nxs-analysis-tools 0.0.46__py3-none-any.whl → 0.0.47__py3-none-any.whl

_meta/__init__.py

@@ -6,5 +6,5 @@ __author__ = 'Steven J. Gomez Alvarado'
 __email__ = 'stevenjgomez@ucsb.edu'
 __copyright__ = f"2023-2025, {__author__}"
 __license__ = 'MIT'
-__version__ = '0.0.46'
+__version__ = '0.0.47'
 __repo_url__ = 'https://github.com/stevenjgomez/nxs_analysis_tools'

nxs_analysis_tools/datareduction.py

@@ -16,7 +16,7 @@ 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', 'rotate_data_2D'
-           'array_to_nxdata', 'Padder']
+                                                       'array_to_nxdata', 'Padder']
 
 
 def load_data(path, print_tree=True):
@@ -107,7 +107,7 @@ def array_to_nxdata(array, data_template, signal_name=None):
                   tuple(d[d.axes[i]] for i in range(len(d.axes))))
 
 
-def plot_slice(data, X=None, Y=None, transpose=False, vmin=None, vmax=None,
+def plot_slice(data, X=None, Y=None, sum_axis=None, transpose=False, vmin=None, vmax=None,
                skew_angle=90, ax=None, xlim=None, ylim=None,
                xticks=None, yticks=None, cbar=True, logscale=False,
                symlogscale=False, cmap='viridis', linthresh=1,
@@ -130,6 +130,10 @@ def plot_slice(data, X=None, Y=None, transpose=False, vmin=None, vmax=None,
         The Y axis values. If None, a default range from 0 to the number of
          rows in `data` is used.
 
+    sum_axis : int, optional
+        If the input data is 3D, this specifies the axis to sum over in order
+        to reduce the data to 2D for plotting. Required if `data` has three dimensions.
+
     transpose : bool, optional
         If True, transpose the dataset and its axes before plotting.
         Default is False.
@@ -199,7 +203,37 @@ def plot_slice(data, X=None, Y=None, transpose=False, vmin=None, vmax=None,
     p : :class:`matplotlib.collections.QuadMesh`
         The `matplotlib` QuadMesh object representing the plotted data.
     """
+    is_array = False
+    is_nxdata = False
+
     if isinstance(data, np.ndarray):
+        is_array = True
+    elif isinstance(data, (NXdata, NXfield)):
+        is_nxdata = True
+    else:
+        raise TypeError(f"Unexpected data type: {type(data)}. "
+                        f"Supported types are np.ndarray and NXdata.")
+
+    # If three-dimensional, demand sum_axis to reduce to two dimensions.
+    if is_array and len(data.shape) == 3:
+        assert sum_axis is not None, "sum_axis must be specified when data is a 3D array"
+
+        data = data.sum(axis=sum_axis)
+
+    if is_nxdata and len(data.shape) == 3:
+        assert sum_axis is not None, "sum_axis must be specified when data is a 3D array"
+
+        arr = data.nxsignal.nxdata
+        arr = arr.sum(axis=sum_axis)
+
+        # Create a 2D template from the original nxdata
+        slice_obj = [slice(None)] * len(data.shape)
+        slice_obj[sum_axis] = 0
+
+        # Use the 2D template to create a new nxdata
+        data = array_to_nxdata(arr, data[slice_obj])
+
+    if is_array:
         if X is None:
             X = NXfield(np.linspace(0, data.shape[0], data.shape[0]), name='x')
         if Y is None:
@@ -209,7 +243,7 @@ def plot_slice(data, X=None, Y=None, transpose=False, vmin=None, vmax=None,
             data = data.transpose()
         data = NXdata(NXfield(data, name='value'), (X, Y))
         data_arr = data[data.signal].nxdata.transpose()
-    elif isinstance(data, (NXdata, NXfield)):
+    elif is_nxdata:
         if X is None:
             X = data[data.axes[0]]
         if Y is None:
@@ -218,9 +252,6 @@ def plot_slice(data, X=None, Y=None, transpose=False, vmin=None, vmax=None,
             X, Y = Y, X
             data = data.transpose()
         data_arr = data[data.signal].nxdata.transpose()
-    else:
-        raise TypeError(f"Unexpected data type: {type(data)}. "
-                        f"Supported types are np.ndarray and NXdata.")
 
     # Display Markdown heading
     if mdheading is None:
@@ -559,22 +590,31 @@ class Scissors:
 
         return self.linecut
 
-    def highlight_integration_window(self, data=None, label=None, highlight_color='red', **kwargs):
+    def highlight_integration_window(self, data=None, width=None, height=None, label=None, highlight_color='red',
+                                     **kwargs):
         """
-        Plots integration window highlighted on the three principal cross sections of the first
-        temperature dataset.
+        Plots the integration window highlighted on the three principal 2D cross-sections of a 3D dataset.
 
         Parameters
         ----------
         data : array-like, optional
-            The 2D heatmap dataset to plot. If not provided, the dataset stored in `self.data` will
-            be used.
+            The 3D dataset to visualize. If not provided, uses `self.data`.
+        width : float, optional
+            Width of the visible x-axis range in each subplot. Used to zoom in on the integration region.
+        height : float, optional
+            Height of the visible y-axis range in each subplot. Used to zoom in on the integration region.
         label : str, optional
-            The label for the integration window plot.
+            Label for the rectangle patch marking the integration window, used in the legend.
         highlight_color : str, optional
-            The edge color used to highlight the integration window. Default is 'red'.
-        **kwargs : keyword arguments, optional
-            Additional keyword arguments to customize the plot.
+            Color of the rectangle edges highlighting the integration window. Default is 'red'.
+        **kwargs : dict, optional
+            Additional keyword arguments passed to `plot_slice` for customizing the plot (e.g., colormap, vmin, vmax).
+
+        Returns
+        -------
+        p1, p2, p3 : matplotlib.collections.QuadMesh
+            The plotted QuadMesh objects for the three cross-sections:
+            XY at fixed Z, XZ at fixed Y, and YZ at fixed X.
 
         """
         data = self.data if data is None else data
@@ -584,7 +624,7 @@ class Scissors:
         # Create a figure and subplots
         fig, axes = plt.subplots(1, 3, figsize=(15, 4))
 
-        # Plot cross section 1
+        # Plot cross-section 1
         slice_obj = [slice(None)] * data.ndim
         slice_obj[2] = center[2]
 
@@ -603,7 +643,12 @@ class Scissors:
         )
         ax.add_patch(rect_diffuse)
 
-        # Plot cross section 2
+        if 'xlim' not in kwargs and width is not None:
+            ax.set(xlim=(center[0] - width / 2, center[0] + width / 2))
+        if 'ylim' not in kwargs and height is not None:
+            ax.set(ylim=(center[1] - height / 2, center[1] + height / 2))
+
+        # Plot cross-section 2
         slice_obj = [slice(None)] * data.ndim
         slice_obj[1] = center[1]
 
@@ -622,7 +667,12 @@ class Scissors:
         )
         ax.add_patch(rect_diffuse)
 
-        # Plot cross section 3
+        if 'xlim' not in kwargs and width is not None:
+            ax.set(xlim=(center[0] - width / 2, center[0] + width / 2))
+        if 'ylim' not in kwargs and height is not None:
+            ax.set(ylim=(center[2] - height / 2, center[2] + height / 2))
+
+        # Plot cross-section 3
         slice_obj = [slice(None)] * data.ndim
         slice_obj[0] = center[0]
 
@@ -641,6 +691,11 @@ class Scissors:
         )
         ax.add_patch(rect_diffuse)
 
+        if 'xlim' not in kwargs and width is not None:
+            ax.set(xlim=(center[1] - width / 2, center[1] + width / 2))
+        if 'ylim' not in kwargs and height is not None:
+            ax.set(ylim=(center[2] - height / 2, center[2] + height / 2))
+
         # Adjust subplot padding
         fig.subplots_adjust(wspace=0.5)
 
@@ -665,7 +720,7 @@ class Scissors:
 
         fig, axes = plt.subplots(1, 3, figsize=(15, 4))
 
-        # Plot cross section 1
+        # Plot cross-section 1
         slice_obj = [slice(None)] * data.ndim
         slice_obj[2] = center[2]
         p1 = plot_slice(data[slice_obj],
@@ -685,7 +740,7 @@ class Scissors:
                         **kwargs)
         axes[1].set_aspect(len(data[data.axes[0]].nxdata) / len(data[data.axes[2]].nxdata))
 
-        # Plot cross section 3
+        # Plot cross-section 3
         slice_obj = [slice(None)] * data.ndim
         slice_obj[0] = center[0]
         p2 = plot_slice(data[slice_obj],
@@ -1015,7 +1070,7 @@ class Padder:
         self.data = data
 
         self.steps = tuple((data[axis].nxdata[1] - data[axis].nxdata[0])
-                            for axis in data.axes)
+                           for axis in data.axes)
 
         # Absolute value of the maximum value; assumes the domain of the input
         # is symmetric (eg, -H_min = H_max)

{nxs_analysis_tools-0.0.46.dist-info → nxs_analysis_tools-0.0.47.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nxs-analysis-tools
-Version: 0.0.46
+Version: 0.0.47
 Summary: Reduce and transform nexus format (.nxs) scattering data.
 Author-email: "Steven J. Gomez Alvarado" <stevenjgomez@ucsb.edu>
 License: MIT License

nxs_analysis_tools-0.0.47.dist-info/RECORD

@@ -0,0 +1,11 @@
+_meta/__init__.py,sha256=MPxIjim0z8Ugh3YLct0a3ThFNGcKhqJCTs5T_tZYZt0,357
+nxs_analysis_tools/__init__.py,sha256=bxbTLpIcKasH3fuRZOvJ9zeu7IBBju82mOTgUV4ZqHE,530
+nxs_analysis_tools/chess.py,sha256=bSSDMAuZLS9se1EJjNa6uuuQFiJZJcWGrEJX0oAm5gc,27470
+nxs_analysis_tools/datareduction.py,sha256=YlfsjFpv9CJl7C8HPlX6AN4ZrWngvMFTBwvl_Axh6oM,44903
+nxs_analysis_tools/fitting.py,sha256=vPx75lKvm5pWOGBtRtff8k6J5dA6kRk3EJyzxCH5Tyk,8809
+nxs_analysis_tools/pairdistribution.py,sha256=CZvXCfCumZp84LQKsJShwgDx5wtDOGpOoOAxjI0jms0,62272
+nxs_analysis_tools-0.0.47.dist-info/licenses/LICENSE,sha256=tbfd7DgSzDiNJpXHXqK6e2usHdJQfLrQKHxti7eyH9k,1107
+nxs_analysis_tools-0.0.47.dist-info/METADATA,sha256=x4opbN0G8rIeAlJfJtFJlSNqJMmBWBALtNSbhCgAdBo,3923
+nxs_analysis_tools-0.0.47.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+nxs_analysis_tools-0.0.47.dist-info/top_level.txt,sha256=8U000GNPzo6T6pOMjRdgOSO5heMzLMGjkxa1CDtyMHM,25
+nxs_analysis_tools-0.0.47.dist-info/RECORD,,

nxs_analysis_tools-0.0.46.dist-info/RECORD

@@ -1,11 +0,0 @@
-_meta/__init__.py,sha256=9BhNnrOTX8WpPVjSzNRyYktMYI7OyHFZowP9aIUuksk,357
-nxs_analysis_tools/__init__.py,sha256=bxbTLpIcKasH3fuRZOvJ9zeu7IBBju82mOTgUV4ZqHE,530
-nxs_analysis_tools/chess.py,sha256=bSSDMAuZLS9se1EJjNa6uuuQFiJZJcWGrEJX0oAm5gc,27470
-nxs_analysis_tools/datareduction.py,sha256=d24_Vw3-0iOZHdd1JK36idjI5CJmqDEjhcZaaire2fU,42403
-nxs_analysis_tools/fitting.py,sha256=vPx75lKvm5pWOGBtRtff8k6J5dA6kRk3EJyzxCH5Tyk,8809
-nxs_analysis_tools/pairdistribution.py,sha256=CZvXCfCumZp84LQKsJShwgDx5wtDOGpOoOAxjI0jms0,62272
-nxs_analysis_tools-0.0.46.dist-info/licenses/LICENSE,sha256=tbfd7DgSzDiNJpXHXqK6e2usHdJQfLrQKHxti7eyH9k,1107
-nxs_analysis_tools-0.0.46.dist-info/METADATA,sha256=Scvtqz8Db5H0C0OC9AwqUj_c8kYmrYgNwWOV1Issod4,3923
-nxs_analysis_tools-0.0.46.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-nxs_analysis_tools-0.0.46.dist-info/top_level.txt,sha256=8U000GNPzo6T6pOMjRdgOSO5heMzLMGjkxa1CDtyMHM,25
-nxs_analysis_tools-0.0.46.dist-info/RECORD,,