nxs-analysis-tools 0.0.40__py3-none-any.whl → 0.0.42__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__ = '0.0.40'
+__version__ = '0.0.42'
 __repo_url__ = 'https://github.com/stevenjgomez/nxs_analysis_tools'

nxs_analysis_tools/chess.py

@@ -8,6 +8,7 @@ import re
 
 import matplotlib.pyplot as plt
 import matplotlib as mpl
+import pandas as pd
 import numpy as np
 from IPython.display import display, Markdown
 from nxs_analysis_tools import load_data, Scissors
@@ -190,8 +191,12 @@ class TempDependence:
 
         # Convert all temperatures to int temporarily to sort temperatures list before loading
         self.temperatures = [int(t) for t in self.temperatures]
-        self.temperatures.sort()
+
+        loading_template = pd.DataFrame({'temperature': self.temperatures, 'filename': items_to_load})
+        loading_template = loading_template.sort_values(by='temperature')
+        self.temperatures = loading_template['temperature']
         self.temperatures = [str(t) for t in self.temperatures]
+        items_to_load = loading_template['filename'].to_list()
 
         for i, item in enumerate(items_to_load):
             path = os.path.join(self.sample_directory, item)

nxs_analysis_tools/datareduction.py

@@ -787,7 +787,8 @@ def rotate_data(data, lattice_angle, rotation_angle, rotation_axis, printout=Fal
 
         p = Padder(sliced_data)
         padding = tuple(len(sliced_data[axis]) for axis in sliced_data.axes)
-        counts = p.pad(padding).counts
+        counts = p.pad(padding)
+        counts = p.padded[p.padded.signal]
 
         counts_skewed = ndimage.affine_transform(counts,
                                                  t.inverted().get_matrix()[:2, :2],
@@ -848,7 +849,7 @@ def rotate_data(data, lattice_angle, rotation_angle, rotation_axis, printout=Fal
         elif rotation_axis == 2:
             output_array[:, :, i] = counts_unpadded
     print('\nDone.')
-    return NXdata(NXfield(output_array, name='counts'),
+    return NXdata(NXfield(output_array, name=p.padded.signal),
                   (data[data.axes[0]], data[data.axes[1]], data[data.axes[2]]))
 
 
@@ -884,7 +885,8 @@ def rotate_data2D(data, lattice_angle, rotation_angle):
 
     p = Padder(data)
     padding = tuple(len(data[axis]) for axis in data.axes)
-    counts = p.pad(padding).counts
+    counts = p.pad(padding)
+    counts = p.padded[p.padded.signal]
 
     counts_skewed = ndimage.affine_transform(counts,
                                              t.inverted().get_matrix()[:2, :2],
@@ -937,7 +939,7 @@ def rotate_data2D(data, lattice_angle, rotation_angle):
     counts_unpadded = p.unpad(counts_unskewed)
 
     print('\nDone.')
-    return NXdata(NXfield(counts_unpadded, name='counts'),
+    return NXdata(NXfield(counts_unpadded, name=p.padded.signal),
                   (data[data.axes[0]], data[data.axes[1]]))
 
 

nxs_analysis_tools/pairdistribution.py

@@ -1140,7 +1140,7 @@ class Interpolator:
         self.tapered = self.interpolated * self.window
 
 
-def fourier_transform_nxdata(data):
+def fourier_transform_nxdata(data, is_2d=False):
     """
     Perform a 3D Fourier Transform on the given NXdata object.
 
@@ -1156,6 +1156,10 @@ def fourier_transform_nxdata(data):
         include the `signal` field for the data and `axes` fields
         specifying the coordinate axes.
 
+    is_2d : bool
+        If true, skip FFT on out-of-plane direction and only do FFT
+        on axes 0 and 1. Default False.
+
     Returns
     -------
     NXdata
@@ -1163,16 +1167,13 @@ def fourier_transform_nxdata(data):
         result includes:
 
         - `dPDF`: The transformed data array.
-        - `x`, `y`, `z`: Arrays representing the frequency components along each axis.
+        - `x`, `y`, `z`: Arrays representing the real-space components along each axis.
 
     Notes
     -----
-    - The FFT is performed in two stages: first along the last dimension of
-    the input array and then along the first two dimensions.
-    - The function uses `pyfftw` for efficient computation of the Fourier
-    Transform.
-    - The output frequency components are computed based on the step sizes
-    of the original data axes.
+    - The FFT is performed in two stages: first along the last dimension of the input array and then along the first two dimensions.
+    - The function uses `pyfftw` for efficient computation of the Fourier Transform.
+    - The output frequency components are computed based on the step sizes of the original data axes.
 
     """
     start = time.time()
@@ -1181,7 +1182,9 @@ def fourier_transform_nxdata(data):
     padded = data[data.signal].nxdata
 
     fft_array = np.zeros(padded.shape)
+
     print("FFT on axes 1,2")
+
     for k in range(0, padded.shape[2]):
         fft_array[:, :, k] = np.real(
             np.fft.fftshift(
@@ -1190,17 +1193,18 @@ def fourier_transform_nxdata(data):
         )
         print(f'k={k}                  ', end='\r')
 
-    print("FFT on axis 3")
-    for i in range(0, padded.shape[0]):
-        for j in range(0, padded.shape[1]):
-            f_slice = fft_array[i, j, :]
-            print(f'i={i}                  ', end='\r')
-            fft_array[i, j, :] = np.real(
-                np.fft.fftshift(
-                    pyfftw.interfaces.numpy_fft.ifftn(np.fft.fftshift(f_slice),
-                                                      planner_effort='FFTW_MEASURE')
+    if not is_2d:
+        print("FFT on axis 3")
+        for i in range(0, padded.shape[0]):
+            for j in range(0, padded.shape[1]):
+                f_slice = fft_array[i, j, :]
+                print(f'i={i}                  ', end='\r')
+                fft_array[i, j, :] = np.real(
+                    np.fft.fftshift(
+                        pyfftw.interfaces.numpy_fft.ifftn(np.fft.fftshift(f_slice),
+                                                          planner_effort='FFTW_MEASURE')
+                    )
                 )
-            )
 
     end = time.time()
     print("FFT complete.")
@@ -1520,7 +1524,7 @@ class DeltaPDF:
         """
         self.padded = self.padder.pad(padding)
 
-    def perform_fft(self):
+    def perform_fft(self, is_2d=False):
         """
         Perform a 3D Fourier Transform on the padded data.
 
@@ -1548,4 +1552,4 @@ class DeltaPDF:
 
 
         """
-        self.fft = fourier_transform_nxdata(self.padded)
+        self.fft = fourier_transform_nxdata(self.padded, is_2d=is_2d)

{nxs_analysis_tools-0.0.40.dist-info → nxs_analysis_tools-0.0.42.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nxs-analysis-tools
-Version: 0.0.40
+Version: 0.0.42
 Summary: Reduce and transform nexus format (.nxs) scattering data.
 Author-email: "Steven J. Gomez Alvarado" <stevenjgomez@ucsb.edu>
 License: MIT License

nxs_analysis_tools-0.0.42.dist-info/RECORD

@@ -0,0 +1,11 @@
+_meta/__init__.py,sha256=RgVI9i9hMP8JG47ZopZMSrPEHTeCD680Z5-BWeTUZzY,352
+nxs_analysis_tools/__init__.py,sha256=bxbTLpIcKasH3fuRZOvJ9zeu7IBBju82mOTgUV4ZqHE,530
+nxs_analysis_tools/chess.py,sha256=LA2z-qk7IgNGPm8ov7JLgIupv__vmHfAc9NFCblI5fQ,24632
+nxs_analysis_tools/datareduction.py,sha256=RcfAqokK04CKuj867MdiF5EhzhhodJx99G40v8wh8W8,41932
+nxs_analysis_tools/fitting.py,sha256=vPx75lKvm5pWOGBtRtff8k6J5dA6kRk3EJyzxCH5Tyk,8809
+nxs_analysis_tools/pairdistribution.py,sha256=bO-Ljst8eD5wmeq6oH8ylhHqaUyu2CvARznDupCygWQ,58245
+nxs_analysis_tools-0.0.42.dist-info/LICENSE,sha256=tdnoYVH1-ogW_5-gGs9bK-IkCamH1ATJqrdL37kWTHk,1102
+nxs_analysis_tools-0.0.42.dist-info/METADATA,sha256=8lqJPJaka29fMmA2GTTtUzCnJnkhjVjKYcLv_gLqmu4,3895
+nxs_analysis_tools-0.0.42.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nxs_analysis_tools-0.0.42.dist-info/top_level.txt,sha256=8U000GNPzo6T6pOMjRdgOSO5heMzLMGjkxa1CDtyMHM,25
+nxs_analysis_tools-0.0.42.dist-info/RECORD,,

{nxs_analysis_tools-0.0.40.dist-info → nxs_analysis_tools-0.0.42.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

nxs_analysis_tools-0.0.40.dist-info/RECORD

@@ -1,11 +0,0 @@
-_meta/__init__.py,sha256=cgRdSYbkbQq7Gw011aNLk8NLfCZBtPjp2VfhtL5KeeE,352
-nxs_analysis_tools/__init__.py,sha256=bxbTLpIcKasH3fuRZOvJ9zeu7IBBju82mOTgUV4ZqHE,530
-nxs_analysis_tools/chess.py,sha256=GUW08BcDUGD88MPZCl4yJTQp4hwd9tVNTJN_afNSUUo,24339
-nxs_analysis_tools/datareduction.py,sha256=e__mBGZIpJ-_-Dr6-T9hJURJazFnBy3PoWfwRxOra4U,41848
-nxs_analysis_tools/fitting.py,sha256=vPx75lKvm5pWOGBtRtff8k6J5dA6kRk3EJyzxCH5Tyk,8809
-nxs_analysis_tools/pairdistribution.py,sha256=AtjllbbakFyo3MnGH18rvr6-h3ONopxXEmZK4F3VzMI,58023
-nxs_analysis_tools-0.0.40.dist-info/LICENSE,sha256=tdnoYVH1-ogW_5-gGs9bK-IkCamH1ATJqrdL37kWTHk,1102
-nxs_analysis_tools-0.0.40.dist-info/METADATA,sha256=H9FqaRexBO4zxSFcunsIieblI5jhUtosugg4sZVCMFU,3895
-nxs_analysis_tools-0.0.40.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-nxs_analysis_tools-0.0.40.dist-info/top_level.txt,sha256=8U000GNPzo6T6pOMjRdgOSO5heMzLMGjkxa1CDtyMHM,25
-nxs_analysis_tools-0.0.40.dist-info/RECORD,,