.1)
+    if not interactive:
 
-        # Setup "Add material" button
-        add_material_btn = Button(
-            plt.axes([0.125, 0.015, 0.1, 0.05]), 'Add material')
-        add_material_cid = add_material_btn.on_clicked(add_material)
-        widget_callbacks.append([(add_material_btn, add_material_cid)])
+        if materials:
+            mat_texts.append(
+                plt.figtext(
+                    0.1, 0.05 + 0.05*len(materials),
+                    'Currently selected materials:',
+                    fontsize='x-large', ha='left', va='center'))
+        plt.subplots_adjust(bottom=0.125 + 0.05*len(materials))
 
-        # Setup "Confirm" button
-        confirm_btn = Button(plt.axes([0.75, 0.015, 0.1, 0.05]), 'Confirm')
-        confirm_cid = confirm_btn.on_clicked(confirm)
-        widget_callbacks.append([(confirm_btn, confirm_cid)])
+    else:
 
-        # Setup material-property-editing buttons for each material
-        for material in _materials:
-            add_material(material=material)
+        if materials:
+            mat_texts.append(
+                plt.figtext(
+                    0.1, 0.125 + 0.05*len(materials),
+                    'Currently selected materials:',
+                    fontsize='x-large', ha='left', va='center'))
+        else:
+            mat_texts.append(
+                plt.figtext(
+                    0.1, 0.125, 'Add at least one material',
+                    fontsize='x-large', ha='left', va='center'))
+        plt.subplots_adjust(bottom=0.2 + 0.05*len(materials))
+
+        # Setup "Add" button
+        add_btn = Button(plt.axes([0.1, 0.025, 0.15, 0.05]), 'Add material')
+        add_cid = add_btn.on_clicked(add)
+        buttons.append((add_btn, add_cid))
+
+        # Setup "Remove" button
+        if materials:
+            remove_btn = Button(
+                plt.axes([0.425, 0.025, 0.15, 0.05]), f'Remove material')
+            remove_cid = remove_btn.on_clicked(remove)
+            buttons.append((remove_btn, remove_cid))
+
+        # Setup "Accept" button
+        accept_btn = Button(
+            plt.axes([0.75, 0.025, 0.15, 0.05]), 'Accept materials')
+        accept_cid = accept_btn.on_clicked(accept)
+        buttons.append((accept_btn, accept_cid))
 
-        # Show figure for user interaction
         plt.show()
 
         # Disconnect all widget callbacks when figure is closed
         # and remove the buttons before returning the figure
-        for group in widget_callbacks:
-            for widget, callback in group:
-                widget.disconnect(callback)
-                widget.ax.remove()
-    else:
-        draw_plot()
-
-    fig.tight_layout()
-
-    new_materials = [
+        for button in buttons:
+            button[0].disconnect(button[1])
+            button[0].ax.remove()
+        buttons.clear()
+
+    if filename is not None:
+        for mat_text in mat_texts:
+            pos = mat_text.get_position()
+            if interactive:
+                mat_text.set_position((pos[0], pos[1]-0.075))
+            else:
+                mat_text.set_position(pos)
+            if mat_text.get_text() == 'Currently selected materials:':
+                mat_text.set_text('Selected materials:')
+            mat_text.set_in_layout(True)
+        fig.tight_layout(rect=(0, 0.05 + 0.05*len(materials), 1, 1))
+        fig.savefig(filename)
+    plt.close()
+
+    if added_material:
+        # Local modules
+        from CHAP.utils.general import (
+            input_int,
+            input_num_list,
+        )
+
+        error = True
+        while error:
+            try:
+                print('\nEnter the name of the material to be added:')
+                name = input()
+                sgnum = input_int(
+                    'Enter the space group for this material',
+                    raise_error=True, log=False)
+                lat_params = input_num_list(
+                    'Enter the lattice properties for this material',
+                    raise_error=True, log=False)
+                print()
+                new_material = MaterialConfig(
+                    material_name=name, sgnum=sgnum,
+                    lattice_parameters=lat_params)
+                error = False
+            except (
+                    ValueError, TypeError, SyntaxError, MemoryError,
+                    RecursionError, IndexError) as e:
+                print(f'{e}: try again')
+            except:
+                raise
+        materials.append(new_material)
+        return select_material_params(
+            x, y, tth, preselected_materials= materials, label=label,
+            interactive=interactive, filename=filename)
+    if removed_material:
+        return select_material_params(
+            x, y, tth,
+            preselected_materials=[
+                m for m in materials if m.name not in removed_material],
+            label=label, interactive=interactive, filename=filename)
+    if not materials:
+        return select_material_params(
+            x, y, tth, label=label, interactive=interactive, filename=filename)
+    return [
         MaterialConfig(
             material_name=m.name, sgnum=m.sgnum,
             lattice_parameters=[
                 m.latticeParameters[i].value for i in range(6)])
-        for m in _materials]
+        for m in materials]
 
-    return fig, new_materials
 
 def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
-        preselected_hkl_indices=[], detector_name=None, ref_map=None,
-        flux_energy_range=None, calibration_bin_ranges=None,
-        label='Reference Data', interactive=False):
+        preselected_hkl_indices=[], num_hkl_min=1, detector_name=None,
+        ref_map=None, flux_energy_range=None, calibration_bin_ranges=None,
+        label='Reference Data', interactive=False, filename=None):
     """Return a matplotlib figure to indicate data ranges and HKLs to
-    include for fitting in EDD Ceria calibration and/or strain
+    include for fitting in EDD energy/tth calibration and/or strain
     analysis.
 
     :param x: MCA channel energies.
@@ -523,6 +798,9 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
     :param preselected_hkl_indices: Preselected unique HKL indices to
         fit peaks for in the calibration routine, defaults to `[]`.
     :type preselected_hkl_indices: list[int], optional
+    :param num_hkl_min: Minimum number of HKLs to select,
+        defaults to `1`.
+    :type num_hkl_min: int, optional
     :param detector_name: Name of the MCA detector element.
     :type detector_name: str, optional
     :param ref_map: Reference map of MCA intensities to show underneath
@@ -534,28 +812,32 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
     :param calibration_bin_ranges: MCA channel index ranges included
         in the detector calibration.
     :type calibration_bin_ranges: list[[int, int]], optional
-    :param interactive: Allows for user interactions, defaults to
-        `False`.
-    :type interactive: bool, optional
     :param label: Legend label for the 1D plot of reference MCA data
         from the parameters `x`, `y`, defaults to `"Reference Data"`
     :type label: str, optional
-    :return: A saveable matplotlib figure, the list of selected data
-        index ranges to include, and the list of HKL indices to
-        include
-    :rtype: matplotlib.figure.Figure, list[list[int]], list[int]
+    :param interactive: Show the plot and allow user interactions with
+        the matplotlib figure, defaults to `True`.
+    :type interactive: bool, optional
+    :param filename: Save a .png of the plot to filename, defaults to
+        `None`, in which case the plot is not saved.
+    :type filename: str, optional
+    :return: The list of selected data index ranges to include, and the
+        list of HKL indices to include
+    :rtype: list[list[int]], list[int]
     """
     # Third party modules
-    import matplotlib.lines as mlines
-    from matplotlib.patches import Patch
+    if interactive or filename is not None:
+        import matplotlib.lines as mlines
+        from matplotlib.patches import Patch
+        from matplotlib.widgets import Button
     import matplotlib.pyplot as plt
-    from matplotlib.widgets import Button, SpanSelector
+    from matplotlib.widgets import SpanSelector
 
     # Local modules
     from CHAP.utils.general import (
         get_consecutive_int_range,
         index_nearest_down,
-        index_nearest_upp,
+        index_nearest_up,
     )
 
     def change_fig_title(title):
@@ -570,10 +852,20 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
             error_texts.pop()
         error_texts.append(plt.figtext(*error_pos, error, **error_props))
 
+    def get_mask():
+        """Return a boolean array that acts as the mask corresponding
+        to the currently-selected index ranges"""
+        mask = np.full(x.shape[0], False)
+        for span in spans:
+            _min, _max = span.extents
+            mask = np.logical_or(
+                mask, np.logical_and(x >= _min, x <= _max))
+        return mask
+
     def hkl_locations_in_any_span(hkl_index):
         """Return the index of the span where the location of a specific
         HKL resides. Return(-1 if outside any span."""
-        if hkl_index < 0 or hkl_index>= len(hkl_locations):
+        if hkl_index < 0 or hkl_index >= len(hkl_locations):
             return -1
         for i, span in enumerate(spans):
             if (span.extents[0] <= hkl_locations[hkl_index] and
@@ -581,15 +873,21 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
                 return i
         return -1
 
+    def position_cax():
+        """Reposition the colorbar axes according to the axes of the
+        reference map"""
+        ((left, bottom), (right, top)) = ax_map.get_position().get_points()
+        cax.set_position([right + 0.01, bottom, 0.01, top - bottom])
+
     def on_span_select(xmin, xmax):
         """Callback function for the SpanSelector widget."""
         removed_hkls = False
-        if not init_flag[0]:
-            for hkl_index in deepcopy(selected_hkl_indices):
-                if hkl_locations_in_any_span(hkl_index) < 0:
+        for hkl_index in deepcopy(selected_hkl_indices):
+            if hkl_locations_in_any_span(hkl_index) < 0:
+                if interactive or filename is not None:
                     hkl_vlines[hkl_index].set(**excluded_hkl_props)
-                    selected_hkl_indices.remove(hkl_index)
-                    removed_hkls = True
+                selected_hkl_indices.remove(hkl_index)
+                removed_hkls = True
         combined_spans = False
         combined_spans_test = True
         while combined_spans_test:
@@ -617,48 +915,39 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
         for hkl_index in range(len(hkl_locations)):
             if (hkl_index not in selected_hkl_indices
                     and hkl_locations_in_any_span(hkl_index) >= 0):
-                hkl_vlines[hkl_index].set(**included_hkl_props)
+                if interactive or filename is not None:
+                    hkl_vlines[hkl_index].set(**included_hkl_props)
                 selected_hkl_indices.append(hkl_index)
                 added_hkls = True
-        if combined_spans:
-            if added_hkls or removed_hkls:
+        if interactive or filename is not None:
+            if combined_spans:
+                if added_hkls or removed_hkls:
+                    change_error_text(
+                        'Combined overlapping spans and selected only HKL(s) '
+                        'inside the selected energy mask')
+                else:
+                    change_error_text('Combined overlapping spans in the '
+                                      'selected energy mask')
+            elif added_hkls and removed_hkls:
                 change_error_text(
-                    'Combined overlapping spans and selected only HKL(s) '
-                    'inside the selected energy mask')
-            else:
+                    'Adjusted the selected HKL(s) to match the selected '
+                    'energy mask')
+            elif added_hkls:
                 change_error_text(
-                    'Combined overlapping spans in the selected energy mask')
-        elif added_hkls and removed_hkls:
-            change_error_text(
-                'Adjusted the selected HKL(s) to match the selected '
-                'energy mask')
-        elif added_hkls:
-            change_error_text(
-                'Added HKL(s) to match the selected energy mask')
-        elif removed_hkls:
-            change_error_text(
-                'Removed HKL(s) outside the selected energy mask')
+                    'Added HKL(s) to match the selected energy mask')
+            elif removed_hkls:
+                change_error_text(
+                    'Removed HKL(s) outside the selected energy mask')
         # If using ref_map, update the colorbar range to min / max of
         # the selected data only
         if ref_map is not None:
             selected_data = ref_map[:,get_mask()]
-            _min, _max = np.argmin(selected_data), np.argmax(selected_data)
             ref_map_mappable = ax_map.pcolormesh(
-                x, np.arange(ref_map.shape[0]), ref_map, vmin=_min, vmax=_max)
+                x, np.arange(ref_map.shape[0]), ref_map,
+                vmin=selected_data.min(), vmax=selected_data.max())
             fig.colorbar(ref_map_mappable, cax=cax)
         plt.draw()
 
-    def get_mask():
-        """Return a boolean array that acts as the mask corresponding
-        to the currently-selected index ranges"""
-        mask = np.full(x.shape[0], False)
-        bin_indices = np.arange(x.shape[0])
-        for span in spans:
-            _min, _max = span.extents
-            mask = np.logical_or(
-                mask, np.logical_and(bin_indices >= _min, bin_indices <= _max))
-        return mask
-
     def add_span(event, xrange_init=None):
         """Callback function for the "Add span" button."""
         spans.append(
@@ -688,17 +977,19 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
                 hkl_vline.set(**excluded_hkl_props)
                 selected_hkl_indices.remove(hkl_index)
                 span = spans[hkl_locations_in_any_span(hkl_index)]
-                span_next_hkl_index = hkl_locations_in_any_span(hkl_index+1)
                 span_prev_hkl_index = hkl_locations_in_any_span(hkl_index-1)
-                if span_next_hkl_index < 0 and span_prev_hkl_index < 0:
+                span_curr_hkl_index = hkl_locations_in_any_span(hkl_index)
+                span_next_hkl_index = hkl_locations_in_any_span(hkl_index+1)
+                if (span_curr_hkl_index != span_prev_hkl_index
+                        and span_curr_hkl_index != span_next_hkl_index):
                     span.set_visible(False)
                     spans.remove(span)
-                elif span_next_hkl_index < 0:
+                elif span_curr_hkl_index != span_next_hkl_index:
                     span.extents = (
                         span.extents[0],
                         0.5*(hkl_locations[hkl_index-1]
                              + hkl_locations[hkl_index]))
-                elif span_prev_hkl_index < 0:
+                elif span_curr_hkl_index != span_prev_hkl_index:
                     span.extents = (
                         0.5*(hkl_locations[hkl_index]
                              + hkl_locations[hkl_index+1]),
@@ -717,19 +1008,54 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
                     f'Adjusted the selected energy mask to reflect the '
                     'removed HKL')
             else:
+                hkl_vline.set(**included_hkl_props)
+                prev_hkl = hkl_index-1 in selected_hkl_indices
+                next_hkl = hkl_index+1 in selected_hkl_indices
+                if prev_hkl and next_hkl:
+                    span_prev = spans[hkl_locations_in_any_span(hkl_index-1)]
+                    span_next = spans[hkl_locations_in_any_span(hkl_index+1)]
+                    span_prev.extents = (
+                        span_prev.extents[0], span_next.extents[1])
+                    span_next.set_visible(False)
+                elif prev_hkl:
+                    span_prev = spans[hkl_locations_in_any_span(hkl_index-1)]
+                    if hkl_index < len(hkl_locations)-1:
+                        max_ = 0.5*(
+                            hkl_locations[hkl_index]
+                            + hkl_locations[hkl_index+1])
+                    else:
+                        max_ = 0.5*(hkl_locations[hkl_index] + max_x)
+                    span_prev.extents = (span_prev.extents[0], max_)
+                elif next_hkl:
+                    span_next = spans[hkl_locations_in_any_span(hkl_index+1)]
+                    if hkl_index > 0:
+                        min_ = 0.5*(
+                            hkl_locations[hkl_index-1]
+                            + hkl_locations[hkl_index])
+                    else:
+                        min_ = 0.5*(min_x + hkl_locations[hkl_index])
+                    span_next.extents = (min_, span_next.extents[1])
+                else:
+                    if hkl_index > 0:
+                        min_ = 0.5*(
+                            hkl_locations[hkl_index-1]
+                            + hkl_locations[hkl_index])
+                    else:
+                        min_ = 0.5*(min_x + hkl_locations[hkl_index])
+                    if hkl_index < len(hkl_locations)-1:
+                        max_ = 0.5*(
+                            hkl_locations[hkl_index]
+                            + hkl_locations[hkl_index+1])
+                    else:
+                        max_ = 0.5*(hkl_locations[hkl_index] + max_x)
+                    add_span(None, xrange_init=(min_, max_))
                 change_error_text(
-                    f'Selected HKL is outside any current span, '
-                    'extend or add spans before adding this value')
+                    f'Adjusted the selected energy mask to reflect the '
+                    'added HKL')
             plt.draw()
 
-    def position_cax():
-        """Reposition the colorbar axes according to the axes of the
-        reference map"""
-        ((left, bottom), (right, top)) = ax_map.get_position().get_points()
-        cax.set_position([right + 0.01, bottom, 0.01, top - bottom])
-
     def reset(event):
-        """Callback function for the "Confirm" button."""
+        """Callback function for the "Reset" button."""
         for hkl_index in deepcopy(selected_hkl_indices):
             hkl_vlines[hkl_index].set(**excluded_hkl_props)
             selected_hkl_indices.remove(hkl_index)
@@ -740,8 +1066,9 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
 
     def confirm(event):
         """Callback function for the "Confirm" button."""
-        if not len(spans) or len(selected_hkl_indices) < 2:
-            change_error_text('Select at least one span and two HKLs')
+        if not len(spans) or len(selected_hkl_indices) < num_hkl_min:
+            change_error_text(
+                f'Select at least one span and {num_hkl_min} HKLs')
             plt.draw()
         else:
             if error_texts:
@@ -760,78 +1087,12 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
     fig_title = []
     error_texts = []
 
+    if ref_map is not None and ref_map.ndim == 1:
+        ref_map = None
+
+    # Make preselected_bin_ranges consistent with selected_hkl_indices 
     hkl_locations = [loc for loc in get_peak_locations(ds, tth)
                      if x[0] <= loc <= x[-1]]
-    hkl_labels = [str(hkl)[1:-1] for hkl, loc in zip(hkls, hkl_locations)]
-
-    title_pos = (0.5, 0.95)
-    title_props = {'fontsize': 'xx-large', 'ha': 'center', 'va': 'bottom'}
-    error_pos = (0.5, 0.90)
-    error_props = {'fontsize': 'x-large', 'ha': 'center', 'va': 'bottom'}
-    excluded_hkl_props = {
-        'color': 'black', 'linestyle': '--','linewidth': 1,
-        'marker': 10, 'markersize': 5, 'fillstyle': 'none'}
-    included_hkl_props = {
-        'color': 'green', 'linestyle': '-', 'linewidth': 2,
-        'marker': 10, 'markersize': 10, 'fillstyle': 'full'}
-    excluded_data_props = {
-        'facecolor': 'white', 'edgecolor': 'gray', 'linestyle': ':'}
-    included_data_props = {
-        'alpha': 0.5, 'facecolor': 'tab:blue', 'edgecolor': 'blue'}
-
-    if flux_energy_range is None:
-        min_x = x.min()
-        max_x = x.max()
-    else:
-        min_x = x[index_nearest_upp(x, max(x.min(), flux_energy_range[0]))]
-        max_x = x[index_nearest_down(x, min(x.max(), flux_energy_range[1]))]
-
-    if ref_map is None:
-        fig, ax = plt.subplots(figsize=(11, 8.5))
-        ax.set(xlabel='Energy (keV)', ylabel='Intensity (counts)')
-    else:
-        # Ensure ref_map is 2D
-        if ref_map.ndim > 2:
-            ref_map = np.reshape(
-                ref_map, (np.prod(ref_map.shape[:-1]), ref_map.shape[-1]))
-        # If needed, abbreviate ref_map to <= 50 spectra to keep
-        # response time of mouse interactions quick.
-        max_ref_spectra = 50
-        if ref_map.shape[0] > max_ref_spectra:
-            choose_i = np.sort(
-                np.random.choice(
-                    ref_map.shape[0], max_ref_spectra, replace=False))
-            ref_map = ref_map[choose_i]
-        fig, (ax, ax_map) = plt.subplots(
-            2, sharex=True, figsize=(11, 8.5), height_ratios=[2, 1])
-        ax.set(ylabel='Intensity (counts)')
-        ref_map_mappable = ax_map.pcolormesh(
-            x, np.arange(ref_map.shape[0]), ref_map)
-        ax_map.set_yticks([])
-        ax_map.set_xlabel('Energy (keV)')
-        ax_map.set_xlim(x[0], x[-1])
-        ((left, bottom), (right, top)) = ax_map.get_position().get_points()
-        cax = plt.axes([right + 0.01, bottom, 0.01, top - bottom])
-        fig.colorbar(ref_map_mappable, cax=cax)
-    handles = ax.plot(x, y, color='k', label=label)
-    if calibration_bin_ranges is not None:
-        ylow = ax.get_ylim()[0]
-        for low, upp in calibration_bin_ranges:
-            ax.plot([x[low], x[upp]], [ylow, ylow], color='r', linewidth=2)
-        handles.append(mlines.Line2D(
-            [], [], label='Energies included in calibration', color='r',
-            linewidth=2))
-    handles.append(mlines.Line2D(
-        [], [], label='Excluded / unselected HKL', **excluded_hkl_props))
-    handles.append(mlines.Line2D(
-        [], [], label='Included / selected HKL', **included_hkl_props))
-    handles.append(Patch(
-        label='Excluded / unselected data', **excluded_data_props))
-    handles.append(Patch(
-        label='Included / selected data', **included_data_props))
-    ax.legend(handles=handles)
-    ax.set_xlim(x[0], x[-1])
-
     if selected_hkl_indices and not preselected_bin_ranges:
         index_ranges = get_consecutive_int_range(selected_hkl_indices)
         for index_range in index_ranges:
@@ -846,30 +1107,109 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
             else:
                 max_ = 0.5*(hkl_locations[j] + max_x)
             preselected_bin_ranges.append(
-                [index_nearest_upp(x, min_), index_nearest_down(x, max_)])
+                [index_nearest_up(x, min_), index_nearest_down(x, max_)])
 
-    for i, (loc, lbl) in enumerate(zip(hkl_locations, hkl_labels)):
-        nearest_index = np.searchsorted(x, loc)
-        if i in selected_hkl_indices:
-            hkl_vline = ax.axvline(loc, **included_hkl_props)
+    if flux_energy_range is None:
+        min_x = x.min()
+        max_x = x.max()
+    else:
+        min_x = x[index_nearest_up(x, max(x.min(), flux_energy_range[0]))]
+        max_x = x[index_nearest_down(x, min(x.max(), flux_energy_range[1]))]
+
+    # Setup the Matplotlib figure
+    if not interactive and filename is None:
+
+        # It is too convenient to not use the Matplotlib SpanSelector
+        # so define a (fig, ax) tuple, despite not creating a figure
+        included_data_props = {}
+        fig, ax = plt.subplots()
+
+    else:
+
+        title_pos = (0.5, 0.95)
+        title_props = {'fontsize': 'xx-large', 'ha': 'center', 'va': 'bottom'}
+        error_pos = (0.5, 0.90)
+        error_props = {'fontsize': 'x-large', 'ha': 'center', 'va': 'bottom'}
+        excluded_hkl_props = {
+            'color': 'black', 'linestyle': '--','linewidth': 1,
+            'marker': 10, 'markersize': 5, 'fillstyle': 'none'}
+        included_hkl_props = {
+            'color': 'green', 'linestyle': '-', 'linewidth': 2,
+            'marker': 10, 'markersize': 10, 'fillstyle': 'full'}
+        included_data_props = {
+            'alpha': 0.5, 'facecolor': 'tab:blue', 'edgecolor': 'blue'}
+        excluded_data_props = {
+            'facecolor': 'white', 'edgecolor': 'gray', 'linestyle': ':'}
+
+        if ref_map is None:
+            fig, ax = plt.subplots(figsize=(11, 8.5))
+            ax.set(xlabel='Energy (keV)', ylabel='Intensity (counts)')
         else:
-            hkl_vline = ax.axvline(loc, **excluded_hkl_props)
-        ax.text(loc, 1, lbl, ha='right', va='top', rotation=90,
-                transform=ax.get_xaxis_transform())
-        hkl_vlines.append(hkl_vline)
+            if ref_map.ndim > 2:
+                ref_map = np.reshape(
+                    ref_map, (np.prod(ref_map.shape[:-1]), ref_map.shape[-1]))
+            # If needed, abbreviate ref_map to <= 50 spectra to keep
+            # response time of mouse interactions quick.
+            max_ref_spectra = 50
+            if ref_map.shape[0] > max_ref_spectra:
+                choose_i = np.sort(
+                    np.random.choice(
+                        ref_map.shape[0], max_ref_spectra, replace=False))
+                ref_map = ref_map[choose_i]
+            fig, (ax, ax_map) = plt.subplots(
+                2, sharex=True, figsize=(11, 8.5), height_ratios=[2, 1])
+            ax.set(ylabel='Intensity (counts)')
+            ref_map_mappable = ax_map.pcolormesh(
+                x, np.arange(ref_map.shape[0]), ref_map)
+            ax_map.set_yticks([])
+            ax_map.set_xlabel('Energy (keV)')
+            ax_map.set_xlim(x[0], x[-1])
+            ((left, bottom), (right, top)) = ax_map.get_position().get_points()
+            cax = plt.axes([right + 0.01, bottom, 0.01, top - bottom])
+            fig.colorbar(ref_map_mappable, cax=cax)
+        handles = ax.plot(x, y, color='k', label=label)
+        if calibration_bin_ranges is not None:
+            ylow = ax.get_ylim()[0]
+            for low, upp in calibration_bin_ranges:
+                ax.plot([x[low], x[upp]], [ylow, ylow], color='r', linewidth=2)
+            handles.append(mlines.Line2D(
+                [], [], label='Energies included in calibration', color='r',
+                linewidth=2))
+        handles.append(mlines.Line2D(
+            [], [], label='Excluded / unselected HKL', **excluded_hkl_props))
+        handles.append(mlines.Line2D(
+            [], [], label='Included / selected HKL', **included_hkl_props))
+        handles.append(Patch(
+            label='Excluded / unselected data', **excluded_data_props))
+        handles.append(Patch(
+            label='Included / selected data', **included_data_props))
+        ax.legend(handles=handles)
+        ax.set_xlim(x[0], x[-1])
 
-    init_flag = [True]
+        # Add HKL lines
+        hkl_labels = [str(hkl)[1:-1] for hkl, loc in zip(hkls, hkl_locations)]
+        for i, (loc, lbl) in enumerate(zip(hkl_locations, hkl_labels)):
+            nearest_index = np.searchsorted(x, loc)
+            if i in selected_hkl_indices:
+                hkl_vline = ax.axvline(loc, **included_hkl_props)
+            else:
+                hkl_vline = ax.axvline(loc, **excluded_hkl_props)
+            ax.text(loc, 1, lbl, ha='right', va='top', rotation=90,
+                    transform=ax.get_xaxis_transform())
+            hkl_vlines.append(hkl_vline)
+
+    # Add initial spans
     for bin_range in preselected_bin_ranges:
         add_span(None, xrange_init=x[bin_range])
-    init_flag = [False]
 
     if not interactive:
 
-        if detector_name is None:
-            change_fig_title('Selected data and HKLs used in fitting')
-        else:
-            change_fig_title(
-                f'Selected data and HKLs used in fitting {detector_name}')
+        if filename is not None:
+            if detector_name is None:
+                change_fig_title('Selected data and HKLs used in fitting')
+            else:
+                change_fig_title(
+                    f'Selected data and HKLs used in fitting {detector_name}')
 
     else:
 
@@ -913,6 +1253,14 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
         reset_btn.ax.remove()
         plt.subplots_adjust(bottom=0.0)
 
+    if filename is not None:
+        fig_title[0].set_in_layout(True)
+        fig.tight_layout(rect=(0, 0, 0.9, 0.9))
+        if ref_map is not None:
+            position_cax()
+        fig.savefig(filename)
+    plt.close()
+
     selected_bin_ranges = [np.searchsorted(x, span.extents).tolist()
                            for span in spans]
     if not selected_bin_ranges:
@@ -922,15 +1270,79 @@ def select_mask_and_hkls(x, y, hkls, ds, tth, preselected_bin_ranges=[],
     else:
         selected_hkl_indices = None
 
-    fig_title[0].set_in_layout(True)
-    fig.tight_layout(rect=(0, 0, 0.9, 0.9))
-    if ref_map is not None:
-        position_cax()
-
-    return fig, selected_bin_ranges, selected_hkl_indices
+    return selected_bin_ranges, selected_hkl_indices
 
 
-def get_spectra_fits(spectra, energies, peak_locations, fit_params):
+def get_rolling_sum_spectra(
+        y, bin_axis, start=0, end=None, width=None, stride=None, num=None,
+        mode='valid'):
+    """
+    Return the rolling sum of the spectra over a specified axis.
+    """
+    y = np.asarray(y)
+    if not 0 <= bin_axis < y.ndim-1:
+        raise ValueError(f'Invalid "bin_axis" parameter ({bin_axis})')
+    size = y.shape[bin_axis]
+    if not 0 <= start < size:
+        raise ValueError(f'Invalid "start" parameter ({start})')
+    if end is None:
+        end = size
+    elif not start < end <= size:
+        raise ValueError('Invalid "start" and "end" combination '
+                         f'({start} and {end})')
+
+    size = end-start
+    if stride is None:
+        if width is None:
+            width = max(1, int(size/num))
+            stride = width
+        else:
+            width = max(1, min(width, size))
+            if num is None:
+                stride = width
+            else:
+                stride = max(1, int((size-width) / (num-1)))
+    else:
+        stride = max(1, min(stride, size-stride))
+        if width is None:
+            width = stride
+    if mode == 'valid':
+        num = 1 + max(0, int((size-width) / stride))
+    else:
+        num = int(size/stride)
+        if num*stride < size:
+            num += 1
+    bin_ranges = [(start+n*stride, min(start+size, start+n*stride+width))
+                  for n in range(num)]
+
+    y_shape = y.shape
+    y_ndim = y.ndim
+    swap_axis = False
+    if y_ndim > 2 and bin_axis != y_ndim-2:
+        y = np.swapaxes(y, bin_axis, y_ndim-2)
+        swap_axis = True
+    if y_ndim > 3:
+        map_shape = y.shape[0:y_ndim-2]
+        y = y.reshape((np.prod(map_shape), *y.shape[y_ndim-2:]))
+    if y_ndim == 2:
+        y = np.expand_dims(y, 0)
+
+    ry = np.zeros((y.shape[0], num, y.shape[-1]), dtype=y.dtype)
+    for dim in range(y.shape[0]):
+        for n in range(num):
+            ry[dim, n] = np.sum(y[dim,bin_ranges[n][0]:bin_ranges[n][1]], 0)
+
+    if y_ndim > 3:
+        ry = np.reshape(ry, (*map_shape, num, y_shape[-1]))
+    if y_ndim == 2:
+        ry = np.squeeze(ry)
+    if swap_axis:
+        ry = np.swapaxes(ry, bin_axis, y_ndim-2)
+
+    return ry
+
+
+def get_spectra_fits(spectra, energies, peak_locations, detector):
     """Return twenty arrays of fit results for the map of spectra
     provided: uniform centers, uniform center errors, uniform
     amplitudes, uniform amplitude errors, uniform sigmas, uniform
@@ -948,8 +1360,8 @@ def get_spectra_fits(spectra, energies, peak_locations, fit_params):
     :param peak_locations: Initial guesses for peak ceneters to use
         for the uniform fit.
     :type peak_locations: list[float]
-    :param fit_params: Detector element fit parameters.
-    :type fit_params: CHAP.edd.models.MCAElementStrainAnalysisConfig
+        :param detector: A single MCA detector element configuration.
+        :type detector: CHAP.edd.models.MCAElementStrainAnalysisConfig
     :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
@@ -961,86 +1373,228 @@ def get_spectra_fits(spectra, energies, peak_locations, fit_params):
         numpy.ndarray, numpy.ndarray, numpy.ndarray, numpy.ndarray,
         numpy.ndarray]
     """
-    from CHAP.utils.fit import FitMap
+    # Third party modules
+    from nexusformat.nexus import NXdata, NXfield
 
-    # Perform fit to get measured peak positions
-    fit = FitMap(spectra, x=energies)
+    # Local modules
+    from CHAP.utils.fit import FitProcessor
+
+    num_proc = detector.num_proc
+    rel_height_cutoff = detector.rel_height_cutoff
     num_peak = len(peak_locations)
-    delta = 0.1 * (energies[-1]-energies[0])
-    centers_range = (
-        max(0.0, energies[0]-delta), energies[-1]+delta)
-    fit.create_multipeak_model(
-        peak_locations,
-        fit_type='uniform',
-        peak_models=fit_params.peak_models,
-        background=fit_params.background,
-        fwhm_min=fit_params.fwhm_min,
-        fwhm_max=fit_params.fwhm_max,
-        centers_range=centers_range)
-    fit.fit(num_proc=fit_params.num_proc)
-    uniform_fit_centers = [
-        fit.best_values[
-            fit.best_parameters().index(f'peak{i+1}_center')]
-        for i in range(num_peak)]
-    uniform_fit_centers_errors = [
-        fit.best_errors[
-            fit.best_parameters().index(f'peak{i+1}_center')]
-        for i in range(num_peak)]
-    uniform_fit_amplitudes = [
-        fit.best_values[
-            fit.best_parameters().index(f'peak{i+1}_amplitude')]
-        for i in range(num_peak)]
-    uniform_fit_amplitudes_errors = [
-        fit.best_errors[
-            fit.best_parameters().index(f'peak{i+1}_amplitude')]
-        for i in range(num_peak)]
-    uniform_fit_sigmas = [
-        fit.best_values[
-            fit.best_parameters().index(f'peak{i+1}_sigma')]
-        for i in range(num_peak)]
-    uniform_fit_sigmas_errors = [
-        fit.best_errors[
-            fit.best_parameters().index(f'peak{i+1}_sigma')]
-        for i in range(num_peak)]
-    uniform_best_fit = fit.best_fit
-    uniform_residuals = fit.residual
-    uniform_redchi = fit.redchi
-    uniform_success = fit.success
+    nxdata = NXdata(NXfield(spectra, 'y'), NXfield(energies, 'x'))
+
+    # 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(peak_locations),
+         'fit_type': 'uniform', 'peak_models': detector.peak_models,
+         'centers_range': detector.centers_range,
+         'fwhm_min': detector.fwhm_min, 'fwhm_max': detector.fwhm_max})
+    config = {
+#        'code': 'lmfit',
+        'models': models,
+#        'plot': True,
+        'num_proc': num_proc,
+        'rel_height_cutoff': rel_height_cutoff,
+#        'method': 'trf',
+        'method': 'leastsq',
+#        'method': 'least_squares',
+    }
+
+    # Perform uniform fit
+    fit = FitProcessor()
+    uniform_fit = fit.process(nxdata, config)
+    uniform_success = uniform_fit.success
+    if spectra.ndim == 1:
+        if uniform_success:
+            if num_peak == 1:
+                uniform_fit_centers = [uniform_fit.best_values['center']]
+                uniform_fit_centers_errors = [
+                    uniform_fit.best_errors['center']]
+                uniform_fit_amplitudes = [
+                    uniform_fit.best_values['amplitude']]
+                uniform_fit_amplitudes_errors = [
+                    uniform_fit.best_errors['amplitude']]
+                uniform_fit_sigmas = [uniform_fit.best_values['sigma']]
+                uniform_fit_centers_errors = [uniform_fit.best_errors['sigma']]
+            else:
+                uniform_fit_centers = [
+                    uniform_fit.best_values[
+                        f'peak{i+1}_center'] for i in range(num_peak)]
+                uniform_fit_centers_errors = [
+                    uniform_fit.best_errors[
+                        f'peak{i+1}_center'] for i in range(num_peak)]
+                uniform_fit_amplitudes = [
+                    uniform_fit.best_values[
+                        f'peak{i+1}_amplitude'] for i in range(num_peak)]
+                uniform_fit_amplitudes_errors = [
+                    uniform_fit.best_errors[
+                        f'peak{i+1}_amplitude'] for i in range(num_peak)]
+                uniform_fit_sigmas = [
+                    uniform_fit.best_values[
+                        f'peak{i+1}_sigma'] for i in range(num_peak)]
+                uniform_fit_sigmas_errors = [
+                    uniform_fit.best_errors[
+                        f'peak{i+1}_sigma'] for i in range(num_peak)]
+        else:
+            uniform_fit_centers = list(peak_locations)
+            uniform_fit_centers_errors = [0]
+            uniform_fit_amplitudes = [0]
+            uniform_fit_amplitudes_errors = [0]
+            uniform_fit_sigmas = [0]
+            uniform_fit_sigmas_errors = [0]
+    else:
+        if num_peak == 1:
+            uniform_fit_centers = [
+                uniform_fit.best_values[
+                    uniform_fit.best_parameters().index('center')]]
+            uniform_fit_centers_errors = [
+                uniform_fit.best_errors[
+                    uniform_fit.best_parameters().index('center')]]
+            uniform_fit_amplitudes = [
+                uniform_fit.best_values[
+                    uniform_fit.best_parameters().index('amplitude')]]
+            uniform_fit_amplitudes_errors = [
+                uniform_fit.best_errors[
+                    uniform_fit.best_parameters().index('amplitude')]]
+            uniform_fit_sigmas = [
+                uniform_fit.best_values[
+                    uniform_fit.best_parameters().index('sigma')]]
+            uniform_fit_sigmas_errors = [
+                uniform_fit.best_errors[
+                    uniform_fit.best_parameters().index('sigma')]]
+        else:
+            uniform_fit_centers = [
+                uniform_fit.best_values[
+                    uniform_fit.best_parameters().index(f'peak{i+1}_center')]
+                for i in range(num_peak)]
+            uniform_fit_centers_errors = [
+                uniform_fit.best_errors[
+                    uniform_fit.best_parameters().index(f'peak{i+1}_center')]
+                for i in range(num_peak)]
+            uniform_fit_amplitudes = [
+                uniform_fit.best_values[
+                    uniform_fit.best_parameters().index(
+                        f'peak{i+1}_amplitude')]
+                for i in range(num_peak)]
+            uniform_fit_amplitudes_errors = [
+                uniform_fit.best_errors[
+                    uniform_fit.best_parameters().index(
+                        f'peak{i+1}_amplitude')]
+                for i in range(num_peak)]
+            uniform_fit_sigmas = [
+                uniform_fit.best_values[
+                    uniform_fit.best_parameters().index(f'peak{i+1}_sigma')]
+                for i in range(num_peak)]
+            uniform_fit_sigmas_errors = [
+                uniform_fit.best_errors[
+                    uniform_fit.best_parameters().index(f'peak{i+1}_sigma')]
+                for i in range(num_peak)]
+        if not np.asarray(uniform_success).all():
+            for n in range(num_peak):
+                uniform_fit_centers[n] = np.where(
+                    uniform_success, uniform_fit_centers[n], peak_locations[n])
+                uniform_fit_centers_errors[n] *= uniform_success
+                uniform_fit_amplitudes[n] *= uniform_success
+                uniform_fit_amplitudes_errors[n] *= uniform_success
+                uniform_fit_sigmas[n] *= uniform_success
+                uniform_fit_sigmas_errors[n] *= uniform_success
+    uniform_best_fit = uniform_fit.best_fit
+    uniform_residuals = uniform_fit.residual
+    uniform_redchi = uniform_fit.redchi
+
+    if num_peak == 1:
+        return (
+            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,
+            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
+        )
 
     # Perform unconstrained fit
-    fit.create_multipeak_model(fit_type='unconstrained')
-    fit.fit(num_proc=fit_params.num_proc,
-            rel_amplitude_cutoff=fit_params.rel_amplitude_cutoff)
-    unconstrained_fit_centers = np.array(
-        [fit.best_values[
-            fit.best_parameters()\
-            .index(f'peak{i+1}_center')]
-         for i in range(num_peak)])
-    unconstrained_fit_centers_errors = np.array(
-        [fit.best_errors[
-            fit.best_parameters()\
-            .index(f'peak{i+1}_center')]
-         for i in range(num_peak)])
-    unconstrained_fit_amplitudes = [
-        fit.best_values[
-            fit.best_parameters().index(f'peak{i+1}_amplitude')]
-        for i in range(num_peak)]
-    unconstrained_fit_amplitudes_errors = [
-        fit.best_errors[
-            fit.best_parameters().index(f'peak{i+1}_amplitude')]
-        for i in range(num_peak)]
-    unconstrained_fit_sigmas = [
-        fit.best_values[
-            fit.best_parameters().index(f'peak{i+1}_sigma')]
-        for i in range(num_peak)]
-    unconstrained_fit_sigmas_errors = [
-        fit.best_errors[
-            fit.best_parameters().index(f'peak{i+1}_sigma')]
-        for i in range(num_peak)]
-    unconstrained_best_fit = fit.best_fit
-    unconstrained_residuals = fit.residual
-    unconstrained_redchi = fit.redchi
-    unconstrained_success = fit.success
+    config['models'][-1]['fit_type'] = 'unconstrained'
+    unconstrained_fit = fit.process(uniform_fit, config)
+    unconstrained_success = unconstrained_fit.success
+    if spectra.ndim == 1:
+        if unconstrained_success:
+            unconstrained_fit_centers = [
+                unconstrained_fit.best_values[
+                    f'peak{i+1}_center'] for i in range(num_peak)]
+            unconstrained_fit_centers_errors = [
+                unconstrained_fit.best_errors[
+                    f'peak{i+1}_center'] for i in range(num_peak)]
+            unconstrained_fit_amplitudes = [
+                unconstrained_fit.best_values[
+                    f'peak{i+1}_amplitude'] for i in range(num_peak)]
+            unconstrained_fit_amplitudes_errors = [
+                unconstrained_fit.best_errors[
+                    f'peak{i+1}_amplitude'] for i in range(num_peak)]
+            unconstrained_fit_sigmas = [
+                unconstrained_fit.best_values[
+                    f'peak{i+1}_sigma'] for i in range(num_peak)]
+            unconstrained_fit_sigmas_errors = [
+                unconstrained_fit.best_errors[
+                    f'peak{i+1}_sigma'] for i in range(num_peak)]
+        else:
+            unconstrained_fit_centers = list(peak_locations)
+            unconstrained_fit_centers_errors = [0]
+            unconstrained_fit_amplitudes = [0]
+            unconstrained_fit_amplitudes_errors = [0]
+            unconstrained_fit_sigmas = [0]
+            unconstrained_fit_sigmas_errors = [0]
+    else:
+        unconstrained_fit_centers = np.array(
+            [unconstrained_fit.best_values[
+                unconstrained_fit.best_parameters().index(f'peak{i+1}_center')]
+             for i in range(num_peak)])
+        unconstrained_fit_centers_errors = np.array(
+            [unconstrained_fit.best_errors[
+                unconstrained_fit.best_parameters().index(f'peak{i+1}_center')]
+             for i in range(num_peak)])
+        unconstrained_fit_amplitudes = [
+            unconstrained_fit.best_values[
+                unconstrained_fit.best_parameters().index(
+                    f'peak{i+1}_amplitude')]
+            for i in range(num_peak)]
+        unconstrained_fit_amplitudes_errors = [
+            unconstrained_fit.best_errors[
+                unconstrained_fit.best_parameters().index(
+                    f'peak{i+1}_amplitude')]
+            for i in range(num_peak)]
+        unconstrained_fit_sigmas = [
+            unconstrained_fit.best_values[
+                unconstrained_fit.best_parameters().index(f'peak{i+1}_sigma')]
+            for i in range(num_peak)]
+        unconstrained_fit_sigmas_errors = [
+            unconstrained_fit.best_errors[
+                unconstrained_fit.best_parameters().index(f'peak{i+1}_sigma')]
+            for i in range(num_peak)]
+        if not np.asarray(unconstrained_success).all():
+            for n in range(num_peak):
+                unconstrained_fit_centers[n] = np.where(
+                    unconstrained_success, unconstrained_fit_centers[n],
+                    peak_locations[n])
+                unconstrained_fit_centers_errors[n] *= unconstrained_success
+                unconstrained_fit_amplitudes[n] *= unconstrained_success
+                unconstrained_fit_amplitudes_errors[n] *= unconstrained_success
+                unconstrained_fit_sigmas[n] *= unconstrained_success
+                unconstrained_fit_sigmas_errors[n] *= unconstrained_success
+    unconstrained_best_fit = unconstrained_fit.best_fit
+    unconstrained_residuals = unconstrained_fit.residual
+    unconstrained_redchi = unconstrained_fit.redchi
 
     return (
         uniform_fit_centers, uniform_fit_centers_errors,