pyTEMlib 0.2025.4.0__py3-none-any.whl → 0.2025.4.2__py3-none-any.whl

pyTEMlib/file_tools.py

@@ -1457,10 +1457,12 @@ def read_adorned_metadata(image):
     root = ET.fromstring(xml_str)
     metadata_dict = etree_to_dict(root)
     detector = 'detector'
-    if 'Detectors' in metadata_dict['Metadata']['Detectors']['ScanningDetector']:
-        if 'ScanningDetector' in metadata_dict['Metadata']['Detectors']['ScanningDetector']:
+    
+    if 'Detectors' in metadata_dict['Metadata']:
+        if 'ScanningDetector' in metadata_dict['Metadata']['Detectors']:
             detector = metadata_dict['Metadata']['Detectors']['ScanningDetector']['DetectorName']
-
+        elif 'ImagingDetector' in metadata_dict['Metadata']['Detectors']:
+            detector = metadata_dict['Metadata']['Detectors']['ImagingDetector']['DetectorName']
     segment = ''
     if 'CustomPropertyGroup' in  metadata_dict['Metadata']:
         if 'CustomProperties' in metadata_dict['Metadata']['CustomPropertyGroup']:
@@ -1476,6 +1478,29 @@ def read_adorned_metadata(image):
                                     segment = '_'+item['@value']
     return detector+segment, metadata_dict['Metadata']
 
+
+def get_metadata_from_adorned(ds):
+    ds.metadata['experiment']= {}
+    if 'Optics' in ds.original_metadata:
+        if 'LastMeasuredScreenCurrent' in ds.original_metadata['Optics']:
+            ds.metadata['experiment']['current'] = float(ds.original_metadata['Optics']['LastMeasuredScreenCurrent'])
+        if 'ConvergenceAngle' in ds.original_metadata['Optics']:
+            ds.metadata['experiment']['convergence_angle'] = float(ds.original_metadata['Optics']['ConvergenceAngle'])  
+        if 'AccelerationVoltage' in ds.original_metadata['Optics']:
+            ds.metadata['experiment']['acceleration_voltage'] = float(ds.original_metadata['Optics']['AccelerationVoltage'])    
+        if 'SpotIndex' in ds.original_metadata['Optics']:
+            ds.metadata['experiment']['spot_size'] = ds.original_metadata['Optics']['SpotIndex']    
+    if' StagesSettings' in ds.original_metadata:
+        if 'StagePosition' in ds.original_metadata['StagesSettings']:
+            ds.metadata['experiment']['stage_position'] = ds.original_metadata['StagesSettings']['StagePosition']
+    if 'Detectors' in ds.original_metadata:
+        if 'ScanningDetector' in ds.original_metadata['Detectors']:
+            ds.metadata['experiment']['detector'] = ds.original_metadata['Detectors']['ScanningDetector']['DetectorName']
+        elif 'ImagingDetector' in ds.original_metadata['Detectors']:
+            ds.metadata['experiment']['detector'] = ds.original_metadata['Detectors']['ImagingDetector']['DetectorName'] 
+            ds.metadata['experiment']['exposure_time'] = ds.original_metadata['Detectors']['ImagingDetector']['ExposureTime']       
+            
+    
 def adorned_to_sidpy(images):
     """
     Convert a list of adorned images to a dictionary of Sidpy datasets.
@@ -1519,6 +1544,7 @@ def adorned_to_sidpy(images):
             ds.set_dimension(1, sidpy.Dimension(np.arange(image.data.shape[1]) * pixel_size_x_nm,
                                           name='x', units='nm', quantity='Length', dimension_type='spatial'))
 
+        get_metadata_from_adorned(ds)
     return data_sets
 
 

pyTEMlib/image_tools.py

@@ -639,8 +639,21 @@ def rigid_registration(dataset, normalization=None):
         normalization = None
 
     if dataset.get_dimensions_by_type('TEMPORAL')[0] != 0:
-        raise TypeError('Image stack does not have correct frame dimension')
-        
+        x = dataset.x
+        y = dataset.y
+        z = dataset.z
+        metadata = dataset.metadata.copy()
+        original_metadata = dataset.original_metadata.copy()
+        arr = np.rollaxis(np.array(dataset), 2, 0)
+        dataset = sidpy.Dataset.from_array(arr, title=dataset.title, data_type='IMAGE_STACK',
+                                           quantity=dataset.quantity, units=dataset.units)
+        dataset.set_dimension(0, sidpy.Dimension(z.values, name='frame', units='frame', quantity='time',       
+                                                  dimension_type='temporal'))
+        dataset.set_dimension(1, x)
+        dataset.set_dimension(2, y)
+        dataset.metadata = metadata
+        dataset.original_metadata = original_metadata
+
     stack_dim = dataset.get_dimensions_by_type('TEMPORAL', return_axis=True)[0]
     image_dim = dataset.get_image_dims(return_axis=True)
     if len(image_dim) != 2:

pyTEMlib/version.py

@@ -1,6 +1,6 @@
 """
 version
 """
-_version = '0.2025.04.0'
+_version = '0.2025.04.2'
 __version__ = _version
-_time = '2025-04-25 19:58:26'
+_time = '2025-05-26 19:58:26'

{pytemlib-0.2025.4.0.dist-info → pytemlib-0.2025.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyTEMlib
-Version: 0.2025.4.0
+Version: 0.2025.4.2
 Summary: pyTEM: TEM Data Quantification library through a model-based approach
 Home-page: https://pycroscopy.github.io/pyTEMlib/about.html
 Author: Gerd Duscher

{pytemlib-0.2025.4.0.dist-info → pytemlib-0.2025.4.2.dist-info}/RECORD

@@ -10,13 +10,13 @@ pyTEMlib/eds_tools.py,sha256=Ilof2Cars-1ILXx5g2RsU2G4BgrPwjOHgQ7-OabmbrU,28000
 pyTEMlib/eels_dialog.py,sha256=QG_PU3uuzus_3I3zjfaxb2a9iYq8B053zYw-B52JklM,32595
 pyTEMlib/eels_dialog_utilities.py,sha256=73W9jFbPx-eeLEiSaBptTgGLr40bIYYfSyzLnZbhfvo,51761
 pyTEMlib/eels_tools.py,sha256=pl75ZDQHz1JngxD84T_595Kfrl5TEJSETPGgkXfBtrA,88688
-pyTEMlib/file_tools.py,sha256=AIeWD3JaB1OI32_pj_RSqQuRGjPM-wiD0zTbL5W17Tc,64559
+pyTEMlib/file_tools.py,sha256=RniTJrcuiyt7PefE5SSY_z2pTZPTNhFRjb2oVXVa4nE,66373
 pyTEMlib/file_tools_qt.py,sha256=tLZACS4JyGH_AOzNR_SGAhjA01y4VJB261opPhGMlm8,7223
 pyTEMlib/graph_tools.py,sha256=VWuTgFGeu4gn4cfRgf-76kO6u2B1ZV_dz6gLfx2k4NY,46570
 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=iBVsAr6-oQY6y2LTSbUIz6nMeAIOsSX5zPBezekJsFg,52334
+pyTEMlib/image_tools.py,sha256=g0P_r0Ygehadi-aVufQs0CahB1N7Teyrx2oTEOBChmA,53007
 pyTEMlib/info_widget.py,sha256=lkzQOuNVlkaasiZDtc5UtYk541-plYNfnW4DQwQB_iA,53467
 pyTEMlib/info_widget3.py,sha256=QSbdSj6m57KQTir2fNhulVgjOu9EQL31c-9SzTlghnE,55495
 pyTEMlib/interactive_image.py,sha256=5PwypcA1OjLAD-fi8bmWWFHuOjdIPVY9Dh59V24WuDA,34
@@ -28,11 +28,11 @@ pyTEMlib/peak_dlg.py,sha256=qcjcnhwpGa4jBCeXzwQz9sCyX-tHsLLQ67ToqfKOiQY,11550
 pyTEMlib/probe_tools.py,sha256=sDW9CW3SMwjvSHYcEufceismHv_LVkqxcS-gCtEklCg,37926
 pyTEMlib/sidpy_tools.py,sha256=0oIx-qMtEmcZmLazQKW19dd-KoxyY3B15aIeMcyHA8E,4878
 pyTEMlib/simulation_tools.py,sha256=RmegD5TpQMU68uASvzZWVplAqs7bM5KkF6bWDWLjyc0,2799
-pyTEMlib/version.py,sha256=znL_4Pt7sBR4l1I39FM04SGxnneUfbZrv9R_6tFaynA,94
+pyTEMlib/version.py,sha256=sLEWA3eeGfLH2FDGCSFBKKzQ7hDmULfKjeBegz_cqAI,94
 pyTEMlib/xrpa_x_sections.py,sha256=m4gaH7gaJiNi-CsIT9aKoH4fB6MQIAe876kxEmzSebI,1825392
-pytemlib-0.2025.4.0.dist-info/licenses/LICENSE,sha256=7HdBF6SXIBd38bHOKkQd4DYR1KV-OYm9mwB16fM-984,1062
-pytemlib-0.2025.4.0.dist-info/METADATA,sha256=mV1ni5hE1q19Z8qOzNfWGb9YAOy0rv69JZd3J1e14MM,3515
-pytemlib-0.2025.4.0.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
-pytemlib-0.2025.4.0.dist-info/entry_points.txt,sha256=zn2yO1IWTutI3c7C9e3GdARCvm43JURoOhqQ8YylV4Y,43
-pytemlib-0.2025.4.0.dist-info/top_level.txt,sha256=rPLVH0UJxrPSPgSoKScTjL1K_X69JFzsYYnDnYTYIlU,9
-pytemlib-0.2025.4.0.dist-info/RECORD,,
+pytemlib-0.2025.4.2.dist-info/licenses/LICENSE,sha256=7HdBF6SXIBd38bHOKkQd4DYR1KV-OYm9mwB16fM-984,1062
+pytemlib-0.2025.4.2.dist-info/METADATA,sha256=C-qYZn0VpCQOyMbwDFbgxjzcBYzz8D76cucXAxq0R7o,3515
+pytemlib-0.2025.4.2.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
+pytemlib-0.2025.4.2.dist-info/entry_points.txt,sha256=zn2yO1IWTutI3c7C9e3GdARCvm43JURoOhqQ8YylV4Y,43
+pytemlib-0.2025.4.2.dist-info/top_level.txt,sha256=rPLVH0UJxrPSPgSoKScTjL1K_X69JFzsYYnDnYTYIlU,9
+pytemlib-0.2025.4.2.dist-info/RECORD,,