update setuppy and change to dictionary for tem readers

.gitignore

@@ -114,3 +114,4 @@ test_scripts/
 /SciFiReaders/readers/microscopy/spm/afm/mdt_reader/MDTdeclaration.py
 /SciFiReaders/readers/microscopy/spm/afm/mdt_reader/MDTfile.py
 .pyTEMlib.files.pkl
+tests/readers/microscopy/em/tem/EMDReader_Spectrum_FEI.emd

SciFiReaders/readers/microscopy/em/tem/emd_reader.py

@@ -100,13 +100,13 @@ def read(self, eds_stream=False):
         if 'Data' not in self._h5_file:
             raise TypeError('Velox EMD File is empty')
 
-        number_of_datasets=0
+        number_of_datasets = 0
         use_tqdm = False
         for key in self._h5_file['Data']:
             if key == 'SpectrumStream':
                 number_of_datasets += len(self._h5_file['Data']['SpectrumStream'].keys())
         if number_of_datasets > 1:
-            progress_bar = tqdm(total=number_of_datasets) # Initialise
+            progress_bar = tqdm(total=number_of_datasets)  # Initialise
             use_tqdm = tqdm_available
         for key in self._h5_file['Data']:
             self.image_key = 'None'
@@ -157,7 +157,7 @@ def get_eds(self, eds_stream=False):
         else:
             data_array = self.get_eds_spectrum()
             if data_array.shape[0] == 1 and data_array.shape[1] == 1:
-                data_array = np.array(data_array).flatten()
+                data_array = np.squeeze(data_array)
                 chunks = 1
             else:
                 chunks= [32, 32, data_array.shape[2]]
@@ -166,7 +166,7 @@ def get_eds(self, eds_stream=False):
                 if data_array.shape[1]> chunks[1]:
                     chunks[1] = data_array.shape[1]
 
-            self.datasets[key] = sidpy.Dataset.from_array(self.data_array, chunks=chunks)
+            self.datasets[key] = sidpy.Dataset.from_array(data_array, chunks=chunks)
 
 
         self.data_array=np.zeros([1,1])

tests/readers/microscopy/em/tem/test_Nion_reader.py

@@ -11,10 +11,12 @@
 import os
 from pywget import wget
 
-sys.path.append("../../../../../SciFiReaders/")
+
+sys.path.insert(0, "../../../../../SciFiReaders/")
 import SciFiReaders
+print(SciFiReaders.__version__)
 
-data_path = 'https://raw.githubusercontent.com/pycroscopy/SciFidataset/main/data/microscopy/em/tem/'
+data_path = 'https://raw.githubusercontent.com/pycroscopy/SciFiDatasets/main/data/microscopy/em/tem/'
 
 
 class TestNionReader(unittest.TestCase):
@@ -24,15 +26,16 @@ def test_load_nion_h5_file(self):
         file_name = wget.download(data_path + '/NionReader_ImageStack_STO_HAADF.h5')
         reader = SciFiReaders.NionReader(file_name)
         datasets = reader.read()
-        dataset  = datasets['Channel_000']
+        dataset = datasets['Channel_000']
         self.assertEqual(dataset.title, '10-Recording of SuperScan (HAADF)')
         self.assertEqual(dataset.source, 'NionReader')
         self.assertEqual(dataset.data_type.name, 'IMAGE_STACK')
         self.assertEqual(float(dataset[1, 200, 200]), 0.3707197606563568)
         self.assertEqual(float(dataset[13, 200, 200]), 0.392993688583374)
         self.assertEqual(float(dataset[17, 200, 200]), 0.4997090995311737)
         self.assertEqual(dataset.shape, (25, 512, 512))
-        self.assertEqual(dataset.original_metadata['dimensional_calibrations'][1], {'offset': -4.0, 'scale': 0.015625, 'units': 'nm'})
+        self.assertEqual(dataset.original_metadata['dimensional_calibrations'][1],
+                         {'offset': -4.0, 'scale': 0.015625, 'units': 'nm'})
 
         os.remove(file_name)
 
@@ -41,7 +44,7 @@ def test_load_nion_ndata_file(self):
         file_name = wget.download(data_path + '/NionReader_Image_STO_HAADF.ndata')
         reader = SciFiReaders.NionReader(file_name)
         datasets = reader.read()
-        dataset  = datasets['Channel_000']
+        dataset = datasets['Channel_000']
         self.assertEqual(dataset.title, '19-SuperScan (HAADF) 9')
         self.assertEqual(dataset.source, 'NionReader')
         self.assertEqual(dataset.data_type.name, 'IMAGE')
@@ -68,6 +71,6 @@ def test_load_wrong_file(self):
         file_name = wget.download(data_path + '/DMReader_Image_SI-Survey.dm3')
         reader = SciFiReaders.NionReader(file_name)
         datasets = reader.read()
-        dataset  = datasets['Channel_000']
+        dataset = datasets['Channel_000']
         self.assertEqual(dataset.data_type.name, 'UNKNOWN')
         os.remove(file_name)

tests/readers/microscopy/em/tem/test_emd_reader.py

@@ -39,7 +39,7 @@ def test_read_spectrum(self):
         os.remove(file_name)
 
         self.assertIsInstance(dataset, sidpy.Dataset)
-        self.assertTrue(datasets.ndim == 1)
+        self.assertTrue(dataset.ndim == 1)
         self.assertTrue(len(datasets) == 1)
         print(datasets['Channel_000'].original_metadata)
 
@@ -311,20 +311,20 @@ def test_read_spectrum_image(self):
         file_name  = wget.download(data_path + '/EMDReader_SpectrumImage_Si.emd')
         emd_reader = SciFiReaders.EMDReader(file_name)
         datasets = emd_reader.read()
-        dataset = datasets['Channel_000']
+        dataset = datasets['Channel_001']
         emd_reader.close()
         os.remove(file_name)
 
         self.assertIsInstance(dataset, sidpy.Dataset)
         self.assertTrue(dataset.data_type.name, 'IMAGE_STACK')
-        self.assertTrue(datasets[1].data_type.name, 'SPECTRAL_IMAGE')
-        self.assertTrue(datasets[1].ndim == 3)
+        self.assertTrue(dataset.data_type.name, 'SPECTRAL_IMAGE')
+        self.assertTrue(dataset.ndim == 3)
         self.assertTrue(len(datasets) == 2)
         print(dataset.original_metadata)
         original_metadata = dataset.original_metadata
 
         self.assertTrue(dataset.units == 'counts')
-        self.assertTrue(dataset.shape == (5, 16, 16))
+        self.assertTrue(datasets['Channel_000'].shape == (5, 16, 16))
         """self.assertTrue(datasets[1].shape == (512, 512, 4096))
         self.assertEqual(float(dataset[1,10,10]), 23053.)
         self.assertEqual(float(dataset[3, 10, 10]), 23228.0)