pyTEMlib 0.2024.2.0__py2.py3-none-any.whl → 0.2024.2.2__py2.py3-none-any.whl

pyTEMlib/file_tools.py

@@ -82,11 +82,12 @@ class FileWidget(ipywidgets.DOMWidget):
 
     """
 
-    def __init__(self, dir_name=None, extension=['*']):
+    def __init__(self, dir_name=None, extension=['*'], sum_frames=False):
         self.save_path = False
         self.dir_dictionary = {}
         self.dir_list = ['.', '..']
         self.display_list = ['.', '..']
+        self.sum_frames = sum_frames
 
         self.dir_name = '.'
         if dir_name is None:
@@ -148,7 +149,7 @@ class FileWidget(ipywidgets.DOMWidget):
         self.datasets = {}
         #self.loaded_datasets.value = self.dataset_list[0]
         self.dataset_list = []
-        self.datasets = open_file(self.file_name)
+        self.datasets = open_file(self.file_name, sum_frames=self.sum_frames)
         self.dataset_list = []
         for key in self.datasets.keys():
             self.dataset_list.append(f'{key}: {self.datasets[key].title}')
@@ -593,7 +594,7 @@ def h5_group_to_dict(group, group_dict={}):
     return group_dict
 
 
-def open_file(filename=None,  h5_group=None, write_hdf_file=False):  # save_file=False,
+def open_file(filename=None,  h5_group=None, write_hdf_file=False, sum_frames=False):  # save_file=False,
     """Opens a file if the extension is .hf5, .ndata, .dm3 or .dm4
 
     If no filename is provided the QT open_file windows opens (if QT_available==True)
@@ -680,7 +681,7 @@ def open_file(filename=None,  h5_group=None, write_hdf_file=False):  # save_file
                 print('This file type needs hyperspy to be installed to be able to be read')
                 return
         elif extension == '.emd':
-            reader = SciFiReaders.EMDReader(filename)
+            reader = SciFiReaders.EMDReader(filename, sum_frames=sum_frames)
 
         elif 'edax' in extension.lower():
             if 'h5' in extension:

pyTEMlib/image_tools.py

@@ -731,15 +731,27 @@ class LineSelector(matplotlib.widgets.PolygonSelector):
             self.line_verts[moved_point] = self.new_point
             self.set_linewidth()
 
-def get_profile(dataset, line):
+def get_profile(dataset, line, spline_order=-1):
+    """
+    This function extracts a line profile from a given dataset. The line profile is a representation of the data values 
+    along a specified line in the dataset. This function works for both image and spectral image data types.
+
+    Args:
+        dataset (sidpy.Dataset): The input dataset from which to extract the line profile.
+        line (list): A list specifying the line along which the profile should be extracted.
+        spline_order (int, optional): The order of the spline interpolation to use. Default is -1, which means no interpolation.
+
+    Returns:
+        profile_dataset (sidpy.Dataset): A new sidpy.Dataset containing the line profile.
+
+
+    """
     xv, yv = get_line_selection_points(line)
-    
-    
     if dataset.data_type.name == 'IMAGE':
         dataset.get_image_dims()
         xv /= (dataset.x[1] - dataset.x[0])
         yv /= (dataset.y[1] - dataset.y[0])
-        profile = scipy.ndimage.map_coordinates(np.array(dataset), [xv,yv])
+        profile = scipy.ndimage.map_coordinates(np.array(dataset), [xv, yv])
         
         profile_dataset = sidpy.Dataset.from_array(profile.sum(axis=0))
         profile_dataset.data_type='spectrum'
@@ -753,19 +765,21 @@ def get_profile(dataset, line):
 
     if dataset.data_type.name == 'SPECTRAL_IMAGE':
         spectral_axis = dataset.get_spectral_dims(return_axis=True)[0]
-        profile = np.zeros([xv.shape[1], 2, len(spectral_axis)])
-        data =np.array(dataset)
-
-        for index_x in range(xv.shape[1]):
-            for  index_y  in range(xv.shape[0]):
-                x = xv[index_y, index_x]
-                y = yv[index_y, index_x]
-                profile[index_x, 0] +=data[int(x),int(y)]
+        if spline_order > -1:
+            xv, yv, zv = get_line_selection_points_interpolated(line, z_length=dataset.shape[2])
+            profile = scipy.ndimage.map_coordinates(np.array(dataset), [xv, yv, zv], order=spline_order)
+            profile = profile.sum(axis=0)
+            profile = np.stack([profile, profile], axis=1)
+            start = xv[0, 0, 0]
+        else:
+            profile = get_line_profile(np.array(dataset), xv, yv, len(spectral_axis))
+            start = xv[0, 0]
+        print(profile.shape)
         profile_dataset = sidpy.Dataset.from_array(profile)
         profile_dataset.data_type='spectral_image'
         profile_dataset.units = dataset.units
         profile_dataset.quantity = dataset.quantity
-        profile_dataset.set_dimension(0, sidpy.Dimension(np.linspace(xv[0,0], xv[-1,-1], profile_dataset.shape[0]), 
+        profile_dataset.set_dimension(0, sidpy.Dimension(np.arange(profile_dataset.shape[0])+start, 
                                                   name='x', units=dataset.x.units, quantity=dataset.x.quantity,
                                                   dimension_type='spatial'))
         profile_dataset.set_dimension(1, sidpy.Dimension([0, 1], 
@@ -776,6 +790,42 @@ def get_profile(dataset, line):
     return profile_dataset
 
 
+
+def get_line_selection_points_interpolated(line, z_length=1):
+    
+    start_point = line.line_verts[3]
+    right_point = line.line_verts[0]
+    low_point = line.line_verts[2]
+
+    if start_point[0] > right_point[0]:
+        start_point = line.line_verts[0]
+        right_point = line.line_verts[3]
+        low_point = line.line_verts[1]
+    m = (right_point[1] - start_point[1]) / (right_point[0] - start_point[0])
+    length_x = int(abs(start_point[0]-right_point[0]))
+    length_v = int(np.linalg.norm(start_point-right_point))
+    
+    linewidth = int(abs(start_point[1]-low_point[1]))
+    x = np.linspace(0,length_x, length_v)
+    y = np.linspace(0,linewidth, line.line_width)
+    if z_length > 1:
+        z = np.linspace(0, z_length, z_length)
+        xv, yv, zv = np.meshgrid(x, y, np.arange(z_length))
+        x = np.atleast_2d(x).repeat(z_length, axis=0).T
+        y = np.atleast_2d(y).repeat(z_length, axis=0).T
+    else:
+        xv, yv = np.meshgrid(x, y)
+    
+    
+    yv = yv + x*m + start_point[1] 
+    xv = (xv.swapaxes(0,1) -y*m ).swapaxes(0,1) + start_point[0]
+
+    if z_length > 1:
+        return xv, yv, zv
+    else:   
+        return xv, yv
+
+
 def get_line_selection_points(line):
     
     start_point = line.line_verts[3]
@@ -801,6 +851,16 @@ def get_line_selection_points(line):
     return xx, yy
 
 
+def get_line_profile(data, xv, yv, z_length):
+    profile = np.zeros([len(xv[0]), 2, z_length])
+    for index_x in range(xv.shape[1]):
+        for  index_y  in range(xv.shape[0]):
+            x = int(xv[index_y, index_x])
+            y = int(yv[index_y, index_x])
+            if x< data.shape[0] and x>0 and y < data.shape[1] and y>0:
+                profile[index_x, 0] +=data[x, y]
+    return profile
+     
 
 def histogram_plot(image_tags):
     """interactive histogram"""

pyTEMlib/version.py

@@ -1,6 +1,6 @@
 """
 version
 """
-_version = '0.2024.02.0'
+_version = '0.2024.02.2'
 __version__ = _version
-_time = '2024-02-08 19:58:26'
+_time = '2024-02-26 19:58:26'

{pyTEMlib-0.2024.2.0.dist-info → pyTEMlib-0.2024.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyTEMlib
-Version: 0.2024.2.0
+Version: 0.2024.2.2
 Summary: pyTEM: TEM Data Quantification library through a model-based approach
 Home-page: https://pycroscopy.github.io/pyTEMlib/about.html
 Author: Gerd Duscher
@@ -24,6 +24,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering :: Information Analysis
+License-File: LICENSE
 Requires-Dist: scipy
 Requires-Dist: numpy
 Requires-Dist: pillow
@@ -51,7 +52,7 @@ pyTEMlib
 .. image:: https://img.shields.io/pypi/v/pyTEMlib.svg
     :target: https://pypi.org/project/pyTEMlib/
     :alt: PyPI
-
+    
 .. image:: https://img.shields.io/conda/vn/conda-forge/pyTEMlib.svg
     :target: https://github.com/conda-forge/pyTEMlib-feedstock
     :alt: conda-forge

{pyTEMlib-0.2024.2.0.dist-info → pyTEMlib-0.2024.2.2.dist-info}/RECORD

@@ -9,13 +9,13 @@ pyTEMlib/eds_tools.py,sha256=34YYoix9rhq0aYnZrHVi0A8gQeu9XZ9fGGT0VxPQo8Y,24882
 pyTEMlib/eels_dialog.py,sha256=x5AOe2SjL4R8aR6X92HOWdC9mL0M-jKtSiNfR-SHQr8,32327
 pyTEMlib/eels_dialog_utilities.py,sha256=srkRvRDUWIzN38EWNGRWimsJLK4YXSnGEfL6Dd1V3IY,51778
 pyTEMlib/eels_tools.py,sha256=pzsiMY-1ZXth5ZIrPaRNOs6R3gMAyZr8TVYf-Lxnn5Y,77781
-pyTEMlib/file_tools.py,sha256=RqYPMAkz7pNorvTUhazXk7aQltjOvQPqo_PhA9Iz-Bw,46371
+pyTEMlib/file_tools.py,sha256=XbtKLWEK-zam4A4u5iS4lFhNw51Vcm8Syoa_133hFyo,46495
 pyTEMlib/file_tools_qt.py,sha256=tLZACS4JyGH_AOzNR_SGAhjA01y4VJB261opPhGMlm8,7223
 pyTEMlib/graph_tools.py,sha256=iu0Y2hIPU6CkQHQEh-dI1vKnUHnSNXx4-CXs2M-1Sr8,44097
 pyTEMlib/graph_viz.py,sha256=m5PwSn6l2r0bsaLWBDSHc9IGR3_PneG2BrZgnEdi07I,13644
 pyTEMlib/image_dialog.py,sha256=F-ZgKq7UnMtPPd1b9eqb7t8MXDfWN-8hVKwB2Il0x28,6235
 pyTEMlib/image_dlg.py,sha256=n5gradDiYOFGEQ3k_Wlk9RUYYzl4bl_hKLzNVcYteNE,5694
-pyTEMlib/image_tools.py,sha256=IoRBmKsL6o4V9xGAKoSUV0hOJhr0QXIPCbEiAPWLOq0,43231
+pyTEMlib/image_tools.py,sha256=Z1ZClIl0nqqPbehJzpLeWd0C_-dMCgzegPFIiNjJDNM,45665
 pyTEMlib/info_widget.py,sha256=G8MArXYI_xdvRY3cD7-3UxUjczEUWPjlrGJOj2BKU2Y,49903
 pyTEMlib/interactive_image.py,sha256=5PwypcA1OjLAD-fi8bmWWFHuOjdIPVY9Dh59V24WuDA,34
 pyTEMlib/kinematic_scattering.py,sha256=CUdJnclkok7d8qm_jDUF92MVHrmaTeMkKdvxxB6AqvA,43309
@@ -25,11 +25,11 @@ pyTEMlib/peak_dlg.py,sha256=qcjcnhwpGa4jBCeXzwQz9sCyX-tHsLLQ67ToqfKOiQY,11550
 pyTEMlib/probe_tools.py,sha256=8tPQuANClLsGAKnZo6Vo4gNIGKfyDR6WUMO3dXcm_4k,27177
 pyTEMlib/sidpy_tools.py,sha256=0oIx-qMtEmcZmLazQKW19dd-KoxyY3B15aIeMcyHA8E,4878
 pyTEMlib/simulation_tools.py,sha256=RmegD5TpQMU68uASvzZWVplAqs7bM5KkF6bWDWLjyc0,2799
-pyTEMlib/version.py,sha256=0VMCRcKqYUmPVFq0CCqmw64JL4otiQC0CzcUsUWQV1Y,94
+pyTEMlib/version.py,sha256=_bRzJnpABIwsBmU7vcbAzkVQOcrs4FDhOj7NU--rmwI,94
 pyTEMlib/xrpa_x_sections.py,sha256=peb2pozcH0T-3zlWITx-5rdyeoP2YhOfBpwsWD1-4T4,1813751
-pyTEMlib-0.2024.2.0.dist-info/LICENSE,sha256=7HdBF6SXIBd38bHOKkQd4DYR1KV-OYm9mwB16fM-984,1062
-pyTEMlib-0.2024.2.0.dist-info/METADATA,sha256=fFKLCe0EnCeRwkFKBHcQvqPl6MjtPRGsb7ygt97l-Co,3280
-pyTEMlib-0.2024.2.0.dist-info/WHEEL,sha256=-G_t0oGuE7UD0DrSpVZnq1hHMBV9DD2XkS5v7XpmTnk,110
-pyTEMlib-0.2024.2.0.dist-info/entry_points.txt,sha256=qiIFPP3ffSz-gxj-TowzbA0Setq5Lo0RJTVtSrqD1IY,44
-pyTEMlib-0.2024.2.0.dist-info/top_level.txt,sha256=rPLVH0UJxrPSPgSoKScTjL1K_X69JFzsYYnDnYTYIlU,9
-pyTEMlib-0.2024.2.0.dist-info/RECORD,,
+pyTEMlib-0.2024.2.2.dist-info/LICENSE,sha256=7HdBF6SXIBd38bHOKkQd4DYR1KV-OYm9mwB16fM-984,1062
+pyTEMlib-0.2024.2.2.dist-info/METADATA,sha256=ysRSA7XOwpB9J7hwnDBzAHaD1GxOpCCyUQFqe0yGkFM,3306
+pyTEMlib-0.2024.2.2.dist-info/WHEEL,sha256=-G_t0oGuE7UD0DrSpVZnq1hHMBV9DD2XkS5v7XpmTnk,110
+pyTEMlib-0.2024.2.2.dist-info/entry_points.txt,sha256=qiIFPP3ffSz-gxj-TowzbA0Setq5Lo0RJTVtSrqD1IY,44
+pyTEMlib-0.2024.2.2.dist-info/top_level.txt,sha256=rPLVH0UJxrPSPgSoKScTjL1K_X69JFzsYYnDnYTYIlU,9
+pyTEMlib-0.2024.2.2.dist-info/RECORD,,