whitespace

Wrappers/Python/cil/utilities/dataexample.py

@@ -33,17 +33,17 @@ class DATA(object):
     @classmethod
     def dfile(cls):
         return None
-    
+
 class CILDATA(DATA):
     data_dir = os.path.abspath(os.path.join(sys.prefix, 'share','cil'))
     @classmethod
     def get(cls, size=None, scale=(0,1), **kwargs):
         ddir = kwargs.get('data_dir', CILDATA.data_dir)
         loader = TestData(data_dir=ddir)
         return loader.load(cls.dfile(), size, scale, **kwargs)
-    
+
 class REMOTEDATA(DATA):
-    
+
     FOLDER = ''
     URL = ''
     FILE_SIZE = ''
@@ -56,7 +56,7 @@ def get(cls, data_dir):
     def _download_and_extract_from_url(cls, data_dir):
         with urlopen(cls.URL) as response:
             with BytesIO(response.read()) as bytes, ZipFile(bytes) as zipfile:
-                zipfile.extractall(path = data_dir) 
+                zipfile.extractall(path = data_dir)
 
     @classmethod
     def download_data(cls, data_dir):
@@ -72,8 +72,8 @@ def download_data(cls, data_dir):
         if os.path.isdir(os.path.join(data_dir, cls.FOLDER)):
             print("Dataset already exists in " + data_dir)
         else:
-            if input("Are you sure you want to download " + cls.FILE_SIZE + " dataset from " + cls.URL + " ? (y/n)") == "y": 
-                print('Downloading dataset from ' + cls.URL) 
+            if input("Are you sure you want to download " + cls.FILE_SIZE + " dataset from " + cls.URL + " ? (y/n)") == "y":
+                print('Downloading dataset from ' + cls.URL)
                 cls._download_and_extract_from_url(os.path.join(data_dir,cls.FOLDER))
                 print('Download complete')
             else:
@@ -185,15 +185,15 @@ def get(cls, **kwargs):
         -------
         ImageData
             The simulated spheres volume
-        '''       
+        '''
         ddir = kwargs.get('data_dir', CILDATA.data_dir)
         loader = NEXUSDataReader()
         loader.set_up(file_name=os.path.join(os.path.abspath(ddir), 'sim_volume.nxs'))
         return loader.read()
-    
+
 class WALNUT(REMOTEDATA):
     '''
-    A microcomputed tomography dataset of a walnut from https://zenodo.org/records/4822516 
+    A microcomputed tomography dataset of a walnut from https://zenodo.org/records/4822516
     '''
     FOLDER = 'walnut'
     URL = 'https://zenodo.org/record/4822516/files/walnut.zip'
@@ -202,7 +202,7 @@ class WALNUT(REMOTEDATA):
     @classmethod
     def get(cls, data_dir):
         '''
-        A microcomputed tomography dataset of a walnut from https://zenodo.org/records/4822516 
+        A microcomputed tomography dataset of a walnut from https://zenodo.org/records/4822516
         This function returns the raw projection data from the .txrm file
 
         Parameters
@@ -222,19 +222,19 @@ def get(cls, data_dir):
         except(FileNotFoundError):
             raise(FileNotFoundError("Dataset .txrm file not found in specifed data_dir: {} \n \
                                     Specify a different data_dir or download data with dataexample.{}.download_data(data_dir)".format(filepath, cls.__name__)))
-     
+
 class USB(REMOTEDATA):
     '''
-    A microcomputed tomography dataset of a usb memory stick from https://zenodo.org/records/4822516 
+    A microcomputed tomography dataset of a usb memory stick from https://zenodo.org/records/4822516
     '''
-    FOLDER = 'USB' 
+    FOLDER = 'USB'
     URL = 'https://zenodo.org/record/4822516/files/usb.zip'
     FILE_SIZE = '3.2 GB'
 
     @classmethod
     def get(cls, data_dir):
         '''
-        A microcomputed tomography dataset of a usb memory stick from https://zenodo.org/records/4822516 
+        A microcomputed tomography dataset of a usb memory stick from https://zenodo.org/records/4822516
         This function returns the raw projection data from the .txrm file
 
         Parameters
@@ -254,7 +254,7 @@ def get(cls, data_dir):
         except(FileNotFoundError):
             raise(FileNotFoundError("Dataset .txrm file not found in: {} \n \
                                     Specify a different data_dir or download data with dataexample.{}.download_data(data_dir)".format(filepath, cls.__name__)))
-        
+
 class KORN(REMOTEDATA):
     '''
     A microcomputed tomography dataset of a sunflower seeds in a box from https://zenodo.org/records/6874123
@@ -319,7 +319,7 @@ class TestData(object):
 
     def __init__(self, data_dir):
         self.data_dir = data_dir
-        
+
     def load(self, which, size=None, scale=(0,1), **kwargs):
         '''
         Return a test data of the requested image
@@ -645,4 +645,4 @@ def scikit_random_noise(image, mode='gaussian', seed=None, clip=True, **kwargs):
         if clip:
             out = np.clip(out, low_clip, 1.0)
 
-        return out
+        return out

Wrappers/Python/test/test_dataexample.py

@@ -25,7 +25,7 @@
 from testclass import CCPiTestClass
 import platform
 import numpy as np
-from unittest.mock import patch, MagicMock 
+from unittest.mock import patch, MagicMock
 from urllib import request
 from zipfile import ZipFile
 from io import StringIO
@@ -151,26 +151,26 @@ def test_load_SIMULATED_CONE_BEAM_DATA(self):
                                          .set_panel((128,128),(64,64))\
                                          .set_angles(np.linspace(0,360,300,False))
 
-        self.assertEqual(ag_expected,image.geometry,msg="Acquisition geometry mismatch")   
+        self.assertEqual(ag_expected,image.geometry,msg="Acquisition geometry mismatch")
 
 class TestRemoteData(unittest.TestCase):
 
     def setUp(self):
-        
+
         self.data_list = ['WALNUT','USB','KORN','SANDSTONE']
         self.tmp_file = 'tmp.txt'
         self.tmp_zip = 'tmp.zip'
         with ZipFile(self.tmp_zip, 'w') as zipped_file:
             zipped_file.writestr(self.tmp_file, np.array([1, 2, 3]))
         with open(self.tmp_zip, 'rb') as zipped_file:
-            self.zipped_bytes = zipped_file.read()        
-    
+            self.zipped_bytes = zipped_file.read()
+
     def tearDown(self):
         for data in self.data_list:
             test_func = getattr(dataexample, data)
             if os.path.exists(os.path.join(test_func.FOLDER)):
                 shutil.rmtree(test_func.FOLDER)
-        
+
         if os.path.exists(self.tmp_zip):
             os.remove(self.tmp_zip)
 
@@ -189,39 +189,39 @@ def test_unzip_remote_data(self, mock_urlopen):
         dataexample.REMOTEDATA._download_and_extract_from_url('.')
         self.assertTrue(os.path.isfile(self.tmp_file))
 
-    @patch('cil.utilities.dataexample.input', return_value='n')    
+    @patch('cil.utilities.dataexample.input', return_value='n')
     @patch('cil.utilities.dataexample.urlopen')
     def test_download_data_input_n(self, mock_urlopen, input):
         self.mock_urlopen(mock_urlopen)
 
         data_list = ['WALNUT','USB','KORN','SANDSTONE']
         for data in data_list:
              # redirect print output
-            capturedOutput = StringIO()                 
-            sys.stdout = capturedOutput  
+            capturedOutput = StringIO()
+            sys.stdout = capturedOutput
             test_func = getattr(dataexample, data)
             test_func.download_data('.')
-            
+
             self.assertFalse(os.path.isfile(self.tmp_file))
             self.assertEqual(capturedOutput.getvalue(),'Download cancelled\n')
-        
+
         # return to standard print output
-        sys.stdout = sys.__stdout__ 
+        sys.stdout = sys.__stdout__
 
-    @patch('cil.utilities.dataexample.input', return_value='y')    
+    @patch('cil.utilities.dataexample.input', return_value='y')
     @patch('cil.utilities.dataexample.urlopen')
     def test_download_data_input_y(self, mock_urlopen, input):
         self.mock_urlopen(mock_urlopen)
 
         # redirect print output
-        capturedOutput = StringIO()                 
-        sys.stdout = capturedOutput         
+        capturedOutput = StringIO()
+        sys.stdout = capturedOutput
+
 
-
         for data in self.data_list:
             test_func = getattr(dataexample, data)
             test_func.download_data('.')
             self.assertTrue(os.path.isfile(os.path.join(test_func.FOLDER,self.tmp_file)))
-        
+
         # return to standard print output
-        sys.stdout = sys.__stdout__ 
+        sys.stdout = sys.__stdout__