added test for asciiimageio.py and test_tiffio.py

added installation of pillow via setup (review based)
minor modification of asciiimageio and tiff

.circleci/requirements_testing.txt

@@ -9,3 +9,4 @@ ipython
 https://github.com/nsdf/nsdf/archive/0.1.tar.gz
 coverage
 coveralls
+pillow

.travis.yml

@@ -10,6 +10,7 @@ install:
   - pip install -r requirements.txt
   - pip install coveralls
   - pip install .
+  - pip install pillow
 # command to run tests, e.g. python setup.py test
 script:
   nosetests --with-coverage --cover-package=neo

neo/core/block.py

@@ -98,6 +98,7 @@ def __init__(self, name=None, description=None, file_origin=None,
         self.file_datetime = file_datetime
         self.rec_datetime = rec_datetime
         self.index = index
+        self.regionsofinterest = []
 
     @property
     def data_children_recur(self):

neo/io/__init__.py

@@ -17,10 +17,10 @@
 
 .. autoclass:: neo.io.AlphaOmegaIO
 
-.. autoclass:: neo.io.AsciiSignalIO
-
 .. autoclass:: neo.io.AsciiImageIO
 
+.. autoclass:: neo.io.AsciiSignalIO
+
 .. autoclass:: neo.io.AsciiSpikeTrainIO
 
 .. autoclass:: neo.io.AxographIO
@@ -85,10 +85,10 @@
 
 .. autoclass:: neo.io.StimfitIO
 
-.. autoclass:: neo.io.TiffIO
-
 .. autoclass:: neo.io.TdtIO
 
+.. autoclass:: neo.io.TiffIO
+
 .. autoclass:: neo.io.WinEdrIO
 
 .. autoclass:: neo.io.WinWcpIO
@@ -114,8 +114,8 @@
     # print("\n loading with API...")
 
 from neo.io.alphaomegaio import AlphaOmegaIO
-from neo.io.asciisignalio import AsciiSignalIO
 from neo.io.asciiimageio import AsciiImageIO
+from neo.io.asciisignalio import AsciiSignalIO
 from neo.io.asciispiketrainio import AsciiSpikeTrainIO
 from neo.io.axographio import AxographIO
 from neo.io.axonio import AxonIO
@@ -152,15 +152,15 @@
 from neo.io.rawmcsio import RawMCSIO
 from neo.io.spike2io import Spike2IO
 from neo.io.stimfitio import StimfitIO
-from neo.io.tiffio import TiffIO
 from neo.io.tdtio import TdtIO
+from neo.io.tiffio import TiffIO
 from neo.io.winedrio import WinEdrIO
 from neo.io.winwcpio import WinWcpIO
 
 iolist = [
     AlphaOmegaIO,
-    AsciiSignalIO,
     AsciiImageIO,
+    AsciiSignalIO,
     AsciiSpikeTrainIO,
     AxographIO,
     AxonIO,
@@ -195,8 +195,8 @@
     RawMCSIO,
     Spike2IO,
     StimfitIO,
-    TiffIO,
     TdtIO,
+    TiffIO,
     WinEdrIO,
     WinWcpIO
 ]

neo/io/asciiimageio.py

@@ -62,13 +62,12 @@ def __init__(self, file_name=None, nb_frame=None, nb_row=None, nb_column=None, u
     def read(self, lazy=False, **kwargs):
         if lazy:
             raise ValueError('This IO module does not support lazy loading')
-        return [self.read_block(lazy=lazy, nb_frame=self.nb_frame, nb_row=self.nb_row,
-                                nb_column=self.nb_column, units=self.units, sampling_rate=self.sampling_rate,
-                                spatial_scale=self.spatial_scale, **kwargs)]
+        return [self.read_block(lazy=lazy, **kwargs)]
 
     def read_block(self, lazy=False, **kwargs):
 
-        data = open(self.filename, 'r').read()
+        file = open(self.filename, 'r')
+        data = file.read()
         print("read block")
         liste_value = []
         record = []
@@ -93,6 +92,7 @@ def read_block(self, lazy=False, **kwargs):
 
         image_sequence = ImageSequence(np.array(data, dtype='float'), units=self.units,
                                        sampling_rate=self.sampling_rate, spatial_scale=self.spatial_scale)
+        file.close()
         print("creating segment")
         segment = Segment(file_origin=self.filename)
         segment.imagesequences = [image_sequence]

neo/io/tiffio.py

@@ -4,6 +4,12 @@
 """
 
 import os
+try:
+    from PIL import Image
+    have_pil = True
+except ImportError:
+    have_pil = False
+
 from PIL import Image
 import numpy as np
 from neo.core import ImageSequence, Segment, Block
@@ -68,6 +74,10 @@ class TiffIO(BaseIO):
 
     def __init__(self, directory_path=None,units=None, sampling_rate=None,
                    spatial_scale=None, **kwargs):
+
+        if not have_pil:
+            raise Exception("Please install the pillow package to use TiffIO")
+
         BaseIO.__init__(self, directory_path, **kwargs)
         self.units = units
         self.sampling_rate = sampling_rate
@@ -76,8 +86,7 @@ def __init__(self, directory_path=None,units=None, sampling_rate=None,
     def read(self, lazy=False, **kwargs):
         if lazy:
             raise ValueError('This IO module does not support lazy loading')
-        return [self.read_block(lazy=lazy, units=self.units, sampling_rate=self.sampling_rate,
-                                spatial_scale=self.spatial_scale, **kwargs)]
+        return [self.read_block(lazy=lazy, **kwargs)]
 
     def read_block(self, lazy=False, **kwargs):
         # to sort file

neo/test/coretest/test_imagesequence.py

@@ -35,13 +35,14 @@ def test_error_spatial_scale(self):
             ImageSequence(self.data, units='V', sampling_rate=500 * pq.Hz)
 
     def test_units(self):
-        with self.assertRaises(ValueError):
+        with self.assertRaises(TypeError):
             ImageSequence(self.data, sampling_rate=500 * pq.Hz, spatial_scale='m')
 
     # test method will be remove are rename
 
     def test_something(self):
-        l = ImageSequence(self.data, sampling_rate=500 * pq.Hz, units='V', spatial_scale='m')
+        l = ImageSequence(self.data, sampling_rate=500 * pq.Hz, units='V',
+                          spatial_scale='m')
 
         self.assertEqual(l.sampling_rate, 500 * pq.Hz)
         self.assertEqual(l.spatial_scale, 'm')
@@ -75,8 +76,6 @@ def test_signal_from_region(self):
         with self.assertRaises(ValueError):
             ImageSequence(self.data, units='V', sampling_rate=500 * pq.Hz, spatial_scale='m').signal_from_region()
 
-        m = ImageSequence(self.data, units='V', sampling_rate=500 * pq.Hz, spatial_scale='m').view()
-        print(m.sampling_rate)
 
 if __name__ == "__main__":
     unittest.main()

neo/test/iotest/test_asciiimageio.py

@@ -0,0 +1,43 @@
+"""
+Test of neo.io.asciiimageio
+"""
+import os
+import unittest
+import quantities as pq
+from neo.io import AsciiImageIO
+import numpy as np
+
+
+class TestAsciiImageIO(unittest.TestCase):
+
+    def test_read_txt(self):
+        img = ''
+        img_list = []
+        for frame in range(20):
+            img_list.append([])
+            for y in range(50):
+                img_list[frame].append([])
+                for x in range(50):
+                    img += str(x)
+                    img += '\t'
+                    img_list[frame][y].append(x)
+        img_list = np.array(img_list)
+        file_name = "txt_test_file.txt"
+        file = open(file_name, mode="w")
+        file.write(str(img))
+        file.close()
+
+        object = AsciiImageIO(file_name='txt_test_file.txt',
+                     nb_frame=20, nb_row=50, nb_column=50, units='V',
+                     sampling_rate=1 * pq.Hz, spatial_scale=1 * pq.micrometer)
+        block = object.read_block()
+        self.assertEqual(len(block.segments), 1)
+        self.assertEqual(len(block.segments[0].imagesequences), 1)
+        self.assertEqual(block.segments[0].imagesequences[0].shape, (20, 50, 50))
+        self.assertEqual(block.segments[0].imagesequences[0].any(), img_list.any())
+
+        file.close()
+        os.remove(file_name)
+
+if __name__ == "__main__":
+    unittest.main()

neo/test/iotest/test_tiffio.py

@@ -0,0 +1,43 @@
+
+import unittest
+import os
+from PIL import Image
+import numpy as np
+import shutil
+from neo.io.tiffio import TiffIO
+import quantities as pq
+
+class TestTiffIO(unittest.TestCase):
+
+
+    def test_read_group_of_tiff_grayscale(self):
+        directory = 'test_tiff'
+        if not os.path.exists(directory):
+            os.makedirs(directory)
+        # directory is live
+        img = []
+        for picture in range(10):
+            img.append([])
+            for y in range(50):
+                img[picture].append([])
+                for x in range(50):
+                    img[picture][y].append(x)
+        img = np.array(img, dtype=float)
+        for image in range(10):
+            Image.fromarray(img[image]).save(directory+'/tiff_exemple'+str(image)+".tif")
+
+        ioclass = TiffIO(directory_path=directory, units='V', sampling_rate=1.0*pq.Hz,
+                         spatial_scale=1.0*pq.micrometer)
+        blck = ioclass.read_block()
+        self.assertEqual(len(blck.segments), 1)
+        self.assertEqual(len(blck.segments[0].imagesequences), 1)
+        self.assertEqual(blck.segments[0].imagesequences[0].any(), img.any())
+        self.assertEqual(blck.segments[0].imagesequences[0].sampling_rate, 1.0*pq.Hz)
+        self.assertEqual(blck.segments[0].imagesequences[0].spatial_scale, 1.0 * pq.micrometer)
+
+        # end of directory
+        shutil.rmtree(directory)
+
+
+if __name__ == "__main__":
+    unittest.main()

setup.py

@@ -14,6 +14,7 @@
     'neomatlabio': ['scipy>=0.12.0'],
     'nixio': ['nixio>=1.5.0b2'],
     'stimfitio': ['stfio'],
+    'tiffio':['pillow']
 }
 
 if os.environ.get('TRAVIS') == 'true' and \