Merge pull request #102 from pycroscopy/switch2dict

Switch2dict
pycroscopy · Sep 30, 2023 · 54aa00b · 54aa00b
2 parents ad2b691 + 673a4ab
commit 54aa00b
Show file tree

Hide file tree

Showing 11 changed files with 194 additions and 1,070 deletions.
diff --git a/SciFiReaders/readers/microscopy/em/tem/dm_reader.py b/SciFiReaders/readers/microscopy/em/tem/dm_reader.py
@@ -187,6 +187,7 @@ def read(self):
         if '1' in self.__stored_tags['ImageList']:
             start=1
         for image_number in self.__stored_tags['ImageList'].keys():
+            print(image_number, start)
             if int(image_number) >= start:
                 dataset = self.get_dataset(self.__stored_tags['ImageList'][image_number])
                 if isinstance(dataset, sidpy.Dataset):
@@ -214,16 +215,17 @@ def read(self):
                     dataset.source = 'SciFiReaders.DMReader'
                     dataset.original_metadata['DM']['full_file_name'] = self.__filename
 
-                    key = f'Channel_{int(image_number):03d}'
+                    key = f"Channel_{int(image_number)-start:03d}"
                     self.datasets[key] = dataset
                     self.extract_crucial_metadata(key)
 
         del self.__stored_tags['ImageList'] 
-        main_dataset_number = 0
-        for index, dataset in self.datasets.items():
-            if 'urvey' in dataset.title:
-                main_dataset_number = index
         main_dataset_key = list(self.datasets.keys())[0]
+        for key, dataset in self.datasets.items():
+            print(key, dataset)
+            if 'urvey' in dataset.title:
+                main_dataset_key = key
+        print(main_dataset_key)
         self.datasets[main_dataset_key].original_metadata.update(self.__stored_tags)
         self.close()
         return self.datasets

diff --git a/SciFiReaders/readers/microscopy/em/tem/emd_reader.py b/SciFiReaders/readers/microscopy/em/tem/emd_reader.py
@@ -215,15 +215,12 @@ def get_eds_spectrum(self):
         if 'Scan' in self.metadata:
             scan = self.metadata['Scan']
             if 'ScanArea' in scan:
-                size_x = float(scan['ScanSize']['width'])
-                size_y = float(scan['ScanSize']['height'])
-                size_x *= (float(scan['ScanArea']['right']) - float(scan['ScanArea']['left']))
-                size_y *= (float(scan['ScanArea']['bottom']) - float(scan['ScanArea']['top']))
-                size_x = int(size_x)
-                size_y = int(size_y)
-            elif 'RasterScanDefinition' in acquisition:
-                size_x = int(acquisition['RasterScanDefinition']['Width'])
-                size_y = int(acquisition['RasterScanDefinition']['Height'])
+                size_x = int(float(scan['ScanSize']['width']) * float(scan['ScanArea']['right'])-float(scan['ScanSize']['width']) * float(scan['ScanArea']['left']))
+                size_y = int(float(scan['ScanSize']['height']) * float(scan['ScanArea']['bottom'])-float(scan['ScanSize']['height']) * float(scan['ScanArea']['top']))
+
+        if 'RasterScanDefinition' in acquisition:
+            size_x = int(acquisition['RasterScanDefinition']['Width'])
+            size_y = int(acquisition['RasterScanDefinition']['Height'])
         spectrum_size = int(acquisition['bincount'])
 
         self.number_of_frames = int(np.ceil((self.data_array[:, 0] == 65535).sum() / (size_x * size_y)))