nxs-analysis-tools 0.0.42__tar.gz → 0.0.44__tar.gz

{nxs_analysis_tools-0.0.42/src/nxs_analysis_tools.egg-info → nxs_analysis_tools-0.0.44}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: nxs-analysis-tools
-Version: 0.0.42
+Version: 0.0.44
 Summary: Reduce and transform nexus format (.nxs) scattering data.
 Author-email: "Steven J. Gomez Alvarado" <stevenjgomez@ucsb.edu>
 License: MIT License
@@ -66,6 +66,7 @@ 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"
+Dynamic: license-file
 
 # nxs-analysis-tools
 

{nxs_analysis_tools-0.0.42 → nxs_analysis_tools-0.0.44}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = 'nxs-analysis-tools'
-version = '0.0.42'
+version = '0.0.44'
 description = 'Reduce and transform nexus format (.nxs) scattering data.'
 readme = 'README.md'
 requires-python = '>=3.7'

{nxs_analysis_tools-0.0.42 → nxs_analysis_tools-0.0.44}/src/_meta/__init__.py

@@ -6,5 +6,5 @@ __author__ = 'Steven J. Gomez Alvarado'
 __email__ = 'stevenjgomez@ucsb.edu'
 __copyright__ = f"2023, {__author__}"
 __license__ = 'MIT'
-__version__ = '0.0.42'
+__version__ = '0.0.44'
 __repo_url__ = 'https://github.com/stevenjgomez/nxs_analysis_tools'

{nxs_analysis_tools-0.0.42 → nxs_analysis_tools-0.0.44}/src/nxs_analysis_tools/chess.py

@@ -50,6 +50,8 @@ class TempDependence:
     -------
     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():
@@ -105,7 +107,7 @@ class TempDependence:
         Initialize the TempDependence class with default values.
         """
 
-        self.sample_directory = ''
+        self.sample_directory = None
         self.xlabel = ''
         self.datasets = {}
         self.temperatures = []
@@ -127,6 +129,31 @@ class TempDependence:
         """
         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.
@@ -172,6 +199,9 @@ class TempDependence:
         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
@@ -179,7 +209,6 @@ class TempDependence:
             pattern = r'_(\d+)\.nxs'
             match = re.search(pattern, item)
             if match:
-                print(f'Found {item}')
                 # Identify temperature
                 temperature = match.group(1)
                 # print(f'Temperature = {temperature}')
@@ -188,7 +217,6 @@ class TempDependence:
                     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]
 
@@ -202,7 +230,13 @@ class TempDependence:
             path = os.path.join(self.sample_directory, item)
 
             # Save dataset
-            self.datasets[self.temperatures[i]] = load_transform(path)
+            try:
+                self.datasets[self.temperatures[i]] = load_transform(path)
+            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()
@@ -232,9 +266,6 @@ class TempDependence:
         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:
@@ -245,9 +276,6 @@ class TempDependence:
             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)
-                    print('-----------------------------------------------')
-                    print('Loading ' + T + ' K indexed .nxs files...')
-                    print('Found ' + filepath)
 
                     # Load dataset at each temperature
                     self.datasets[T] = load_data(filepath)

{nxs_analysis_tools-0.0.42 → nxs_analysis_tools-0.0.44}/src/nxs_analysis_tools/datareduction.py

@@ -15,7 +15,7 @@ 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',
+           'reciprocal_lattice_params', 'rotate_data', 'rotate_data_2D'
            'array_to_nxdata', 'Padder']
 
 
@@ -185,14 +185,14 @@ def plot_slice(data, X=None, Y=None, transpose=False, vmin=None, vmax=None,
     """
     if isinstance(data, np.ndarray):
         if X is None:
-            X = NXfield(np.linspace(0, data.shape[1], data.shape[1]), name='x')
+            X = NXfield(np.linspace(0, data.shape[0], data.shape[0]), name='x')
         if Y is None:
-            Y = NXfield(np.linspace(0, data.shape[0], data.shape[0]), name='y')
+            Y = NXfield(np.linspace(0, data.shape[1], data.shape[1]), name='y')
         if transpose:
             X, Y = Y, X
             data = data.transpose()
         data = NXdata(NXfield(data, name='value'), (X, Y))
-        data_arr = data
+        data_arr = data[data.signal].nxdata.transpose()
     elif isinstance(data, (NXdata, NXfield)):
         if X is None:
             X = data[data.axes[0]]
@@ -853,7 +853,7 @@ def rotate_data(data, lattice_angle, rotation_angle, rotation_axis, printout=Fal
                   (data[data.axes[0]], data[data.axes[1]], data[data.axes[2]]))
 
 
-def rotate_data2D(data, lattice_angle, rotation_angle):
+def rotate_data_2D(data, lattice_angle, rotation_angle):
     """
     Rotates 2D data.
 

{nxs_analysis_tools-0.0.42 → nxs_analysis_tools-0.0.44}/src/nxs_analysis_tools/pairdistribution.py

@@ -185,23 +185,58 @@ class Symmetrizer2D:
         q1 = data_padded[data.axes[0]]
         q2 = data_padded[data.axes[1]]
 
-        # Define signal to be symmetrized
-        counts = data_padded[data.signal].nxdata
-
         # Calculate the angle for each data point
         theta = np.arctan2(q1.reshape((-1, 1)), q2.reshape((1, -1)))
         # Create a boolean array for the range of angles
         symmetrization_mask = np.logical_and(theta >= theta_min * np.pi / 180,
                                              theta <= theta_max * np.pi / 180)
-        self.symmetrization_mask = NXdata(NXfield(p.unpad(symmetrization_mask),
-                                                  name='mask'),
-                                          (data[data.axes[0]], data[data.axes[1]])
-                                          )
 
-        self.wedge = NXdata(NXfield(p.unpad(counts * symmetrization_mask),
-                                    name=data.signal),
-                            (data[data.axes[0]], data[data.axes[1]])
-                            )
+        # Define signal to be transformed
+        counts = symmetrization_mask
+
+        # Scale and skew counts
+        skew_angle_adj = 90 - self.skew_angle
+
+        scale2 = q1.max()/q2.max()
+        counts_unscaled2 = ndimage.affine_transform(counts,
+                                                    Affine2D().scale(scale2, 1).inverted().get_matrix()[:2, :2],
+                                                    offset=[-(1 - scale2) * counts.shape[
+                                                        0] / 2 / scale2, 0],
+                                                    order=0,
+                                                    )
+
+        scale1 = np.cos(skew_angle_adj * np.pi / 180)
+        counts_unscaled1 = ndimage.affine_transform(counts_unscaled2,
+                                                    Affine2D().scale(scale1, 1).inverted().get_matrix()[:2, :2],
+                                                    offset=[-(1 - scale1) * counts.shape[
+                                                        0] / 2 / scale1, 0],
+                                                    order=0,
+                                                    )
+
+        mask = ndimage.affine_transform(counts_unscaled1,
+                                        t.get_matrix()[:2, :2],
+                                        offset=[-counts.shape[0] / 2
+                                                * np.sin(skew_angle_adj * np.pi / 180), 0],
+                                        order=0,
+                                        )
+
+        # Convert mask to nxdata
+        mask = array_to_nxdata(mask, data_padded)
+
+        # Save mask for user interaction
+        self.symmetrization_mask = p.unpad(mask)
+
+        # Perform masking
+        wedge = mask * data_padded
+
+        # Save wedge for user interaction
+        self.wedge = p.unpad(wedge)
+
+        # Convert wedge back to array for further transformations
+        wedge = wedge[data.signal].nxdata
+
+        # Define signal to be transformed
+        counts = wedge
 
         # Scale and skew counts
         skew_angle_adj = 90 - self.skew_angle
@@ -216,9 +251,9 @@ class Symmetrizer2D:
                                          Affine2D().scale(scale1, 1).get_matrix()[:2, :2],
                                          offset=[(1 - scale1) * counts.shape[0] / 2, 0],
                                          order=0,
-                                         ) * symmetrization_mask
+                                         )
 
-        scale2 = counts.shape[0] / counts.shape[1]
+        scale2 = q1.max()/q2.max()
         wedge = ndimage.affine_transform(wedge,
                                          Affine2D().scale(scale2, 1).get_matrix()[:2, :2],
                                          offset=[(1 - scale2) * counts.shape[0] / 2, 0],
@@ -325,15 +360,24 @@ class Symmetrizer2D:
         symm_test = s.symmetrize_2d(data)
         fig, axesarr = plt.subplots(2, 2, figsize=(10, 8))
         axes = axesarr.reshape(-1)
+
+        # Plot the data
         plot_slice(data, skew_angle=s.skew_angle, ax=axes[0], title='data', **kwargs)
-        plot_slice(s.symmetrization_mask, skew_angle=s.skew_angle, ax=axes[1], title='mask')
+
+        # Filter kwargs to exclude 'vmin' and 'vmax'
+        filtered_kwargs = {key: value for key, value in kwargs.items() if key not in ('vmin', 'vmax')}
+        # Plot the mask
+        plot_slice(s.symmetrization_mask, skew_angle=s.skew_angle, ax=axes[1], title='mask', **filtered_kwargs)
+
+        # Plot the wedge
         plot_slice(s.wedge, skew_angle=s.skew_angle, ax=axes[2], title='wedge', **kwargs)
+
+        # Plot the symmetrized data
         plot_slice(symm_test, skew_angle=s.skew_angle, ax=axes[3], title='symmetrized', **kwargs)
         plt.subplots_adjust(wspace=0.4)
         plt.show()
         return fig, axesarr
 
-
 class Symmetrizer3D:
     """
     A class to symmetrize 3D datasets by performing sequential 2D symmetrization on
@@ -433,7 +477,7 @@ class Symmetrizer3D:
         q1, q2, q3 = self.q1, self.q2, self.q3
         out_array = np.zeros(data[data.signal].shape)
 
-        if self.plane1symmetrizer.theta_max:
+        if self.plane1symmetrizer.theta_max is not None:
             print('Symmetrizing ' + self.plane1 + ' planes...')
             for k, value in enumerate(q3):
                 print(f'Symmetrizing {q3.nxname}={value:.02f}...', end='\r')
@@ -441,7 +485,7 @@ class Symmetrizer3D:
                 out_array[:, :, k] = data_symmetrized[data.signal].nxdata
             print('\nSymmetrized ' + self.plane1 + ' planes.')
 
-        if self.plane2symmetrizer.theta_max:
+        if self.plane2symmetrizer.theta_max is not None:
             print('Symmetrizing ' + self.plane2 + ' planes...')
             for j, value in enumerate(q2):
                 print(f'Symmetrizing {q2.nxname}={value:.02f}...', end='\r')
@@ -451,7 +495,7 @@ class Symmetrizer3D:
                 out_array[:, j, :] = data_symmetrized[data.signal].nxdata
             print('\nSymmetrized ' + self.plane2 + ' planes.')
 
-        if self.plane3symmetrizer.theta_max:
+        if self.plane3symmetrizer.theta_max is not None:
             print('Symmetrizing ' + self.plane3 + ' planes...')
             for i, value in enumerate(q1):
                 print(f'Symmetrizing {q1.nxname}={value:.02f}...', end='\r')
@@ -492,7 +536,7 @@ class Symmetrizer3D:
         print("Output file saved to: " + os.path.join(os.getcwd(), fout_name))
 
 
-def generate_gaussian(H, K, L, amp, stddev, lattice_params, coeffs=None):
+def generate_gaussian(H, K, L, amp, stddev, lattice_params, coeffs=None, center=None):
     """
     Generate a 3D Gaussian distribution.
 
@@ -514,16 +558,23 @@ def generate_gaussian(H, K, L, amp, stddev, lattice_params, coeffs=None):
         Coefficients for the Gaussian expression, including cross-terms between axes.
          Default is [1, 0, 1, 0, 1, 0],
          corresponding to (1*H**2 + 0*H*K + 1*K**2 + 0*K*L + 1*L**2 + 0*L*H).
+    center : tuple
+        Tuple of coordinates for the center of the Gaussian. Default is (0,0,0).
 
     Returns
     -------
     gaussian : ndarray
         3D Gaussian distribution array.
     """
+    if center is None:
+        center=(0,0,0)
     if coeffs is None:
         coeffs = [1, 0, 1, 0, 1, 0]
     a, b, c, al, be, ga = lattice_params
     a_, b_, c_, _, _, _ = reciprocal_lattice_params((a, b, c, al, be, ga))
+    H = H-center[0]
+    K = K-center[1]
+    L = L-center[2]
     H, K, L = np.meshgrid(H, K, L, indexing='ij')
     gaussian = amp * np.exp(-(coeffs[0] * H ** 2 +
                               coeffs[1] * (b_ * a_ / (a_ ** 2)) * H * K +
@@ -537,7 +588,6 @@ def generate_gaussian(H, K, L, amp, stddev, lattice_params, coeffs=None):
         gaussian = gaussian.transpose()
     return gaussian.transpose(1, 0, 2)
 
-
 class Puncher:
     """
     A class for applying masks to 3D datasets, typically for data processing in reciprocal space.

{nxs_analysis_tools-0.0.42 → nxs_analysis_tools-0.0.44/src/nxs_analysis_tools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: nxs-analysis-tools
-Version: 0.0.42
+Version: 0.0.44
 Summary: Reduce and transform nexus format (.nxs) scattering data.
 Author-email: "Steven J. Gomez Alvarado" <stevenjgomez@ucsb.edu>
 License: MIT License
@@ -66,6 +66,7 @@ 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"
+Dynamic: license-file
 
 # nxs-analysis-tools
 

{nxs_analysis_tools-0.0.42 → nxs_analysis_tools-0.0.44}/src/nxs_analysis_tools.egg-info/SOURCES.txt

@@ -19,4 +19,7 @@ tests/test_chess_fitting.py
 tests/test_datareduction.py
 tests/test_fitting.py
 tests/test_lmfit.py
-tests/test_pairdistribution.py
+tests/test_mask_plotting.py
+tests/test_pairdistribution.py
+tests/test_plot_slice_with_ndarray.py
+tests/test_symmetrizer_rectangular_plane.py