pyTEMlib 0.2024.1.1__py2.py3-none-any.whl → 0.2024.2.0__py2.py3-none-any.whl

pyTEMlib/eds_tools.py

@@ -424,7 +424,7 @@ def fit_model(spectrum, elements, use_detector_efficiency=False):
     y = np.array(spectrum)  # .compute()
     [p, _] = leastsq(residuals, pin, args=(y))
 
-    print(pin[-6:], p[-6:])
+    # print(pin[-6:], p[-6:])
 
     update_fit_values(out_tags, p)
 

pyTEMlib/image_tools.py

@@ -23,6 +23,7 @@ from tqdm.auto import trange, tqdm
 from itertools import product
 
 from scipy import fftpack
+import scipy
 # from scipy import signal
 from scipy.interpolate import interp1d  # , interp2d
 import scipy.optimize as optimization
@@ -730,6 +731,76 @@ class LineSelector(matplotlib.widgets.PolygonSelector):
             self.line_verts[moved_point] = self.new_point
             self.set_linewidth()
 
+def get_profile(dataset, line):
+    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_dataset = sidpy.Dataset.from_array(profile.sum(axis=0))
+        profile_dataset.data_type='spectrum'
+        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]), 
+                                                  name='x', units=dataset.x.units, quantity=dataset.x.quantity,
+                                                  dimension_type='spatial'))
+
+        profile_dataset
+
+    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)]
+        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]), 
+                                                  name='x', units=dataset.x.units, quantity=dataset.x.quantity,
+                                                  dimension_type='spatial'))
+        profile_dataset.set_dimension(1, sidpy.Dimension([0, 1], 
+                                                  name='y', units=dataset.x.units, quantity=dataset.x.quantity,
+                                                  dimension_type='spatial'))
+        
+        profile_dataset.set_dimension(2, spectral_axis)
+    return profile_dataset
+
+
+def get_line_selection_points(line):
+    
+    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)
+    xv, yv = np.meshgrid(x, y)
+    
+    yy = yv +x*m+start_point[1] 
+    xx = (xv.T -y*m ).T + start_point[0]
+    
+    return xx, yy
+
+
 
 def histogram_plot(image_tags):
     """interactive histogram"""

pyTEMlib/version.py

@@ -1,6 +1,6 @@
 """
 version
 """
-_version = '0.2024.01.1'
+_version = '0.2024.02.0'
 __version__ = _version
-_time = '2024-01-08 19:58:26'
+_time = '2024-02-08 19:58:26'

{pyTEMlib-0.2024.1.1.dist-info → pyTEMlib-0.2024.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyTEMlib
-Version: 0.2024.1.1
+Version: 0.2024.2.0
 Summary: pyTEM: TEM Data Quantification library through a model-based approach
 Home-page: https://pycroscopy.github.io/pyTEMlib/about.html
 Author: Gerd Duscher

{pyTEMlib-0.2024.1.1.dist-info → pyTEMlib-0.2024.2.0.dist-info}/RECORD

@@ -5,7 +5,7 @@ pyTEMlib/config_dir.py,sha256=4evlo9P2Yht-AnqaLI-WweLjDQcislbAP3I7P7EZsPU,2085
 pyTEMlib/crystal_tools.py,sha256=g4OXyvd5NLw7vaXhjDP3P6VZpVV6eiyuPn8MdgR2amI,61652
 pyTEMlib/diffraction_plot.py,sha256=pM5d3bdBGa8LlPZ5lw8sLT94mlYTXELxPLv-jUP2FWY,27959
 pyTEMlib/dynamic_scattering.py,sha256=O9MxnxfndWJ2VhQRjksKNQ4yY7y-gN_hitRQ4Qox4ns,9472
-pyTEMlib/eds_tools.py,sha256=NFip6RKr-z3Ea2JlG_OVmr3YQRYeradea-NaGYFppF8,24880
+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
@@ -15,7 +15,7 @@ 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=7t-zqK0eB_h6-6t0xosamwtL0Upqnd0xO0B_zTX4lvg,40228
+pyTEMlib/image_tools.py,sha256=IoRBmKsL6o4V9xGAKoSUV0hOJhr0QXIPCbEiAPWLOq0,43231
 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=Hv4aDOpFP2K3b5yCBeQXcOIKZWB-6YVJSwRt6aTk_iY,94
+pyTEMlib/version.py,sha256=0VMCRcKqYUmPVFq0CCqmw64JL4otiQC0CzcUsUWQV1Y,94
 pyTEMlib/xrpa_x_sections.py,sha256=peb2pozcH0T-3zlWITx-5rdyeoP2YhOfBpwsWD1-4T4,1813751
-pyTEMlib-0.2024.1.1.dist-info/LICENSE,sha256=7HdBF6SXIBd38bHOKkQd4DYR1KV-OYm9mwB16fM-984,1062
-pyTEMlib-0.2024.1.1.dist-info/METADATA,sha256=cnmLfVHeXr1BVb2X-w-7SpoW3Ult018jbcWVaQbih8k,3280
-pyTEMlib-0.2024.1.1.dist-info/WHEEL,sha256=-G_t0oGuE7UD0DrSpVZnq1hHMBV9DD2XkS5v7XpmTnk,110
-pyTEMlib-0.2024.1.1.dist-info/entry_points.txt,sha256=qiIFPP3ffSz-gxj-TowzbA0Setq5Lo0RJTVtSrqD1IY,44
-pyTEMlib-0.2024.1.1.dist-info/top_level.txt,sha256=rPLVH0UJxrPSPgSoKScTjL1K_X69JFzsYYnDnYTYIlU,9
-pyTEMlib-0.2024.1.1.dist-info/RECORD,,
+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,,