def lucid_transforms(img, jitter=None, scale=.5, degrees=45, **kwargs):
h,w = img.shape[-2], img.shape[-1]
if jitter is None:
jitter = min(h,w)//2
fastai_image = vision.Image(img.squeeze())
# pad
fastai_image._flow = gpu_affine_grid(fastai_image.shape)
vision.transform.pad()(fastai_image, jitter)
# jitter
first_jitter = int((jitter*(2/3)))
vision.transform.crop_pad()(fastai_image,
(h+first_jitter,w+first_jitter),
row_pct=np.random.rand(), col_pct=np.random.rand())
# scale
percent = scale * 100 # scale up to integer to avoid float repr errors
scale_factors = [(100 - percent + percent/5. * i)/100 for i in range(11)]
rand_scale = scale_factors[int(np.random.rand()*len(scale_factors))]
fastai_image._flow = gpu_affine_grid(fastai_image.shape)
vision.transform.zoom()(fastai_image, rand_scale)
# rotate
rotate_factors = list(range(-degrees, degrees+1)) + degrees//2 * [0]
rand_rotate = rotate_factors[int(np.random.rand()*len(rotate_factors))]
fastai_image._flow = gpu_affine_grid(fastai_image.shape)
vision.transform.rotate()(fastai_image, rand_rotate)
# jitter
vision.transform.crop_pad()(fastai_image, (h,w), row_pct=np.random.rand(), col_pct=np.random.rand())
return fastai_image.data[None,:]
def visualize_feature(model, layer, feature, start_image=None, last_hook_out=None,
size=200, steps=500, lr=0.004, weight_decay=0.1, grad_clip=1,
debug=False, frames=10, show=True, **kwargs):
h,w = size if type(size) is tuple else (size,size)
if start_image is not None:
fastai_image = vision.Image(start_image.squeeze())
fastai_image._flow = gpu_affine_grid((3,h,w)) # resize
img_buf = fastai_image.data[None,:]
img_buf = normalize(img_buf)
img_buf = rgb_to_lucid_colorspace(img_buf)
img_buf = rgb_to_fft(h, w, img_buf, **kwargs)
else:
img_buf = init_fft_buf(h, w, **kwargs)
img_buf.requires_grad_()
opt = torch.optim.AdamW([img_buf], lr=lr, weight_decay=weight_decay)
hook_out = None
def callback(m, i, o):
nonlocal hook_out
hook_out = o
hook = layer.register_forward_hook(callback)
for i in range(1,steps+1):
opt.zero_grad()
img = fft_to_rgb(h, w, img_buf, **kwargs)
img = lucid_colorspace_to_rgb(img)
stats = tensor_stats(img)
img = torch.sigmoid(img)*2 - 1
img = lucid_transforms(img, **kwargs)
model(img.cuda())
if feature is None:
loss = -1 * hook_out[0].pow(2).mean()
else:
loss = -1 * hook_out[0][feature].mean()
if last_hook_out is not None:
simularity = cossim(hook_out[0], last_hook_out, **kwargs)
loss = loss + loss * simularity
loss.backward()
torch.nn.utils.clip_grad_norm_(img_buf,grad_clip)
opt.step()
if debug and (i)%(int(steps/frames))==0:
clear_output(wait=True)
label = f"step: {i} loss: {loss:.2f} stats:{stats}"
show_rgb(image_buf_to_rgb(h, w, img_buf, **kwargs),
label=label, **kwargs)
hook.remove()
retval = image_buf_to_rgb(h, w, img_buf, **kwargs)
if show:
if not debug: show_rgb(retval, **kwargs)
return retval, hook_out[0].clone().detach()
def open_nii_image(fn):
x = None
if str(fn).split('.')[-1] == 'nrrd':
_nrrd = nrrd.read(str(fn))
x = _nrrd[0]
else:
load_data = LoadNifti(image_only=True)
x = load_data(fn)
if x is None: raise TypeError
return fvision.Image(torch.Tensor(x[None]))
def Forward(inputImgName: str, Color):
outputImgName = inputImgName.with_name(str(inputImgName.stem) + "-seg.png")
Img = fv.open_image(inputImgName)
originalSize = Img.size
Img = Img.resize(500)
Res = Learn.predict(Img)[0]
# Colorization
Mask = (Res.data == 255)
R, G, B, A = [
torch.zeros((1, 500, 500), dtype=torch.uint8) for _ in range(4)
]
R[Mask], G[Mask], B[Mask] = Color
A[Mask] = 255
ColorMask = fv.Image(torch.cat([R, G, B, A]))
Pil_Img = to_pil(ColorMask.data.detach().cpu().type(torch.ByteTensor))
Pil_Img = Pil_Img.resize(originalSize[::-1])
Pil_Img.save(outputImgName)
return outputImgName
def open_tiff(fn: faiv.PathOrStr) -> faiv.Image:
""" open a 1 channel tif image and transform it into a fastai image """
return faiv.Image(
torch.Tensor(np.asarray(Image.open(fn), dtype=np.float32)[None, ...]))
def open_nii(fn: str) -> faiv.Image:
""" Return fastai `Image` object created from NIfTI image in file `fn`."""
x = nib.load(str(fn)).get_data()
return faiv.Image(torch.Tensor(x))
def reconstruct(self, t: torch.Tensor):
return ImageTuple(faiv.Image(t[0]), faiv.Image(t[1]))
def reconstruct(self, t: torch.Tensor):
if len(t.size()) == 0: return t
return ImageTuple(faiv.Image(t[0]), faiv.Image(t[1]))
def to_one(self):
return faiv.Image(torch.cat(self.data, 2))
def open_tiff(fn: str) -> faiv.Image:
""" Return fastai `Image` object created from Tiff image in file `fn`."""
return faiv.Image(
torch.Tensor(np.asarray(Image.open(fn), dtype=np.float32)[None, ...]))