def downscale(data, downscale_factor):
new_data = []
for i, (stk,roi) in enumerate(data):
new_stk = downscale_local_mean(stk, (1,downscale_factor,downscale_factor))
new_roi = downscale_local_mean(roi, (1,downscale_factor,downscale_factor))
new_data.append((new_stk, new_roi))
return new_data
def test_downscale_local_mean():
image1 = np.arange(4 * 6).reshape(4, 6)
out1 = downscale_local_mean(image1, (2, 3))
expected1 = np.array([[4., 7.], [16., 19.]])
assert_array_equal(expected1, out1)
image2 = np.arange(5 * 8).reshape(5, 8)
out2 = downscale_local_mean(image2, (4, 5))
expected2 = np.array([[14., 10.8], [8.5, 5.7]])
assert_array_equal(expected2, out2)
def main(): args = vars(parser.parse_args()) filename = os.path.join(os.getcwd(), args["image"][0]) image = skimage.img_as_uint(color.rgb2gray(io.imread(filename))) subsample = 1 if (not args["subsample"] == 1): subsample = args["subsample"][0] image = transform.downscale_local_mean(image, (subsample, subsample)) image = transform.pyramid_expand(image, subsample, 0, 0) image = exposure.rescale_intensity(image, out_range=(0,args["depth"][0])) if (args["visualize"]): io.imshow(image) io.show() source = generate_face(image, subsample, args["depth"][0], FLICKER_SPEED) if source: with open(args["output"][0], 'w') as file_: file_.write(source) else: print "Attempted to generate source code, failed."
def make_hips_allsky_jpeg_file(order):
log.info(f'Making HiPS allsky image for order {order}')
tiles = []
for ipix in range(healpix_order_to_npix(order=order)):
log.info(f'Processing tile {ipix}')
meta = HipsTileMeta(order=order, ipix=ipix, file_format='jpg', frame='galactic', width=2 ** shift_order)
filename = DATA_DIR / 'maps' / 'Fermi10GeV' / meta.tile_default_path
tile = HipsTile.read(meta, filename)
# Downsample the tile
factor = 2 ** allsky_downsample_order
# import IPython; IPython.embed(); 1/0
data = downscale_local_mean(tile.data, factors=(factor, factor, 1))
meta.order -= allsky_downsample_order
meta.width //= factor
# This is to debug when all-sky is shown
data[:, :, 0] = 255
tile = HipsTile.from_numpy(meta, data.astype('uint8'))
# print(tile.data.shape, tile.meta)
tiles.append(tile)
allsky = HipsTileAllskyArray.from_tiles(tiles)
path = DATA_DIR / 'maps' / 'Fermi10GeV' / f'Norder{order}' / 'Allsky.jpg'
# path.parent.mkdir(exist_ok=True, parents=True)
log.info(f'Writing {path}')
allsky.write(path)
def load_and_downscale(input_filename):
"""Load the image, covert to grayscale and downscale as needed."""
image = Image.from_file(input_filename)
blue_channel = image[:,:,2]
downscaled = downscale_local_mean(blue_channel, (2, 2))
return downscaled
def downscale_in_chunks(im, downscale_tuple=None, nfrchunk=1000, print_status=True):
cL = []
if print_status: print('downscaling frames... ', end='')
for iC in range(int(np.ceil(im.shape[0]/nfrchunk))):
maxfr = np.min((nfrchunk*(iC+1),im.shape[0]))
cL.append(transform.downscale_local_mean(im[nfrchunk*iC:maxfr,:,:],
downscale_tuple))
if print_status: print(maxfr, end=' ')
if print_status: print('done.')
return(np.concatenate(cL,axis=0))
def generate_column(numbers):
images = []
for i in numbers:
i = selected[i]
image_fpath = dataset.item_content_abspath(i)
images.append(
downscale_local_mean(Image.from_file(image_fpath), (5, 5, 1))
)
column = join_horizontally(images)
return column
def preprocess(data, radius):
for i, (stk,roi) in enumerate(data):
# Normalize
low_p = np.percentile(stk.flatten(), 3)
high_p = np.percentile(stk.flatten(), 99)
#print np.min(stk.flatten()), low_p, high_p, np.max(stk.flatten())
# plt.figure()
# plt.hist(stk.flatten())
# plt.figure()
# plt.imshow(downscale_local_mean(stk[0], (DOWNSCALE_FACTOR, DOWNSCALE_FACTOR)), cmap="gray")
# plt.figure()
# plt.imshow(downscale_local_mean(np.mean(stk, axis=0), (DOWNSCALE_FACTOR, DOWNSCALE_FACTOR)), cmap="gray")
stk = np.clip(stk, low_p, high_p)
stk = stk - stk.mean()
stk = np.divide(stk-np.min(stk), np.max(stk) - np.min(stk))
#print np.min(stk.flatten()), np.max(stk.flatten())
# plt.figure()
# plt.hist(stk.flatten())
# Downscale
stk = downscale_local_mean(stk, (1,DOWNSCALE_FACTOR,DOWNSCALE_FACTOR))
roi = downscale_local_mean(roi, (1,DOWNSCALE_FACTOR,DOWNSCALE_FACTOR))
new_stk = np.zeros((stk.shape[1], stk.shape[2], IMG_CHANNELS))
# Uncomment following 2 lines to use more channels
#new_stk[:,:,2] = stk.max(axis=0)
#new_stk[:,:,1] = np.std(stk, axis=0)
new_stk[:,:,0] = np.mean(stk, axis=0)
# plt.figure()
# plt.imshow(stk[0], cmap="gray")
# plt.figure()
# plt.imshow(new_stk[:,:,0], cmap="gray")
# plt.show()
roi_centroids = get_centroids(roi, radius).max(axis=0)
data[i] = (new_stk, roi.max(axis=0), roi.max(axis=0))#(new_stk, roi_centroids, roi.max(axis=0))
return data
def auto_centre(self, window=400, downsample_y=2, plot=True):
"""
Automatic method for finding the centre of rotation.
# window: Window width to search across (pixels).
"""
downsample = (downsample_y, 1)
half_win = window // 2
win_range = range(-half_win, half_win)
# Compare ref image with flipped 180deg counterpart
ref_image = self.im_stack[:, half_win:-half_win, self.p0]
ref = downscale_local_mean(ref_image, downsample)
im_180_image = self.im_stack[:, :, self.num_images // 2 + self.p0]
im_180 = downscale_local_mean(im_180_image, downsample)
flipped = np.fliplr(im_180)
diff = np.nan * np.zeros(len(win_range))
# Flip win_range as we are working on flipped data
for idx, i in enumerate(win_range[::-1]):
cropped = flipped[:, half_win + i: -half_win + i]
tmp = cropped - ref
diff[idx] = tmp.std()
minima = np.argmin(diff)
self.cor_offset = win_range[minima]
print('COR = %i' % self.cor_offset)
if plot:
fig, ax = plt.subplots()
fig.canvas.set_window_title('Centre Analysis')
ax.plot([i for i in win_range], diff)
ax.plot(self.cor_offset, np.min(diff), '*')
ax.set_ylabel('Standard deviation (original v 180deg flipped)')
ax.set_xlabel('2 * Centre correction (pixels)')
im_copy = np.copy(self.im_stack[:, :, self.p0])
recentre_plot(im_copy, self.cor_offset)
def load_dir(dir_name, ext='.tif'):
X, Y = [], []
fns = glob.glob(dir_name+'/*' + ext)
random.shuffle(fns)
for fn in fns:
img = np.array(io.imread(fn), dtype='float32')
scaled = img / np.float32(255.0)
scaled = downscale_local_mean(scaled, factors=(2,2))
X.append(scaled)
Y.append(os.path.basename(fn).split('_')[0])
return X, Y
def process_line(t):
i, row = t
image_urls = row[0].split(',')
for image_url in image_urls:
if 'http' in image_url:
try:
image_data = imread(image_url)
grayed = rgb2gray(image_data)
image_resized = resize(grayed, (100, 100))
descriptor = local_binary_pattern(image_resized, 3, 20, 'uniform')
descriptor = downscale_local_mean(descriptor, (10, 10))
descriptor_list = np.floor(descriptor.flatten()).tolist()
return [image_url, row[2], descriptor_list]
except:
return [image_url, row[2], []]
def resample_binary_majority(raster, factor):
resampled = downscale_local_mean(raster, factors=factor)
resampled_bool = np.zeros_like(resampled)
resampled_bool[resampled >= 0.5] = 1
mask = np.ones_like(resampled)
if raster.shape[0] % factor[0] != 0:
y = (factor[0] - (raster.shape[0] % factor[0])) * -1
mask[y:,:] = 0
if raster.shape[1] % factor[1] != 0:
x = (factor[1] - (raster.shape[1] % factor[1])) * -1
mask[:,x:] = 0
# Create mask
mask = mask.astype(bool)
return [factor, resampled_bool, mask]
def _build_expected_output(self):
funcs = (grey.erosion, grey.dilation, grey.opening, grey.closing,
grey.white_tophat, grey.black_tophat)
selems_2D = (selem.square, selem.diamond,
selem.disk, selem.star)
with expected_warnings(['Possible precision loss']):
image = img_as_ubyte(transform.downscale_local_mean(
color.rgb2gray(data.coffee()), (20, 20)))
output = {}
for n in range(1, 4):
for strel in selems_2D:
for func in funcs:
key = '{0}_{1}_{2}'.format(strel.__name__, n, func.__name__)
output[key] = func(image, strel(n))
return output
def render(img, color_samples):
print("Rendering...")
h, w = [2*x for x in img.shape[:2]]
xx, yy = np.meshgrid(np.arange(h), np.arange(w))
pixel_coords = np.c_[xx.ravel(), yy.ravel()]
colors = np.empty([h, w, 3])
coords = []
for color_sample in color_samples:
coord = tuple(x*2 for x in color_sample[:2][::-1])
colors[coord] = color_sample[2:]
coords.append(coord)
tree = KDTree(coords)
idxs = tree.query(pixel_coords)[1]
data = colors[tuple(tree.data[idxs].astype(int).T)].reshape((w, h, 3))
data = np.transpose(data, (1, 0, 2))
return downscale_local_mean(data, (2, 2, 1))
def test():
test_images, test_categories = [], []
for fn in glob.glob('data/splits/test/*.tif'):
img = np.array(io.imread(fn), dtype='float32')
scaled = img / np.float32(255.0)
scaled = downscale_local_mean(scaled, factors=(2,2))
test_images.append(scaled)
test_categories.append(os.path.basename(fn).split('_')[0])
label_encoder = pickle.load( open('models/' + MODEL_NAME + '/label_encoder.p', 'rb'))
print('-> Working on classes:', label_encoder.classes_)
test_int_labels = label_encoder.transform(test_categories)
model = model_from_json(open('models/' + MODEL_NAME + '/architecture.json').read())
model.load_weights('models/' + MODEL_NAME + '/weights.hdf5')
test_preds = []
for img in test_images:
X = utils.augment_test_image(image=img,
nb_rows=NB_ROWS,
nb_cols=NB_COLS,
nb_patches=NB_TEST_PATCHES)
preds = np.array(model.predict(X), dtype='float64')
av_pred = preds.mean(axis=0)
test_preds.append(np.argmax(av_pred, axis=0))
print('Test accuracy:', accuracy_score(test_int_labels, test_preds))
# confusion matrix
plt.clf()
T = label_encoder.inverse_transform(test_int_labels)
P = label_encoder.inverse_transform(test_preds)
cm = confusion_matrix(T, P, labels=label_encoder.classes_)
cm_normalized = cm.astype('float') / cm.sum(axis=1)[:, np.newaxis]
np.set_printoptions(precision=2)
sns.plt.figure()
utils.plot_confusion_matrix(cm_normalized, target_names=label_encoder.classes_)
sns.plt.savefig('models/' + MODEL_NAME + '/test_conf_matrix.pdf')
def DetectLargeImage(img_path, div_shape, sigma, neighborhood_size, threshold):
ds, ysize, xsize, yblocks, xblocks, block_size = div_shape
xcoord = []
ycoord = []
for n in range(yblocks):
for m in range(xblocks):
try:
# Read part image
print('Block: n={}, m={}'.format(n, m))
extra = 100
img_extended = np.uint8(
ip.read_image_part_extra(img_path, div_shape, n, m, extra))
img = np.uint8(img_extended[:, extra:-extra, :])
# Convert to a* channel and Cb channel
img_a = cv2.cvtColor(img_extended, cv2.COLOR_BGR2Lab)[:, :, 1]
img_gauss = np.uint8(
ndimage.gaussian_filter(downscale_local_mean(
img, (10, 10, 1)),
sigma=(2.0, 2.0, 0.0)))
#img = None
img_gauss_Cb = cv2.cvtColor(img_gauss, cv2.COLOR_BGR2Lab)[:, :,
2]
img_gauss = None
img_gauss_Cb_bin = img_gauss_Cb < 140
img_gauss_Cb = None
img_gauss_Cb_bin_inv = np.invert(img_gauss_Cb_bin)
img_gauss_Cb_bin = None
img_temp = np.zeros((img_gauss_Cb_bin_inv.shape[0] + 2,
img_gauss_Cb_bin_inv.shape[1] + 2),
dtype=bool)
img_temp[1:-1, 1:-1] = img_gauss_Cb_bin_inv
img_gauss_Cb_bin = np.invert(
ndimage.morphology.binary_fill_holes(img_temp))[1:-1, 1:-1]
img_temp = None
img_gauss_Cb_bin_inv = None
# =============================================================================
# img_plot = ip.Otsu(cv2.cvtColor(img, cv2.COLOR_BGR2Lab)[:,:,1],rev=True)
# grass_plot = resize(img_gauss_Cb_bin,img_plot.shape)
# img_p = np.multiply(img_plot, grass_plot)
# ip.show_image(img_p)
# =============================================================================
# Detect plants using local maxima
try:
xy = Detect(img_a, sigma, neighborhood_size, threshold)
x_arr, y_arr = Filter(xy, block_size, extra=100)
except IndexError:
print('Algorithm found zero points')
continue
img_a = None
sort_idx = y_arr.argsort()
y_arr_sort = y_arr[sort_idx]
x_arr_sort = x_arr[sort_idx]
pos_arr = np.zeros((block_size // 10, block_size // 10),
dtype=int)
pos_arr[np.array(y_arr_sort // 10, dtype=int),
np.array(x_arr_sort // 10, dtype=int)] = np.arange(
0, len(x_arr), 1, dtype=int) + 1
plant_pos = np.multiply(pos_arr, img_gauss_Cb_bin)
pos = np.nonzero(plant_pos)
x_plant = x_arr_sort[plant_pos[pos] - 1]
y_plant = y_arr_sort[plant_pos[pos] - 1]
xcoord += list(x_plant + m * block_size)
ycoord += list(y_plant + n * block_size)
except ValueError:
print(
'Moving on to next block, since this block ({}, {}) is not part of the image'
.format(n, m))
return np.array(xcoord), np.array(ycoord)
def preprocess(self, s):
s = color.rgb2gray(s).astype('float16')
s = s.reshape(list(s.shape) + [1])
s = transf.downscale_local_mean(s, (2, 2, 1)) # Downsample
s = s[17:-8, :, :]
return s
print len(data)
print len(labels)
data = np.array(data)
print data.shape
new_data = []
data = np.array(data)
des = data.shape[0] / 100
if (whichdata == 2):
data = []
labels = []
for i in range(1, 12):
folder = "./Face_data/" + str(i) + "/"
for face in os.listdir(folder):
if ("yale" in face and "info" not in face):
f = misc.imread(folder + face)
f = downscale_local_mean(f, (12, 12))
if (f.shape == (16, 14)):
data.append(f.ravel())
labels.append(i)
data = np.array(data)
labels = np.array(labels)
print data.shape
des = data.shape[0]
data = np.array(data)
acc = []
FPRS = []
TPRS = []
models = []
for _ in range(5):
i_train = random.sample(range(0, data.shape[0]),
def ds(img):
il, ih, iw = img.shape
img_tmp = np.zeros((il, ih / 2, iw / 2))
for i in range(len(img)):
img_tmp[i] = downscale_local_mean(img[i], (2, 2))
return img_tmp
def initialize_components(Y,
K=30,
gSig=[5, 5],
gSiz=None,
ssub=1,
tsub=1,
nIter=5,
maxIter=5,
nb=1,
kernel=None,
use_hals=True,
normalize=True,
img=None,
method='greedy_roi',
max_iter_snmf=500,
alpha_snmf=10e2,
sigma_smooth_snmf=(.5, .5, .5),
perc_baseline_snmf=20):
"""Initalize components
This method uses a greedy approach followed by hierarchical alternative least squares (HALS) NMF.
Optional use of spatio-temporal downsampling to boost speed.
Parameters
----------
Y: np.ndarray
d1 x d2 [x d3] x T movie, raw data.
K: [optional] int
number of neurons to extract (default value: 30).
tau: [optional] list,tuple
standard deviation of neuron size along x and y [and z] (default value: (5,5).
gSiz: [optional] list,tuple
size of kernel (default 2*tau + 1).
nIter: [optional] int
number of iterations for shape tuning (default 5).
maxIter: [optional] int
number of iterations for HALS algorithm (default 5).
ssub: [optional] int
spatial downsampling factor recommended for large datasets (default 1, no downsampling).
tsub: [optional] int
temporal downsampling factor recommended for long datasets (default 1, no downsampling).
kernel: [optional] np.ndarray
User specified kernel for greedyROI (default None, greedy ROI searches for Gaussian shaped neurons)
use_hals: [optional] bool
Whether to refine components with the hals method
normalize: [optional] bool
Whether to normalize data before running the initialization
img: optional [np 2d array]
Image with which to normalize. If not present use the mean + offset
method: str
Initialization method 'greedy_roi' or 'sparse_nmf'
max_iter_snmf: int
Maximum number of sparse NMF iterations
alpha_snmf: scalar
Sparsity penalty
Returns
--------
Ain: np.ndarray
(d1*d2[*d3]) x K , spatial filter of each neuron.
Cin: np.ndarray
T x K , calcium activity of each neuron.
center: np.ndarray
K x 2 [or 3] , inferred center of each neuron.
bin: np.ndarray
(d1*d2[*d3]) x nb, initialization of spatial background.
fin: np.ndarray
nb x T matrix, initalization of temporal background.
"""
if gSiz is None:
gSiz = 2 * np.asarray(gSig) + 1
d, T = np.shape(Y)[:-1], np.shape(Y)[-1]
# rescale according to downsampling factor
gSig = np.round(np.asarray(gSig) // ssub).astype(np.int)
gSiz = np.round(np.asarray(gSiz) // ssub).astype(np.int)
print('Noise Normalization')
if normalize is True:
if img is None:
img = np.mean(Y, axis=-1)
img += np.median(img)
Y = old_div(Y, np.reshape(img, d + (-1, ), order='F'))
alpha_snmf /= np.mean(img)
# spatial downsampling
mean_val = np.mean(Y)
if ssub != 1 or tsub != 1:
print("Spatial Downsampling ...")
Y_ds = downscale_local_mean(Y,
tuple([ssub] * len(d) + [tsub]),
cval=mean_val)
else:
Y_ds = Y
print('Roi Extraction...')
if method == 'greedy_roi':
Ain, Cin, _, b_in, f_in = greedyROI(Y_ds,
nr=K,
gSig=gSig,
gSiz=gSiz,
nIter=nIter,
kernel=kernel,
nb=nb)
if use_hals:
print('Refining Components...')
Ain, Cin, b_in, f_in = hals(Y_ds,
Ain,
Cin,
b_in,
f_in,
maxIter=maxIter)
elif method == 'sparse_nmf':
Ain, Cin, _, b_in, f_in = sparseNMF(Y_ds,
nr=K,
nb=nb,
max_iter_snmf=max_iter_snmf,
alpha=alpha_snmf,
sigma_smooth=sigma_smooth_snmf,
remove_baseline=True,
perc_baseline=perc_baseline_snmf)
# print np.sum(Ain), np.sum(Cin)
# print 'Refining Components...'
# Ain, Cin, b_in, f_in = hals(Y_ds, Ain, Cin, b_in, f_in, maxIter=maxIter)
# print np.sum(Ain), np.sum(Cin)
elif method == 'pca_ica':
Ain, Cin, _, b_in, f_in = ICA_PCA(Y_ds, nr = K, sigma_smooth=sigma_smooth_snmf, truncate = 2, fun='logcosh',\
max_iter=max_iter_snmf, tol=1e-10,remove_baseline=True, perc_baseline=perc_baseline_snmf, nb=nb)
else:
print(method)
raise Exception("Unsupported method")
K = np.shape(Ain)[-1]
ds = Y_ds.shape[:-1]
Ain = np.reshape(Ain, ds + (K, ), order='F')
if len(ds) == 2:
Ain = resize(Ain, d + (K, ), order=1)
else: # resize only deals with 2D images, hence apply resize twice
Ain = np.reshape([resize(a, d[1:] + (K, ), order=1) for a in Ain],
(ds[0], d[1] * d[2], K),
order='F')
Ain = resize(Ain, (d[0], d[1] * d[2], K), order=1)
Ain = np.reshape(Ain, (np.prod(d), K), order='F')
#import pdb
# pdb.set_trace()
b_in = np.reshape(b_in, ds + (nb, ), order='F')
if len(ds) == 2:
b_in = resize(b_in, d + (nb, ), order=1)
else:
b_in = np.reshape([resize(b, d[1:] + (nb, ), order=1) for b in b_in],
(ds[0], d[1] * d[2], nb),
order='F')
b_in = resize(b_in, (d[0], d[1] * d[2], nb), order=1)
b_in = np.reshape(b_in, (np.prod(d), nb), order='F')
Cin = resize(Cin, [K, T])
f_in = resize(np.atleast_2d(f_in), [nb, T])
# center = com(Ain, *d)
center = np.asarray(
[center_of_mass(a.reshape(d, order='F')) for a in Ain.T])
if normalize is True:
#import pdb
# pdb.set_trace()
Ain = Ain * np.reshape(img, (np.prod(d), -1), order='F')
b_in = b_in * np.reshape(img, (np.prod(d), -1), order='F')
# b_in = np.atleast_2d(b_in * img.flatten('F')) #np.reshape(img,
# (np.prod(d), -1),order='F')
Y = Y * np.reshape(img, d + (-1, ), order='F')
return Ain, Cin, b_in, f_in, center
def _forward(self, input_act):
act = downscale_local_mean(np.rollaxis(input_act, 0, 4), (self.pool_size, self.pool_size, 1, 1))
return np.rollaxis(act, 3, 0)
def pre_processing(img):
return transform.downscale_local_mean(img, (2, 2))
def read_and_downscale(f):
img = plt.imread(f)
ds = downscale_local_mean(img[:, :, 2], (10, 10))
return ds[:225, :300]
# There are lots of details to be worked out here, still -- mainly trying to select overlapping image patches. # In[ ]: from skimage.transform import downscale_local_mean img1 = plt.imread(set175[1])[:, :, 2] img2 = plt.imread(set175[3])[:, :, 2] # In[ ]: np.shape(img1), np.shape(img2) # In[ ]: img1ds = downscale_local_mean(img1, (10, 10)) img2ds = downscale_local_mean(img2, (10, 10)) plt.figure(figsize=(8, 10)) plt.subplot(121) plt.imshow(img1ds[:225, :300]) plt.subplot(122) plt.imshow(img2ds[:225, :300]) # For prototyping my goal is to get a bunch of downscaled images so that I can feed them in to test # plausibility of basic NN architecture decisions. # # Dims are subsampled and hard-coded for now so we don't have wrong dimensions showing up here and there. # In[ ]:
def process_image(state):
state = color.rgb2gray(state)
state = np.resize(downscale_local_mean(state, (4, 4)), (1, 60, 64, 1))
return state
def sk_downscale(imageIn, factors):
"""
use the scikit-image method for downsampling
needs a tuple with same number of factors as dim of imgIn
"""
return downscale_local_mean(imageIn, factors)
def downsample(image, factors):
return downscale_local_mean(image, tuple(factors))
def train_model(train_set, images_folder, valid_set):
print('Start training model...')
# Number of training samples
m = train_set.shape[0]
print('Number of samples: ', m)
# Create empty dataframe
x = np.empty((0, 64 * 64 * 3), float)
y = np.empty((0, 384 * 384), float)
for i in range(m):
#print(train_set.iloc[i, 0])
# Read image
image_path = images_folder + '/' + train_set.iloc[i, 0]
img = io.imread(image_path)
# Downscale
img_t = transform.downscale_local_mean(img, (12, 12, 1))
img_t = img_t.astype(np.uint8)
#plt.imshow(img_t.astype(np.uint8))
#plt.show()
#exit(0)
img_norm = img_t.astype(float) / 255.0
# Append to dataframe
rgb = np.reshape(img_norm, (-1, 3))
array = np.concatenate((rgb[:, 0], rgb[:, 1], rgb[:, 2]))
x = np.vstack((x, array))
mask = get_mask(train_set.iloc[i, 1])
y = np.vstack((y, mask))
# Setup the classifier
model = MLPClassifier(hidden_layer_sizes=(4096, 2048),
activation='relu',
max_iter=1000,
learning_rate_init=0.001,
verbose=10)
# Training the model
print('Training model...')
model.fit(x, y)
# Save the model on hard disk for future uses
joblib.dump(model, 'model.joblib')
# Plot loss
fig = plt.figure()
plt.plot(model.loss_curve_)
plt.xlabel('Iteration')
plt.ylabel('Cost')
plt.show()
fig.savefig('error_plot.png')
return model
def __getitem__(self, idx):
if torch.is_tensor(idx):
idx = idx.tolist()
img_name = os.path.join(self.root_dir, "t1/",
self.list_of_images.iloc[idx, 0])
image_t1 = np.load(img_name)
image_t2 = np.load(
os.path.join(self.root_dir, "t2/", self.list_of_images.iloc[idx,
0]))
image_t3 = np.load(
os.path.join(self.root_dir, "t3/", self.list_of_images.iloc[idx,
0]))
image_t4 = np.load(
os.path.join(self.root_dir, "t4/", self.list_of_images.iloc[idx,
0]))
image_t5 = np.load(
os.path.join(self.root_dir, "t5/", self.list_of_images.iloc[idx,
0]))
poss_targets = [image_t1, image_t2, image_t3, image_t4, image_t5]
mediana = [
image_t1.mean(),
image_t2.mean(),
image_t3.mean(),
image_t4.mean(),
image_t5.mean()
]
for i in range(len(mediana)):
for j in range(len(mediana) - 1):
if mediana[i] > mediana[j + 1]:
var = poss_targets[i]
poss_targets[i] = poss_targets[j + 1]
poss_targets[j + 1] = var
target = np.copy(poss_targets[2])
image_t1 = np.transpose(image_t1, (1, 2, 0)) # formato HWC
image_t1 = transform.downscale_local_mean(image_t1, (2, 2, 1))
image_t1 = np.transpose(image_t1, (2, 0, 1)) # formato CHW
image_t2 = np.transpose(image_t2, (1, 2, 0)) # formato HWC
image_t2 = transform.downscale_local_mean(image_t2, (2, 2, 1))
image_t2 = np.transpose(image_t2, (2, 0, 1)) # formato CHW
image_t3 = np.transpose(image_t3, (1, 2, 0)) # formato HWC
image_t3 = transform.downscale_local_mean(image_t3, (2, 2, 1))
image_t3 = np.transpose(image_t3, (2, 0, 1)) # formato CHW
image_t4 = np.transpose(image_t4, (1, 2, 0)) # formato HWC
image_t4 = transform.downscale_local_mean(image_t4, (2, 2, 1))
image_t4 = np.transpose(image_t4, (2, 0, 1)) # formato CHW
image_t5 = np.transpose(image_t5, (1, 2, 0)) # formato HWC
image_t5 = transform.downscale_local_mean(image_t5, (2, 2, 1))
image_t5 = np.transpose(image_t5, (2, 0, 1)) # formato CHW
if self.norm == True:
image_t1 = image_t1 / 32767
image_t2 = image_t2 / 32767
image_t3 = image_t3 / 32767
image_t4 = image_t4 / 32767
image_t5 = image_t5 / 32767
target = target / 32767
if self.stand == True:
image_t1_mean = image_t1.mean(keepdims=True, axis=(1, 2))
image_t1_stddev = image_t1.std(keepdims=True, axis=(1, 2))
image_t1 = (image_t1 - image_t1_mean) / image_t1_stddev
image_t2_mean = image_t2.mean(keepdims=True, axis=(1, 2))
image_t2_stddev = image_t2.std(keepdims=True, axis=(1, 2))
image_t2 = (image_t2 - image_t2_mean) / image_t2_stddev
image_t3_mean = image_t3.mean(keepdims=True, axis=(1, 2))
image_t3_stddev = image_t3.std(keepdims=True, axis=(1, 2))
image_t3 = (image_t3 - image_t3_mean) / image_t3_stddev
image_t4_mean = image_t4.mean(keepdims=True, axis=(1, 2))
image_t4_stddev = image_t4.std(keepdims=True, axis=(1, 2))
image_t4 = (image_t4 - image_t4_mean) / image_t4_stddev
image_t5_mean = image_t5.mean(keepdims=True, axis=(1, 2))
image_t5_stddev = image_t5.std(keepdims=True, axis=(1, 2))
image_t5 = (image_t5 - image_t5_mean) / image_t5_stddev
target_mean = target.mean(keepdims=True, axis=(1, 2))
target_stddev = target.std(keepdims=True, axis=(1, 2))
target = (target - target_mean) / target_stddev
samples = {
'image_1': image_t1.astype('float32'),
'image_2': image_t2.astype('float32'),
'image_3': image_t3.astype('float32'),
'image_4': image_t4.astype('float32'),
'image_5': image_t5.astype('float32')
}
t = {'target': target.astype('float32')}
if self.transform != None:
samples, t = self.transform(samples, t)
return samples, t
def initialize_components(Y, K=30, gSig=[5, 5], gSiz=None, ssub=1, tsub=1, nIter=5, maxIter=5, nb=1,
kernel=None, use_hals=True, normalize=True, img=None, method='greedy_roi', max_iter_snmf=500, alpha_snmf=10e2, sigma_smooth_snmf=(.5, .5, .5), perc_baseline_snmf=20):
"""Initalize components
This method uses a greedy approach followed by hierarchical alternative least squares (HALS) NMF.
Optional use of spatio-temporal downsampling to boost speed.
Parameters
----------
Y: np.ndarray
d1 x d2 [x d3] x T movie, raw data.
K: [optional] int
number of neurons to extract (default value: 30).
tau: [optional] list,tuple
standard deviation of neuron size along x and y [and z] (default value: (5,5).
gSiz: [optional] list,tuple
size of kernel (default 2*tau + 1).
nIter: [optional] int
number of iterations for shape tuning (default 5).
maxIter: [optional] int
number of iterations for HALS algorithm (default 5).
ssub: [optional] int
spatial downsampling factor recommended for large datasets (default 1, no downsampling).
tsub: [optional] int
temporal downsampling factor recommended for long datasets (default 1, no downsampling).
kernel: [optional] np.ndarray
User specified kernel for greedyROI (default None, greedy ROI searches for Gaussian shaped neurons)
use_hals: [optional] bool
Whether to refine components with the hals method
normalize: [optional] bool
Whether to normalize data before running the initialization
img: optional [np 2d array]
Image with which to normalize. If not present use the mean + offset
method: str
Initialization method 'greedy_roi' or 'sparse_nmf'
max_iter_snmf: int
Maximum number of sparse NMF iterations
alpha_snmf: scalar
Sparsity penalty
Returns
--------
Ain: np.ndarray
(d1*d2[*d3]) x K , spatial filter of each neuron.
Cin: np.ndarray
T x K , calcium activity of each neuron.
center: np.ndarray
K x 2 [or 3] , inferred center of each neuron.
bin: np.ndarray
(d1*d2[*d3]) x nb, initialization of spatial background.
fin: np.ndarray
nb x T matrix, initalization of temporal background.
"""
if gSiz is None:
gSiz = 2 * np.asarray(gSig) + 1
d, T = np.shape(Y)[:-1], np.shape(Y)[-1]
# rescale according to downsampling factor
gSig = np.round(np.asarray(gSig) // ssub).astype(np.int)
gSiz = np.round(np.asarray(gSiz) // ssub).astype(np.int)
print('Noise Normalization')
if normalize is True:
if img is None:
img = np.mean(Y, axis=-1)
img += np.median(img)
Y = old_div(Y, np.reshape(img, d + (-1,), order='F'))
alpha_snmf /= np.mean(img)
# spatial downsampling
mean_val = np.mean(Y)
if ssub != 1 or tsub != 1:
print("Spatial Downsampling ...")
Y_ds = downscale_local_mean(Y, tuple([ssub] * len(d) + [tsub]), cval=mean_val)
else:
Y_ds = Y
print('Roi Extraction...')
if method == 'greedy_roi':
Ain, Cin, _, b_in, f_in = greedyROI(
Y_ds, nr=K, gSig=gSig, gSiz=gSiz, nIter=nIter, kernel=kernel, nb=nb)
if use_hals:
print('Refining Components...')
Ain, Cin, b_in, f_in = hals(Y_ds, Ain, Cin, b_in, f_in, maxIter=maxIter)
elif method == 'sparse_nmf':
Ain, Cin, _, b_in, f_in = sparseNMF(Y_ds, nr=K, nb=nb, max_iter_snmf=max_iter_snmf, alpha=alpha_snmf,
sigma_smooth=sigma_smooth_snmf, remove_baseline=True, perc_baseline=perc_baseline_snmf)
# print np.sum(Ain), np.sum(Cin)
# print 'Refining Components...'
# Ain, Cin, b_in, f_in = hals(Y_ds, Ain, Cin, b_in, f_in, maxIter=maxIter)
# print np.sum(Ain), np.sum(Cin)
else:
print(method)
raise Exception("Unsupported method")
K = np.shape(Ain)[-1]
ds = Y_ds.shape[:-1]
Ain = np.reshape(Ain, ds + (K,), order='F')
if len(ds) == 2:
Ain = resize(Ain, d + (K,), order=1)
else: # resize only deals with 2D images, hence apply resize twice
Ain = np.reshape([resize(a, d[1:] + (K,), order=1)
for a in Ain], (ds[0], d[1] * d[2], K), order='F')
Ain = resize(Ain, (d[0], d[1] * d[2], K), order=1)
Ain = np.reshape(Ain, (np.prod(d), K), order='F')
#import pdb
# pdb.set_trace()
b_in = np.reshape(b_in, ds + (nb,), order='F')
if len(ds) == 2:
b_in = resize(b_in, d + (nb,), order=1)
else:
b_in = np.reshape([resize(b, d[1:] + (nb,), order=1)
for b in b_in], (ds[0], d[1] * d[2], nb), order='F')
b_in = resize(b_in, (d[0], d[1] * d[2], nb), order=1)
b_in = np.reshape(b_in, (np.prod(d), nb), order='F')
Cin = resize(Cin, [K, T])
f_in = resize(np.atleast_2d(f_in), [nb, T])
# center = com(Ain, *d)
center = np.asarray([center_of_mass(a.reshape(d, order='F')) for a in Ain.T])
if normalize is True:
#import pdb
# pdb.set_trace()
Ain = Ain * np.reshape(img, (np.prod(d), -1), order='F')
b_in = b_in * np.reshape(img, (np.prod(d), -1), order='F')
# b_in = np.atleast_2d(b_in * img.flatten('F')) #np.reshape(img,
# (np.prod(d), -1),order='F')
Y = Y * np.reshape(img, d + (-1,), order='F')
return Ain, Cin, b_in, f_in, center
def reconstruct(self, downsample=(4, 4), crop=True, median_filter=False,
kernel=9, recon_alg='fbp', sart_iters=1,
crop_circle=False, save=True, fancy_out=True):
"""
Reconstruct the data using a radon transform. Reconstructed slices
saved in folder specified upon class creation.
# downsample: Downsample (local mean) data before reconstructing.
Specify mean kernel size (height, width).
# pre_filter: If True apply median filter to data before reconstructing
# kernel: Kernel size to use for median filter
"""
if self.cor_offset >= 0:
images = self.im_stack[:, self.cor_offset:]
else:
images = self.im_stack[:, :self.cor_offset]
images = images[:, :, self.p0:self.num_images + self.p0]
if crop:
left, right, top, bottom = self.crop
images = images[top:bottom, left:right]
images = downscale_local_mean(images, downsample + (1, ))
recon_height, recon_width = images.shape[:2]
self.recon_data = np.zeros((recon_width, recon_width, recon_height))
if median_filter:
print('Applying median filter...')
for i in range(images.shape[-1]):
sys.stdout.write('\rProgress: [{0:20s}] {1:.0f}%'.format('#' *
int(20 * (i + 1) / images.shape[-1]),
100 * ((i + 1) / images.shape[-1])))
sys.stdout.flush()
images[:, :, i] = medfilt(images[:, :, i], kernel_size=kernel)
print('\nReconstructing...')
if save:
save_folder = os.path.join(self.folder, 'reconstruction')
if not os.path.exists(save_folder):
os.makedirs(save_folder)
for the_file in os.listdir(save_folder):
file_path = os.path.join(save_folder, the_file)
if os.path.isfile(file_path):
os.unlink(file_path)
if fancy_out:
fig, ax = plt.subplots(figsize=(4, 4))
fig.canvas.set_window_title('Reconstruction')
patch = Wedge((.5, .5), .375, 90, 90, width=0.1)
ax.add_patch(patch)
ax.axis('equal')
ax.set_xlim([0, 1])
ax.set_ylim([0, 1])
ax.axis('off')
t = ax.text(0.5, 0.5, '0%%', fontsize=15, ha='center', va='center')
for j in range(recon_height):
# Update figure every other slice
if fancy_out and j % 2 == 0:
patch.set_theta1(90 - 360 * (j + 1) / recon_height)
progress = 100 * (j + 1) / recon_height
t.set_text('%02d%%' % progress)
plt.pause(0.001)
else:
sys.stdout.write('\rProgress: [{0:20s}] {1:.0f}%'.format('#' *
int(20 * (j + 1) / recon_height),
100 * ((j + 1) / recon_height)))
sys.stdout.flush()
sino_tmp = np.squeeze(images[j, :, :])
if recon_alg is 'sart':
image_tmp = iradon_sart(sino_tmp, theta=self.angles)
for i in range(sart_iters - 1):
image_tmp = iradon_sart(sino_tmp, theta=self.angles,
image=image_tmp)
else:
image_tmp = iradon(sino_tmp, theta=self.angles,
filter=None, circle=True)
# if crop_circle:
# image_tmp = image_tmp[w0:wf, w0:wf]
self.recon_data[:, :, j] = image_tmp
if crop_circle:
w = int((recon_width**2 / 2)**0.5)
w = w if (w - recon_width) % 2 == 0 else w - 1
w0 = int((recon_width - w) / 2 )
wf = int(w0 + w)
self.recon_data = self.recon_data[w0:wf, w0:wf]
if save:
for j in range(recon_height):
image_tmp = self.recon_data[:, :, j]
imsave(os.path.join(save_folder, '%04d.tif' % j), image_tmp)
if fancy_out:
plt.close()
abs_pix = np.sqrt((x**2 + y**2)).ravel()
angle_pix = np.arctan2(y, x).ravel()
angle_array, abs_array = np.meshgrid(np.linspace(-np.pi, np.pi, 900),
np.linspace(0, np.sqrt(2), 900))
polar_image = griddata((angle_pix, abs_pix),
image.ravel(), (angle_array.ravel(), abs_array.ravel()),
method='nearest') #nearest cubic linear
polar_image = polar_image.reshape(900, 900)
grad_r, grad_fi = np.gradient(polar_image)
grad_r = downscale_local_mean(grad_r, (30, 30))
grad_fi = downscale_local_mean(grad_fi, (30, 30))
abs_array = abs_array[::30, ::30]
angle_array = angle_array[::30, ::30]
polar_image = np.zeros((30, 30), dtype=np.float)
grad_r_na = grad_r[:, :450]
grad_r_na = np.fliplr(grad_r_na)
polar_image[:, :450] = np.fliplr(cumtrapz(grad_r_na, axis=0, initial=0))
polar_image[:, 450:] = cumtrapz(grad_r[:, 450:], axis=0, initial=0)
# polar_image = cumtrapz(grad_r, axis=0, initial=0)
# integral_over_fi = 0
# for i in range( grad_fi.shape[1] - 2 ):
# integral_over_fi += cumtrapz(np.roll(grad_fi, i+1, axis=1), axis=1, initial=0)
# integral_over_fi /= (i+1)
def downsample_4_image(path):
image = io.imread(path, as_grey=True)
image_downsampled = downscale_local_mean(image, (4, 4))
plt.gray()
matplotlib.image.imsave(path + "_downsampled.jpg", image_downsampled)
def _prepare_data(idx, batch_idx):
# --------------------------------------------------------------------------------------------------------------
# Preparation of the image data
if len(im_list_raw) > idx:
# Check whether the result exists if a target folder is given here
if target_folder is not None:
if os.path.isfile(os.path.join(target_folder, os.path.split(im_list_raw[idx])[1])):
# Return Nones for each slice that was already computed
if verbose:
print('{} already exists, nothing to do...'.format(os.path.split(im_list_raw[idx])[1]))
return None, None, None, None
# Load the raw data slice
im = imread(im_list_raw[idx])
assert im.dtype in ['uint8', 'uint16'], 'Only the data types uint8 and uint16 are supported!'
else:
# This happens if the number of images does not divide by the number of batches (smaller last batch)
# Return Nones for each missing slice to fill up the batch
if verbose:
print('Filling up batch...')
return None, None, None, None
# Start end end indices for the median filter, idx being the current slice position in the center
start_id = idx - median_radius
end_id = idx + median_radius + 1
# Load the necessary data for the z-median filtered slice
for load_idx, slice_idx in enumerate(range(start_id, end_id)):
load_idx += idx - batch_idx
# print('load_idx = {}; slice_idx = {}'.format(load_idx, slice_idx))
if 0 <= slice_idx < len(im_list_pre):
if template_data[load_idx] is None:
template_data[load_idx] = imread(im_list_pre[slice_idx])
assert template_data[load_idx].dtype == 'uint8', 'Only 8bit template data is supported!'
# else:
# print('Template data is not None')
# else:
# print('slice_idx < 0')
# Do the median smoothing to obtain one composition image at the current z-position
ims = [x for x in template_data[idx - batch_idx: idx - batch_idx + median_radius * 2 + 1] if x is not None]
median_z = np.median(ims, axis=0).astype('uint8')
del ims
# The sift doesn't like images of different size. This fixes some cases by cropping away areas from the raw data
# that are zero and padding it with zeros to the size of the template image
# We are assuming here that the template data slices are larger than the non-zero region of interest in the raw
# data.
if im.shape != median_z.shape:
try:
bounds = _crop_zero_padding(im)
cropped_im = im[bounds]
t_im = np.zeros(median_z.shape, dtype=im.dtype)
t_im[0:cropped_im.shape[0], 0:cropped_im.shape[1]] = cropped_im
im = t_im
except ValueError as e:
# This happened when a white slice was present (no zero pixel)
warnings.warn('Cropping zero-padding failed with ValueError: {}'.format(str(e)))
print('This happens if a completely black slice is present in the data. ')
print('Affected slice: {}'.format(im_list_raw[idx]))
print('Replacing with empty slice ...')
im = np.zeros(median_z.shape, dtype=im.dtype)
# Gaussian smooth the image and the median_z for the SIFT step
if sift_sigma is not None:
median_z_smooth = gaussianSmoothing(median_z, sift_sigma)
if im.dtype == 'uint8':
im_smooth = gaussianSmoothing(im, sift_sigma)
else:
# vigra.gaussianSmoothing cannot handle 16 bit data
im_smooth = gaussianSmoothing(im.astype('float32'), sift_sigma)
# The data for the sift step does not require to be 16 bit
im_smooth = (im_smooth / (2 ** 16) * (2 ** 8)).astype('uint8')
else:
median_z_smooth = median_z.copy()
im_smooth = im.copy()
if im_smooth.dtype == 'uint16':
# The data for the sift step does not require to be 16 bit
im_smooth = (im_smooth.astype('float32') / (2 ** 16) * (2 ** 8)).astype('uint8')
# Downsample for SIFT step for speed-up of computation
if sift_downsample is not None:
median_z_smooth = downscale_local_mean(median_z_smooth, sift_downsample).astype('uint8')
im_smooth = downscale_local_mean(im_smooth, sift_downsample).astype('uint8')
# --------------------------------------------------------------------------------------------------------------
# Return the results
assert im.dtype in ['uint8', 'uint16']
assert im_smooth.dtype == 'uint8'
assert median_z.dtype == 'uint8'
assert median_z_smooth.dtype == 'uint8'
return im, im_smooth, median_z, median_z_smooth
def cascadeCorners(img_path, georef_path, truth_corners, plot,
downscale_factor):
img = imread(img_path, as_gray=True)
georef_img = imread(georef_path, as_gray=True)
# downscale images
img_small = downscale_local_mean(img, (downscale_factor, downscale_factor))
georef_img_small = downscale_local_mean(
georef_img, (downscale_factor, downscale_factor))
# blurring adds 0.8s (6.7->7.5) per image on average, but helps with correct corner identification (even though 3,3 gaussian is a bit much...)
img_small = filters.gaussian(img_small, sigma=(3, 3), truncate=1.0)
georef_img_small = filters.gaussian(georef_img_small,
sigma=(3, 3),
truncate=1.0)
# rescale truth corners to small resolution
scaled_corners = [(x // downscale_factor, y // downscale_factor)
for (x, y) in truth_corners]
# find corners in small image
corner_points = findCorners(img_small,
georef_img_small,
scaled_corners,
template_size=20,
plot=plot)
# rescale found coordinates to original resolution
corner_points = [(x * downscale_factor, y * downscale_factor)
for (x, y) in corner_points]
corner_coords = []
for idx, corner in enumerate(corner_points):
roi_size = 100
template_size = 20
# extract ROI from original size image
x_min = max(0, corner[1] - roi_size)
x_max = max(0, corner[1] + roi_size)
y_min = max(0, corner[0] - roi_size)
y_max = max(0, corner[0] + roi_size)
roi = georef_img[x_min:x_max, y_min:y_max]
ref_corner = truth_corners[idx]
template = img[ref_corner[1] - template_size:ref_corner[1] +
template_size, ref_corner[0] -
template_size:ref_corner[0] + template_size]
# match again in ROIs
match = match_corner(roi, template)
match = (match[0] + (y_min), match[1] + (x_min)
) # scale match to non-ROI positions
corner_coords.append(get_coords_from_raster(georef_path, match))
if plot:
# show corners
ax = plt.subplot(2, 4, idx + 1)
ax.set_title("original")
plt.xticks([], [])
plt.yticks([], [])
plt.gray()
plt.imshow(template)
ax = plt.subplot(2, 4, idx + 5)
ax.set_title("warped")
plt.xticks([], [])
plt.yticks([], [])
plt.gray()
x_min = max(0, match[1] - template_size)
x_max = min(georef_img.shape[0], match[1] + template_size)
y_min = max(0, match[0] - template_size)
y_max = min(georef_img.shape[1], match[0] + template_size)
plt.imshow(georef_img[x_min:x_max, y_min:y_max])
# plt.imshow(georef_img[match[1]-template_size:match[1]+template_size, match[0]-template_size:match[0]+template_size])
# TODO: plot center point, to show pixel perfect location
if plot:
plt.show()
return corner_coords
img = mpimg.imread(x[i][2])
gray_img = segment(img).ravel()
trainX = np.vstack((trainX, gray_img))
trainY.append(int(x[i][0]))
trainY = np.array(trainY)
f = open('test','r')
x = f.readlines()
testY = []
testX = np.array([]).reshape(0, 300*400)
for i in range(len(x)):
x[i] = x[i].strip().split('\t')
path = x[i][2]
img = imread(x[i][2])
print(i)
gray_img = segment(img)
gray_img = downscale_local_mean(gray_img, (4,4)).ravel()
testX = np.vstack((testX, gray_img))
testY.append(int(x[i][0]))
testY = np.array(testY)
np.save('testX.npy', testX)
np.save('testY.npy', testY)
# np.save('trainX.npy', trainX)
# np.save('trainY.npy', trainY)
def preproc_field(field,
mask,
inpaint=True,
median=True,
med_size=(3, 1),
downscale=True,
dscale_size=(2, 2),
sigmoid=False,
scale=None,
expon=None,
only_inpaint=False,
gradient=False,
log_scale=False):
"""
Preprocess an input field image with a series of steps:
1. Inpainting
2. Median
3. Downscale
4. Sigmoid
5. Scale
6. Remove mean
Parameters
----------
field : np.ndarray
mask : np.ndarray
Data mask. True = masked
inpaint : bool, optional
if True, inpaint masked values
median : bool, optional
If True, apply a median filter
med_size : tuple
Median window to apply
downscale : bool, optional
If True downscale the image
dscale_size : tuple, optional
Size to rescale by
scale : float
Scale the SSTa values by this multiplicative factor
expon : float
Exponate the SSTa values by this exponent
gradient : bool, optional
If True, apply a Sobel gradient enhancing filter
Returns
-------
pp_field, meta_dict : np.ndarray, dict
Pre-processed field, mean temperature
"""
meta_dict = {}
# Inpaint?
if inpaint:
if mask.dtype.name != 'uint8':
mask = np.uint8(mask)
field = sk_inpaint.inpaint_biharmonic(field, mask, multichannel=False)
if only_inpaint:
if np.any(np.isnan(field)):
return None, None
else:
return field, None
# Capture more metadata
srt = np.argsort(field.flatten())
meta_dict['Tmax'] = field.flatten()[srt[-1]]
meta_dict['Tmin'] = field.flatten()[srt[0]]
i10 = int(0.1 * field.size)
i90 = int(0.9 * field.size)
meta_dict['T10'] = field.flatten()[srt[i10]]
meta_dict['T90'] = field.flatten()[srt[i90]]
# Median
if median:
field = median_filter(field, size=med_size)
# Reduce to 64x64
if downscale:
field = downscale_local_mean(field, dscale_size)
# Check for junk
if np.any(np.isnan(field)):
return None, None
# De-mean the field
mu = np.mean(field)
pp_field = field - mu
meta_dict['mu'] = mu
# Sigmoid?
if sigmoid:
pp_field = special.erf(pp_field)
# Scale?
if scale is not None:
pp_field *= scale
# Exponate?
if expon is not None:
neg = pp_field < 0.
pos = np.logical_not(neg)
pp_field[pos] = pp_field[pos]**expon
pp_field[neg] = -1 * (-1 * pp_field[neg])**expon
# Sobel Gradient?
if gradient:
pp_field = filters.sobel(pp_field)
# Log?
if log_scale:
if not gradient:
raise IOError("Only implemented with gradient=True so far")
# Set 0 values to the lowest non-zero value
zero = pp_field == 0.
if np.any(zero):
min_nonz = np.min(pp_field[np.logical_not(zero)])
pp_field[zero] = min_nonz
# Take log
pp_field = np.log(pp_field)
# Return
return pp_field, meta_dict
def trip_diffusion_convolution(self, img, trip_filter):
n = DESTINATION_PROFILE_SPATIAL_AGGREGATION
M = downscale_local_mean(img, (n, n))
M = np.tensordot(trip_filter, M)
M = resize(M, img.shape, mode='edge')
return M
# 4. Register
###
path = sys.argv[1]
nframes = int(sys.argv[2])
#'/media/timrudge/tjr34_ntfs/Microscopy/Cavendish/10.01.16/Pos0000'
infile = os.path.join(path, 'Frame%04dStep%04d.tiff')
outfile = os.path.join(path, 'aligned_Frame%04dStep%04d.tiff')
outfile_mask = os.path.join(path, 'aligned_mask_Frame%04dStep%04d.tiff')
startframe = 0
step = 1
scale = 2
im1 = imread(infile % (0, startframe), plugin='tifffile').astype(np.float32)
im1 = gaussian_filter(im1, 1)
im1 = downscale_local_mean(im1, (scale, scale))
# Use first image to compute background of 1st channel
bgmean = np.mean(im1.ravel())
bgstd = np.std(im1.ravel())
bgval = bgmean + bgstd * 2
print(bgmean)
im2 = imread(infile % (2, startframe + step),
plugin='tifffile').astype(np.float32)
im2 = gaussian_filter(im2, 1)
im2 = downscale_local_mean(im2, (scale, scale))
shifts = np.zeros((nframes - step, 2))
# Offset images to align to sequentially
def rasterize(shp, ext_outline=False, ext_fill=True, int_outline=False,
int_fill=False, scale_factor=4):
"""Convert a vector shape to a raster. Assumes the shape has already
been transformed in to a pixel based coordinate system. The algorithm
checks for the intersection of each point in the shape with
a pixel grid created by the bounds of the shape. Partial overlaps
are estimated by scaling the image in X and Y by the scale factor,
rasterizing the shape, and downscaling (using mean), back to the
bounds of the original shape.
Parameters
----------
shp: shapely.Polygon or Multipolygon
The shape to rasterize
ext_outline: boolean (default False)
Include the outline of the shape in the raster
ext_fill: boolean (default True)
Fill the shape in the raster
int_outline: booelan (default False)
Include the outline of the interior shapes
int_fill: boolean (default False):
Fill the interior shapes
scale_factor: int (default 4)
The amount to scale the shape in X, Y before downscaling. The
higher this number, the more precise the estimate of the overlap.
Returns
-------
np.ndarray representing the rasterized shape.
"""
sf = scale_factor
minx, miny, maxx, maxy = map(int, shp.bounds)
if minx == maxx and miny == maxy:
return np.array([[1.]])
elif maxy > miny and minx == maxx:
n = maxy - miny + 1
return np.zeros([n, 1]) + 1./n
elif maxy == miny and minx < maxx:
n = maxx - minx + 1
return np.zeros([1, n]) + 1./n
if ((maxx - minx + 1) + (maxy - miny + 1)) <= 2*sf:
sf = 1.0
shp = scale(shp, xfact=sf, yfact=sf)
minx, miny, maxx, maxy = shp.bounds
width = int(maxx - minx + 1)
height = int(maxy - miny + 1)
img = Image.new('L', (width, height), 0)
_shp = shp.geoms if hasattr(shp, "geoms") else [shp]
ext_outline = int(ext_outline)
ext_fill = int(ext_fill)
int_outline = int(int_outline)
int_fill = int(int_fill)
for pg in _shp:
ext_pg = [(x-minx, y-miny) for x, y in pg.exterior.coords]
ImageDraw.Draw(img).polygon(ext_pg, outline=ext_outline, fill=ext_fill)
for s in pg.interiors:
int_pg = [(x-minx, y-miny) for x, y in s.coords]
ImageDraw.Draw(img).polygon(int_pg, outline=int_outline,
fill=int_fill)
return downscale_local_mean(np.array(img), (sf, sf))
def initialize_components(Y, K=30, gSig=[5, 5], gSiz=None, ssub=1, tsub=1, nIter=5, maxIter=5,
kernel=None, use_hals=True, Cn=None, sn=None):
"""Initalize components
This method uses a greedy approach followed by hierarchical alternative least squares (HALS) NMF.
Optional use of spatio-temporal downsampling to boost speed.
Parameters
----------
Y: np.ndarray
d1 x d2 [x d3] x T movie, raw data.
K: [optional] int
number of neurons to extract (default value: 30).
tau: [optional] list,tuple
standard deviation of neuron size along x and y [and z] (default value: (5,5).
gSiz: [optional] list,tuple
size of kernel (default 2*tau + 1).
nIter: [optional] int
number of iterations for shape tuning (default 5).
maxIter: [optional] int
number of iterations for HALS algorithm (default 5).
ssub: [optional] int
spatial downsampling factor recommended for large datasets (default 1, no downsampling).
tsub: [optional] int
temporal downsampling factor recommended for long datasets (default 1, no downsampling).
kernel: [optional] np.ndarray
User specified kernel for greedyROI (default None, greedy ROI searches for Gaussian shaped neurons)
use_hals: [bool]
Whether to refine components with the hals method
Returns
--------
Ain: np.ndarray
(d1*d2[*d3]) x K , spatial filter of each neuron.
Cin: np.ndarray
T x K , calcium activity of each neuron.
center: np.ndarray
K x 2 [or 3] , inferred center of each neuron.
bin: np.ndarray
(d1*d2[*d3]) x nb, initialization of spatial background.
fin: np.ndarray
nb x T matrix, initalization of temporal background.
"""
if gSiz is None:
gSiz = 2 * np.asarray(gSig) + 1
d, T = np.shape(Y)[:-1], np.shape(Y)[-1]
# rescale according to downsampling factor
gSig = np.round(np.asarray(gSig) / ssub).astype(np.int)
gSiz = np.round(np.asarray(gSiz) / ssub).astype(np.int)
print 'Noise Normalization'
if sn is not None:
min_noise = np.percentile(sn, 2)
noise = np.maximum(sn, min_noise)
Y = Y / np.reshape(noise, d + (-1,),order='F')
# spatial downsampling
mean_val = np.mean(Y)
if ssub != 1 or tsub != 1:
print "Spatial Downsampling ..."
Y_ds = downscale_local_mean(Y, tuple([ssub] * len(d) + [tsub]), cval=mean_val)
if Cn is not None:
Cn = downscale_local_mean(Cn, tuple([ssub] * len(d)), cval=mean_val)
else:
Y_ds = Y
print 'Roi Extraction...'
Ain, Cin, _, b_in, f_in = greedyROI(
Y_ds, nr=K, gSig=gSig, gSiz=gSiz, nIter=nIter, kernel=kernel)
if use_hals:
print 'Refining Components...'
Ain, Cin, b_in, f_in = hals(Y_ds, Ain, Cin, b_in, f_in, maxIter=maxIter)
ds = Y_ds.shape[:-1]
Ain = np.reshape(Ain, ds + (K,), order='F')
if len(ds) == 2:
Ain = resize(Ain, d + (K,), order=1)
else: # resize only deals with 2D images, hence apply resize twice
Ain = np.reshape([resize(a, d[1:] + (K,), order=1) for a in Ain], (ds[0], d[1] * d[2], K), order='F')
Ain = resize(Ain, (d[0], d[1] * d[2], K), order=1)
Ain = np.reshape(Ain, (np.prod(d), K), order='F')
b_in = np.reshape(b_in, ds, order='F')
# b_in = resize(b_in, ds)
b_in = resize(b_in, d)
b_in = np.reshape(b_in, (-1, 1), order='F')
Cin = resize(Cin, [K, T])
f_in = resize(np.atleast_2d(f_in), [1, T])
# center = com(Ain, *d)
center = np.asarray([center_of_mass(a.reshape(d, order='F')) for a in Ain.T])
if sn is not None:
Ain = Ain * np.reshape(noise, (np.prod(d), -1),order='F')
b_in = b_in * np.atleast_2d(noise).T
Y = Y * np.reshape(noise, d + (-1,),order='F')
return Ain, Cin, b_in, f_in, center
# antialias not yet in skimage 0.13.1 ....
imm = rescale(imgray, 1.0 / 4.0, mode="reflect") # , anti_aliasing=False)
lb = "Resscale / 4"
iml.append(imm)
lbl.append(lb)
print("shape: ", imm.shape, ", dtype: ", imm.dtype)
imm = resize(imgray, (imgray.shape[0] / 4, imgray.shape[1] / 4),
mode="reflect") #, anti_aliasing=True)
lb = "Resize to size"
iml.append(imm)
lbl.append(lb)
print("shape: ", imm.shape, ", dtype: ", imm.dtype)
print(lb)
imm = downscale_local_mean(imgray, (4, 3))
lb = "Downscale 4/3"
iml.append(imm)
lbl.append(lb)
print("shape: ", imm.shape, ", dtype: ", imm.dtype)
print(lb)
imm = rotate(imgray, 90, resize=True, mode="reflect")
lb = "Rotate"
iml.append(imm)
lbl.append(lb)
print("shape: ", imm.shape, ", dtype: ", imm.dtype)
print(lb)
imm = imgray > filters.threshold_li(imgray)
lb = "Threshold"
#! /usr/bin/env python
from skimage import io, feature, transform
startlong=-8.
startlat=43.
scale=10.
dbpic=io.imread("./example.jpg",as_grey=True)
dbpic=transform.downscale_local_mean(dbpic, (10, 10))
edges=feature.canny(dbpic)
with open("./out.csv","w+") as out:
out.write("point,latitude,longitude\n")
for ni,i in enumerate(edges):
for nj,j in enumerate(i):
if j:
out.write("%02i-%02i,"%(ni,nj))
out.write("%f,%f\n"%(startlat-(ni/scale),startlong+(nj/scale)))
def rebin(img):
img = img.reshape(inpshape)
if crop_left:
img = img[crop_left:,crop_left:]
ret=downscale_local_mean(img, factors)
return ret
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from skimage import data, io
from skimage.filters import threshold_otsu
from skimage.segmentation import clear_border
from skimage.measure import label, regionprops
from skimage.morphology import closing, square
from skimage.color import label2rgb, rgb2gray
from skimage.transform import downscale_local_mean
im_file = io.imread("photo.bmp")
#image = data.coins()[50:-50, 50:-50]
# image = scaled[:, :, 0]
im_gray = rgb2gray(im_file)
image = downscale_local_mean(im_gray, (10, 10))
# io.imsave("photo.png", image)
# apply threshold
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(5))
# remove artifacts connected to image border
cleared = clear_border(bw)
# label image regions
label_image = label(bw)
image_label_overlay = label2rgb(label_image, image=image)
fig, ax = plt.subplots(figsize=(10, 6))
ax.imshow(image) #_label_overlay)
def filter_and_voxelise(corrected_path):
mean_filtered_stack = mean_filter(corrected_path)
print 'Voxelising stack'
voxelised_stack = tf.downscale_local_mean(mean_filtered_stack, (1, 4, 4))
return voxelised_stack
def generate(csv_file, images_folder, fraction):
print("Generating input...")
# Read dataset
df = pd.read_csv(csv_file)
# Add label
df.loc[df['EncodedPixels'].notnull(), 'EncodedPixels'] = 1
df.loc[df['EncodedPixels'].isnull(), 'EncodedPixels'] = 0
# Change column name
df.columns = ['ImageId', 'Label']
# Remove duplicates
df_dropped = df.drop_duplicates(['ImageId'], keep='first')
# Select a fraction of samples
df_set = df_dropped.sample(frac=fraction, random_state=1)
m = df_set.shape[0]
print("Number of samples: ", m)
# Create empty dataframe
x = np.empty((0, 128 * 128), float)
for i in range(m):
# Read image
image_path = images_folder + '/' + df_set.iloc[i, 0]
img = io.imread(image_path)
# Convert to grayscale
img_gray = rgb2gray(img)
# Compute FFT
img_fft = fftpack.fft2(img_gray)
img_abs = np.abs(img_fft) / (768 * 768)
# Downscale
fft_t = transform.downscale_local_mean(img_abs, (6, 6))
# Append to dataframe
array = np.reshape(fft_t, (-1))
x = np.vstack((x, array))
# Column names
column_names = ['ImageId', 'Label']
for i in range(x.shape[1]):
column_names.append('Pixel_' + str(i))
# Create dataframe from pixels values
df_pixels = pd.DataFrame(x, columns=column_names[2:])
# Concatenate the pixels values
df_set.reset_index(drop=True, inplace=True)
df_set = pd.concat([df_set, df_pixels], axis=1, ignore_index=True)
# Add column names
df_set.columns = column_names
# Save csv
df_set.to_csv('train_modified.csv', index=False)
def image_to_patches(self,
path,
patch_size=7,
iterations=500,
batch_size=20,
color=False,
downscale_factor=2,
is_matrix=False,
is_recons=False):
'''
#*****
args:
path (string): Path and filename of input image
patch_size (int): Pixel dimension of square patches taken of image
color (boolean): Specifies conversion of image to RGB (True) or grayscale (False).
Default value = false. When color = True, images in gray colorspace will still appear
gray, but will thereafter be represented in RGB colorspace using three channels.
downscale_factor: Specifies the extent to which the image will be downscaled. Greater values
will result in more downscaling but faster speed. For no downscaling, use downscale_factor=1.
returns: #***
'''
#open image and convert it to either RGB (three channel) or grayscale (one channel)
if is_matrix:
img = np.load(path)
data = (img + 1) / 2 # it was +-1 matrix; now it is 0-1 matrix
else:
img = Image.open(path)
if color:
img = img.convert('RGB')
img = tl_unfold(img, mode=2).T
print('img.shape_color_after_unfolding', img.shape)
else:
img = img.convert('L')
# normalize pixel values (range 0-1)
data = np.asarray(img) / 255
'''
img = np.load(path)
data = (img + 1) / 2 # it was +-1 matrix; now it is 0-1 matrix
'''
if DEBUG:
print(np.asarray(img))
# downscale image for speed
if downscale_factor > 1:
data = downscale_local_mean(data,
(downscale_factor, downscale_factor))
# show_array(data)
if not is_recons:
patches = extract_patches_2d(data, (patch_size, patch_size),
max_patches=iterations * batch_size)
else: # for reconstruction we need to use all patches not to mess up with the ordering
patches = extract_patches_2d(data, (patch_size, patch_size))
# we do not need more than iterations*batch_size patches for training dictionaries
# convert 7x7 squares to 1d (49,) vectors
patches_flat = patches.reshape(len(patches), -1).T
# (Num patches)*(7*7) array
# .reshape(len(patches),-1) makes it two dimensional -- (Num patches)*(whatever that's correct)
# take transpose to make it 49 * (Num patches)
print(patches_flat.shape)
return patches_flat
def downscale_channel(self, channel):
return downscale_local_mean(channel, (self.down_factor, self.down_factor)).astype(np.uint8)
def main():
"""
This script converts MRI scans in nifti format from a specified data path to numpy arrays (.npy). This is the
required format to be used in the data generators of the Keras deep learning model created for the MRI-based
classification of Alzheimer's Disease.
In the settings can be specified which data set and data type should be converted. Also can be specified whether
images should be converted to whole brain and/or down sampled images. A mask is applied to all images so that
the area outside the brain is set to zero. Furthermore the images are cropped to this mask.
This script should be run to create data before a model can be trained on this data with the 'main.py' script.
"""
# SETTINGS
dataset = "PSI" # ADNI / PSI
datatype = "GM" # T1 / T1m / GM
WB = False # if True: whole brain images, if False: downsampled by factor 4
testing = True # if True: only applied to 4 subjects
# create output dir
if WB:
save_path_WB = f"path/to/WB/"
create_data_directory(save_path_WB)
else:
save_path_f4 = f"path/to/f4/"
create_data_directory(save_path_f4)
# set path to data
if dataset == "ADNI":
if datatype == "GM":
data_path = f"path/to/cartesius_mount/Template_space/*/Brain_image_in_template_space/gmModulatedJacobian.nii.gz"
elif datatype == "T1":
data_path = "/mnt/cartesius/ADNI/Template_space/*_bl/Brain_image_in_MNI_space/result.nii.gz"
elif datatype == "T1m":
data_path = "/mnt/cartesius/ADNI/Template_space/*_bl/Brain_image_in_template_space/T1wModulatedJacobian.nii.gz"
elif dataset == "PSI":
if datatype == "GM":
data_path = f"path/to/cartesius_mount_parelsnoer/Template_space/*/Brain_image_in_template_space/gmModulatedJacobian.nii.gz"
elif datatype == "T1":
data_path = "/mnt/cartesius/Parelsnoer/Template_space/PSI_*/Brain_image_in_MNI_space/result.nii.gz"
elif datatype == "T1m":
data_path = "/mnt/cartesius/Parelsnoer/Template_space/PSI_*/Brain_image_in_template_space/T1wModulatedJacobian.nii.gz"
# create mask of brain
template_file = f"path/to/cartesius_mount/Template_space/brain_mask_in_template_space.nii.gz"
template = nib.load(template_file).get_fdata()
mask = np.zeros(template.shape)
mask[np.where(template != 0)] = 1
cnt = 0
# loop over all files in data path
for filename in glob.glob(data_path):
cnt += 1
# get subject ID
if dataset == "ADNI":
# format: ".../Template_space/*/Brain_image_in_template_space/..."
common_substring_1 = "Template_space"
common_substring_2 = "Brain_image_in_template_space"
x1 = filename.index(common_substring_1)
x2 = filename.index(common_substring_2)
subject = filename[x1+15:x2-1]
elif dataset == "PSI":
#subject = filename[41:50]
common_substring_1 = "Template_space"
common_substring_2 = "Brain_image_in_template_space"
x1 = filename.index(common_substring_1)
x2 = filename.index(common_substring_2)
subject = filename[x1+15:x2-1]
if WB:
if os.path.exists(save_path_WB + subject + ".h5py"):
continue
else:
if os.path.exists(save_path_f4 + subject + ".h5py"):
continue
# for testing break early
if testing:
if cnt % 5 == 0:
break
print(subject)
# print progress
if cnt % 50 == 0:
print('\n----- Working on subject number ' + str(cnt) + ' -----')
# load .nii data as 3d numpy array
image = nib.load(filename).get_fdata()
# normalization for signal intensity
if datatype == "T1":
image = normalize(operator.mul(image, mask))
# apply mask + crop image
masked = apply_mask(image, mask)
# save as .npy
if WB:
# .npy to .h5py in order to save storage space
with h5py.File(save_path_WB + subject + ".h5py", "w") as hf:
hf.create_dataset(subject, data=masked, compression="gzip", compression_opts=9)
#np.save(save_path_WB + subject + '.npy', masked)
else:
# down sample by factor 4 based on local mean
downsampled = downscale_local_mean(masked, (4, 4, 4))
# .npy to .h5py in order to save storage space
with h5py.File(save_path_f4 + subject + ".h5py", "w") as hf:
hf.create_dataset(subject, data=downsampled, compression="gzip", compression_opts=9)
def initialize_components(Y, K=30, gSig=[5,5], gSiz=None, ssub=1, tsub=1, nIter = 5, maxIter=5, kernel = None, use_hals=True,Cn=None,sn=None):
"""Initalize components
This method uses a greedy approach followed by hierarchical alternative least squares (HALS) NMF.
Optional use of spatio-temporal downsampling to boost speed.
Parameters
----------
Y: np.ndarray
d1 x d2 x T movie, raw data.
K: [optional] int
number of neurons to extract (default value: 30).
tau: [optional] list,tuple
standard deviation of neuron size along x and y (default value: (5,5).
gSiz: [optional] list,tuple
size of kernel (default 2*tau + 1).
nIter: [optional] int
number of iterations for shape tuning (default 5).
maxIter: [optional] int
number of iterations for HALS algorithm (default 5).
ssub: [optional] int
spatial downsampling factor recommended for large datasets (default 1, no downsampling).
tsub: [optional] int
temporal downsampling factor recommended for long datasets (default 1, no downsampling).
kernel: [optional] np.ndarray
User specified kernel for greedyROI (default None, greedy ROI searches for Gaussian shaped neurons)
use_hals: [bool]
Whether to refine components with the hals method
Returns
--------
Ain: np.ndarray
(d1*d2) x K , spatial filter of each neuron.
Cin: np.ndarray
T x K , calcium activity of each neuron.
center: np.ndarray
K x 2 , inferred center of each neuron.
bin: np.ndarray
(d1*d2) X nb, initialization of spatial background.
fin: np.ndarray
nb X T matrix, initalization of temporal background.
"""
if gSiz is None:
gSiz=(2*gSig[0] + 1,2*gSig[1] + 1)
d1,d2,T=np.shape(Y)
# rescale according to downsampling factor
gSig = np.round([gSig[0]/ssub,gSig[1]/ssub]).astype(np.int)
gSiz = np.round([gSiz[0]/ssub,gSiz[1]/ssub]).astype(np.int)
print 'Noise Normalization'
if sn is not None:
min_noise=np.percentile(sn,2)
noise=np.maximum(sn,min_noise)
Y=Y/np.reshape(noise,(d1,d2))[:,:,np.newaxis]
# spatial downsampling
mean_val=np.mean(Y)
if ssub!=1 or tsub!=1:
print "Spatial Downsampling ..."
Y_ds = downscale_local_mean(Y,(ssub,ssub,tsub),cval=mean_val)
if Cn is not None:
Cn = downscale_local_mean(Cn,(ssub,ssub),cval=mean_val)
else:
Y_ds = Y
print 'Roi Extraction...'
Ain, Cin, _, b_in, f_in = greedyROI2d(Y_ds, nr = K, gSig = gSig, gSiz = gSiz, nIter=nIter, kernel = kernel)
if use_hals:
print 'Refining Components...'
Ain, Cin, b_in, f_in = hals_2D(Y_ds, Ain, Cin, b_in, f_in,maxIter=maxIter);
#center = ssub*com(Ain,d1s,d2s)
d1s,d2s,Ts=np.shape(Y_ds)
Ain = np.reshape(Ain, (d1s, d2s,K),order='F')
Ain = resize(Ain, [d1, d2, K],order=1)
Ain = np.reshape(Ain, (d1*d2, K),order='F')
b_in=np.reshape(b_in,(d1s, d2s),order='F')
b_in = resize(b_in, [d1, d2]);
b_in = np.reshape(b_in, (d1*d2, 1),order='F')
Cin = resize(Cin, [K, T])
f_in = resize(np.atleast_2d(f_in), [1, T])
center = com(Ain,d1,d2)
if sn is not None:
Ain=Ain*np.reshape(noise,(d1*d2,))[:,np.newaxis]
b_in=b_in*np.reshape(noise,(d1*d2,))
Y=Y*np.reshape(noise,(d1,d2))[:,:,np.newaxis]
return Ain, Cin, b_in, f_in, center
`Downscale` operation serves the purpose of downsampling an
n-dimensional image by calculating local mean on the elements of
each block of the size factors given as a parameter to the function.
"""
import matplotlib.pyplot as plt
from skimage import data
from skimage.transform import rescale, resize, downscale_local_mean
image = data.camera()
image_rescaled = rescale(image, 0.5)
image_resized = resize(image, (400, 400), mode='reflect')
image_downscaled = downscale_local_mean(image, (2, 3))
fig, axes = plt.subplots(nrows=2, ncols=2,
sharex=True, sharey=True)
ax = axes.ravel()
ax[0].imshow(image, cmap='gray')
ax[0].set_title("Original image")
ax[1].imshow(image_rescaled, cmap='gray')
ax[1].set_title("Rescaled image")
ax[2].imshow(image_resized, cmap='gray')
ax[2].set_title("Resized image")
def normalize(x):
# utility function to normalize a tensor by its L2 norm
return x / (K.sqrt(K.mean(K.square(x))) + 1e-5)
if os.path.isdir('crop_viz'):
shutil.rmtree('crop_viz')
os.mkdir('crop_viz')
test_crops = []
for fn in glob.glob('data/splits/dev/*.tif'):
img = None
img = np.array(io.imread(fn), dtype='float32')
scaled = None
scaled = img / np.float32(255.0)
scaled = downscale_local_mean(scaled, factors=(2,2))
test_crops.extend(utils.augment_test_image(scaled, img_width, img_height, NB_TEST_PATCHES))
print(len(test_crops))
if LAYER_NAME == 'prediction':
label_encoder = pickle.load( open('models/' + MODEL_NAME + '/label_encoder.p', 'rb'))
print('-> Working on classes:', label_encoder.classes_)
NB_FILTERS = len(label_encoder.classes_)
for filter_idx in range(0, NB_FILTERS):
print('Processing filter', filter_idx)
layer_output = layer_dict[LAYER_NAME].output
if LAYER_NAME == 'prediction':
loss = K.mean(layer_output[:, filter_idx])
example_dir = os.path.splitext(os.path.basename(FILEPATH))[0]
try:
shutil.rmtree('viz/' + example_dir)
except:
pass
os.mkdir('viz/' + example_dir)
img = io.imread(FILEPATH)
img = np.array(io.imread(FILEPATH), dtype='float32')
print(img.shape)
scipy.misc.imsave('viz/' + example_dir + '/orig.tiff', img)
scaled = img / np.float32(255.0)
scaled = downscale_local_mean(scaled, factors=(2, 2))
scipy.misc.imsave('viz/' + example_dir + '/downscaled' + '.tiff', scaled * 255)
train_crops, _ = utils.augment_train_images([scaled], [0], NB_ROWS, NB_COLS,
NB_PATCHES)
for idx, x in enumerate(train_crops):
x = x.reshape((x.shape[1], x.shape[2]))
x *= 255
scipy.misc.imsave(
'viz/' + example_dir + '/train_crop_' + str(idx) + '.tiff', x)
test_crops = utils.augment_test_image(scaled, NB_ROWS, NB_COLS, NB_PATCHES)
for idx, x in enumerate(test_crops):
x = x.reshape((x.shape[1], x.shape[2]))
x *= 255
print(report)
'''Show the classified validation images'''
if ShowValidation:
for s in range(len(ValidationSites.index)):
UAVRaster = io.imread(DataFolder+'Cropped_'+ValidationSites.Abbrev[s]+'_'+str(ValidationSites.Month[s])+'_'+str(ValidationSites.Year[s])+'_UAVCLS.tif')
UAVRaster[UAVRaster>3] =0
UAVRaster[UAVRaster<1] =0
UAVRasterRGB = np.zeros((UAVRaster.shape[0], UAVRaster.shape[1], 4))
UAVRasterRGB[:,:,0]=255*(UAVRaster==3)
UAVRasterRGB[:,:,1]=255*(UAVRaster==2)
UAVRasterRGB[:,:,2]=255*(UAVRaster==1)
UAVRasterRGB[:,:,3] = 255*np.float32(UAVRaster != 0.0)
UAVRasterRGB= downscale_local_mean(UAVRasterRGB, (10,10,1))
ValidRasterName = DataFolder+'Cropped_'+ValidationSites.Abbrev[s]+'_'+str(ValidationSites.Month[s])+'_'+str(ValidationSites.Year[s])+'_S2.tif'
ValidRaster = io.imread(ValidRasterName)
ValidRasterIR = np.uint8(np.zeros((ValidRaster.shape[0], ValidRaster.shape[1],4)))
stretch=2
ValidRasterIR[:,:,0] = np.int16(stretch*255*ValidRaster[:,:,10])
ValidRasterIR[:,:,1] = np.int16(stretch*255*ValidRaster[:,:,5])
ValidRasterIR[:,:,2] = np.int16(stretch*255*ValidRaster[:,:,4])
ValidRasterIR[:,:,3]= 255*np.int16((ValidRasterIR[:,:,0] != 0.0)&(ValidRasterIR[:,:,1] != 0.0))
ValidTensor = slide_raster_to_tiles(ValidRaster, size)
Valid=np.zeros(12)
for n in range(1,13):
if ('B'+str(n)) in FeatureSet:
Valid[n-1]=1
ValidTensor = np.compress(Valid, ValidTensor, axis=3)
def plot_both(
id_to_match,
data_tree,
data_pop,
true_tree,
true_pop,
img_crop,
widths=[14, 28, 56, 112, 224],
save_dir=None,
):
"""Plot image, scene-level label, and super-res predictions at multiple scales.
Parameters
----------
id_to_match : str ("int,int")
The grid ID of the image to plot
data_[tree,pop] : :class:`numpy.ndarray`
The pixel-level superresolution predictions as arrays for treecover and
population.
true_[tree,pop] : float
The scene-level labels for treecover and population
img_crop : len-2 tuple
The amount to crop the image along left/top and right/bottom dimensions. This is
needed right, top, bottom. This is needed both because the feature extraction
causes the predictions to be slightly smaller than the image (e.g. 256x256
image --> 254x254 predictions with a 3x3 filter), and because we may have
cropped the predictions to be divisible by each scale of superresolution factor
that we are displaying.
widths : list of int
The widths (in pixels) of the superresolution predictions to make. The last
element should be equal to the length of the dimensions of ``data_[tree,pop]``
save_dir : str
Path to directory where these images are saved. If None, do not save
"""
# plotting contexts
context = sns.plotting_context("paper", font_scale=2)
lines = True
style = {
"axes.grid": False,
"axes.edgecolor": "0.0",
"axes.labelcolor": "0.0",
"axes.spines.right": lines,
"axes.spines.top": lines,
"axes.spines.left": lines,
"axes.spines.bottom": lines,
}
sns.set_context(context)
sns.set_style(style)
# set plotting context
plot_bounds_tree = TREECOVER_CMAP_BOUNDS
plot_bounds_pop = [0, 1000]
plot_bounds = [plot_bounds_tree, plot_bounds_pop]
names = ["treecover", "population"]
names_disp = ["% Forest", "Pop. Dens."]
# grab plotting constants from config file
c_plotting = getattr(config, "plotting")
cmap_fxn = c_plotting["cmap_fxn"]
cmaps = [cmap_fxn(getattr(config, task)["color"]) for task in names]
# get the image (returning blank if imagery is not saved)
image_dir = Path(config.data_dir) / "raw" / "imagery" / "CONTUS_UAR"
try:
image_this = io.load_img_from_ids_local(id_to_match, image_dir, c=config)
except FileNotFoundError:
image_this = None
for t, data_this in enumerate([(data_tree, true_tree), (data_pop, true_pop)]):
pred_map = data_this[0]
label_this = data_this[1]
task_this = names[t]
# get clipping bounds
c_app = getattr(config, task_this)
if c_app["logged"]:
bounds = [np.exp(i) for i in c_app["us_bounds_log_pred"]]
else:
bounds = c_app["us_bounds_pred"]
# collect maps by downscale level
superres_preds_by_scale = []
for w in widths:
# downscale
assert pred_map.shape[0] % w == 0
this_preds = downscale_local_mean(pred_map, (w, w))
# clip if both bounds aren't None for this outcome
if not (np.asarray(bounds) == None).all():
this_preds = np.clip(this_preds, *bounds)
superres_preds_by_scale.append(this_preds)
# plot for this variable
cmap_this = cmaps[t]
bounds_this = plot_bounds[t]
plot_img_and_heatmap_and_preds_multiscale(
image_this,
superres_preds_by_scale,
widths,
label_this,
cmap=cmap_this,
vmin=bounds_this[0],
vmax=bounds_this[1],
name=names_disp[t],
)
# save with descriptive name
if save_dir is not None:
plt.savefig(
"{2}/{1}_multires_{0}.pdf".format(id_to_match, names[t], save_dir),
bbox_inches="tight",
)