def predict_image(self, test_img):
"""
predicts classes of input image
:param test_img: filepath to image to predict on
:param show: displays segmentation results
:return: segmented result
"""
img = np.array(
rgb2gray(imread(test_img).astype('float')).reshape(5, 216,
160)[-2]) / 256
plist = []
# create patches from an entire slice
img_1 = adjust_sigmoid(img).astype(float)
edges_1 = adjust_sigmoid(img, inv=True).astype(float)
edges_2 = img_1
edges_5_n = normalize(laplace(img_1))
edges_5_n = img_as_float(img_as_ubyte(edges_5_n))
plist.append(extract_patches_2d(edges_1, (23, 23)))
plist.append(extract_patches_2d(edges_2, (23, 23)))
plist.append(extract_patches_2d(edges_5_n, (23, 23)))
patches = np.array(
zip(np.array(plist[0]), np.array(plist[1]), np.array(plist[2])))
# predict classes of each pixel based on model
full_pred = self.model.predict_classes(patches)
fp1 = full_pred.reshape(194, 138)
return fp1
def predict_image(self, test_img):
"""
predicts classes of input image
:param test_img: filepath to image to predict on
:param show: displays segmentation results
:return: segmented result
"""
img = np.array( rgb2gray( imread( test_img ).astype( 'float' ) ).reshape( 5, 216, 160 )[-2] ) / 256
plist = []
# create patches from an entire slice
img_1 = adjust_sigmoid( img ).astype( float )
edges_1 = adjust_sigmoid( img, inv=True ).astype( float )
edges_2 = img_1
edges_5_n = normalize( laplace( img_1 ) )
edges_5_n = img_as_float( img_as_ubyte( edges_5_n ) )
plist.append( extract_patches_2d( edges_1, (23, 23) ) )
plist.append( extract_patches_2d( edges_2, (23, 23) ) )
plist.append( extract_patches_2d( edges_5_n, (23, 23) ) )
patches = np.array( zip( np.array( plist[0] ), np.array( plist[1] ), np.array( plist[2] ) ) )
# predict classes of each pixel based on model
full_pred = self.model.predict_classes( patches )
fp1 = full_pred.reshape( 194, 138 )
return fp1
def improve_scenebkp(sub_templateg, alg=1):
ref = np.asarray(PIL.Image.fromarray(np.asarray(pd.read_pickle('./AuxFiles/refhist.pkl'))))
#if alg==1:
#sub_templateg = cv2.fastNlMeansDenoising(sub_templateg,None,10,7,21)
if is_low_contrast(sub_templateg, 0.35):
temp_img = np.copy(sub_templateg).astype(float)
temp_img[temp_img <= 30] = np.nan
temp_img_std = np.nanstd(temp_img)
del temp_img
if temp_img_std <= 30:
print('Scene is low contrasted, improving...')
sub_templateg = hist.adjust_gamma(sub_templateg, gamma=1.7)
sub_templateg = adjust_sigmoid(sub_templateg)
sub_templateg = hist.adjust_gamma(sub_templateg, gamma=1.2)
hist1 = cv2.calcHist([sub_templateg], [0], None, [256], [0, 256])
hist2 = cv2.calcHist([ref], [0], None, [256], [0, 256])
sim = cv2.compareHist(hist1, hist2, 0)
if sim < 0.8:
if alg == 1:
print('Computing large objects.')
sub_templateg = cv2.medianBlur(sub_templateg, 5)
sub_templateg = cv2.bilateralFilter(sub_templateg, 3, 3, 3)
sub_templateg = hist.adjust_gamma(sub_templateg, gamma=3.0)
sub_templateg = adjust_sigmoid(sub_templateg)
sub_templateg = hist.adjust_gamma(sub_templateg, gamma=1.0)
if alg == 2:
print('Computing small objects')
sub_templateg = hist.adjust_gamma(sub_templateg, gamma=1.5)
else:
if alg ==1:
print('Computing large objects.')
sub_templateg = hist.adjust_gamma(sub_templateg, gamma=1.5)
sub_templateg = adjust_sigmoid(sub_templateg)
sub_templateg = hist.adjust_gamma(sub_templateg, gamma=1.0)
else:
print('Computing small objects.')
sub_templateg = match_histograms(sub_templateg, ref)
sub_templateg = convert(sub_templateg, 0, 255, np.uint8)
return sub_templateg
def preproc(self, img, size, pixel_spacing, equalize=True, crop=True):
"""crop center and resize"""
# TODO: this is stupid, you could crop out the heart
# But should test this
if img.shape[0] < img.shape[1]:
img = img.T
# Standardize based on pixel spacing
img = transform.resize(img, (int(img.shape[0]*(1.0/np.float32(pixel_spacing[0]))), int(img.shape[1]*(1.0/np.float32(pixel_spacing[1])))))
# we crop image from center
short_egde = min(img.shape[:2])
yy = int((img.shape[0] - short_egde) / 2)
xx = int((img.shape[1] - short_egde) / 2)
if crop:
crop_img = img[yy : yy + short_egde, xx : xx + short_egde]
# resize to 64, 64
resized_img = transform.resize(crop_img, (size, size))
else:
resized_img = img
#resized_img = gaussian_filter(resized_img, sigma=1)
#resized_img = median_filter(resized_img, size=(3,3))
if equalize:
resized_img = equalize_hist(resized_img)
resized_img = adjust_sigmoid(resized_img)
resized_img *= 255.
return resized_img.astype("float32")
def run(self, img=misc.lena(), increase=True):
img = misc.imread('/Users/Daniel/Desktop/p0.jpg')
img_blurred = self.__blur(img)
img = self.__divide(img, img_blurred)
if False:
img = exposure.adjust_sigmoid(img)
misc.imsave('/Users/Daniel/Desktop/p1.jpg', img)
def img_exposure_sigmoid(image, sigmoid, prob=1):
generator = generator_class(prob)
if generator:
img = exposure.adjust_sigmoid(image, sigmoid)
else:
img = []
return img
def proc_mbi(imgarray):
# Normalize image:
img = img_as_float(imgarray,force_copy=True)
# Image equalization (Contrast stretching):
p2,p98 = np.percentile(img, (2,98))
img = exposure.rescale_intensity(img, in_range=(p2, p98), out_range=(0, 1))
# Gamma correction:
#img = exposure.adjust_gamma(img, 0.5)
# Or Sigmoid correction:
img = exposure.adjust_sigmoid(img)
print "Init Morph Proc..."
sizes = range(2,40,5)
angles = [0,18,36,54,72,90,108,126,144,162]
szimg = img.shape
all_thr = np.zeros((len(sizes),szimg[0], szimg[1])).astype('float64')
all_dmp = np.zeros((len(sizes) - 1,szimg[0], szimg[1])).astype('float64')
idx = 0
for sz in sizes:
print sz
builds_by_size = np.zeros(szimg).astype('float64')
for ang in angles:
print ang
stel = ia870.iaseline(sz, ang)
oprec = opening_by_reconstruction(img, stel)
thr = np.absolute(img-oprec)
builds_by_size += thr
all_thr[idx,:,:] = (builds_by_size / len(angles))
if idx>0:
all_dmp[idx-1,:,:] = all_thr[idx,:,:] - all_thr[idx-1,:,:]
idx += 1
mbi = np.mean(all_dmp, axis=0)
return mbi
def Hist_sigmoid(self):
self.temp = self.temp + 1
img = img_as_float(self.img)
sigmoid_corrected = adjust_sigmoid(img)
io.imsave('static/Image/temp' + str(self.temp) + '.' + self.format,
sigmoid_corrected)
return 'static/Image/temp' + str(self.temp) + '.' + self.format
def preprocessing(chunk, processing_type):
"""
performing preprocessing before motion correction
:param chunk: 3d array, frame * y * x
:param processing_type: int, type of preprocessing
0: nothing, no preprocessing
1: histogram equlization, return uint8 bit chunk
2: rectifyinng with a certain threshold
3: gamma correct each frame by gamma=0.1
4: brightness contrast adjustment
5: spatial filtering
6: tukey window with alpha 0.1
:return: preprocessed chunk
"""
if processing_type == 0:
return chunk
elif processing_type == 1:
chunk_eh = np.zeros(chunk.shape, dtype=np.uint8)
for i in range(chunk.shape[0]):
frame = chunk[i].astype(np.float32)
frame = (frame - np.amin(frame)) / (np.amax(frame) - np.amin(frame))
chunk_eh[i] = cv2.equalizeHist((frame * 255).astype(np.uint8))
return chunk_eh
elif processing_type == 2:
low_thr = -200
high_thr = 2000
chunk[chunk < low_thr] = low_thr
chunk[chunk > high_thr] = high_thr
return chunk
elif processing_type == 3:
chunk_gamma = np.zeros(chunk.shape, dtype=np.float32)
for i in range(chunk.shape[0]):
frame = chunk[i].astype(np.float32)
frame = (frame - np.amin(frame)) / (np.amax(frame) - np.amin(frame))
chunk_gamma[i] = exp.adjust_gamma(frame, gamma=0.1)
return chunk_gamma.astype(chunk.dtype)
elif processing_type == 4:
chunk_sigmoid = np.zeros(chunk.shape, dtype=np.float32)
for i in range(chunk.shape[0]):
frame = chunk[i].astype(np.float32)
frame = (frame - np.amin(frame)) / (np.amax(frame) - np.amin(frame))
frame_sigmoid = exp.adjust_sigmoid(frame, cutoff=0.1, gain=10, inv=False)
# plt.imshow(frame_sigmoid)
# plt.show()
chunk_sigmoid[i] = frame_sigmoid
return chunk_sigmoid.astype(chunk.dtype)
elif processing_type == 5:
chunk_filtered = np.zeros(chunk.shape, dtype=np.float32)
for i in range(chunk.shape[0]):
frame = chunk[i].astype(np.float32)
frame_filtered = ni.gaussian_filter(frame, sigma=10.)
chunk_filtered[i] = frame_filtered
return chunk_filtered.astype(chunk.dtype)
elif processing_type == 6:
window = tukey_2d(shape=(chunk.shape[1], chunk.shape[2]), alpha=0.1, sym=True)
window = np.array([window])
return (chunk * window).astype(chunk.dtype)
else:
raise LookupError('Do not understand framewise preprocessing type.')
def process_frame(frame, bbox):
# crop frame (assuming CROP_X and Y are set in env)
#frame = frame[CROP_Y[0]:CROP_Y[1], CROP_X[0]:CROP_X[1], :]
frame = frame[bbox[1]:bbox[1] + bbox[2], bbox[0]:bbox[0] + bbox[3], :]
# Adjust contrast
frame = adjust_sigmoid(frame, gain=5, cutoff=0.1)
return frame
print('defined')
def gray_process(img, dsize=25, cutoff=0.5, gain=10):
img_gr = np.zeros_like(img[:, :, 0])
img_gr = (img[:, :, 0] + img[:, :, 1] + img[:, :, 2]) / 3
selem = morphology.disk(dsize)
img_gr = filters.rank.equalize(img_gr, selem=selem)
img_gr = img_as_float(img_gr)
img_gr = exposure.adjust_sigmoid(img_gr, cutoff=cutoff, gain=gain)
return img_gr
def transform(src_dir, city, s, gamma, method='CLAHE'):
"""Scales all images of given city
@param: src_dir is directory the tiles are in
@param: city is the positive filter for the city you're looking for
@param: s is vector of color scalings for that city
@param: gamma is exponent for scaling
@param: type of method to transform by"""
imList = [f for f in os.listdir(src_dir) if ('RGB' in f
and city in f
and 'tif' in f)]
path = src_dir + 'transformed_{}/'.format(method)
try: os.mkdir(path)
except: pass
if method == 'WB2': #transformations considering entire city of data
threshold = 0.005
cum_hist = {}
for i in range(3): #each color channel
histSum = 0
cumSum = 0
for file in imList:
image = imio.imread(src_dir + file)
hist, bins = np.histogram(image[...,i].ravel(), 256, (0,255))
histSum += hist.sum()
cumSum += np.cumsum(hist)
cum_hist[i] = cumSum / histSum
for file in imList:
name = file[0].upper() + file[1:]
image = imio.imread(src_dir + file)
if method == 'gamma_correction':
new_image = gammaCorrect(image, s, gamma)
elif method == 'scale_only':
new_image = gamma(image, s, gamma=1.0)
elif method == 'CLAHE':
new_image = exposure.equalize_adapthist(image, clip_limit=0.01)
new_image = img_as_uint(new_image)
elif method == 'log':
new_image = exposure.adjust_log(image)
elif method == 'sigmoid':
new_image = exposure.adjust_sigmoid(image, gain=4, cutoff=0.35)
elif method == 'KyleWb2':
new_image = KyleWB2(image)
elif method == 'WB2':
new_image = np.zeros_like(image) #Initialize final image
for i in range(3): #each color channel
bmin = np.where(cum_hist[i]>threshold)[0][0]
bmax = np.where(cum_hist[i]>1-threshold)[0][0]
new_image[...,i] = np.clip(image[...,i], bmin, bmax)
new_image[...,i] = (new_image[...,i]-bmin) / (bmax - bmin) * 255
new_image = new_image.round().astype('uint8')
print(name)
imio.imwrite(path + name, new_image)
def bw_transform_special(img):
#Tratamiento especial para imágenes
image = rgb2gray(img)
image = invert(image)
image = adjust_gamma(image, 2)
image = adjust_sigmoid(image, .95)
threshold_image = threshold_otsu(image)
image = image > threshold_image
return image
def gammacorection():
image = load_a_picture()
# ima = exposure.adjust_gamma(image, 2)
ima = exposure.adjust_sigmoid(image, 0.8)
add_to_stack(ima)
show_img(actual_loaded)
processing_menu()
def random_transform(self, x, seed=None):
x = super(MyImageDataGenerator, self).random_transform(x, seed)
if self.contrast_stretching_perc != 0.:
contrast_p = np.random.uniform(1. - self.contrast_stretching_perc,
1. + self.contrast_stretching_perc)
x = adjust_sigmoid(x.astype(np.float) / 255., cutoff=0.5,
gain=5 * contrast_p, inv=False)
x *= 255
return x
def plot_image(img, ax):
from skimage import exposure
h, w, _ = img.shape
img = img[100:h - 100, 100:w - 100, :]
plt.setp(ax.get_yticklabels(), visible=False)
plt.setp(ax.get_xticklabels(), visible=False)
ax.imshow(exposure.adjust_sigmoid(img, 0.40, 8))
ax.set_xticks([])
ax.set_yticks([])
return
def saturation_rectified_intensity(image):
assert (type(image) is np.ndarray and image.dtype == np.uint8 and len(
image.shape) == 3), "The input image has to be a uint8 2D numpy array."
image_hsv = cv2.cvtColor(image, cv2.COLOR_BGR2HSV)
saturation = img_as_float(image_hsv[:, :, 1])
intensity = img_as_float(image_hsv[:, :, 2])
adjust = adjust_sigmoid(saturation, 0.08, 25)
signal = invert(intensity)
image_out = invert(adjust * signal)
return img_as_ubyte(image_out)
def callPeaks(lane, gain=7, hamming=5, filt=0.2, order=9):
""" Identify peaks in the lane
:Args:
:param lane: The lane which to call peaks.
:type lane: tapeAnalyst.gel_processing.GelLane
:param gain: The gain value to use for increasing contrast (see
skimage.exposure.adjust_sigmoid)
:type gain: int
:param hamming: The value to use Hamming convolution (see
scipy.signal.hamming)
:type gain: int
:param filt: Remove all pixels whose intensity is below this value.
:type filt: float
:param order: The distance allowed for finding maxima (see scipy.signal.argrelmax)
:type order: int
"""
# Increase contrast to help with peak calling
ladj = exposure.adjust_sigmoid(lane.lane, cutoff=0.5, gain=gain)
# Tack the max pixel intensity for each row in then lane's gel image.
laneDist = ladj.max(axis=1)
# Smooth the distribution
laneDist = signal.convolve(laneDist, signal.hamming(hamming))
# Get the locations of the dye front and dye end. Peak calling is difficult
# here because dyes tend to plateau. To aid peak calling, add an artificial
# spike in dye regions. Also remove all peaks outside of the dyes
try:
dyeFrontPeak = int(np.ceil(np.mean([lane.dyeFrontStart, lane.dyeFrontEnd])))
laneDist[dyeFrontPeak] = laneDist[dyeFrontPeak] + 2
laneDist[dyeFrontPeak+1:] = 0
except:
logger.warn('No Dye Front - Lane {}: {}'.format(lane.index, lane.wellID))
try:
dyeEndPeak = int(np.ceil(np.mean([lane.dyeEndStart, lane.dyeEndEnd])))
laneDist[dyeEndPeak] = laneDist[dyeEndPeak] + 2
laneDist[:dyeEndPeak-1] = 0
except:
logger.warn('No Dye End - Lane {}: {}'.format(lane.index, lane.wellID))
# Filter out low levels
laneDist[laneDist < filt] = 0
# Find local maxima
peaks = signal.argrelmax(laneDist, order=order)[0]
return peaks
def callPeaks(lane, gain=7, hamming=5, filt=0.2, order=9):
""" Identify peaks in the lane
:Args:
:param lane: The lane which to call peaks.
:type lane: tapeAnalyst.gel_processing.GelLane
:param gain: The gain value to use for increasing contrast (see
skimage.exposure.adjust_sigmoid)
:type gain: int
:param hamming: The value to use Hamming convolution (see
scipy.signal.hamming)
:type gain: int
:param filt: Remove all pixels whose intensity is below this value.
:type filt: float
:param order: The distance allowed for finding maxima (see scipy.signal.argrelmax)
:type order: int
"""
# Increase contrast to help with peak calling
ladj = exposure.adjust_sigmoid(lane.lane, cutoff=0.5, gain=gain)
# Tack the max pixel intensity for each row in then lane's gel image.
laneDist = ladj.max(axis=1)
# Smooth the distribution
laneDist = signal.convolve(laneDist, signal.hamming(hamming))
# Get the locations of the dye front and dye end. Peak calling is difficult
# here because dyes tend to plateau. To aid peak calling, add an artificial
# spike in dye regions. Also remove all peaks outside of the dyes
try:
dyeFrontPeak = int(np.ceil(np.mean([lane.dyeFrontStart, lane.dyeFrontEnd])))
laneDist[dyeFrontPeak] = laneDist[dyeFrontPeak] + 2
laneDist[dyeFrontPeak+1:] = 0
except:
logger.warn('No Dye Front - Lane {}: {}'.format(lane.index, lane.wellID))
try:
dyeEndPeak = int(np.ceil(np.mean([lane.dyeEndStart, lane.dyeEndEnd])))
laneDist[dyeEndPeak] = laneDist[dyeEndPeak] + 2
laneDist[:dyeEndPeak-1] = 0
except:
logger.warn('No Dye End - Lane {}: {}'.format(lane.index, lane.wellID))
# Filter out low levels
laneDist[laneDist < filt] = 0
# Find local maxima
peaks = signal.argrelmax(laneDist, order=order)[0]
return peaks
def m6():
Image.MAX_IMAGE_PIXELS = None
for fn in os.listdir("all"):
if fn.endswith("TIF"):
adj_fn = fn.split("_B")[1]
if len(adj_fn) == 5:
adj_fn = "0" + adj_fn
adj_fn = "A_" + adj_fn[:-4]
print(adj_fn)
image = io.imread("all/" + fn)
print(image.shape)
if fn.endswith("8.TIF"):
pass
region = image[3500 * 2:3900 * 2, 800 * 2:1200 * 2]
else:
region = image[3500:3900, 800:1200]
region = transform.resize(region, (800, 800),
anti_aliasing=False)
io.imsave("edited/" + adj_fn + ".png", region)
adhist = exposure.equalize_adapthist(region)
io.imsave("edited/" + adj_fn + "adj_adhist.png", adhist)
exp = exposure.adjust_sigmoid(adhist)
io.imsave("edited/" + adj_fn + "adj_adsig.png", exp)
#roberts, sobel, scharr, prewitt
edges = filters.roberts(adhist)
io.imsave("edited/" + adj_fn + "f_rob.png", edges)
edges = filters.sobel(adhist)
io.imsave("edited/" + adj_fn + "f_sob.png", edges)
edges = filters.scharr(adhist)
io.imsave("edited/" + adj_fn + "f_sch.png", edges)
edges = filters.prewitt(adhist)
io.imsave("edited/" + adj_fn + "f_prew.png", edges)
adhist = exposure.equalize_hist(region)
io.imsave("edited/" + adj_fn + "adj_hist.png", adhist)
exp = exposure.adjust_sigmoid(adhist)
io.imsave("edited/" + adj_fn + "adj_sig.png", exp)
def process_image(img, sig_param=.85):
image = rgb2gray(img)
image = pyramid_expand(image, order=3)
theta = ImageSignalDigitalizer.skew_detect(image)
image = rotate(image,
np.rad2deg(theta) + ImageSignalDigitalizer.CONST_ANGLE,
resize=True)
image = invert(image)
image = adjust_sigmoid(image, sig_param)
image = ImageSignalDigitalizer.bw_transform(image)
image = resize(image, (2048, 2048 * 2))
return image
def sigmoid(self):
"""sigmoid exposure added to image
Parameters
----------
image : n-dimensional array
Input image folder.
Returns
-------
Image with sigmoid exposure.
"""
return exposure.adjust_sigmoid(self)
def _augment(xs):
"""Image adjustment doesn't change image shape, but for intensity.
Return:
images: 4-d tensor with shape [depth, height, width, channels]
"""
# `xs` has shape [depth, height, width] with value in [0, 1].
brt_gamma, brt_gain = np.random.uniform(low=0.9, high=1.1, size=2)
aj_bright = adjust_gamma(xs, brt_gamma, brt_gain)
contrast_gain = np.random.uniform(low=5, high=10)
aj_contrast = adjust_sigmoid(aj_bright, gain=contrast_gain)
return aj_contrast
def run(self, imgin_path, imgout_path=None, increase_exposure=False):
imgin_path = self.__expand_user(imgin_path)
img = misc.imread(imgin_path)
img_blurred = self.__blur(img)
img = self.__divide(img, img_blurred)
if increase_exposure:
img = exposure.adjust_sigmoid(img)
if not imgout_path:
imgout_path = self.__add_suffix(imgin_path)
misc.imsave(imgout_path, img)
print("Saved to", imgout_path)
def rescale(initial_data, log_scale=True, method='adaptive_equalization'):
norm = (initial_data-initial_data.min())/initial_data.max()
exponent = 1000
log = np.log(exponent*norm+1)/np.log(exponent) if log_scale else norm
if method == 'adaptive_equalization':
return exposure.equalize_adapthist(log/log.max(), nbins=2048, kernel_size=64)
elif method == 'adjust_sigmoid':
return exposure.adjust_sigmoid(log/log.max(), cutoff=0.5, gain=20)
elif method == 'global_equalization':
return exposure.equalize_hist(log / log.max(), nbins=1024)
elif method == 'local_equalization':
return rank.equalize(log / log.max(), selem=disk(30 ))
return
def test_adjust_sigmoid_cutoff_one():
"""Verifying the output with expected results for sigmoid correction
with cutoff equal to one and gain of 5"""
image = np.arange(0, 255, 4, np.uint8).reshape((8, 8))
expected = np.array(
[[1, 1, 1, 2, 2, 2, 2, 2], [3, 3, 3, 4, 4, 4, 5, 5],
[5, 6, 6, 7, 7, 8, 9, 10], [10, 11, 12, 13, 14, 15, 16, 18],
[19, 20, 22, 24, 25, 27, 29, 32], [34, 36, 39, 41, 44, 47, 50, 54],
[57, 61, 64, 68, 72, 76, 80, 85],
[89, 94, 99, 104, 108, 113, 118, 123]],
dtype=np.uint8)
result = exposure.adjust_sigmoid(image, 1, 5)
assert_array_equal(result, expected)
def create_dataset():
dataset = []
os.chdir("Car")
img_list = os.listdir()
for img in img_list:
image = io.imread(img)
img_gray = color.rgb2gray(image)
img_contrast = exposure.adjust_sigmoid(img_gray,
cutoff=0.5,
gain=100,
inv=False)
dataset.append((image, img_contrast))
os.chdir(os.getcwd() + "/../")
return dataset
def augmentations(image_array: ndarray):
v_min, v_max = np.percentile(image_array, (0.2, 99.8))
return (
image_array,
transform.rotate(image_array, random.uniform(-50, 50)),
exposure.rescale_intensity(image_array, in_range=(v_min, v_max)),
util.random_noise(image_array),
ndimage.gaussian_filter(image_array, 2),
exposure.adjust_log(image_array),
exposure.adjust_sigmoid(image_array),
#color.rgb2gray(image_array), (FOR COLORED IMAGES)
#np.invert(image_array), (FOR COLORED IMAGES)
exposure.adjust_gamma(image_array, gamma=0.4, gain=0.9),
image_array[:, ::-1],
image_array[::-1, :])
def adjust(frame, method, **kwargs):
if method == "equalize":
adjusted = exp.equalize_hist(frame, **kwargs)
elif method == "gamma":
adjusted = exp.adjust_gamma(frame, **kwargs)
elif method == "log":
adjusted = exp.adjust_log(frame, **kwargs)
elif method == "sigmoid":
adjusted = exp.adjust_sigmoid(frame, **kwargs)
elif method == "adaptive":
adjusted = exp.equalize_adapthist(frame, **kwargs)
else:
raise ValueError(
"method can be equalize, gamma, log, sigmoid or adaptive")
return adjusted
def test_adjust_inv_sigmoid_cutoff_half():
"""Verifying the output with expected results for inverse sigmoid
correction with cutoff equal to half and gain of 10"""
image = np.arange(0, 255, 4, np.uint8).reshape((8, 8))
expected = np.array(
[[253, 253, 252, 252, 251, 251, 250, 249],
[249, 248, 247, 245, 244, 242, 240, 238],
[235, 232, 229, 225, 220, 215, 210, 204],
[197, 190, 182, 174, 165, 155, 146, 136],
[126, 116, 106, 96, 87, 78, 70, 62], [55, 49, 43, 37, 33, 28, 25, 21],
[18, 16, 14, 12, 10, 8, 7, 6], [5, 4, 4, 3, 3, 2, 2, 1]],
dtype=np.uint8)
result = exposure.adjust_sigmoid(image, 0.5, 10, True)
assert_array_equal(result, expected)
def test_adjust_sigmoid_cutoff_one():
"""Verifying the output with expected results for sigmoid correction
with cutoff equal to one and gain of 5"""
image = np.arange(0, 255, 4, np.uint8).reshape(8,8)
expected = np.array([[ 1, 1, 1, 2, 2, 2, 2, 2],
[ 3, 3, 3, 4, 4, 4, 5, 5],
[ 5, 6, 6, 7, 7, 8, 9, 10],
[ 10, 11, 12, 13, 14, 15, 16, 18],
[ 19, 20, 22, 24, 25, 27, 29, 32],
[ 34, 36, 39, 41, 44, 47, 50, 54],
[ 57, 61, 64, 68, 72, 76, 80, 85],
[ 89, 94, 99, 104, 108, 113, 118, 123]], dtype=np.uint8)
result = exposure.adjust_sigmoid(image, 1, 5)
assert_array_equal(result, expected)
def test_adjust_sigmoid_cutoff_zero():
"""Verifying the output with expected results for sigmoid correction
with cutoff equal to zero and gain of 10"""
image = np.arange(0, 255, 4, np.uint8).reshape(8,8)
expected = np.array([[127, 137, 147, 156, 166, 175, 183, 191],
[198, 205, 211, 216, 221, 225, 229, 232],
[235, 238, 240, 242, 244, 245, 247, 248],
[249, 250, 250, 251, 251, 252, 252, 253],
[253, 253, 253, 253, 254, 254, 254, 254],
[254, 254, 254, 254, 254, 254, 254, 254],
[254, 254, 254, 254, 254, 254, 254, 254],
[254, 254, 254, 254, 254, 254, 254, 254]], dtype=np.uint8)
result = exposure.adjust_sigmoid(image, 0, 10)
assert_array_equal(result, expected)
def test_adjust_sigmoid_cutoff_half():
"""Verifying the output with expected results for sigmoid correction
with cutoff equal to half and gain of 10"""
image = np.arange(0, 255, 4, np.uint8).reshape(8,8)
expected = np.array([[ 1, 1, 2, 2, 3, 3, 4, 5],
[ 5, 6, 7, 9, 10, 12, 14, 16],
[ 19, 22, 25, 29, 34, 39, 44, 50],
[ 57, 64, 72, 80, 89, 99, 108, 118],
[128, 138, 148, 158, 167, 176, 184, 192],
[199, 205, 211, 217, 221, 226, 229, 233],
[236, 238, 240, 242, 244, 246, 247, 248],
[249, 250, 250, 251, 251, 252, 252, 253]], dtype=np.uint8)
result = exposure.adjust_sigmoid(image, 0.5, 10)
assert_array_equal(result, expected)
def test_adjust_inv_sigmoid_cutoff_half():
"""Verifying the output with expected results for inverse sigmoid
correction with cutoff equal to half and gain of 10"""
image = np.arange(0, 255, 4, np.uint8).reshape(8,8)
expected = np.array([[253, 253, 252, 252, 251, 251, 250, 249],
[249, 248, 247, 245, 244, 242, 240, 238],
[235, 232, 229, 225, 220, 215, 210, 204],
[197, 190, 182, 174, 165, 155, 146, 136],
[126, 116, 106, 96, 87, 78, 70, 62],
[ 55, 49, 43, 37, 33, 28, 25, 21],
[ 18, 16, 14, 12, 10, 8, 7, 6],
[ 5, 4, 4, 3, 3, 2, 2, 1]], dtype=np.uint8)
result = exposure.adjust_sigmoid(image, 0.5, 10, True)
assert_array_equal(result, expected)
def test_adjust_sigmoid_cutoff_half():
"""Verifying the output with expected results for sigmoid correction
with cutoff equal to half and gain of 10"""
image = np.arange(0, 255, 4, np.uint8).reshape((8, 8))
expected = np.array(
[[1, 1, 2, 2, 3, 3, 4, 5], [5, 6, 7, 9, 10, 12, 14, 16],
[19, 22, 25, 29, 34, 39, 44, 50], [57, 64, 72, 80, 89, 99, 108, 118],
[128, 138, 148, 158, 167, 176, 184, 192],
[199, 205, 211, 217, 221, 226, 229, 233],
[236, 238, 240, 242, 244, 246, 247, 248],
[249, 250, 250, 251, 251, 252, 252, 253]],
dtype=np.uint8)
result = exposure.adjust_sigmoid(image, 0.5, 10)
assert_array_equal(result, expected)
def pre_image_processing(resized_image):
equal_adapt_hist_image = exposure.equalize_adapthist(resized_image)
rescale_intensity_image = exposure.rescale_intensity(equal_adapt_hist_image)
adjust_sigmoid_image = exposure.adjust_sigmoid(rescale_intensity_image)
gray_scale_image = rgb2gray(adjust_sigmoid_image)
mean_image = mean(gray_scale_image, disk(1))
mean_image = mean(mean_image, disk(1))
mean_image = mean(mean_image, disk(1))
median_image = dilation(median(mean_image, disk(1)), square(2))
otsu_image = filters.threshold_otsu(median_image)
closing_image = closing(median_image > otsu_image, square(1))
# opening_image = opening(closing_image, square(2))
opening_image = invert(closing_image)
return opening_image
def test_adjust_sigmoid_cutoff_zero():
"""Verifying the output with expected results for sigmoid correction
with cutoff equal to zero and gain of 10"""
image = np.arange(0, 255, 4, np.uint8).reshape((8, 8))
expected = np.array([[127, 137, 147, 156, 166, 175, 183, 191],
[198, 205, 211, 216, 221, 225, 229, 232],
[235, 238, 240, 242, 244, 245, 247, 248],
[249, 250, 250, 251, 251, 252, 252, 253],
[253, 253, 253, 253, 254, 254, 254, 254],
[254, 254, 254, 254, 254, 254, 254, 254],
[254, 254, 254, 254, 254, 254, 254, 254],
[254, 254, 254, 254, 254, 254, 254, 254]],
dtype=np.uint8)
result = exposure.adjust_sigmoid(image, 0, 10)
assert_array_equal(result, expected)
def image_transformation(X, method_type='blur', **kwargs):
# https://www.kaggle.com/tomahim/image-manipulation-augmentation-with-skimage
q = kwargs['percentile'] if 'percentile' in kwargs else (0.2, 99.8)
angle = kwargs['angle'] if 'angle' in kwargs else 60
transformation_dict = {
'blur': normalize(ndimage.uniform_filter(X)),
'invert': normalize(util.invert(X)),
'rotate': rotate(X, angle=angle),
'rescale_intensity': _rescale_intensity(X, q=q),
'gamma_correction': exposure.adjust_gamma(X, gamma=0.4, gain=0.9),
'log_correction': exposure.adjust_log(X),
'sigmoid_correction': exposure.adjust_sigmoid(X),
'horizontal_flip': X[:, ::-1],
'vertical_flip': X[::-1, :],
'rgb2gray': skimage.color.rgb2gray(X)
}
return transformation_dict[method_type]
def image_transformation(X, method_type='blur', **kwargs):
# https://www.kaggle.com/tomahim/image-manipulation-augmentation-with-skimage
q = kwargs['percentile'] if 'percentile' in kwargs else (0.2, 99.8)
angle = kwargs['angle'] if 'angle' in kwargs else 60
transformation_dict = {
'blur': normalize(ndimage.uniform_filter(X)),
'invert': normalize(util.invert(X)),
'rotate': rotate(X, angle=angle),
'rescale_intensity': _rescale_intensity(X, q=q),
'gamma_correction': exposure.adjust_gamma(X, gamma=0.4, gain=0.9),
'log_correction': exposure.adjust_log(X),
'sigmoid_correction': exposure.adjust_sigmoid(X),
'horizontal_flip': X[:, ::-1],
'vertical_flip': X[::-1, :],
'rgb2gray': skimage.color.rgb2gray(X)
}
return transformation_dict[method_type]
def intensity_correction(img):
mean_val = np.mean(img)
mean_val = mean_val / 255.
#print(mean_val)
#sigmoid correction
img2 = exp.adjust_sigmoid(img, cutoff = mean_val, gain=5)
#draw(img2, "Sigmoid correction", 4, 3, 4, 4, 3, 5)
#robust linear correction
left, right = np.percentile(img2, (10, 90))
img3 = exp.rescale_intensity(img2, in_range=(left, right))
#draw(img3, "Linear correction", 4, 3, 7, 4, 3, 8)
img4 = filters.gaussian(img3, sigma=.5)
#draw(img4, "Gaussian filter", 4, 3, 10, 4, 3, 11)
return img4
def image_equalization(image_file):
'''
in testing
'''
# Load an example image
img = io.imread(image_file)
#img = data.moon()
#img = 'new.jpg'
# Contrast stretching
p2, p98 = np.percentile(img, (2, 98))
img_rescale = exposure.rescale_intensity(img, in_range=(p2, p98))
img_rescale = exposure.adjust_sigmoid(img_rescale, 0.5, 5)
# Equalization
img_eq = exposure.equalize_hist(img)
# Adaptive Equalization
img_adapteq = exposure.equalize_adapthist(img, clip_limit=0.03)
'''
cv2.imshow('image', img)
cv2.waitKey(0)
'''
cv2.imshow('image', img_rescale)
cv2.waitKey(0)
'''
cv2.imshow('image', img_eq)
cv2.waitKey(0)
cv2.imshow('image', img_adapteq)
cv2.waitKey(0)
'''
cv2.imwrite('new_adj.jpg', img_rescale)
'''
cv2.imwrite('new_adj2.jpg', img_eq)
cv2.imwrite('new_adj3.jpg', img_adapteq)
'''
return ['new_adj.jpg', 1, 2] #'new_adj2.jpg', 'new_adj3.jpg']
# <codecell>
# Original image
A = io.imread("../data/" + l[2])
io.imshow(A)
# <codecell>
# Colour Deconvolution
deconv = ski.img_as_float(color.separate_stains(A, np.linalg.inv(qstain)))
io.imshow(exposure.adjust_sigmoid(
filter.gaussian_filter(
exposure.rescale_intensity(
deconv[:, :, 0] + deconv[:, :, 2],
out_range=(0, 1)),
17),
gain=7, cutoff=0.6))
# <codecell>
# Blood
blood = \
morphology.remove_small_objects(
filter.threshold_adaptive(
exposure.adjust_sigmoid(
filter.gaussian_filter(
exposure.rescale_intensity(
deconv[:, :, 0] + deconv[:, :, 2],
def contrast_enhance(img):
return adjust_sigmoid(img, cutoff=0.5, gain=10)
offset = 1000 lengthscale = 301 image = exposure.equalize_adapthist(io.imread(files[4])) #image = io.imread(files[4]) io.imshow(image) plt.grid(False) # <codecell> #binary = np.logical_or(filter.threshold_adaptive(exposure.adjust_sigmoid(image[:, :, 0], cutoff=0.4, gain=20), lengthscale), \ # filter.threshold_adaptive(exposure.adjust_sigmoid(image[:, :, 2], cutoff=0.5, gain=20), lengthscale)) binary = filter.threshold_adaptive(exposure.adjust_sigmoid(image[:, :, 0], cutoff=0.4, gain = 30), 301).astype(bool) clean = morphology.binary_closing(binary, morphology.disk(3)).astype(bool) clean = morphology.remove_small_objects(clean, 200) clean = morphology.remove_small_objects( (1-clean).astype(bool), 200) io.imshow(clean) plt.grid(False) # <codecell> (xdim, ydim, _) = image.shape xdim /= 10 ydim /= 10
# <codecell>
A = io.imread("../data/" + l[5])
io.imshow(A)
# <codecell>
#B = exposure.adjust_sigmoid(filter.gaussian_filter(A[:, :, 0], 19), cutoff=.45, gain=15)
B = exposure.adjust_sigmoid(
filter.gaussian_filter(
exposure.rescale_intensity(
color.separate_stains(
A,
np.linalg.inv(qstain)),
out_range=(0, 1))[:, :, 1],
29),
cutoff=.35, gain=20)
io.imshow(B)
# <codecell>
#b = morphology.remove_small_objects(filter.threshold_adaptive(filter.gaussian_filter(exposure.adjust_sigmoid(A[:,:,1]), 31), 501, offset=-0.05), 2000)
C = morphology.remove_small_objects(
filter.threshold_adaptive(B, 301, offset=-0.025),
4000)
#io.imshow(morphology.binary_closing(np.logical_or(morphology.binary_dilation(C, morphology.disk(11)), b), morphology.disk(31)))
io.imshow(C)
cov_point_density = [] var_area_density = [] cov_area_density = [] fs_area = [] pairwise = [] image = exposure.equalize_adapthist(A) io.imshow(image) plt.grid(False) # <codecell> # Process for nuclei binary = filter.threshold_adaptive(exposure.adjust_sigmoid(A[:, :, 0], cutoff=0.4, gain = 30), 301).astype(bool) clean = morphology.binary_closing(binary, morphology.disk(3)).astype(bool) clean = morphology.remove_small_objects(clean, 200) clean = morphology.remove_small_objects( (1-clean).astype(bool), 200) io.imshow(clean) plt.grid(False) # <codecell> # Find contour of inflammatory zone local_density = filter.gaussian_filter(clean, 61) local_density -= local_density.min() local_density /= local_density.max()
def sigmoid_transform(img, cutoff=0.5):
return exposure.adjust_sigmoid(img, cutoff)
c.z_sun
# In[ ]:
# In[ ]:
cube.imshow(data=out)
# In[ ]:
out2 = adjust_sigmoid(out)
# In[ ]:
equal = equalize_adapthist(out2)
# In[ ]:
cube.imshow(equal)
# In[ ]:
meta = pd.read_csv('/Users/klay6683/Dropbox/DDocuments/UVIS/straws/coiss_ahires.015.list.txt',
for k in range(0,len(image_file_list),n):
X = []
Y = []
for fname in image_file_list[k:k+n]:
label = label_dict[fname.split('.')[0]]
cur_img = imread(folder+'/'+fname , as_grey=True)
cur_img = 1 - cur_img
# randomly add samples
r_for_eq = random()
if r_for_eq<0.3:
cur_img = equalize_adapthist(cur_img,ntiles_x=5,ntiles_y=5,clip_limit=0.1)
if 0.3<r_for_eq<0.4:
cur_img = adjust_sigmoid(cur_img,cutoff=0.5, gain=10, inv=False)
if 0.5<r_for_eq<0.6:
cur_img = adjust_gamma(cur_img,gamma=0.5, gain=1)
X.append([cur_img.tolist()])
label_vec = [0]*5
label_vec[label] = 1
"""
label_vec = [0]*3
if label == 0 or label == 1:
label_vec[0] = 1
elif label == 2 or label == 3 :
label_vec[1] = 1
else:
# There are plenty of ways of combining the different grey-level images into a
# false-color representation (it's a bit of an art!). This is a very simple
# pipeline, that mainly tweaks intensities, and that does nothing fancy along
# the lines of denoising, sharpening, etc.
import numpy as np
import matplotlib.pyplot as plt
from skimage import img_as_float, io, exposure
ic = io.ImageCollection('m8_050507_*.png')
ic = [img_as_float(img) for img in ic]
H, B, G, R, L = ic
H = exposure.adjust_sigmoid(H, cutoff=0.05, gain=35)
L = exposure.adjust_sigmoid(L, cutoff=0.05, gain=15)
R = exposure.adjust_gamma(R, 0.1)
# Merge R, G, B channels
out = np.dstack((H, L, R))
out = exposure.adjust_gamma(out, 2.1)
io.imsave('m8_recon.png', out)
f, ax = plt.subplots()
ax.imshow(out)
plt.show()
27) inflammation = \ maximum_filter( morphology.remove_small_objects( filter.threshold_adaptive( exposure.adjust_sigmoid( filter.gaussian_filter( exposure.equalize_adapthist( exposure.rescale_intensity( deconv[:, :, 1], out_range = (0, 1)), ntiles_y = 1), 5), cutoff = 0.6), 75, offset = -0.12), 250), 29) # Labelled
print files # <codecell> # <codecell> A = io.imread(files[0]) As = transform.rescale(A, 0.25) io.imshow(A) plt.grid(False) # <codecell> #B = exposure.adjust_sigmoid(A, gain=12) Bs = exposure.adjust_sigmoid(ski.img_as_float(As), gain=12) #io.imshow(B - exposure.adjust_sigmoid(ski.img_as_float(A), gain=12)) # <codecell> #C = color.rgb2xyz(B)[:, :, 1] Cs = color.rgb2xyz(Bs)[:, :, 1] io.imshow(Cs) plt.grid(0) # <codecell> #D = filter.threshold_adaptive(C, 301) Ds = filter.threshold_adaptive(Cs, 75) io.imshow(Ds) plt.grid(0)
def _find_patches(self, class_number, per_class):
"""
this function in dependence of the class number search for patches with the edge pattern
:param per_class: number of patches to find
:param class_number the class number
:return:
a numpy array of patches and a numpy array of labels
"""
print()
patches = []
labels = np.ones( per_class * self.augmentation_multiplier ) * class_number
ten_percent_black = 0
ten_percent_black_value = int( float( per_class ) * 0.0001 )
start_value_extraction = 0
full = False
if isdir( 'patches/' ) and isdir( 'patches/sigma_{}/'.format( self.sigma
) ) and isdir(
'patches/sigma_{}/class_{}/'.format( self.sigma,
class_number ) ):
# load all patches
# check if quantity is enough to work
path_to_patches = sorted( glob( './patches/sigma_{}/class_{}/**.png'.format( self.sigma,
class_number ) ),
key=get_right_order )
for path_index in xrange( len( path_to_patches ) ):
if path_index < per_class:
patch_to_load = np.array( rgb2gray( imread( path_to_patches[path_index],
dtype=float ) ).reshape( 3,
self.patch_size[0],
self.patch_size[1] ) ).astype(
float )
patches.append( patch_to_load )
for el in xrange( len( patch_to_load ) ):
if np.max( patch_to_load[el] ) > 1:
patch_to_load[el] /= np.max( patch_to_load[el] )
print( '*---> patch {}/{} loaded and added '.format( path_index, per_class ) )
else:
full = True
break
if len( path_to_patches ) < per_class:
# change start_value_extraction
start_value_extraction = len( path_to_patches )
else:
full = True
else:
mkdir_p( 'patches/sigma_{}/class_{}'.format( self.sigma,
class_number ) )
patch_to_extract = 25000
if not full:
for i in range( start_value_extraction, per_class ):
extracted = False
random_image = self.images[randint( 0, len( self.images ) - 1 )]
while np.array_equal( random_image, np.zeros( random_image.shape ) ):
random_image = self.images[randint( 0, len( self.images ) - 1 )]
patches_from_random = np.array( extract_patches_2d( random_image, self.patch_size, patch_to_extract ) )
counter = 0
while not extracted:
if counter > per_class / 2:
random_image = self.images[randint( 0, len( self.images ) - 1 )]
patches_from_random = np.array(
extract_patches_2d( random_image, self.patch_size, patch_to_extract ) )
counter = 0
patch = np.array( patches_from_random[randint( 0, patch_to_extract - 1 )].astype( float ) )
if patch.max() > 1:
patch = normalize( patch )
patch_1 = adjust_sigmoid( patch )
edges_1 = adjust_sigmoid( patch, inv=True )
edges_2 = patch_1
edges_5_n = normalize( laplace( patch ) )
edges_5_n = img_as_float( img_as_ubyte( edges_5_n ) )
choosing_cond = is_boarder( patch=patch_1, sigma=self.sigma )
if class_number == 1 and choosing_cond:
final_patch = np.array( [edges_1, edges_2, edges_5_n] )
patches.append( final_patch )
try:
imsave( './patches/sigma_{}/class_{}/{}.png'.format( self.sigma,
class_number,
i ),
final_patch.reshape( (3 * self.patch_size[0], self.patch_size[1]) ),
dtype=float )
except:
print( 'problem occurred in save for class {}'.format( class_number ) )
exit( 0 )
print( '*---> patch {}/{} added and saved '.format( i, per_class ) )
extracted = True
elif class_number == 0 and not choosing_cond:
if np.array_equal( patch, np.zeros( patch.shape ) ):
if ten_percent_black < ten_percent_black_value:
final_patch = np.array( [patch, edges_2, edges_5_n] )
patches.append( final_patch )
try:
imsave( './patches/sigma_{}/class_{}/{}.png'.format( self.sigma,
class_number,
i ),
final_patch.reshape( (3 * self.patch_size[0], self.patch_size[1]) ),
dtype=float )
except:
print( 'problem occurred in save for class {}'.format( class_number ) )
exit( 0 )
print( '*---> patch {}/{} added and saved '.format( i, per_class ) )
ten_percent_black += 1
extracted = True
else:
pass
else:
final_patch = np.array( [edges_1, edges_2, edges_5_n] )
patches.append( final_patch )
try:
imsave( './patches/sigma_{}/class_{}/{}.png'.format( self.sigma,
class_number,
i ),
final_patch.reshape( (3 * self.patch_size[0], self.patch_size[1]) ),
dtype=float )
except:
print( 'problem occurred in save for class {}'.format( class_number ) )
exit( 0 )
print( '*---> patch {}/{} added and saved '.format( i, per_class ) )
extracted = True
counter += 1
if self.augmentation_angle != 0:
print( "\n *_*_*_*_* proceeding with data augmentation for class {} *_*_*_*_* \n".format( class_number ) )
if isdir( './patches/sigma_{}/class_{}/rotations'.format( self.sigma,
class_number ) ):
print( "rotations folder present " )
else:
mkdir_p( './patches/sigma_{}/class_{}/rotations'.format( self.sigma,
class_number ) )
print( "rotations folder created" )
for el_index in xrange( len( patches ) ):
for j in range( 1, self.augmentation_multiplier ):
try:
patch_rotated = np.array( rgb2gray( imread(
('./patches/sigma_{}/class_{}/'
'rotations/{}_{}.png'.format( self.sigma,
class_number,
el_index,
self.augmentation_angle * j )) ) ).reshape( 3,
self.patch_size[
0],
self.patch_size[
1]
) ).astype(
float ) / (
256 * 256)
patches.append( patch_rotated )
print( '*---> patch {}/{} loaded and added '
'with rotation of {} degrees'.format( el_index, per_class,
self.augmentation_angle * j ) )
except:
final_rotated_patch = rotate_patches( patches[el_index][0],
patches[el_index][1],
patches[el_index][2],
self.augmentation_angle * j )
patches.append( final_rotated_patch )
imsave( './patches/sigma_{}/class_{}/'
'rotations/{}_{}.png'.format( self.sigma,
class_number,
el_index,
self.augmentation_angle * j ),
final_rotated_patch.reshape( 3 * self.patch_size[0], self.patch_size[1] ),
dtype=float )
print( ('*---> patch {}/{} saved and added '
'with rotation of {} degrees '.format( el_index, per_class,
self.augmentation_angle * j )) )
print()
print( 'augmentation done \n' )
print( 'extraction for class {} complete\n'.format( class_number ) )
return np.array( patches ), labels