nxs-analysis-tools 0.0.43__py3-none-any.whl → 0.0.45__py3-none-any.whl

_meta/__init__.py

@@ -6,5 +6,5 @@ __author__ = 'Steven J. Gomez Alvarado'
 __email__ = 'stevenjgomez@ucsb.edu'
 __copyright__ = f"2023, {__author__}"
 __license__ = 'MIT'
-__version__ = '0.0.43'
+__version__ = '0.0.45'
 __repo_url__ = 'https://github.com/stevenjgomez/nxs_analysis_tools'

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]
 
@@ -238,9 +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:
@@ -251,9 +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/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']
 
 
@@ -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/pairdistribution.py

@@ -197,7 +197,7 @@ class Symmetrizer2D:
         # Scale and skew counts
         skew_angle_adj = 90 - self.skew_angle
 
-        scale2 = counts.shape[0] / counts.shape[1]
+        scale2 = 1 # q1.max()/q2.max() # TODO: Need to double check this
         counts_unscaled2 = ndimage.affine_transform(counts,
                                                     Affine2D().scale(scale2, 1).inverted().get_matrix()[:2, :2],
                                                     offset=[-(1 - scale2) * counts.shape[
@@ -253,7 +253,7 @@ class Symmetrizer2D:
                                          order=0,
                                          )
 
-        scale2 = counts.shape[0] / counts.shape[1]
+        scale2 = counts.shape[0]/counts.shape[1]
         wedge = ndimage.affine_transform(wedge,
                                          Affine2D().scale(scale2, 1).get_matrix()[:2, :2],
                                          offset=[(1 - scale2) * counts.shape[0] / 2, 0],
@@ -477,7 +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')
@@ -485,7 +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')
@@ -495,7 +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')
@@ -536,7 +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.
 
@@ -558,16 +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 +
@@ -581,7 +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-0.0.43.dist-info → nxs_analysis_tools-0.0.45.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: nxs-analysis-tools
-Version: 0.0.43
+Version: 0.0.45
 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-0.0.45.dist-info/RECORD

@@ -0,0 +1,11 @@
+_meta/__init__.py,sha256=_FU9nkOG1MKsIB1CYm_1yIt6hHVXjoLMxh9CqkZr_sQ,352
+nxs_analysis_tools/__init__.py,sha256=bxbTLpIcKasH3fuRZOvJ9zeu7IBBju82mOTgUV4ZqHE,530
+nxs_analysis_tools/chess.py,sha256=Jtycq4b897bKQSwvf2zig2dA2ToPgQnsKEjHNCqK7wY,25825
+nxs_analysis_tools/datareduction.py,sha256=4yk-UZIdEwlEHj9iEEyeJHM820MHdGyVf4VlKSx3YUI,41982
+nxs_analysis_tools/fitting.py,sha256=vPx75lKvm5pWOGBtRtff8k6J5dA6kRk3EJyzxCH5Tyk,8809
+nxs_analysis_tools/pairdistribution.py,sha256=SDkxAWschiIBZX1Kvzex77LEgX4YlgnB-8DB_7Yo9mU,60293
+nxs_analysis_tools-0.0.45.dist-info/licenses/LICENSE,sha256=tdnoYVH1-ogW_5-gGs9bK-IkCamH1ATJqrdL37kWTHk,1102
+nxs_analysis_tools-0.0.45.dist-info/METADATA,sha256=AKCAQZFj7ErkOPLy1_eOr_TGMxzJGq2o3Nz8uLiiM3Y,3918
+nxs_analysis_tools-0.0.45.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+nxs_analysis_tools-0.0.45.dist-info/top_level.txt,sha256=8U000GNPzo6T6pOMjRdgOSO5heMzLMGjkxa1CDtyMHM,25
+nxs_analysis_tools-0.0.45.dist-info/RECORD,,

{nxs_analysis_tools-0.0.43.dist-info → nxs_analysis_tools-0.0.45.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

nxs_analysis_tools-0.0.43.dist-info/RECORD

@@ -1,11 +0,0 @@
-_meta/__init__.py,sha256=kxRgW9usOeluI-Bk-1GiZ0pt5jesv-HKRThTZKAvTtI,352
-nxs_analysis_tools/__init__.py,sha256=bxbTLpIcKasH3fuRZOvJ9zeu7IBBju82mOTgUV4ZqHE,530
-nxs_analysis_tools/chess.py,sha256=e3ZnyepnLATXZRk2cgh6iCZ7Pk3NKJ4IvRf4xNLuu94,24984
-nxs_analysis_tools/datareduction.py,sha256=arEWF8VI8qJfT--G77OJL37C_3usjfd3-wT2gTCtwZM,41964
-nxs_analysis_tools/fitting.py,sha256=vPx75lKvm5pWOGBtRtff8k6J5dA6kRk3EJyzxCH5Tyk,8809
-nxs_analysis_tools/pairdistribution.py,sha256=8E1grptUMb4UXVT9mBSk45xk2JwjCvTG0Rl6BlbJAdo,60013
-nxs_analysis_tools-0.0.43.dist-info/LICENSE,sha256=tdnoYVH1-ogW_5-gGs9bK-IkCamH1ATJqrdL37kWTHk,1102
-nxs_analysis_tools-0.0.43.dist-info/METADATA,sha256=aBNS2AJAECd6RLqqQCFBjJgrW0piIhFaDxQCekvMqFc,3895
-nxs_analysis_tools-0.0.43.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nxs_analysis_tools-0.0.43.dist-info/top_level.txt,sha256=8U000GNPzo6T6pOMjRdgOSO5heMzLMGjkxa1CDtyMHM,25
-nxs_analysis_tools-0.0.43.dist-info/RECORD,,