def test_encoder_header(self):
roi_obj_write = ROIRect(20, 30, 40, 50, name='test_name_header')
temp_path = 'temp_file.roi'
roi_obj_write.header = {
'C_POSITION': 1,
'Z_POSITION': 2,
'T_POSITION': 3,
'POSITION': 4
}
with ROIEncoder(temp_path, roi_obj_write) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj_read = roi.get_roi()
self.assertIsInstance(roi_obj_read, ROIRect)
self.assertEqual(roi_obj_read.top, 20)
self.assertEqual(roi_obj_read.left, 30)
self.assertEqual(roi_obj_read.bottom, 40)
self.assertEqual(roi_obj_read.right, 50)
self.assertEqual(roi_obj_read.name, 'test_name_header')
#todo name not properly displayed if loaded into imagej (issue)
self.assertEqual(roi_obj_read.header['C_POSITION'], 1)
self.assertEqual(roi_obj_read.header['Z_POSITION'], 2)
self.assertEqual(roi_obj_read.header['T_POSITION'], 3)
self.assertEqual(roi_obj_read.header['POSITION'], 4)
def test_encoder_polyline(self):
x_coords = np.array([1, 2, 3, 10, 15])
y_coords = np.array([4, 5, 6, 8, 20])
roi_obj = ROIPolyline(20,
40,
20 + x_coords.max(),
40 + y_coords.max(),
x_coords,
y_coords,
name='polyline_test')
temp_path = 'temp_file.roi'
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj_read = roi.get_roi()
self.assertIsInstance(roi_obj_read, ROIPolyline)
self.assertEqual(roi_obj_read.top, 20)
self.assertEqual(roi_obj_read.left, 40)
self.assertTrue(np.allclose(roi_obj_read.x_coords, x_coords))
self.assertTrue(np.allclose(roi_obj_read.y_coords, y_coords))
self.assertEqual(roi_obj_read.name, 'polyline_test')
os.remove(temp_path)
def test_encoder_polygon(self):
y_coords = np.array([45, 30, 0, 12, 20])
x_coords = np.array([0, 13, 25, 60, 5])
left = 22
top = 30
right = left + np.max(x_coords) - np.min(x_coords) + 1
bottom = top + np.max(y_coords) - np.min(y_coords) + 1
roi_obj = ROIPolygon(top,
left,
bottom,
right,
x_coords,
y_coords,
name='polygon_test')
temp_path = tempfile.mkstemp()[1]
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIPolygon)
self.assertEqual(roi_obj.top, top)
self.assertEqual(roi_obj.left, left)
self.assertEqual(roi_obj.bottom, bottom)
self.assertEqual(roi_obj.right, right)
self.assertTrue(np.allclose(x_coords, roi_obj.x_coords))
self.assertTrue(np.allclose(y_coords, roi_obj.y_coords))
self.assertEqual('polygon_test', roi_obj.name)
def test_decoder_line(self):
with ROIDecoder('line.roi') as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROILine)
self.assertEqual(roi_obj.x1, 134.75)
self.assertEqual(roi_obj.y1, 254.0)
self.assertEqual(roi_obj.x2, 195.75)
self.assertEqual(roi_obj.y2, 289.625)
self.assertEqual(roi_obj.name, 'line')
def test_decoder_rect(self):
with ROIDecoder('rect.roi') as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIRect)
self.assertEqual(roi_obj.top, 0)
self.assertEqual(roi_obj.left, 0)
self.assertEqual(roi_obj.bottom, 55)
self.assertEqual(roi_obj.right, 114)
self.assertEqual(roi_obj.area, 6270)
def test_decoder_header(self):
with ROIDecoder('rect_slice4.roi') as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIRect)
self.assertEqual(roi_obj.top, 67)
self.assertEqual(roi_obj.left, 124)
self.assertEqual(roi_obj.bottom, 130)
self.assertEqual(roi_obj.right, 187)
self.assertEqual(roi_obj.name, 'rect_slice4')
self.assertEqual(roi_obj.header['POSITION'], 4)
def test_decoder_oval(self):
with ROIDecoder(os.path.join(directory, 'oval.roi')) as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIOval)
self.assertEqual(roi_obj.top, 57)
self.assertEqual(roi_obj.left, 25)
self.assertEqual(roi_obj.bottom, 98)
self.assertEqual(roi_obj.right, 115)
self.assertEqual(roi_obj.area, np.pi * (115 - 25) * (98 - 57) / 4)
def test_decoder_rect(self):
with ROIDecoder('rect.roi') as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIRect)
self.assertEqual(roi_obj.top, 119)
self.assertEqual(roi_obj.left, 136)
self.assertEqual(roi_obj.bottom, 194)
self.assertEqual(roi_obj.right, 247)
self.assertEqual(roi_obj.area, 8325)
self.assertEqual(roi_obj.name, 'rectangle')
def test_decoder_oval(self):
with ROIDecoder('oval.roi') as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIOval)
self.assertEqual(roi_obj.width, 61)
self.assertEqual(roi_obj.height, 33)
self.assertEqual(roi_obj.left, 143)
self.assertEqual(roi_obj.bottom, 248)
self.assertEqual(roi_obj.right, 204)
self.assertEqual(roi_obj.name, 'oval')
def test_decoder_rounded_rect(self):
with ROIDecoder('rounded_rectangle.roi') as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIRect)
self.assertEqual(roi_obj.top, 276)
self.assertEqual(roi_obj.left, 145)
self.assertEqual(roi_obj.bottom, 301)
self.assertEqual(roi_obj.right, 191)
self.assertAlmostEqual(roi_obj.area, 1064.15926536)
self.assertEqual(roi_obj.name, 'rounded_rectangle')
def test_decoder_polygon(self):
with ROIDecoder(os.path.join(directory, 'polygon.roi')) as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIPolygon)
self.assertEqual(roi_obj.top, 81)
self.assertEqual(roi_obj.left, 34)
self.assertEqual(roi_obj.bottom, 126)
self.assertEqual(roi_obj.right, 86)
self.assertTrue(np.allclose([6, 0, 35, 51, 25, 14], roi_obj.x_coords))
self.assertTrue(np.allclose([14, 44, 42, 17, 1, 0], roi_obj.y_coords))
def test_encoder_oval(self):
roi_obj = ROIOval(100, 25, 150, 50, name='oval_test')
temp_path = tempfile.mkstemp()[1]
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIOval)
self.assertEqual(roi_obj.top, 100)
self.assertEqual(roi_obj.left, 25)
self.assertEqual(roi_obj.bottom, 150)
self.assertEqual(roi_obj.right, 50)
self.assertEqual(roi_obj.area, np.pi * (50 - 25) * (150 - 100) / 4)
self.assertEqual(roi_obj.name, 'oval_test')
def test_encoder_rect(self):
roi_obj = ROIRect(20, 30, 40, 50, name='rect_test')
temp_path = tempfile.mkstemp()[1]
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_out = roi.get_roi()
self.assertIsInstance(roi_out, ROIRect)
self.assertEqual(roi_out.top, 20)
self.assertEqual(roi_out.left, 30)
self.assertEqual(roi_out.bottom, 40)
self.assertEqual(roi_out.right, 50)
self.assertEqual(roi_out.area, 400)
self.assertEqual(roi_out.name, 'rect_test')
def test_encoder_rect(self):
roi_obj = ROIRect(20, 30, 40, 50)
temp_path = tempfile.mkstemp()[1]
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIRect)
self.assertEqual(roi_obj.top, 20)
self.assertEqual(roi_obj.left, 30)
self.assertEqual(roi_obj.bottom, 40)
self.assertEqual(roi_obj.right, 50)
self.assertEqual(roi_obj.area, 400)
os.remove(temp_path)
def test_decoder_polygon(self):
with ROIDecoder('polygon.roi') as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIPolygon)
self.assertEqual(roi_obj.top, 49)
self.assertEqual(roi_obj.left, 120)
self.assertEqual(roi_obj.bottom, 137)
self.assertEqual(roi_obj.right, 228)
print(roi_obj.width)
print(roi_obj.left - roi_obj.right)
#todo figure out this difference
self.assertEqual(len(roi_obj.x_coords), 9)
self.assertEqual(len(roi_obj.y_coords), 9)
self.assertArrayEqual(roi_obj.x_coords,
np.array([29, 19, 55, 89, 93, 107, 108, 0, 4]))
self.assertArrayEqual(roi_obj.y_coords,
np.array([56, 88, 86, 37, 76, 70, 0, 17, 46]))
def test_encoder_line(self):
x1, y1, x2, y2 = 23., 256., 200, 305.
roi_obj = ROILine(x1, y1, x2, y2, name='Line_test')
temp_path = tempfile.mkstemp()[1]
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj_read = roi.get_roi()
self.assertIsInstance(roi_obj_read, ROILine)
self.assertEqual(roi_obj_read.x1, x1)
self.assertEqual(roi_obj_read.x2, x2)
self.assertEqual(roi_obj_read.y1, y1)
self.assertEqual(roi_obj_read.y2, y2)
self.assertEqual(roi_obj_read.name, 'Line_test')
self.assertEqual(roi_obj_read.area, 0)
def test_encoder_polygon(self):
x_coords = [1, 2, 3]
y_coords = [4, 5, 6]
roi_obj = ROIPolygon(20, 40, x_coords, y_coords, name='polygon_test')
temp_path = 'temp_file.roi'
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj_read = roi.get_roi()
self.assertIsInstance(roi_obj_read, ROIPolygon)
self.assertEqual(roi_obj_read.top, 20)
self.assertEqual(roi_obj_read.left, 40)
self.assertArrayEqual(roi_obj_read.x_coords, x_coords)
self.assertArrayEqual(roi_obj_read.y_coords, y_coords)
self.assertEqual(roi_obj_read.name, 'polygon_test')
def test_encoder_oval(self):
top, left, bottom, right = 230, 240, 255, 280
roi_obj = ROIOval(top, left, bottom, right, name='Oval_test')
temp_path = 'temp_file.roi'
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj_read = roi.get_roi()
self.assertIsInstance(roi_obj_read, ROIOval)
self.assertEqual(roi_obj_read.top, top)
self.assertEqual(roi_obj_read.left, left)
self.assertArrayEqual(roi_obj_read.bottom, bottom)
self.assertArrayEqual(roi_obj_read.right, right)
self.assertEqual(roi_obj_read.name, 'Oval_test')
self.assertEqual(roi_obj_read.area, roi_obj.area)
def test_encoder_rect(self):
roi_obj_write = ROIRect(20, 30, 40, 50, name='test_name')
temp_path = 'temp_file.roi'
with ROIEncoder(temp_path, roi_obj_write) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj_read = roi.get_roi()
self.assertIsInstance(roi_obj_read, ROIRect)
self.assertEqual(roi_obj_read.top, 20)
self.assertEqual(roi_obj_read.left, 30)
self.assertEqual(roi_obj_read.bottom, 40)
self.assertEqual(roi_obj_read.right, 50)
self.assertEqual(roi_obj_read.area, 400)
self.assertEqual(roi_obj_read.name, 'test_name')
os.remove(temp_path)
def test_encoder_line(self):
x1, y1, x2, y2 = 23.5, 256.8, 200, 305.756
roi_obj = ROILine(x1, y1, x2, y2, name='Line_test')
temp_path = 'temp_file.roi'
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj_read = roi.get_roi()
self.assertIsInstance(roi_obj_read, ROILine)
self.assertEqual(roi_obj_read.x1, x1)
self.assertEqual(roi_obj_read.x2, x2)
self.assertAlmostEqual(roi_obj_read.y1, y1, places=1)
self.assertAlmostEqual(roi_obj_read.y2, y2, places=1)
#todo warn about inaccuracy?
self.assertEqual(roi_obj_read.name, 'Line_test')
self.assertEqual(roi_obj_read.area, 0)
def test_encoder_freeline(self):
x_coords = [1, 2, 3, 10, 15]
y_coords = [4, 5, 6, 8, 20]
roi_obj = ROIFreeLine(20, 40, x_coords, y_coords, name='freeline_test')
temp_path = 'temp_file.roi'
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj_read = roi.get_roi()
self.assertIsInstance(roi_obj_read, ROIFreeLine)
self.assertEqual(roi_obj_read.top, 20)
self.assertEqual(roi_obj_read.left, 40)
self.assertArrayEqual(roi_obj_read.x_coords, x_coords)
self.assertArrayEqual(roi_obj_read.y_coords, y_coords)
self.assertEqual(roi_obj_read.name, 'freeline_test')
os.remove(temp_path)
def test_encoder_freehand(self):
x_coords = np.array([1, 2, 3, 10, 15])
y_coords = np.array([4, 5, 6, 8, 20])
roi_obj = ROIFreehand(20,
40,
20 + x_coords.max(),
40 + y_coords.max(),
x_coords,
y_coords,
name='freehand_test')
temp_path = tempfile.mkstemp()[1]
with ROIEncoder(temp_path, roi_obj) as roi:
roi.write()
with ROIDecoder(temp_path) as roi:
roi_obj_read = roi.get_roi()
self.assertIsInstance(roi_obj_read, ROIFreehand)
self.assertEqual(roi_obj_read.top, 20)
self.assertEqual(roi_obj_read.left, 40)
self.assertTrue(np.allclose(roi_obj_read.x_coords, x_coords))
self.assertTrue(np.allclose(roi_obj_read.y_coords, y_coords))
self.assertEqual(roi_obj_read.name, 'freehand_test')
def test_decoder_freehand(self):
with ROIDecoder('freehand.roi') as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIFreehand)
self.assertEqual(len(roi_obj.x_coords), 117)
def test_decoder_polyline(self):
with ROIDecoder(os.path.join(directory, 'polyline.roi')) as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIPolyline)
self.assertEqual(len(roi_obj.x_coords), 8)
self.assertEqual(roi_obj.name, 'polyline')
def test_decoder_freeline(self):
with ROIDecoder('freehand_line.roi') as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIFreeLine)
def test_decoder_polyline(self):
with ROIDecoder('polyline.roi') as roi:
roi_obj = roi.get_roi()
self.assertIsInstance(roi_obj, ROIPolyline)
self.assertEqual(len(roi_obj.x_coords), 18)
self.assertEqual(roi_obj.name, 'polyline')