nxs-analysis-tools 0.1.6__tar.gz → 0.1.7__tar.gz

{nxs_analysis_tools-0.1.6 → nxs_analysis_tools-0.1.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nxs-analysis-tools
-Version: 0.1.6
+Version: 0.1.7
 Summary: Reduce and transform nexus format (.nxs) scattering data.
 Author-email: "Steven J. Gomez Alvarado" <stevenjgomez@ucsb.edu>
 License-Expression: MIT

{nxs_analysis_tools-0.1.6 → nxs_analysis_tools-0.1.7}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = 'nxs-analysis-tools'
-version = '0.1.6'
+version = '0.1.7'
 description = 'Reduce and transform nexus format (.nxs) scattering data.'
 readme = 'README.md'
 requires-python = '>=3.7'
@@ -71,7 +71,7 @@ dev = [
 'DOI' = 'https://doi.org/10.5281/zenodo.15186359'
 
 [tool.bumpver]
-current_version = "0.1.6"
+current_version = "0.1.7"
 version_pattern = "MAJOR.MINOR.PATCH[-TAG]"
 tag_pattern = "vMAJOR.MINOR.PATCH[-TAG]"
 commit_message = "Bump version {old_version} -> {new_version}"

{nxs_analysis_tools-0.1.6 → nxs_analysis_tools-0.1.7}/src/_meta/__init__.py

@@ -6,5 +6,5 @@ __author__ = 'Steven J. Gomez Alvarado'
 __email__ = 'stevenjgomez@ucsb.edu'
 __copyright__ = f"2023-2025, {__author__}"
 __license__ = 'MIT'
-__version__ = '0.1.6'
+__version__ = '0.1.7'
 __repo_url__ = 'https://github.com/stevenjgomez/nxs_analysis_tools'

{nxs_analysis_tools-0.1.6 → nxs_analysis_tools-0.1.7}/src/nxs_analysis_tools/__init__.py

@@ -11,4 +11,5 @@ from .chess import TempDependence
 __all__ = ['load_data', 'load_transform', 'plot_slice', 'Scissors',
            'reciprocal_lattice_params', 'rotate_data', 'rotate_data_2D',
            'convert_to_inverse_angstroms', 'array_to_nxdata', 'Padder',
-           'rebin_nxdata', 'rebin_3d', 'rebin_1d'] + ['TempDependence']
+           'rebin_nxdata', 'rebin_3d', 'rebin_1d', 'TempDependence',
+           'animate_slice_temp', 'animate_slice_axis']

{nxs_analysis_tools-0.1.6 → nxs_analysis_tools-0.1.7}/src/nxs_analysis_tools/chess.py

@@ -103,18 +103,28 @@ class TempDependence:
         Plot raw data and fitted models for each temperature.
     fit_peak_simple():
         Perform a basic fit using a pseudo-Voigt peak shape, linear background, and no constraints.
-    plot_order_parameter():
+    plot_order_parameter(ax, **kwargs):
         Plot the temperature dependence of the peakheight parameter.
     print_fit_report():
         Print the fit report for each temperature.
     """
 
-    def __init__(self):
+    def __init__(self, sample_directory=None):
         """
-        Initialize the TempDependence class with default values.
+        Initialize the TempDependence class.
+
+        Parameters
+        ----------
+        sample_directory : str, optional
+            Path to the directory containing the temperature folders.
+            If None, no directory is set initially.
         """
 
-        self.sample_directory = None
+        if sample_directory is None:
+            self.sample_directory = None
+        else:
+            self.set_sample_directory(sample_directory)
+
         self.xlabel = ''
         self.datasets = {}
         self.temperatures = []
@@ -138,7 +148,7 @@ class TempDependence:
 
     def find_temperatures(self):
         """
-        Set the list of temperatures by automatically scanning the sample directory.
+        Set the list of temperatures by automatically scanning the sample directory for .nxs files from nxrefine.
         """
 
         # Assert that self.sample_directory must exist
@@ -454,7 +464,7 @@ class TempDependence:
 
         Parameters
         ----------
-        ax : matplotlib.axes.Axes, optional
+        ax : :class:`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
@@ -707,7 +717,7 @@ class TempDependence:
             Amount to vertically offset each linecut for clarity.
         cmap : str, default='viridis'
             Name of the matplotlib colormap used to distinguish different temperatures.
-        ax : matplotlib.axes.Axes or None, default=None
+        ax : :class:`matplotlib.axes.Axes` or None, default=None
             Axis object to plot on. If None, a new figure and axis are created.
 
         The function:
@@ -754,9 +764,10 @@ class TempDependence:
                                                 LinearModel(prefix='background')])
             linecutmodel.make_params()
             linecutmodel.guess()
+            linecutmodel.params.set('peakamplitude', min=0)
             linecutmodel.fit()
 
-    def plot_order_parameter(self):
+    def plot_order_parameter(self, ax=None, **kwargs):
         """
         Plot the temperature dependence of the peak height (order parameter).
 
@@ -764,6 +775,14 @@ class TempDependence:
         line cut fit stored in `linecutmodels` and plots it as a function
         of temperature using matplotlib.
 
+        Parameters
+        ----------
+        ax : :class:`matplotlib.axes.Axes`, optional
+            Axis object to plot on. If None, a new figure and axis are created.
+        **kwargs
+            Keyword arguments to be passed to the plot function.
+
+
         Returns
         -------
         Figure
@@ -786,11 +805,19 @@ class TempDependence:
 
         # Extract the peakheight at every temperature
         for T in self.temperatures:
+            
+            # Verify that the fit has already been completed
+            if self.linecutmodels[T].modelresult is None:
+                raise AttributeError("Model result is empty. Have you fit the data to a model?")
+            
             peakheights.append(self.linecutmodels[T].modelresult.params['peakheight'].value)
 
         # Plot the peakheights vs. temperature
-        fig, ax = plt.subplots()
-        ax.plot(temperatures, peakheights)
+        if ax is None:
+            fig, ax = plt.subplots()
+        else:
+            fig = ax.figure
+        ax.plot(temperatures, peakheights, **kwargs)
         ax.set(xlabel='$T$ (K)', ylabel='peakheight')
         return fig, ax
 

{nxs_analysis_tools-0.1.6 → nxs_analysis_tools-0.1.7}/src/nxs_analysis_tools/datareduction.py

@@ -2,22 +2,27 @@
 Reduces scattering data into 2D and 1D datasets.
 """
 import os
+import io
+import warnings
 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.transforms import Affine2D
 from matplotlib.markers import MarkerStyle
 from matplotlib.ticker import MultipleLocator
+import matplotlib.animation as animation
 from matplotlib import colors
 from matplotlib import patches
-from IPython.display import display, Markdown
+from IPython.display import display, Markdown, HTML, Image
 from nexusformat.nexus import NXfield, NXdata, nxload, NeXusError, NXroot, NXentry, nxsave
 from scipy import ndimage
 
+
 # Specify items on which users are allowed to perform standalone imports
 __all__ = ['load_data', 'load_transform', 'plot_slice', 'Scissors',
            'reciprocal_lattice_params', 'rotate_data', 'rotate_data_2D',
            'convert_to_inverse_angstroms', 'array_to_nxdata', 'Padder',
-           'rebin_nxdata', 'rebin_3d', 'rebin_1d']
+           'rebin_nxdata', 'rebin_3d', 'rebin_1d', 'animate_slice_temp',
+           'animate_slice_axis']
 
 
 def load_data(path, print_tree=True):
@@ -407,6 +412,9 @@ def plot_slice(data, X=None, Y=None, sum_axis=None, transpose=False, vmin=None,
             # Use the 2D template to create a new nxdata
             data = array_to_nxdata(arr, data[slice_obj])
 
+    if data.ndim != 2:
+        raise ValueError("Slice data must be 2D.")
+
     # If the data is of type ndarray, then convert to NXdata
     if is_array:
         # Convert X to NXfield if it is not already
@@ -600,6 +608,175 @@ def plot_slice(data, X=None, Y=None, sum_axis=None, transpose=False, vmin=None,
     # Return the quadmesh object
     return p
 
+def animate_slice_temp(temp_dependence, slice_obj, ax=None, interval=500, save_gif=False, filename='animation',
+                       title=True, title_fmt='d', plot_slice_kwargs=None, ax_kwargs=None):
+    """
+    Animate 2D slices from a temperature-dependent dataset.
+
+    Creates a matplotlib animation by extracting 2D slices from each dataset 
+    in a TempDependence object and animating them in sequence by temperature.
+    Optionally displays the animation inline and/or saves it as a GIF.
+
+    Parameters
+    ----------
+    temp_dependence : nxs_analysis_tools.chess.TempDependence
+        Object holding datasets at various temperatures.
+    slice_obj : list of slice or None
+        Slice object to apply to each dataset; None entries are treated as ':'.
+    ax : matplotlib.axes.Axes, optional
+        The axes object to plot on. If None, a new figure and axes will be created.
+    interval : int, optional
+        Delay between frames in milliseconds. Default is 500.
+    save_gif : bool, optional
+        If True, saves the animation to a .gif file. Default is False.
+    filename : str, optional
+        Filename (without extension) for saved .gif. Default is 'animation'.
+    title : bool, optional
+        If True, displays the temperature in the title of each frame. Default is True.
+    title_fmt : str, optional
+        Format string for temperature values (e.g., '.2f' for 2 decimals). Default is 'd' (integer).
+    plot_slice_kwargs : dict, optional
+        Additional keyword arguments passed to `plot_slice`.
+    ax_kwargs : dict, optional
+        Keyword arguments passed to `ax.set`.
+
+    Returns
+    -------
+    ani : matplotlib.animation.FuncAnimation
+        The resulting animation object.
+    """
+    if ax is None:
+        fig,ax = plt.subplots() # Generate a new figure and axis
+    else:
+        fig = ax.figure  # Get the figure from the provided axis
+
+
+    if plot_slice_kwargs is None:
+        plot_slice_kwargs = {}
+    if ax_kwargs is None:
+        ax_kwargs = {}
+
+    # Normalize the slice object
+    normalized_slice = [slice(None) if s is None else s for s in slice_obj]
+
+    # Warn if colorbar is requested
+    if plot_slice_kwargs.get('cbar', False):
+        warnings.warn("Colorbar is not supported in animation and will be ignored.", UserWarning)
+        plot_slice_kwargs['cbar'] = False
+    elif 'cbar' not in plot_slice_kwargs.keys():
+        plot_slice_kwargs['cbar'] = False
+
+    def update(temp):
+        ax.clear()
+        dataset = temp_dependence.datasets[temp]
+        plot_slice(dataset[tuple(normalized_slice)], ax=ax, **plot_slice_kwargs)
+        ax.set(**ax_kwargs)
+
+        if title:
+            try:
+                formatted_temp = f"{int(temp):{title_fmt}}"
+            except ValueError:
+                raise ValueError(f"Invalid title_fmt '{title_fmt}' for temperature value '{temp}'")
+            ax.set(title=f'$T$={formatted_temp}')
+
+    ani = animation.FuncAnimation(fig, update,
+                                  frames=temp_dependence.temperatures,
+                                  interval=interval, repeat=False)
+
+    display(HTML(ani.to_jshtml()))
+
+    if save_gif:
+        gif_file = f'{filename}.gif'
+        writer = animation.PillowWriter(fps=1000 / interval)
+        ani.save(gif_file, writer=writer)
+        with open(gif_file, 'rb') as f:
+            display(Image(f.read(), format='gif'))
+
+    return ani
+
+def animate_slice_axis(data, axis, axis_values, ax=None, interval=500, save_gif=False, filename='animation', title=True, title_fmt='.2f', plot_slice_kwargs={}, ax_kwargs={}):
+    """
+    Animate 2D slices of a 3D dataset along a given axis.
+
+    Creates a matplotlib animation by sweeping through 2D slices of a 3D 
+    dataset along the specified axis. Optionally displays the animation 
+    inline (e.g., in Jupyter) and/or saves it as a GIF.
+
+    Parameters
+    ----------
+    data : nexusformat.nexus.NXdata
+        The 3D dataset to visualize.
+    axis : int
+        The axis along which to animate (must be 0, 1, or 2).
+    axis_values : iterable
+        The values along the animation axis to use as animation frames.
+    ax : matplotlib.axes.Axes, optional
+        The axes object to plot on. If None, a new figure and axes will be created.
+    interval : int, optional
+        Delay between frames in milliseconds. Default is 500.
+    save_gif : bool, optional
+        If True, saves the animation as a .gif file. Default is False.
+    filename : str, optional
+        Filename (without extension) to use for the saved .gif. Default is 'animation'.
+    title : bool, optional
+        If True, displays the axis value as a title for each frame. Default is True.
+    title_fmt : str, optional
+        Format string for axis value in the title (e.g., '.2f' for 2 decimals). Default is '.2f'.
+    plot_slice_kwargs : dict, optional
+        Additional keyword arguments passed to `plot_slice`.
+    ax_kwargs : dict, optional
+        Keyword arguments passed to `ax.set` to update axis settings.
+
+    Returns
+    -------
+    ani : matplotlib.animation.FuncAnimation
+        The animation object.
+    """
+    if ax is None:
+        fig,ax = plt.subplots() # Generate a new figure and axis
+    else:
+        fig = ax.figure  # Get the figure from the provided axis
+
+    if axis not in [0, 1, 2]:
+        raise ValueError("axis must be either 0, 1, or 2.")
+
+    if plot_slice_kwargs.get('cbar', False):
+        warnings.warn("Colorbar is not supported in animation and will be ignored.", UserWarning)
+        plot_slice_kwargs['cbar'] = False
+    elif 'cbar' not in plot_slice_kwargs.keys():
+        plot_slice_kwargs['cbar'] = False
+
+    
+
+    def update(parameter):
+        ax.clear()
+
+        # Construct slicing object for the selected axis
+        slice_obj = [slice(None)] * 3
+        slice_obj[axis] = parameter
+
+        # Plot the 2D slice
+        plot_slice(data[tuple(slice_obj)], ax=ax, **plot_slice_kwargs)
+        ax.set(**ax_kwargs)
+
+        if title:
+            axis_label = data.axes[axis]
+            ax.set(title=f'${axis_label}$={parameter:{title_fmt}}')
+
+    ani = animation.FuncAnimation(fig, update, frames=axis_values, interval=interval, repeat=False)
+
+    display(HTML(ani.to_jshtml()))
+
+    if save_gif:
+        gif_file = f'{filename}.gif'
+        writergif = animation.PillowWriter(fps=1000/interval)
+        ani.save(gif_file, writer=writergif)
+        display(HTML(ani.to_jshtml()))
+        with open(gif_file, 'rb') as file:
+            display(Image(file.read(), format='gif'))
+
+    return ani
+
 
 class Scissors:
     """