nxs-analysis-tools 0.1.9__tar.gz → 0.1.11__tar.gz

{nxs_analysis_tools-0.1.9 → nxs_analysis_tools-0.1.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nxs-analysis-tools
-Version: 0.1.9
+Version: 0.1.11
 Summary: Reduce and transform nexus format (.nxs) scattering data.
 Author-email: "Steven J. Gomez Alvarado" <stevenjgomez@ucsb.edu>
 License-Expression: MIT
@@ -14,11 +14,10 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering :: Image Processing
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.7
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: matplotlib>=3.10.0
@@ -46,6 +45,7 @@ Requires-Dist: sphinx-autobuild>=2021.3.14; extra == "dev"
 Requires-Dist: sphinx-copybutton>=0.5.0; extra == "dev"
 Requires-Dist: sphinxext-opengraph>=0.6.3; extra == "dev"
 Requires-Dist: twine>=4.0.1; extra == "dev"
+Requires-Dist: pooch>=1.8.2; extra == "dev"
 Dynamic: license-file
 
 # nxs-analysis-tools
@@ -56,7 +56,7 @@ Dynamic: license-file
 
 ## Overview
 
-nxs-analysis-tools provides a suite of tools for slicing (2D), cutting (1D), and transforming (_e.g._, symmetrization, interpolation, delta-PDF) nexus format (.nxs) scattering data.
+nxs-analysis-tools provides a suite of tools for performing slices (2D), cuts (1D), and transformations (_e.g._, symmetrization, interpolation, delta-PDF) on nexus format (.nxs) scattering data.
 
 View the documentation [here](https://nxs-analysis-tools.readthedocs.io/en/stable/).
 
@@ -76,4 +76,14 @@ git clone https://github.com/stevenjgomez/nxs-analysis-tools.git
 
 ## License
 
-This project is licensed under the MIT License.
+This project is licensed under the MIT License. If you find the nxs-analysis-tools package useful in your scientific publications, please cite the relevant DOI.
+
+To cite the most recent version, use:
+
+[![DOI](https://zenodo.org/badge/644189683.svg)](https://doi.org/10.5281/zenodo.15186359)
+
+To cite all versions, use:
+
+```
+10.5281/zenodo.15186359
+```

{nxs_analysis_tools-0.1.9 → nxs_analysis_tools-0.1.11}/README.md

@@ -6,7 +6,7 @@
 
 ## Overview
 
-nxs-analysis-tools provides a suite of tools for slicing (2D), cutting (1D), and transforming (_e.g._, symmetrization, interpolation, delta-PDF) nexus format (.nxs) scattering data.
+nxs-analysis-tools provides a suite of tools for performing slices (2D), cuts (1D), and transformations (_e.g._, symmetrization, interpolation, delta-PDF) on nexus format (.nxs) scattering data.
 
 View the documentation [here](https://nxs-analysis-tools.readthedocs.io/en/stable/).
 
@@ -26,4 +26,14 @@ git clone https://github.com/stevenjgomez/nxs-analysis-tools.git
 
 ## License
 
-This project is licensed under the MIT License.
+This project is licensed under the MIT License. If you find the nxs-analysis-tools package useful in your scientific publications, please cite the relevant DOI.
+
+To cite the most recent version, use:
+
+[![DOI](https://zenodo.org/badge/644189683.svg)](https://doi.org/10.5281/zenodo.15186359)
+
+To cite all versions, use:
+
+```
+10.5281/zenodo.15186359
+```

{nxs_analysis_tools-0.1.9 → nxs_analysis_tools-0.1.11}/pyproject.toml

@@ -6,10 +6,10 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = 'nxs-analysis-tools'
-version = '0.1.9'
+version = '0.1.11'
 description = 'Reduce and transform nexus format (.nxs) scattering data.'
 readme = 'README.md'
-requires-python = '>=3.7'
+requires-python = '>=3.10'
 license = "MIT"
 license-files = ['LICENSE']
 authors = [{ name = 'Steven J. Gomez Alvarado', email = 'stevenjgomez@ucsb.edu' }]
@@ -27,7 +27,6 @@ classifiers = [
     'Intended Audience :: Science/Research',
     'Programming Language :: Python',
     'Programming Language :: Python :: 3',
-    'Programming Language :: Python :: 3.9',
     'Programming Language :: Python :: 3.10',
     'Topic :: Scientific/Engineering :: Image Processing',
     'Topic :: Scientific/Engineering',
@@ -61,6 +60,7 @@ dev = [
     'sphinx-copybutton >= 0.5.0',
     'sphinxext-opengraph >= 0.6.3',
     'twine >= 4.0.1',
+    'pooch >= 1.8.2',
 ]
 
 [project.urls]
@@ -71,7 +71,7 @@ dev = [
 'DOI' = 'https://doi.org/10.5281/zenodo.15186359'
 
 [tool.bumpver]
-current_version = "0.1.9"
+current_version = "0.1.11"
 version_pattern = "MAJOR.MINOR.PATCH[-TAG]"
 tag_pattern = "vMAJOR.MINOR.PATCH[-TAG]"
 commit_message = "Bump version {old_version} -> {new_version}"

{nxs_analysis_tools-0.1.9 → nxs_analysis_tools-0.1.11}/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__ = '0.1.9'
+__version__ = '0.1.11'
 __repo_url__ = 'https://github.com/stevenjgomez/nxs_analysis_tools'

{nxs_analysis_tools-0.1.9 → nxs_analysis_tools-0.1.11}/src/nxs_analysis_tools/__init__.py

@@ -9,7 +9,7 @@ from .chess import TempDependence
 
 # What to import when running "from nxs_analysis_tools import *"
 __all__ = ['load_data', 'load_transform', 'plot_slice', 'Scissors',
-           'reciprocal_lattice_params', 'rotate_data', 'rotate_data_2D',
+           'reciprocal_lattice_params', 'rotate_data',
            'convert_to_inverse_angstroms', 'array_to_nxdata', 'Padder',
            'rebin_nxdata', 'rebin_3d', 'rebin_1d', 'TempDependence',
            'animate_slice_temp', 'animate_slice_axis']

{nxs_analysis_tools-0.1.9 → nxs_analysis_tools-0.1.11}/src/nxs_analysis_tools/chess.py

@@ -1,7 +1,7 @@
 """
 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.
+(ID4B) with temperature dependence. It includes functions for loading temperature series and 
+performing operations on all datasets in the series at once (e.g., cutting, fitting). 
 """
 import os
 import re
@@ -59,10 +59,11 @@ class TempDependence:
         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_transforms(temperatures_list=None, exclude_temperatures=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.
+    load_datasets(file_ending='hkli.nxs', temperatures_list=None, exclude_temperatures=None, 
+                  print_tree=True):
+        Load datasets (legacy CHESS format) from the specified folder.
     get_sample_directory():
         Get the folder path where the datasets are located.
     clear_datasets():
@@ -99,11 +100,12 @@ class TempDependence:
         Fit the line cut models for each temperature.
     plot_fit(mdheadings=False, **kwargs):
         Plot the fit results for each temperature.
-    overlay_fits(numpoints=None, vertical_offset=0, cmap='viridis', ax=ax):
+    overlay_fits(numpoints=None, vertical_offset=0, cmap='viridis', ax=ax, 
+                 data_kwargs=None, fit_kwargs=None):
         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(ax, **kwargs):
+    plot_order_parameter(ax, param_name='peakheight', **kwargs):
         Plot the temperature dependence of the peakheight parameter.
     print_fit_report():
         Print the fit report for each temperature.
@@ -188,6 +190,8 @@ class TempDependence:
         """
         for temperature in self.temperatures:
             self.scissors[temperature] = Scissors()
+            if temperature in self.datasets.keys():
+                self.scissors[temperature].set_data(self.datasets[temperature])
             self.linecutmodels[temperature] = LinecutModel()
 
     def set_data(self, temperature, data):
@@ -203,7 +207,7 @@ class TempDependence:
         """
         self.datasets[temperature] = data
 
-    def load_transforms(self, temperatures_list=None, print_tree=True, use_nxlink=False):
+    def load_transforms(self, temperatures_list=None, exclude_temperatures=None, print_tree=True, use_nxlink=False):
         """
         Load transform datasets (from nxrefine) based on temperature.
 
@@ -211,6 +215,9 @@ class TempDependence:
         ----------
         temperatures_list : list of int or None, optional
             List of temperatures to load. If None, all available temperatures are loaded.
+
+        exclude_temperatures : int, str, optional
+            Temperatures to skip. Applied after filtering with `temperatures_list`, if provided.
         
         print_tree : bool, optional
             Whether to print the data tree upon loading. Default True.
@@ -223,6 +230,10 @@ class TempDependence:
         # Convert all temperatures to strings
         if temperatures_list:
             temperatures_list = [str(t) for t in temperatures_list]
+        if exclude_temperatures:
+            if isinstance(exclude_temperatures, str):
+                exclude_temperatures = [exclude_temperatures]
+            exclude_temperatures = [str(t) for t in list(exclude_temperatures)]
 
         # Clear existing temperatures before loading files
         self.temperatures = []
@@ -237,7 +248,15 @@ class TempDependence:
                 # Identify temperature
                 temperature = match.group(1)
                 # print(f'Temperature = {temperature}')
-                if (temperatures_list is None) or (temperature in temperatures_list):
+                if temperatures_list is not None:
+                    incl_temp = temperature in temperatures_list
+                else:
+                    incl_temp = True
+                if exclude_temperatures is not None:
+                    not_excl_temp = temperature not in exclude_temperatures
+                else:
+                    not_excl_temp = True
+                if incl_temp and not_excl_temp:
                     # Prepare file to be loaded
                     self.temperatures.append(temperature)
                     items_to_load.append(item)
@@ -269,40 +288,38 @@ class TempDependence:
                       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]])
+        self.initialize()
 
-            # Initialize linecutmodel object
-            self.linecutmodels[self.temperatures[i]] = LinecutModel()
-
-    def load_datasets(self, file_ending='hkli.nxs', temperatures_list=None, print_tree=True):
+    def load_datasets(self, file_ending='hkli.nxs', temperatures_list=None, exclude_temperatures=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.
+            File extension of datasets to load. Default is 'hkli.nxs'.
+        temperatures_list : list of int or str, optional
+            Specific temperatures to load. If None, all temperatures are loaded.
+        exclude_temperatures : list of int or str, optional
+            Temperatures to skip. Applied after filtering with `temperatures_list`, if provided.
         print_tree : bool, optional
-            Whether to print the data tree upon loading. Default True.
+            If True, prints the NeXus tree structure for each file. Default is 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]
+        else:
+            self.temperatures = []  # Empty list to store temperature folder names
+            for item in os.listdir(self.sample_directory):
+                try:
+                    self.temperatures.append(int(item))  # If folder name can be int, add it
+                except ValueError:
+                    pass  # Otherwise don't add it
+            self.temperatures.sort()  # Sort from low to high T
+            self.temperatures = [str(i) for i in self.temperatures]  # Convert to strings
+            
+        if exclude_temperatures is not None:
+            [self.temperatures.remove(str(t)) for t in exclude_temperatures]
 
         # Load .nxs files
         for T in self.temperatures:
@@ -313,12 +330,7 @@ class TempDependence:
                     # 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()
+        self.initialize()
 
     def get_sample_directory(self):
         """
@@ -437,11 +449,16 @@ class TempDependence:
         # Get the Viridis colormap
         cmap = mpl.colormaps.get_cmap('viridis')
 
+        # Reverse zorder
+        zorder = 0
+
         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.plot(x_data, y_data, color=cmap(i / len(self.linecuts)), label=self.temperatures[i], 
+                    zorder=zorder, **kwargs)
+            zorder -= 1
 
         ax.set(xlabel=self.xlabel,
                ylabel=self.linecuts[self.temperatures[0]].signal)
@@ -704,7 +721,8 @@ class TempDependence:
                                   title=f"{T} K",
                                   **kwargs)
 
-    def overlay_fits(self, numpoints=None, vertical_offset=0, cmap='viridis', ax=None):
+    def overlay_fits(self, numpoints=None, vertical_offset=0, cmap='viridis', ax=None,
+                     data_kwargs=None, fit_kwargs=None):
         """
         Plot raw data and fitted models for each temperature with optional vertical offsets.
 
@@ -719,6 +737,11 @@ class TempDependence:
             Name of the matplotlib colormap used to distinguish different temperatures.
         ax : :class:`matplotlib.axes.Axes` or None, default=None
             Axis object to plot on. If None, a new figure and axis are created.
+        data_kwargs : dict
+            Keyword arguments to be passed to the data plot function.
+        fit_kwargs : dict
+            Keyword arguments to be passed to the fit plot function.
+
 
         The function:
         - Uses a colormap to assign unique colors to each temperature.
@@ -731,19 +754,24 @@ class TempDependence:
         # Create a figure and axes if an axis is not already provided
         _, ax = plt.subplots() if ax is None else (None, ax)
 
+        if data_kwargs is None:
+            data_kwargs = {}
+        if fit_kwargs is None:
+            fit_kwargs = {}
+
         # Generate a color palette for the various temperatures
         cmap = plt.get_cmap(cmap)
         colors = [cmap(i / len(self.temperatures)) for i, _ in enumerate(self.temperatures)]
 
         for i, lm in enumerate(self.linecutmodels.values()):
             # Plot the raw data
-            ax.plot(lm.x, lm.y + vertical_offset * i, '.', c=colors[i])
+            ax.plot(lm.x, lm.y + vertical_offset * i, '.', c=colors[i], **data_kwargs)
 
             # Evaluate the fit
             numpoints = len(lm.x) if numpoints is None else numpoints
             x_eval = np.linspace(lm.x.min(), lm.x.max(), numpoints)
             y_eval = lm.modelresult.eval(x=x_eval)
-            ax.plot(x_eval, y_eval + vertical_offset * i, '-', c=colors[i], label=self.temperatures[i])
+            ax.plot(x_eval, y_eval + vertical_offset * i, '-', c=colors[i], label=self.temperatures[i], **fit_kwargs)
 
         # Reverse legend entries to match top-to-bottom stacking
         handles, labels = ax.get_legend_handles_labels()
@@ -767,18 +795,19 @@ class TempDependence:
             linecutmodel.params['peakamplitude'].set(min=0)
             linecutmodel.fit()
 
-    def plot_order_parameter(self, ax=None, **kwargs):
+    def plot_order_parameter(self, param_name='peakheight', ax=None, **kwargs):
         """
         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.
+        This method extracts the values of a chosen parameter from each temperature-dependent
+        line cut fit stored in `linecutmodels` and plots it as a function of temperature.
 
         Parameters
         ----------
         ax : :class:`matplotlib.axes.Axes`, optional
             Axis object to plot on. If None, a new figure and axis are created.
+        param_name : str, optional
+            The name of the lmfit parameter to extract. Default is 'peakheight'.
         **kwargs
             Keyword arguments to be passed to the plot function.
 
@@ -810,7 +839,7 @@ class TempDependence:
             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)
+            peakheights.append(self.linecutmodels[T].modelresult.params[param_name].value)
 
         # Plot the peakheights vs. temperature
         if ax is None:
@@ -818,7 +847,7 @@ class TempDependence:
         else:
             fig = ax.figure
         ax.plot(temperatures, peakheights, **kwargs)
-        ax.set(xlabel='$T$ (K)', ylabel='peakheight')
+        ax.set(xlabel='$T$ (K)', ylabel=param_name)
         return fig, ax
 
     def print_fit_report(self):