nxs-analysis-tools 0.0.29__py3-none-any.whl → 0.0.31__py3-none-any.whl

nxs_analysis_tools/chess.py

@@ -1,363 +1,363 @@
-"""
-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 matplotlib.pyplot as plt
-import matplotlib as mpl
-from IPython.display import display, Markdown
-from nxs_analysis_tools import load_data, Scissors
-from nxs_analysis_tools.fitting import LinecutModel
-
-class TempDependence:
-    """
-    Class for analyzing scattering datasets collected at CHESS (ID4B) with temperature dependence.
-    """
-
-    def __init__(self):
-        """
-        Initialize TempDependence class.
-        """
-        self.xlabel = None
-        self.datasets = {}
-        self.folder = None
-        self.temperatures = None
-        self.scissors = {}
-        self.linecuts = {}
-        self.linecutmodels = {}
-
-    def get_folder(self):
-        """
-        Get the folder path where the datasets are located.
-
-        Returns
-        -------
-            str:
-                The folder path.
-        """
-        return self.folder
-
-    def clear_datasets(self):
-        """
-        Clear the datasets stored in the TempDependence instance.
-        """
-        self.datasets = {}
-
-    def load_datasets(self, folder, file_ending='hkli.nxs', temperatures_list=None):
-        """
-        Load scattering datasets from the specified folder.
-
-        Parameters
-        ----------
-        folder : str
-            The path to the folder where the datasets are located.
-        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.
-        """
-        self.folder = os.path.normpath(folder)
-        temperature_folders = []  # Empty list to store temperature folder names
-        for item in os.listdir(self.folder):
-            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
-
-        print('Found temperature folders:')
-        [print('[' + str(i) + '] ' + folder) for i, folder in enumerate(temperature_folders)]
-
-        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.folder, T)):
-                if file.endswith(file_ending):
-                    filepath = os.path.join(self.folder, T, file)
-                    print('-----------------------------------------------')
-                    print('Loading ' + T + ' K indexed .nxs files...')
-                    print('Found ' + filepath)
-
-                    # Load dataset at each temperature
-                    self.datasets[T] = load_data(filepath)
-
-                    # 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 set_window(self, window):
-        """
-        Set the extents of the integration window.
-
-        Parameters
-        ----------
-        window : tuple
-            Extents of the window for integration along each axis.
-        """
-        for T in self.temperatures:
-            print("----------------------------------")
-            print("T = " + T + " K")
-            self.scissors[T].set_window(window)
-
-    def set_center(self, center):
-        """
-        Set the central coordinate for the linecut.
-
-        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):
-        """
-        Perform data cutting for each temperature dataset.
-
-        Parameters
-        ----------
-        center : tuple
-            The center point for cutting the data.
-        window : tuple
-            The window size for cutting the data.
-        axis : int or None, optional
-            The axis along which to perform the cutting. If None, cutting is performed along the
-            longest axis in `window`. The default is None.
-
-        Returns
-        -------
-        list
-            A list of linecuts obtained from the cutting operation.
-        """
-
-        center = center if center is not None else self.scissors[self.temperatures[0]].center
-        window = window if window is not None else self.scissors[self.temperatures[0]].window
-
-        for T in self.temperatures:
-            print("-------------------------------")
-            print("Cutting T = " + T + " K data...")
-            self.scissors[T].cut_data(center, window, axis)
-            self.linecuts[T] = self.scissors[T].linecut
-            self.linecutmodels[T].set_data(self.linecuts[T])
-
-        xlabel_components = [self.linecuts[self.temperatures[0]].axes[0]
-                             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[0]].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 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():
-            fig, ax = plt.subplots()
-            ax.set(title=T + ' K')
-            linecutmodel.plot_initial_guess()
-
-    def fit(self):
-        """
-        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.
-
-        """
-        for T, linecutmodel in self.linecutmodels.items():
-            print(f"Fitting {T} K  data...")
-            linecutmodel.fit()
-            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 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 matplotlib.pyplot as plt
+import matplotlib as mpl
+from IPython.display import display, Markdown
+from nxs_analysis_tools import load_data, Scissors
+from nxs_analysis_tools.fitting import LinecutModel
+
+class TempDependence:
+    """
+    Class for analyzing scattering datasets collected at CHESS (ID4B) with temperature dependence.
+    """
+
+    def __init__(self):
+        """
+        Initialize TempDependence class.
+        """
+        self.xlabel = None
+        self.datasets = {}
+        self.folder = None
+        self.temperatures = None
+        self.scissors = {}
+        self.linecuts = {}
+        self.linecutmodels = {}
+
+    def get_folder(self):
+        """
+        Get the folder path where the datasets are located.
+
+        Returns
+        -------
+            str:
+                The folder path.
+        """
+        return self.folder
+
+    def clear_datasets(self):
+        """
+        Clear the datasets stored in the TempDependence instance.
+        """
+        self.datasets = {}
+
+    def load_datasets(self, folder, file_ending='hkli.nxs', temperatures_list=None):
+        """
+        Load scattering datasets from the specified folder.
+
+        Parameters
+        ----------
+        folder : str
+            The path to the folder where the datasets are located.
+        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.
+        """
+        self.folder = os.path.normpath(folder)
+        temperature_folders = []  # Empty list to store temperature folder names
+        for item in os.listdir(self.folder):
+            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
+
+        print('Found temperature folders:')
+        [print('[' + str(i) + '] ' + folder) for i, folder in enumerate(temperature_folders)]
+
+        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.folder, T)):
+                if file.endswith(file_ending):
+                    filepath = os.path.join(self.folder, T, file)
+                    print('-----------------------------------------------')
+                    print('Loading ' + T + ' K indexed .nxs files...')
+                    print('Found ' + filepath)
+
+                    # Load dataset at each temperature
+                    self.datasets[T] = load_data(filepath)
+
+                    # 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 set_window(self, window):
+        """
+        Set the extents of the integration window.
+
+        Parameters
+        ----------
+        window : tuple
+            Extents of the window for integration along each axis.
+        """
+        for T in self.temperatures:
+            print("----------------------------------")
+            print("T = " + T + " K")
+            self.scissors[T].set_window(window)
+
+    def set_center(self, center):
+        """
+        Set the central coordinate for the linecut.
+
+        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):
+        """
+        Perform data cutting for each temperature dataset.
+
+        Parameters
+        ----------
+        center : tuple
+            The center point for cutting the data.
+        window : tuple
+            The window size for cutting the data.
+        axis : int or None, optional
+            The axis along which to perform the cutting. If None, cutting is performed along the
+            longest axis in `window`. The default is None.
+
+        Returns
+        -------
+        list
+            A list of linecuts obtained from the cutting operation.
+        """
+
+        center = center if center is not None else self.scissors[self.temperatures[0]].center
+        window = window if window is not None else self.scissors[self.temperatures[0]].window
+
+        for T in self.temperatures:
+            print("-------------------------------")
+            print("Cutting T = " + T + " K data...")
+            self.scissors[T].cut_data(center, window, axis)
+            self.linecuts[T] = self.scissors[T].linecut
+            self.linecutmodels[T].set_data(self.linecuts[T])
+
+        xlabel_components = [self.linecuts[self.temperatures[0]].axes[0]
+                             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 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():
+            fig, ax = plt.subplots()
+            ax.set(title=T + ' K')
+            linecutmodel.plot_initial_guess()
+
+    def fit(self):
+        """
+        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.
+
+        """
+        for T, linecutmodel in self.linecutmodels.items():
+            print(f"Fitting {T} K  data...")
+            linecutmodel.fit()
+            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 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()