def test_gray2rgba_dtype():
img_f64 = np.random.random((5, 5))
img_f32 = img_f64.astype('float32')
img_u8 = img_as_ubyte(img_f64)
img_int = img_u8.astype(int)
for img in [img_f64, img_f32, img_u8, img_int]:
assert gray2rgba(img).dtype == img.dtype
def test_gray2rgba_alpha():
img = np.random.random((5, 5))
img_u8 = img_as_ubyte(img)
# Default
alpha = None
rgba = gray2rgba(img, alpha)
assert_equal(rgba[..., :3], gray2rgb(img))
assert_equal(rgba[..., 3], 1.0)
# Scalar
alpha = 0.5
rgba = gray2rgba(img, alpha)
assert_equal(rgba[..., :3], gray2rgb(img))
assert_equal(rgba[..., 3], alpha)
# Array
alpha = np.random.random((5, 5))
rgba = gray2rgba(img, alpha)
assert_equal(rgba[..., :3], gray2rgb(img))
assert_equal(rgba[..., 3], alpha)
# Warning about alpha cast
alpha = 0.5
with expected_warnings(["alpha can't be safely cast to image dtype"]):
rgba = gray2rgba(img_u8, alpha)
assert_equal(rgba[..., :3], gray2rgb(img_u8))
# Invalid shape
alpha = np.random.random((5, 5, 1))
expected_err_msg = ("could not broadcast input array from shape (5,5,1) "
"into shape (5,5)")
with pytest.raises(ValueError) as err:
rgba = gray2rgba(img, alpha)
assert expected_err_msg == str(err.value)
def colorize(image, T):
"""Colorize image
Parameters
----------
image : (M, N) array
Returns
-------
rescaled : rgba float array
Color transformed image
"""
# Convert to rgba
rgba = color.gray2rgba(image, alpha=True)
# Apply transform
transformed = np.dot(rgba, T)
rescaled = exposure.rescale_intensity(transformed)
return rescaled
def test_gray2rgba(shape):
# nD case
img = np.random.random(shape)
rgba = gray2rgba(img)
# Shape check
assert_equal(rgba.shape, shape + (4, ))
# dtype check
assert rgba.dtype == img.dtype
# RGB channels check
for channel in range(3):
assert_equal(rgba[..., channel], img)
# Alpha channel check
assert_equal(rgba[..., 3], 1.0)
def __init__(self, parent, imgPaths, fov_id_list,
image_dir): #,frame_index,peak_id,fov_id):
super(PhaseWidget, self).__init__(parent)
self.image_dir = image_dir
self.imgPaths = imgPaths
self.fov_id_list = fov_id_list
self.fovIndex = 0
self.fov_id = self.fov_id_list[self.fovIndex]
self.imgIndex = 0
self.phaseImgPath = self.imgPaths[self.fov_id][self.imgIndex][0]
self.phaseStack = io.imread(self.phaseImgPath)
self.frameIndex = 0
self.img = self.phaseStack[self.frameIndex, :, :]
self.originalImgMax = np.max(self.img)
# self.originalImgMax = np.max(self.phaseStack)
originalRGBImg = color.gray2rgb(self.img)
self.originalPhaseQImage = QImage(originalRGBImg,
originalRGBImg.shape[1],
originalRGBImg.shape[0],
originalRGBImg.strides[0],
QImage.Format_RGBA64)
rescaledImg = self.img / self.originalImgMax * (2**16 - 1)
RGBImg = color.gray2rgba(rescaledImg)
self.originalHeight, self.originalWidth, self.originalChannelNumber = RGBImg.shape
self.phaseQimage = QImage(
RGBImg, RGBImg.shape[1], RGBImg.shape[0], RGBImg.strides[0],
QImage.Format_RGBA64).scaled(1024,
1024,
aspectRatioMode=Qt.KeepAspectRatio)
self.phaseQpixmap = QPixmap(self.phaseQimage)
# rescaledImg = self.img/self.originalImgMax*255
# RGBImg = color.gray2rgb(rescaledImg).astype('uint8')
# self.originalHeight, self.originalWidth, self.originalChannelNumber = RGBImg.shape
# self.phaseQimage = QImage(RGBImg, RGBImg.shape[1], RGBImg.shape[0], RGBImg.strides[0], QImage.Format_RGB888).scaled(1024, 1024, aspectRatioMode=Qt.KeepAspectRatio)
# self.phaseQpixmap = QPixmap(self.phaseQimage)
self.label = QLabel(self)
self.label.setPixmap(self.phaseQpixmap)
def test_gray2rgba(shape, channel_axis):
# nD case
img = np.random.random(shape)
rgba = gray2rgba(img, channel_axis=channel_axis)
assert rgba.ndim == img.ndim + 1
# Shape check
new_axis_loc = channel_axis % rgba.ndim
assert_equal(rgba.shape,
shape[:new_axis_loc] + (4, ) + shape[new_axis_loc:])
# dtype check
assert rgba.dtype == img.dtype
# RGB channels check
for channel in range(3):
assert_equal(rgba[slice_at_axis(channel, axis=new_axis_loc)], img)
# Alpha channel check
assert_equal(rgba[slice_at_axis(3, axis=new_axis_loc)], 1.0)