Fix bug in NikonReader when ROI is not set (#1457)

* fix bug when ROI is None Signed-off-by: Laura Murgatroyd <[email protected]> * update change log * basic unit tests * Exception types --------- Signed-off-by: Laura Murgatroyd <[email protected]> Co-authored-by: gfardell <[email protected]>
TomographicImaging · Mar 27, 2023 · bc5608d · bc5608d
1 parent 01f0fee
commit bc5608d
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Showing 3 changed files with 44 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,6 @@
+* 23.0.1
+  - Fix bug with NikonReader requiring ROI to be set in constructor.
+
 * 23.0.0
   - Partitioner is now able to create batches even if angle is not the outer dimension
   - Renamed `max_iteration_stop_cryterion` method in the Algorithm class to `max_iteration_stop_criterion`

diff --git a/Wrappers/Python/cil/io/NikonDataReader.py b/Wrappers/Python/cil/io/NikonDataReader.py
@@ -102,22 +102,22 @@ def set_up(self,
         self.fliplr = fliplr
 
         if self.file_name is None:
-            raise Exception('Path to xtekct file is required.')
+            raise ValueError('Path to xtekct file is required.')
 
         # check if xtekct file exists
         if not(os.path.isfile(self.file_name)):
-            raise Exception('File\n {}\n does not exist.'.format(self.file_name))
+            raise FileNotFoundError('File\n {}\n does not exist.'.format(self.file_name))
 
         if os.path.basename(self.file_name).split('.')[-1].lower() != 'xtekct':
             raise TypeError('This reader can only process xtekct files. Got {}'.format(os.path.basename(self.file_name)))
+
+        if self.roi is None:
+            self.roi= {'angle': -1, 'horizontal': -1, 'vertical': -1}
 
         # check labels     
         for key in self.roi.keys():
             if key not in ['angle', 'horizontal', 'vertical']:
-                raise Exception("Wrong label. One of the following is expected: angle, horizontal, vertical")
-
-        if self.roi is None:
-            self.roi= {'angle': -1, 'horizontal': -1, 'vertical': -1}
+                raise ValueError("Wrong label. One of the following is expected: angle, horizontal, vertical")            
 
         roi = self.roi.copy()
 

diff --git a/Wrappers/Python/test/test_io.py b/Wrappers/Python/test/test_io.py
@@ -24,7 +24,7 @@
 import numpy as np
 import os
 from cil.framework import ImageGeometry
-from cil.io import TXRMDataReader, NEXUSDataReader
+from cil.io import TXRMDataReader, NEXUSDataReader, NikonDataReader, ZEISSDataReader
 from cil.io import TIFFWriter, TIFFStackReader
 from cil.io.utilities import HDF5_utilities
 from cil.processors import Slicer
@@ -522,3 +522,37 @@ def test_read_to(self):
 
         HDF5_utilities.read_to(self.path, self.dset_path, data_partial, source_sel=subset, dest_sel=subset)
         np.testing.assert_allclose(data_partial_by_hand,data_partial)
+
+
+class TestNikonReader(unittest.TestCase):
+
+    def test_setup(self):
+
+        reader = NikonDataReader()
+        self.assertEqual(reader.file_name, None)
+        self.assertEqual(reader.roi, None)
+        self.assertTrue(reader.normalise)
+        self.assertEqual(reader.mode, 'bin')
+        self.assertFalse(reader.fliplr)
+
+        roi = {'vertical':(1,-1),'horizontal':(1,-1),'angle':(1,-1)}
+        reader = NikonDataReader(file_name=None, roi=roi, normalise=False, mode='slice', fliplr=True)
+        self.assertEqual(reader.file_name, None)
+        self.assertEqual(reader.roi, roi)
+        self.assertFalse(reader.normalise)
+        self.assertEqual(reader.mode, 'slice')
+        self.assertTrue(reader.fliplr)
+
+        with self.assertRaises(FileNotFoundError):
+            reader = NikonDataReader(file_name='no-file')
+
+
+class TestZeissReader(unittest.TestCase):
+
+    def test_setup(self):
+
+        reader = ZEISSDataReader()
+        self.assertEqual(reader.file_name, None)
+
+        with self.assertRaises(FileNotFoundError):
+            reader = ZEISSDataReader(file_name='no-file')