nxs-analysis-tools 0.0.47__py3-none-any.whl → 0.1.0__py3-none-any.whl

nxs_analysis_tools/chess.py

@@ -1,697 +1,703 @@
-"""
-This module provides classes and functions for analyzing scattering datasets collected at CHESS
-(ID4B) with temperature dependence. It includes functions for loading data, cutting data, and
-plotting linecuts.
-"""
-import os
-import re
-
-import matplotlib.pyplot as plt
-import matplotlib as mpl
-import pandas as pd
-import numpy as np
-from IPython.display import display, Markdown
-from nxs_analysis_tools import load_data, Scissors
-from nxs_analysis_tools.fitting import LinecutModel
-from nxs_analysis_tools.datareduction import load_transform, reciprocal_lattice_params
-
-
-class TempDependence:
-    """
-    A class for analyzing temperature-dependent scattering datasets collected at CHESS (ID4B).
-
-    The `TempDependence` class facilitates the loading, processing, and analysis of scattering
-    data across different temperatures. It includes methods for handling datasets, setting
-    lattice parameters, performing linecuts, modeling the data, and visualizing the results.
-
-    Attributes
-    ----------
-    sample_directory : str
-        Path to the directory containing the datasets.
-    xlabel : str
-        Label for the x-axis of plots, determined by the axis of the linecuts.
-    datasets : dict
-        Dictionary storing datasets keyed by temperature.
-    temperatures : list of str
-        List of temperatures for which data is available.
-    scissors : dict
-        Dictionary of Scissors objects, one for each temperature, used for data manipulation and
-        linecut operations.
-    linecuts : dict
-        Dictionary storing the linecut data for each temperature.
-    linecutmodels : dict
-        Dictionary of LinecutModel objects, one for each temperature, used for fitting the linecuts.
-    a, b, c, al, be, ga : float or None
-        Lattice parameters (a, b, c, alpha, beta, gamma) of the crystal.
-    a_star, b_star, c_star, al_star, be_star, ga_star : float or None
-        Reciprocal lattice parameters (a*, b*, c*, alpha*, beta*, gamma*).
-
-    Methods
-    -------
-    set_temperatures(temperatures):
-        Set the list of temperatures for the datasets.
-    find_temperatures():
-        Set the list of temperatures by automatically scanning the sample directory.
-    set_sample_directory(path):
-        Set the directory path where the datasets are located.
-    initialize():
-        Initialize Scissors and LinecutModel objects for each temperature.
-    set_data(temperature, data):
-        Set the dataset for a specific temperature.
-    load_transforms(temperatures_list=None, print_tree=True):
-        Load transform datasets (from nxrefine) based on temperature.
-    load_datasets(file_ending='hkli.nxs', temperatures_list=None, print_tree=True):
-        Load datasets (CHESS format) from the specified folder.
-    get_sample_directory():
-        Get the folder path where the datasets are located.
-    clear_datasets():
-        Clear the datasets stored in the TempDependence instance.
-    set_Lattice_params(lattice_params):
-        Set lattice parameters and calculate reciprocal lattice parameters.
-    set_window(window, verbose=False):
-        Set the extents of the integration window for each temperature.
-    set_center(center):
-        Set the central coordinate for the linecut for each temperature.
-    cut_data(center=None, window=None, axis=None, verbose=False):
-        Perform data cutting for each temperature dataset.
-    plot_linecuts(vertical_offset=0, **kwargs):
-        Plot the linecuts obtained from data cutting.
-    plot_linecuts_heatmap(ax=None, **kwargs):
-        Plot a heatmap of the linecuts obtained from data cutting.
-    highlight_integration_window(temperature=None, **kwargs):
-        Display the integration window plot for a specific temperature.
-    plot_integration_window(temperature=None, **kwargs):
-        Plot the integration window cross-sections for a specific temperature.
-    set_model_components(model_components):
-        Set the model components for all line cut models.
-    set_param_hint(*args, **kwargs):
-        Set parameter hints for all line cut models.
-    make_params():
-        Create parameters for all line cut models.
-    guess():
-        Make initial parameter guesses for all line cut models.
-    print_initial_params():
-        Print the initial parameter values for all line cut models.
-    plot_initial_guess():
-        Plot the initial guess for all line cut models.
-    fit(verbose=False):
-        Fit the line cut models for each temperature.
-    plot_fit(mdheadings=False, **kwargs):
-        Plot the fit results for each temperature.
-    plot_order_parameter(self):
-        Plot the temperature dependence of the peakheight parameter.
-    print_fit_report():
-        Print the fit report for each temperature.
-    """
-
-    def __init__(self):
-        """
-        Initialize the TempDependence class with default values.
-        """
-
-        self.sample_directory = None
-        self.xlabel = ''
-        self.datasets = {}
-        self.temperatures = []
-        self.scissors = {}
-        self.linecuts = {}
-        self.linecutmodels = {}
-        self.a, self.b, self.c, self.al, self.be, self.ga, \
-            self.a_star, self.b_star, self.c_star, self.al_star, self.be_star, self.ga_star \
-            = [None] * 12
-
-    def set_temperatures(self, temperatures):
-        """
-        Set the list of temperatures for the datasets.
-
-        Parameters
-        ----------
-        temperatures : list
-            List of temperatures to set.
-        """
-        self.temperatures = temperatures
-
-    def find_temperatures(self):
-        """
-        Set the list of temperatures by automatically scanning the sample directory.
-        """
-
-        # Assert that self.sample_directory must exist
-        if self.sample_directory is None:
-            raise ValueError("Sample directory is not set. Use set_sample_directory(path) first.")
-
-        # Clear existing temperatures
-        self.temperatures = []
-
-        # Search for nxrefine .nxs files
-        for item in os.listdir(self.sample_directory):
-            pattern = r'_(\d+)\.nxs'
-            match = re.search(pattern, item)
-            if match:
-                # Identify temperature
-                temperature = match.group(1)
-                self.temperatures.append(temperature)
-        # Convert all temperatures to int temporarily to sort temperatures list
-        self.temperatures = [int(t) for t in self.temperatures]
-        self.temperatures.sort()
-        self.temperatures = [str(t) for t in self.temperatures]
-
-    def set_sample_directory(self, path):
-        """
-        Set the directory path where the datasets are located.
-
-        Parameters
-        ----------
-        path : str
-            Path to the sample directory.
-        """
-        self.sample_directory = os.path.normpath(path)
-
-    def initialize(self):
-        """
-        Initialize Scissors and LinecutModel objects for each temperature.
-        """
-        for temperature in self.temperatures:
-            self.scissors[temperature] = Scissors()
-            self.scissors[temperature] = LinecutModel()
-
-    def set_data(self, temperature, data):
-        """
-        Set the dataset for a specific temperature.
-
-        Parameters
-        ----------
-        temperature : str
-            Temperature for which to set the data.
-        data : object
-            The dataset to be set.
-        """
-        self.datasets[temperature] = data
-
-    def load_transforms(self, temperatures_list=None, print_tree=True):
-        """
-        Load transform datasets (from nxrefine) based on temperature.
-
-        Parameters
-        ----------
-        temperatures_list : list of int or None, optional
-            List of temperatures to load. If None, all available temperatures are loaded.
-        print_tree : bool, optional
-            Whether to print the data tree upon loading. Default True.
-        """
-        # Convert all temperatures to strings
-        if temperatures_list:
-            temperatures_list = [str(t) for t in temperatures_list]
-
-        # Clear existing temperatures before loading files
-        self.temperatures = []
-
-        # Identify files to load
-        items_to_load = []
-        # Search for nxrefine .nxs files
-        for item in os.listdir(self.sample_directory):
-            pattern = r'_(\d+)\.nxs'
-            match = re.search(pattern, item)
-            if match:
-                # Identify temperature
-                temperature = match.group(1)
-                # print(f'Temperature = {temperature}')
-                if (temperatures_list is None) or (temperature in temperatures_list):
-                    # Prepare file to be loaded
-                    self.temperatures.append(temperature)
-                    items_to_load.append(item)
-                    # print(f'Preparing to load {temperature} K data: {item}')
-        # Convert all temperatures to int temporarily to sort temperatures list before loading
-        self.temperatures = [int(t) for t in self.temperatures]
-
-        loading_template = pd.DataFrame({'temperature': self.temperatures, 'filename': items_to_load})
-        loading_template = loading_template.sort_values(by='temperature')
-        self.temperatures = loading_template['temperature']
-        self.temperatures = [str(t) for t in self.temperatures]
-        items_to_load = loading_template['filename'].to_list()
-
-        for i, item in enumerate(items_to_load):
-            path = os.path.join(self.sample_directory, item)
-
-            # Save dataset
-            try:
-                self.datasets[self.temperatures[i]] = load_transform(path, print_tree)
-            except Exception as e:
-                # Report temperature that was unable to load, then raise exception.
-                temp_failed = self.temperatures[i]
-                print(f"Failed to load data for temperature {temp_failed} K from file {item}. Error: {e}")
-                raise  # Re-raise the exception
-
-            # Initialize scissors object
-            self.scissors[self.temperatures[i]] = Scissors()
-            self.scissors[self.temperatures[i]].set_data(self.datasets[self.temperatures[i]])
-
-            # Initialize linecutmodel object
-            self.linecutmodels[self.temperatures[i]] = LinecutModel()
-
-    def load_datasets(self, file_ending='hkli.nxs', temperatures_list=None, print_tree=True):
-        """
-        Load datasets (CHESS format) from the specified folder.
-
-        Parameters
-        ----------
-        file_ending : str, optional
-            The file extension of the datasets to be loaded. The default is 'hkli.nxs'.
-        temperatures_list : list of int or None, optional
-            The list of specific temperatures to load. If None, all available temperatures are
-            loaded. The default is None.
-        print_tree : bool, optional
-            Whether to print the data tree upon loading. Default True.
-        """
-        temperature_folders = []  # Empty list to store temperature folder names
-        for item in os.listdir(self.sample_directory):
-            try:
-                temperature_folders.append(int(item))  # If folder name can be int, add it
-            except ValueError:
-                pass  # Otherwise don't add it
-        temperature_folders.sort()  # Sort from low to high T
-        temperature_folders = [str(i) for i in temperature_folders]  # Convert to strings
-
-        self.temperatures = temperature_folders
-
-        if temperatures_list is not None:
-            self.temperatures = [str(t) for t in temperatures_list]
-
-        # Load .nxs files
-        for T in self.temperatures:
-            for file in os.listdir(os.path.join(self.sample_directory, T)):
-                if file.endswith(file_ending):
-                    filepath = os.path.join(self.sample_directory, T, file)
-
-                    # Load dataset at each temperature
-                    self.datasets[T] = load_data(filepath, print_tree)
-
-                    # Initialize scissors object at each temperature
-                    self.scissors[T] = Scissors()
-                    self.scissors[T].set_data(self.datasets[T])
-
-                    # Initialize linecutmodel object at each temperature
-                    self.linecutmodels[T] = LinecutModel()
-
-    def get_sample_directory(self):
-        """
-        Get the folder path where the datasets are located.
-
-        Returns
-        -------
-        str
-            The folder path.
-        """
-        return self.sample_directory
-
-    def clear_datasets(self):
-        """
-        Clear the datasets stored in the TempDependence instance.
-        """
-        self.datasets = {}
-
-    def set_lattice_params(self, lattice_params):
-        """
-        Set lattice parameters and calculate reciprocal lattice parameters.
-
-        Parameters
-        ----------
-        lattice_params : tuple
-            Tuple containing lattice parameters (a, b, c, al, be, ga).
-        """
-        self.a, self.b, self.c, self.al, self.be, self.ga = lattice_params
-        self.a_star, self.b_star, self.c_star, \
-            self.al_star, self.be_star, self.ga_star = reciprocal_lattice_params(lattice_params)
-
-    def set_window(self, window, verbose=False):
-        """
-        Set the extents of the integration window for each temperature.
-
-        Parameters
-        ----------
-        window : tuple
-            Extents of the window for integration along each axis.
-        verbose : bool, optional
-            Enables printout of linecut axis and integrated axes. Default is False.
-        """
-        for T in self.temperatures:
-            if verbose:
-                print("----------------------------------")
-                print("T = " + T + " K")
-            self.scissors[T].set_window(window, verbose)
-
-    def set_center(self, center):
-        """
-        Set the central coordinate for the linecut for each temperature.
-
-        Parameters
-        ----------
-        center : tuple
-            Central coordinate around which to perform the linecut.
-        """
-        for T in self.temperatures:
-            self.scissors[T].set_center(center)
-
-    def cut_data(self, center=None, window=None, axis=None, verbose=False):
-        """
-        Perform data cutting for each temperature dataset.
-
-        Parameters
-        ----------
-        center : tuple, optional
-            The center point for cutting the data.
-            Defaults to the first temperature's center if None.
-        window : tuple, optional
-            The window size for cutting the data.
-            Defaults to the first temperature's window if None.
-        axis : int or None, optional
-            The axis along which to perform the cutting.
-            Defaults to the longest axis in `window` if None.
-        verbose : bool, optional
-            Enables printout of linecut progress. Default is False.
-
-        Returns
-        -------
-        dict
-            A dictionary of linecuts obtained from the cutting operation.
-        """
-
-        for T in self.temperatures:
-            if verbose:
-                print("-------------------------------")
-                print("Cutting T = " + T + " K data...")
-            self.scissors[T].set_center(center)
-            self.scissors[T].set_window(window)
-            self.scissors[T].cut_data(axis=axis, verbose=verbose)
-            self.linecuts[T] = self.scissors[T].linecut
-            self.linecutmodels[T].set_data(self.linecuts[T])
-
-        xlabel_components = [self.linecuts[self.temperatures[0]].axes
-                             if i == self.scissors[self.temperatures[0]].axis
-                             else str(c) for i, c in
-                             enumerate(self.scissors[self.temperatures[0]].center)]
-        self.xlabel = ' '.join(xlabel_components)
-
-        return self.linecuts
-
-    def plot_linecuts(self, vertical_offset=0, **kwargs):
-        """
-        Plot the linecuts obtained from data cutting.
-
-        Parameters
-        ----------
-        vertical_offset : float, optional
-            The vertical offset between linecuts on the plot. The default is 0.
-        **kwargs
-            Additional keyword arguments to be passed to the plot function.
-        """
-        fig, ax = plt.subplots()
-
-        # Get the Viridis colormap
-        cmap = mpl.colormaps.get_cmap('viridis')
-
-        for i, linecut in enumerate(self.linecuts.values()):
-            x_data = linecut[linecut.axes].nxdata
-            y_data = linecut[linecut.signal].nxdata + i * vertical_offset
-            ax.plot(x_data, y_data, color=cmap(i / len(self.linecuts)), label=self.temperatures[i],
-                    **kwargs)
-
-        ax.set(xlabel=self.xlabel,
-               ylabel=self.linecuts[self.temperatures[0]].signal)
-
-        # Get the current legend handles and labels
-        handles, labels = plt.gca().get_legend_handles_labels()
-
-        # Reverse the order of handles and labels
-        handles = handles[::-1]
-        labels = labels[::-1]
-
-        # Create a new legend with reversed order
-        plt.legend(handles, labels)
-
-        return fig, ax
-
-    def plot_linecuts_heatmap(self, ax=None, **kwargs):
-        """
-        Plot the linecuts obtained from data cutting.
-
-        Parameters
-        ----------
-        ax : matplotlib.axes.Axes, optional
-            The axes on which to plot the heatmap. If None, a new figure and axes
-            are created. The default is None.
-        **kwargs
-            Additional keyword arguments to be passed to the `pcolormesh` function.
-
-        Returns
-        -------
-        QuadMesh
-            The plotted heatmap object.
-        """
-
-        # Retrieve linecut data for the first temperature and extract x-axis data
-        cut = self.linecuts[self.temperatures[0]]
-        x = cut[cut.axes].nxdata
-
-        # Convert the list of temperatures to a NumPy array for the y-axis
-        y = np.array([int(t) for t in self.temperatures])
-
-        # Collect counts from each temperature and ensure they are numpy arrays
-        v = [self.linecuts[T].counts.nxdata for T in self.temperatures]
-
-        # Convert list of arrays to a 2D array for the heatmap
-        v_2d = np.array(v)
-
-        # Create the grid for the heatmap
-        X, Y = np.meshgrid(x, y)
-
-        # Plot using pcolormesh
-        if ax is None:
-            _, ax = plt.subplots()
-        p = ax.pcolormesh(X, Y, v_2d, **kwargs)
-        plt.colorbar(p, label='counts')
-        ax.set(xlabel=self.xlabel, ylabel=r'$T$ (K)')
-
-        return p
-
-    def highlight_integration_window(self, temperature=None, **kwargs):
-        """
-        Displays the integration window plot for a specific temperature,
-        or for the first temperature if none is provided.
-
-        Parameters
-        ----------
-        temperature : str, optional
-            The temperature at which to display the integration window plot. If provided, the plot
-            will be generated using the dataset corresponding to the specified temperature. If not
-            provided, the integration window plots will be generated for the first temperature.
-        **kwargs : keyword arguments, optional
-            Additional keyword arguments to customize the plot.
-        """
-
-        if temperature is not None:
-            p = self.scissors[
-                self.temperatures[0]].highlight_integration_window(
-                data=self.datasets[temperature], **kwargs
-            )
-        else:
-            p = self.scissors[self.temperatures[0]].highlight_integration_window(
-                data=self.datasets[self.temperatures[0]], **kwargs
-            )
-
-        return p
-
-    def plot_integration_window(self, temperature=None, **kwargs):
-        """
-        Plots the three principal cross-sections of the integration volume on
-        a single figure for a specific temperature, or for the first temperature
-        if none is provided.
-
-        Parameters
-        ----------
-        temperature : str, optional
-            The temperature at which to plot the integration volume. If provided,
-            the plot will be generated using the dataset corresponding to the
-            specified temperature. If not provided, the integration window plots
-            will be generated for the first temperature.
-
-        **kwargs : keyword arguments, optional
-            Additional keyword arguments to customize the plot.
-        """
-
-        if temperature is not None:
-            p = self.scissors[self.temperatures[0]].plot_integration_window(**kwargs)
-        else:
-            p = self.scissors[self.temperatures[0]].plot_integration_window(**kwargs)
-
-        return p
-
-    def set_model_components(self, model_components):
-        """
-        Set the model components for all line cut models.
-
-        This method sets the same model components for all line cut models in the
-        analysis. It iterates over each line cut model and calls their respective
-        `set_model_components` method with the provided `model_components`.
-
-        Parameters
-        ----------
-        model_components : Model or iterable of Model
-            The model components to set for all line cut models.
-
-        """
-        [linecutmodel.set_model_components(model_components) for
-         linecutmodel in self.linecutmodels.values()]
-
-    def set_param_hint(self, *args, **kwargs):
-        """
-        Set parameter hints for all line cut models.
-
-        This method sets the parameter hints for all line cut models in the analysis.
-        It iterates over each line cut model and calls their respective `set_param_hint` method
-        with the provided arguments and keyword arguments.
-
-        Parameters
-        ----------
-        *args
-            Variable length argument list.
-        **kwargs
-            Arbitrary keyword arguments.
-
-        """
-        [linecutmodel.set_param_hint(*args, **kwargs)
-         for linecutmodel in self.linecutmodels.values()]
-
-    def make_params(self):
-        """
-        Make parameters for all line cut models.
-
-        This method creates the parameters for all line cut models in the analysis.
-        It iterates over each line cut model and calls their respective `make_params` method.
-        """
-        [linecutmodel.make_params() for linecutmodel in self.linecutmodels.values()]
-
-    def guess(self):
-        """
-        Make initial parameter guesses for all line cut models.
-
-        This method generates initial parameter guesses for all line cut models in the analysis.
-        It iterates over each line cut model and calls their respective `guess` method.
-
-        """
-        [linecutmodel.guess() for linecutmodel in self.linecutmodels.values()]
-
-    def print_initial_params(self):
-        """
-        Print the initial parameter values for all line cut models.
-
-        This method prints the initial parameter values for all line cut models
-        in the analysis. It iterates over each line cut model and calls their
-        respective `print_initial_params` method.
-
-        """
-        [linecutmodel.print_initial_params() for linecutmodel in self.linecutmodels.values()]
-
-    def plot_initial_guess(self):
-        """
-        Plot the initial guess for all line cut models.
-
-        This method plots the initial guess for all line cut models in the analysis.
-        It iterates over each line cut model and calls their respective `plot_initial_guess` method.
-
-        """
-        for T, linecutmodel in self.linecutmodels.items():
-            _, ax = plt.subplots()
-            ax.set(title=T + ' K')
-            linecutmodel.plot_initial_guess()
-
-    def fit(self, verbose=False):
-        """
-        Fit the line cut models.
-
-        This method fits the line cut models for each temperature in the analysis.
-        It iterates over each line cut model, performs the fit, and prints the fitting progress.
-
-        Parameters
-        ----------
-       verbose : bool, optional
-            Enables printout of fitting progress. Default False.
-
-        """
-        for T, linecutmodel in self.linecutmodels.items():
-            if verbose:
-                print(f"Fitting {T} K  data...")
-            linecutmodel.fit()
-            if verbose:
-                print("Done.")
-        print("Fits completed.")
-
-    def plot_fit(self, mdheadings=False, **kwargs):
-        """
-        Plot the fit results.
-
-        This method plots the fit results for each temperature in the analysis.
-        It iterates over each line cut model, calls their respective `plot_fit` method,
-        and sets the xlabel, ylabel, and title for the plot.
-
-        """
-        for T, linecutmodel in self.linecutmodels.items():
-            # Create a markdown heading for the plot
-            if mdheadings:
-                display(Markdown(f"### {T} K Fit Results"))
-            # Plot fit
-            linecutmodel.plot_fit(xlabel=self.xlabel,
-                                  ylabel=self.datasets[self.temperatures[0]].signal,
-                                  title=f"{T} K",
-                                  **kwargs)
-
-    def plot_order_parameter(self):
-        """
-        Plot the temperature dependence of the peak height (order parameter).
-
-        This method extracts the peak height from each temperature-dependent
-        line cut fit stored in `linecutmodels` and plots it as a function
-        of temperature using matplotlib.
-
-        Returns
-        -------
-        Figure
-            Matplotlib Figure object containing the peak height vs. temperature plot.
-        Axes
-            Matplotlib Axes object associated with the figure.
-
-        Notes
-        -----
-        - Temperature values are converted to integers for plotting.
-        - Peak heights are extracted from the 'peakheight' parameter in the model results.
-        - The plot uses standard axes labels with temperature in Kelvin.
-        """
-
-        # Create an array of temperature values
-        temperatures = [int(T) for T in self.temperatures]
-
-        # Create an empty list for the peak heights
-        peakheights = []
-
-        # Extract the peakheight at every temperature
-        for T in self.temperatures:
-            peakheights.append(self.linecutmodels[T].modelresult.params['peakheight'].value)
-
-        # Plot the peakheights vs. temperature
-        fig, ax = plt.subplots()
-        ax.plot(temperatures, peakheights)
-        ax.set(xlabel='$T$ (K)', ylabel='peakheight')
-        return fig, ax
-
-    def print_fit_report(self):
-        """
-        Plot the fit results.
-
-        This method plots the fit results for each temperature in the analysis.
-        It iterates over each line cut model, calls their respective `plot_fit` method,
-        and sets the xlabel, ylabel, and title for the plot.
-
-        """
-        for T, linecutmodel in self.linecutmodels.items():
-            print(f"[[[{T} K Fit Report]]]")
-            linecutmodel.print_fit_report()
+"""
+This module provides classes and functions for analyzing scattering datasets collected at CHESS
+(ID4B) with temperature dependence. It includes functions for loading data, cutting data, and
+plotting linecuts.
+"""
+import os
+import re
+
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+import pandas as pd
+import numpy as np
+from IPython.display import display, Markdown
+from nxs_analysis_tools import load_data, Scissors
+from nxs_analysis_tools.fitting import LinecutModel
+from nxs_analysis_tools.datareduction import load_transform, reciprocal_lattice_params
+
+
+class TempDependence:
+    """
+    A class for analyzing temperature-dependent scattering datasets collected at CHESS (ID4B).
+
+    The `TempDependence` class facilitates the loading, processing, and analysis of scattering
+    data across different temperatures. It includes methods for handling datasets, setting
+    lattice parameters, performing linecuts, modeling the data, and visualizing the results.
+
+    Attributes
+    ----------
+    sample_directory : str
+        Path to the directory containing the datasets.
+    xlabel : str
+        Label for the x-axis of plots, determined by the axis of the linecuts.
+    datasets : dict
+        Dictionary storing datasets keyed by temperature.
+    temperatures : list of str
+        List of temperatures for which data is available.
+    scissors : dict
+        Dictionary of Scissors objects, one for each temperature, used for data manipulation and
+        linecut operations.
+    linecuts : dict
+        Dictionary storing the linecut data for each temperature.
+    linecutmodels : dict
+        Dictionary of LinecutModel objects, one for each temperature, used for fitting the linecuts.
+    a, b, c, al, be, ga : float or None
+        Lattice parameters (a, b, c, alpha, beta, gamma) of the crystal.
+    a_star, b_star, c_star, al_star, be_star, ga_star : float or None
+        Reciprocal lattice parameters (a*, b*, c*, alpha*, beta*, gamma*).
+
+    Methods
+    -------
+    set_temperatures(temperatures):
+        Set the list of temperatures for the datasets.
+    find_temperatures():
+        Set the list of temperatures by automatically scanning the sample directory.
+    set_sample_directory(path):
+        Set the directory path where the datasets are located.
+    initialize():
+        Initialize Scissors and LinecutModel objects for each temperature.
+    set_data(temperature, data):
+        Set the dataset for a specific temperature.
+    load_transforms(temperatures_list=None, print_tree=True):
+        Load transform datasets (from nxrefine) based on temperature.
+    load_datasets(file_ending='hkli.nxs', temperatures_list=None, print_tree=True):
+        Load datasets (CHESS format) from the specified folder.
+    get_sample_directory():
+        Get the folder path where the datasets are located.
+    clear_datasets():
+        Clear the datasets stored in the TempDependence instance.
+    set_Lattice_params(lattice_params):
+        Set lattice parameters and calculate reciprocal lattice parameters.
+    set_window(window, verbose=False):
+        Set the extents of the integration window for each temperature.
+    set_center(center):
+        Set the central coordinate for the linecut for each temperature.
+    cut_data(center=None, window=None, axis=None, verbose=False):
+        Perform data cutting for each temperature dataset.
+    plot_linecuts(vertical_offset=0, **kwargs):
+        Plot the linecuts obtained from data cutting.
+    plot_linecuts_heatmap(ax=None, **kwargs):
+        Plot a heatmap of the linecuts obtained from data cutting.
+    highlight_integration_window(temperature=None, **kwargs):
+        Display the integration window plot for a specific temperature.
+    plot_integration_window(temperature=None, **kwargs):
+        Plot the integration window cross-sections for a specific temperature.
+    set_model_components(model_components):
+        Set the model components for all line cut models.
+    set_param_hint(*args, **kwargs):
+        Set parameter hints for all line cut models.
+    make_params():
+        Create parameters for all line cut models.
+    guess():
+        Make initial parameter guesses for all line cut models.
+    print_initial_params():
+        Print the initial parameter values for all line cut models.
+    plot_initial_guess():
+        Plot the initial guess for all line cut models.
+    fit(verbose=False):
+        Fit the line cut models for each temperature.
+    plot_fit(mdheadings=False, **kwargs):
+        Plot the fit results for each temperature.
+    plot_order_parameter(self):
+        Plot the temperature dependence of the peakheight parameter.
+    print_fit_report():
+        Print the fit report for each temperature.
+    """
+
+    def __init__(self):
+        """
+        Initialize the TempDependence class with default values.
+        """
+
+        self.sample_directory = None
+        self.xlabel = ''
+        self.datasets = {}
+        self.temperatures = []
+        self.scissors = {}
+        self.linecuts = {}
+        self.linecutmodels = {}
+        self.a, self.b, self.c, self.al, self.be, self.ga, \
+            self.a_star, self.b_star, self.c_star, self.al_star, self.be_star, self.ga_star \
+            = [None] * 12
+
+    def set_temperatures(self, temperatures):
+        """
+        Set the list of temperatures for the datasets.
+
+        Parameters
+        ----------
+        temperatures : list
+            List of temperatures to set.
+        """
+        self.temperatures = temperatures
+
+    def find_temperatures(self):
+        """
+        Set the list of temperatures by automatically scanning the sample directory.
+        """
+
+        # Assert that self.sample_directory must exist
+        if self.sample_directory is None:
+            raise ValueError("Sample directory is not set. Use set_sample_directory(path) first.")
+
+        # Clear existing temperatures
+        self.temperatures = []
+
+        # Search for nxrefine .nxs files
+        for item in os.listdir(self.sample_directory):
+            pattern = r'_(\d+)\.nxs'
+            match = re.search(pattern, item)
+            if match:
+                # Identify temperature
+                temperature = match.group(1)
+                self.temperatures.append(temperature)
+        # Convert all temperatures to int temporarily to sort temperatures list
+        self.temperatures = [int(t) for t in self.temperatures]
+        self.temperatures.sort()
+        self.temperatures = [str(t) for t in self.temperatures]
+
+    def set_sample_directory(self, path):
+        """
+        Set the directory path where the datasets are located.
+
+        Parameters
+        ----------
+        path : str
+            Path to the sample directory.
+        """
+        self.sample_directory = os.path.normpath(path)
+
+    def initialize(self):
+        """
+        Initialize Scissors and LinecutModel objects for each temperature.
+        """
+        for temperature in self.temperatures:
+            self.scissors[temperature] = Scissors()
+            self.scissors[temperature] = LinecutModel()
+
+    def set_data(self, temperature, data):
+        """
+        Set the dataset for a specific temperature.
+
+        Parameters
+        ----------
+        temperature : str
+            Temperature for which to set the data.
+        data : object
+            The dataset to be set.
+        """
+        self.datasets[temperature] = data
+
+    def load_transforms(self, temperatures_list=None, print_tree=True):
+        """
+        Load transform datasets (from nxrefine) based on temperature.
+
+        Parameters
+        ----------
+        temperatures_list : list of int or None, optional
+            List of temperatures to load. If None, all available temperatures are loaded.
+        print_tree : bool, optional
+            Whether to print the data tree upon loading. Default True.
+        """
+        # Convert all temperatures to strings
+        if temperatures_list:
+            temperatures_list = [str(t) for t in temperatures_list]
+
+        # Clear existing temperatures before loading files
+        self.temperatures = []
+
+        # Identify files to load
+        items_to_load = []
+        # Search for nxrefine .nxs files
+        for item in os.listdir(self.sample_directory):
+            pattern = r'_(\d+)\.nxs'
+            match = re.search(pattern, item)
+            if match:
+                # Identify temperature
+                temperature = match.group(1)
+                # print(f'Temperature = {temperature}')
+                if (temperatures_list is None) or (temperature in temperatures_list):
+                    # Prepare file to be loaded
+                    self.temperatures.append(temperature)
+                    items_to_load.append(item)
+                    # print(f'Preparing to load {temperature} K data: {item}')
+
+        # Convert all temperatures to int temporarily to sort temperatures list before loading
+        self.temperatures = [int(t) for t in self.temperatures]
+
+        loading_template = pd.DataFrame({'temperature': self.temperatures,
+                                         'filename': items_to_load})
+        loading_template = loading_template.sort_values(by='temperature')
+        self.temperatures = loading_template['temperature']
+        self.temperatures = [str(t) for t in self.temperatures]
+        items_to_load = loading_template['filename'].to_list()
+
+        for i, item in enumerate(items_to_load):
+            path = os.path.join(self.sample_directory, item)
+
+            # Ensure path is a string before using it
+            path = str(path)
+
+            # Save dataset
+            try:
+                self.datasets[self.temperatures[i]] = load_transform(path, print_tree)
+            except Exception as e:
+                # Report temperature that was unable to load, then raise exception.
+                temp_failed = self.temperatures[i]
+                print(f"Failed to load data for temperature {temp_failed} K from file {item}."
+                      f" Error: {e}")
+                raise  # Re-raise the exception
+
+            # Initialize scissors object
+            self.scissors[self.temperatures[i]] = Scissors()
+            self.scissors[self.temperatures[i]].set_data(self.datasets[self.temperatures[i]])
+
+            # Initialize linecutmodel object
+            self.linecutmodels[self.temperatures[i]] = LinecutModel()
+
+    def load_datasets(self, file_ending='hkli.nxs', temperatures_list=None, print_tree=True):
+        """
+        Load datasets (CHESS format) from the specified folder.
+
+        Parameters
+        ----------
+        file_ending : str, optional
+            The file extension of the datasets to be loaded. The default is 'hkli.nxs'.
+        temperatures_list : list of int or None, optional
+            The list of specific temperatures to load. If None, all available temperatures are
+            loaded. The default is None.
+        print_tree : bool, optional
+            Whether to print the data tree upon loading. Default True.
+        """
+        temperature_folders = []  # Empty list to store temperature folder names
+        for item in os.listdir(self.sample_directory):
+            try:
+                temperature_folders.append(int(item))  # If folder name can be int, add it
+            except ValueError:
+                pass  # Otherwise don't add it
+        temperature_folders.sort()  # Sort from low to high T
+        temperature_folders = [str(i) for i in temperature_folders]  # Convert to strings
+
+        self.temperatures = temperature_folders
+
+        if temperatures_list is not None:
+            self.temperatures = [str(t) for t in temperatures_list]
+
+        # Load .nxs files
+        for T in self.temperatures:
+            for file in os.listdir(os.path.join(self.sample_directory, T)):
+                if file.endswith(file_ending):
+                    filepath = os.path.join(self.sample_directory, T, file)
+
+                    # Load dataset at each temperature
+                    self.datasets[T] = load_data(filepath, print_tree)
+
+                    # Initialize scissors object at each temperature
+                    self.scissors[T] = Scissors()
+                    self.scissors[T].set_data(self.datasets[T])
+
+                    # Initialize linecutmodel object at each temperature
+                    self.linecutmodels[T] = LinecutModel()
+
+    def get_sample_directory(self):
+        """
+        Get the folder path where the datasets are located.
+
+        Returns
+        -------
+        str
+            The folder path.
+        """
+        return self.sample_directory
+
+    def clear_datasets(self):
+        """
+        Clear the datasets stored in the TempDependence instance.
+        """
+        self.datasets = {}
+
+    def set_lattice_params(self, lattice_params):
+        """
+        Set lattice parameters and calculate reciprocal lattice parameters.
+
+        Parameters
+        ----------
+        lattice_params : tuple
+            Tuple containing lattice parameters (a, b, c, al, be, ga).
+        """
+        self.a, self.b, self.c, self.al, self.be, self.ga = lattice_params
+        self.a_star, self.b_star, self.c_star, \
+            self.al_star, self.be_star, self.ga_star = reciprocal_lattice_params(lattice_params)
+
+    def set_window(self, window, verbose=False):
+        """
+        Set the extents of the integration window for each temperature.
+
+        Parameters
+        ----------
+        window : tuple
+            Extents of the window for integration along each axis.
+        verbose : bool, optional
+            Enables printout of linecut axis and integrated axes. Default is False.
+        """
+        for T in self.temperatures:
+            if verbose:
+                print("----------------------------------")
+                print("T = " + T + " K")
+            self.scissors[T].set_window(window, verbose)
+
+    def set_center(self, center):
+        """
+        Set the central coordinate for the linecut for each temperature.
+
+        Parameters
+        ----------
+        center : tuple
+            Central coordinate around which to perform the linecut.
+        """
+        for T in self.temperatures:
+            self.scissors[T].set_center(center)
+
+    def cut_data(self, center=None, window=None, axis=None, verbose=False):
+        """
+        Perform data cutting for each temperature dataset.
+
+        Parameters
+        ----------
+        center : tuple, optional
+            The center point for cutting the data.
+            Defaults to the first temperature's center if None.
+        window : tuple, optional
+            The window size for cutting the data.
+            Defaults to the first temperature's window if None.
+        axis : int or None, optional
+            The axis along which to perform the cutting.
+            Defaults to the longest axis in `window` if None.
+        verbose : bool, optional
+            Enables printout of linecut progress. Default is False.
+
+        Returns
+        -------
+        dict
+            A dictionary of linecuts obtained from the cutting operation.
+        """
+
+        for T in self.temperatures:
+            if verbose:
+                print("-------------------------------")
+                print("Cutting T = " + T + " K data...")
+            self.scissors[T].set_center(center)
+            self.scissors[T].set_window(window)
+            self.scissors[T].cut_data(axis=axis, verbose=verbose)
+            self.linecuts[T] = self.scissors[T].linecut
+            self.linecutmodels[T].set_data(self.linecuts[T])
+
+        xlabel_components = [self.linecuts[self.temperatures[0]].axes
+                             if i == self.scissors[self.temperatures[0]].axis
+                             else str(c) for i, c in
+                             enumerate(self.scissors[self.temperatures[0]].center)]
+        self.xlabel = ' '.join(xlabel_components)
+
+        return self.linecuts
+
+    def plot_linecuts(self, vertical_offset=0, **kwargs):
+        """
+        Plot the linecuts obtained from data cutting.
+
+        Parameters
+        ----------
+        vertical_offset : float, optional
+            The vertical offset between linecuts on the plot. The default is 0.
+        **kwargs
+            Additional keyword arguments to be passed to the plot function.
+        """
+        fig, ax = plt.subplots()
+
+        # Get the Viridis colormap
+        cmap = mpl.colormaps.get_cmap('viridis')
+
+        for i, linecut in enumerate(self.linecuts.values()):
+            x_data = linecut[linecut.axes].nxdata
+            y_data = linecut[linecut.signal].nxdata + i * vertical_offset
+            ax.plot(x_data, y_data, color=cmap(i / len(self.linecuts)), label=self.temperatures[i],
+                    **kwargs)
+
+        ax.set(xlabel=self.xlabel,
+               ylabel=self.linecuts[self.temperatures[0]].signal)
+
+        # Get the current legend handles and labels
+        handles, labels = plt.gca().get_legend_handles_labels()
+
+        # Reverse the order of handles and labels
+        handles = handles[::-1]
+        labels = labels[::-1]
+
+        # Create a new legend with reversed order
+        plt.legend(handles, labels)
+
+        return fig, ax
+
+    def plot_linecuts_heatmap(self, ax=None, **kwargs):
+        """
+        Plot the linecuts obtained from data cutting.
+
+        Parameters
+        ----------
+        ax : matplotlib.axes.Axes, optional
+            The axes on which to plot the heatmap. If None, a new figure and axes
+            are created. The default is None.
+        **kwargs
+            Additional keyword arguments to be passed to the `pcolormesh` function.
+
+        Returns
+        -------
+        QuadMesh
+            The plotted heatmap object.
+        """
+
+        # Retrieve linecut data for the first temperature and extract x-axis data
+        cut = self.linecuts[self.temperatures[0]]
+        x = cut[cut.axes].nxdata
+
+        # Convert the list of temperatures to a NumPy array for the y-axis
+        y = np.array([int(t) for t in self.temperatures])
+
+        # Collect counts from each temperature and ensure they are numpy arrays
+        v = [self.linecuts[T].counts.nxdata for T in self.temperatures]
+
+        # Convert list of arrays to a 2D array for the heatmap
+        v_2d = np.array(v)
+
+        # Create the grid for the heatmap
+        X, Y = np.meshgrid(x, y)
+
+        # Plot using pcolormesh
+        if ax is None:
+            _, ax = plt.subplots()
+        p = ax.pcolormesh(X, Y, v_2d, **kwargs)
+        plt.colorbar(p, label='counts')
+        ax.set(xlabel=self.xlabel, ylabel=r'$T$ (K)')
+
+        return p
+
+    def highlight_integration_window(self, temperature=None, **kwargs):
+        """
+        Displays the integration window plot for a specific temperature,
+        or for the first temperature if none is provided.
+
+        Parameters
+        ----------
+        temperature : str, optional
+            The temperature at which to display the integration window plot. If provided, the plot
+            will be generated using the dataset corresponding to the specified temperature. If not
+            provided, the integration window plots will be generated for the first temperature.
+        **kwargs : keyword arguments, optional
+            Additional keyword arguments to customize the plot.
+        """
+
+        if temperature is not None:
+            p = self.scissors[
+                self.temperatures[0]].highlight_integration_window(
+                data=self.datasets[temperature], **kwargs
+            )
+        else:
+            p = self.scissors[self.temperatures[0]].highlight_integration_window(
+                data=self.datasets[self.temperatures[0]], **kwargs
+            )
+
+        return p
+
+    def plot_integration_window(self, temperature=None, **kwargs):
+        """
+        Plots the three principal cross-sections of the integration volume on
+        a single figure for a specific temperature, or for the first temperature
+        if none is provided.
+
+        Parameters
+        ----------
+        temperature : str, optional
+            The temperature at which to plot the integration volume. If provided,
+            the plot will be generated using the dataset corresponding to the
+            specified temperature. If not provided, the integration window plots
+            will be generated for the first temperature.
+
+        **kwargs : keyword arguments, optional
+            Additional keyword arguments to customize the plot.
+        """
+
+        if temperature is not None:
+            p = self.scissors[self.temperatures[0]].plot_integration_window(**kwargs)
+        else:
+            p = self.scissors[self.temperatures[0]].plot_integration_window(**kwargs)
+
+        return p
+
+    def set_model_components(self, model_components):
+        """
+        Set the model components for all line cut models.
+
+        This method sets the same model components for all line cut models in the
+        analysis. It iterates over each line cut model and calls their respective
+        `set_model_components` method with the provided `model_components`.
+
+        Parameters
+        ----------
+        model_components : Model or iterable of Model
+            The model components to set for all line cut models.
+
+        """
+        [linecutmodel.set_model_components(model_components) for
+         linecutmodel in self.linecutmodels.values()]
+
+    def set_param_hint(self, *args, **kwargs):
+        """
+        Set parameter hints for all line cut models.
+
+        This method sets the parameter hints for all line cut models in the analysis.
+        It iterates over each line cut model and calls their respective `set_param_hint` method
+        with the provided arguments and keyword arguments.
+
+        Parameters
+        ----------
+        *args
+            Variable length argument list.
+        **kwargs
+            Arbitrary keyword arguments.
+
+        """
+        [linecutmodel.set_param_hint(*args, **kwargs)
+         for linecutmodel in self.linecutmodels.values()]
+
+    def make_params(self):
+        """
+        Make parameters for all line cut models.
+
+        This method creates the parameters for all line cut models in the analysis.
+        It iterates over each line cut model and calls their respective `make_params` method.
+        """
+        [linecutmodel.make_params() for linecutmodel in self.linecutmodels.values()]
+
+    def guess(self):
+        """
+        Make initial parameter guesses for all line cut models.
+
+        This method generates initial parameter guesses for all line cut models in the analysis.
+        It iterates over each line cut model and calls their respective `guess` method.
+
+        """
+        [linecutmodel.guess() for linecutmodel in self.linecutmodels.values()]
+
+    def print_initial_params(self):
+        """
+        Print the initial parameter values for all line cut models.
+
+        This method prints the initial parameter values for all line cut models
+        in the analysis. It iterates over each line cut model and calls their
+        respective `print_initial_params` method.
+
+        """
+        [linecutmodel.print_initial_params() for linecutmodel in self.linecutmodels.values()]
+
+    def plot_initial_guess(self):
+        """
+        Plot the initial guess for all line cut models.
+
+        This method plots the initial guess for all line cut models in the analysis.
+        It iterates over each line cut model and calls their respective `plot_initial_guess` method.
+
+        """
+        for T, linecutmodel in self.linecutmodels.items():
+            _, ax = plt.subplots()
+            ax.set(title=T + ' K')
+            linecutmodel.plot_initial_guess()
+
+    def fit(self, verbose=False):
+        """
+        Fit the line cut models.
+
+        This method fits the line cut models for each temperature in the analysis.
+        It iterates over each line cut model, performs the fit, and prints the fitting progress.
+
+        Parameters
+        ----------
+       verbose : bool, optional
+            Enables printout of fitting progress. Default False.
+
+        """
+        for T, linecutmodel in self.linecutmodels.items():
+            if verbose:
+                print(f"Fitting {T} K  data...")
+            linecutmodel.fit()
+            if verbose:
+                print("Done.")
+        print("Fits completed.")
+
+    def plot_fit(self, mdheadings=False, **kwargs):
+        """
+        Plot the fit results.
+
+        This method plots the fit results for each temperature in the analysis.
+        It iterates over each line cut model, calls their respective `plot_fit` method,
+        and sets the xlabel, ylabel, and title for the plot.
+
+        """
+        for T, linecutmodel in self.linecutmodels.items():
+            # Create a markdown heading for the plot
+            if mdheadings:
+                display(Markdown(f"### {T} K Fit Results"))
+            # Plot fit
+            linecutmodel.plot_fit(xlabel=self.xlabel,
+                                  ylabel=self.datasets[self.temperatures[0]].signal,
+                                  title=f"{T} K",
+                                  **kwargs)
+
+    def plot_order_parameter(self):
+        """
+        Plot the temperature dependence of the peak height (order parameter).
+
+        This method extracts the peak height from each temperature-dependent
+        line cut fit stored in `linecutmodels` and plots it as a function
+        of temperature using matplotlib.
+
+        Returns
+        -------
+        Figure
+            Matplotlib Figure object containing the peak height vs. temperature plot.
+        Axes
+            Matplotlib Axes object associated with the figure.
+
+        Notes
+        -----
+        - Temperature values are converted to integers for plotting.
+        - Peak heights are extracted from the 'peakheight' parameter in the model results.
+        - The plot uses standard axes labels with temperature in Kelvin.
+        """
+
+        # Create an array of temperature values
+        temperatures = [int(T) for T in self.temperatures]
+
+        # Create an empty list for the peak heights
+        peakheights = []
+
+        # Extract the peakheight at every temperature
+        for T in self.temperatures:
+            peakheights.append(self.linecutmodels[T].modelresult.params['peakheight'].value)
+
+        # Plot the peakheights vs. temperature
+        fig, ax = plt.subplots()
+        ax.plot(temperatures, peakheights)
+        ax.set(xlabel='$T$ (K)', ylabel='peakheight')
+        return fig, ax
+
+    def print_fit_report(self):
+        """
+        Plot the fit results.
+
+        This method plots the fit results for each temperature in the analysis.
+        It iterates over each line cut model, calls their respective `plot_fit` method,
+        and sets the xlabel, ylabel, and title for the plot.
+
+        """
+        for T, linecutmodel in self.linecutmodels.items():
+            print(f"[[[{T} K Fit Report]]]")
+            linecutmodel.print_fit_report()