def reload(self, n=None):
"""Reload one or more images from file.
Parameters
----------
n : None or int
The number of the image to reload. If None (default), all images in
memory are reloaded. If `n` specifies an image not yet in memory,
it is loaded.
Returns
-------
None
Notes
-----
`reload` is used to reload all images in memory when `as_grey` is
changed.
"""
if n is not None:
n = self._check_numimg(n)
idx = n % len(self.data)
self.data[idx] = imread(self.files[n], self.as_grey, dtype=self._dtype)
else:
for idx, img in enumerate(self.data):
if img is not None:
self.data[idx] = imread(self.files[idx], self.as_grey, dtype=self._dtype)
def __getitem__(self, idx):
assert isinstance(idx, int)
img_name = os.path.join(self.root_dir, self.image_dir, f'{idx}.png')
image = io.imread(img_name)
msk_name = os.path.join(self.root_dir, self.mask_dir, f'{idx}.png')
mask = io.imread(msk_name)
sample = {'image': image, 'mask': mask}
if self.transform:
return self.transform(sample)
return sample
def output_image_points_for_leaf_teeth(input_image, contour_tuples,
index_list_a, index_list_b,
output_suffix):
"""
Outputs an image to file with points highlighted
:param input_image: the input image to draw on.
:param contour_tuples: the contour tuples giving xy coords.
:param index_list_a: list a that indexes contour tuples.
:param index_list_b: list b that indexes contour tuples.
:param output_suffix: the suffix for the output (not including .jpg)
:return: None
"""
# open the input image.
img = io.imread(input_image)
# iterate through the indexes and add a circle point for each tuple.
for i in index_list_a:
cv2.circle(img,
contour_tuples[i],
3,
thickness=-1,
color=(255, 0, 0))
# iterate though the indexes and add a circle point for each tuple.
for i in index_list_b:
cv2.circle(img,
contour_tuples[i],
3,
thickness=-1,
color=(0, 255, 0))
# save the image.
io.imsave(input_image + "." + output_suffix + ".jpg", img)
def __getitem__(self, idx):
img_name = os.path.join(self.root_dir,
self.frame.iloc[idx, 0])
image = torch.from_numpy(io.imread(img_name))
empty = int(self.frame.iloc[idx, 1:])
image = image.permute(2, 0, 1).float()
sample = (image, empty)
return sample
def load_image(self, image, unchanged=False, anydepth=False):
"""Load image pixels as numpy array.
The array is 3D, indexed by y-coord, x-coord, channel.
The channels are in RGB order.
"""
a = io.imread(self._image_file(image),
unchanged=unchanged,
anydepth=anydepth)
return a
def write_QC(full_QC_model_path):
with open(os.path.join(full_QC_model_path, 'Quality Control',
'QC_metrics_' + args.name + '.csv'),
"w",
newline='') as file:
writer = csv.writer(file)
writer.writerow(["File name", "IoU", "IoU-optimised threshold"])
# Initialise the lists
filename_list = []
best_threshold_list = []
best_IoU_score_list = []
for filename in os.listdir(args.testInputPath):
if not os.path.isdir(os.path.join(args.testInputPath, filename)):
print('Running QC on: ' + filename)
test_input = io.imread(os.path.join(args.testInputPath,
filename),
as_gray=True)
test_ground_truth_image = io.imread(os.path.join(
args.testGroundTruthPath, filename),
as_gray=True)
(threshold_list, iou_scores_per_threshold) = getIoUvsThreshold(
os.path.join(prediction_QC_folder,
prediction_prefix + filename),
os.path.join(args.testGroundTruthPath, filename))
# Here we find which threshold yielded the highest IoU score for image n.
best_IoU_score = max(iou_scores_per_threshold)
best_threshold = iou_scores_per_threshold.index(best_IoU_score)
# Write the results in the CSV file
writer.writerow(
[filename,
str(best_IoU_score),
str(best_threshold)])
# Here we append the best threshold and score to the lists
filename_list.append(filename)
best_IoU_score_list.append(best_IoU_score)
best_threshold_list.append(best_threshold)
def __getitem__(self, idx):
if torch.is_tensor(idx):
idx = idx.tolist()
img_name = self.data_paths[idx]
image = io.imread(img_name)
sample = {'image': image, 'label': self.data_labels['label'][idx]}
return sample
def infer(self, img_file):
tik = time.time()
img = io.imread(img_file)
img = Image.fromarray(img.astype(np.uint8))
preprocess = transforms.Compose([
transforms.Resize(224),
transforms.CenterCrop(224),
transforms.ToTensor(),
transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225])
])
img = preprocess(img)
img.unsqueeze_(0)
img = img.to(self.device)
outputs = self.model.forward(img)
outputs = F.softmax(outputs, dim=1)
# get TOP-K output labels and corresponding probabilities
topK_prob, topK_label = torch.topk(outputs, self.topK)
prob = topK_prob.to("cpu").detach().numpy().tolist()
_, predicted = torch.max(outputs.data, 1)
tok = time.time()
if prob[0][0] >= cfg['thresholds']['plant_recognition']:
return {
'status': 0,
'message': 'success',
'elapse': tok - tik,
'results': [
{
'name': self.key_type[int(topK_label[0][i].to("cpu"))],
'category_id': int(topK_label[0][i].data.to("cpu").numpy()) + 1,
'prob': round(prob[0][i], 4)
} for i in range(self.topK)
]
}
else:
return {
'status': 0,
'message': 'success',
'elapse': tok - tik,
'results': [
{
'name': "Unknown",
'category_id': -1,
'prob': round(prob[0][0], 4)
}
]
}
def load_mask(self, image):
"""Load image mask if it exists, otherwise return None."""
if image in self.mask_files: ## 여기 안들어감
mask_path = self.mask_files[image]
mask = io.imread(mask_path, grayscale=True)
if mask is None:
raise IOError("Unable to load mask for image {} "
"from file {}".format(image, mask_path))
else:
mask = None
return mask
def __getitem__(self, idx):
img_name = os.path.join(self.root_dir,
self.landmarks_frame.iloc[idx, 0])
image = io.imread(img_name)
landmarks = self.landmarks_frame.iloc[idx, 1:].as_matrix()
landmarks = landmarks.astype('float').reshape(-1, 2)
sample = {'image': image, 'landmarks': landmarks}
if self.transform:
sample = self.transform(sample)
return sample
def image_from_url(url):
"""
Read an image from a URL. Returns a numpy array with the pixel data.
We write the image to a temporary file then read it back. Kinda gross.
"""
try:
img = io.imread(url)
return img
except urllib.error.URLError as e:
print('URL Error: ', e.reason, url)
except urllib.error.HTTPError as e:
print('HTTP Error: ', e.code, url)
def test_data():
"""Return an image for testing purposes.
Returns
-------
I : ndarray of uint8
512x512 test image.
"""
import os
f = os.path.join(os.path.dirname(__file__),
'lib/pywt/demo/data/aero.png')
return io.imread(f)
def load(self, path):
from skimage import io
if not io.util.is_url(path):
path = os.path.abspath(path)
self._path = path
ext = path[-3:].lower()
if ext == 'pdf':
data = read_pdf(path)
else:
with io.util.file_or_url_context(path) as context:
data = io.imread(context)
mode = guessmode(data)
self._set(data, mode)
return self
def __getitem__(self, idx):
if torch.is_tensor(idx):
idx = idx.tolist()
entry = self.data_list[idx]
img_name = entry['file']
answer = entry['answer']
img_path = os.path.join(self.root_dir, img_name)
image = io.imread(img_path).transpose(2, 0, 1).astype(np.float32)
if self.transform:
image = self.transform(image)
return [image, answer]
def bounding_box(url, texts):
"""
add bounding box
"""
img = io.imread(url) # read image from url
for text in texts[1:]: # 0th bounding box is whole picture
vertices = [
(vertex.x, vertex.y) for vertex in text.bounding_poly.vertices
] # get coordinates
# plot line
cv2.polylines(img, [np.array(vertices)], True, (0, 255, 0), 2)
plt.figure(figsize=(10, 10))
plt.imshow(img)
plt.show()
def run():
print('toto')
import io
import os
import sys
import argparse
from skimage import io
from skimage import filter
from skimage import restoration
from skimage import measure
kidney_image = io.imread('manu.jpg')
# estimate the noise in the image
# do a test denosing using a total variation filter
kidney_image_denoised_tv = restoration.denoise_tv_chambolle( kidney_image, weight=0.1)
io.imsave('denoise_image.jpg', kidney_image_denoised_tv)
def pickle_image_data(y, ylabels, imageDirectory, pickleDirectory):
# Extract all training images from a directory
# Use skimage to put all the training data into a big array which is IMAGES,LEFT,RIGHT,CHANNEL
iterator = 0
for (image_name, labels) in ylabels:
raw_data = io.imread(imageDirectory + image_name + ".tif")
np.save(file=pickleDirectory + "train_" + str(iterator),
arr=np.swapaxes(raw_data, 0, 2))
iterator += 1
if (iterator % 500 == 0):
print("image" + str(iterator))
def preprocessing(img_name, trans_all):
# get some random training images
image = io.imread(img_name)
input = image[:, :288, :]
normals = image[:, 288:2 * 288, :]
diffuse = image[:, 2 * 288:3 * 288, :]
roughness = image[:, 3 * 288:4 * 288, :]
specular = image[:, 4 * 288:5 * 288, :]
#label = np.concatenate((normals,diffuse,roughness,specular),axis = 2)
if trans_all:
input_t = trans_all(input)
normals_t = trans_all(normals)
sample = {'input': input_t, 'label': normals_t}
else:
sample = {'input': input, 'label': normals}
images, labels = sample["input"].unsqueeze(0), sample["label"].unsqueeze(0)
return images, labels
def load_data(validation_percent):
all_images = []
counter = 0
for image_path in os.listdir('charts'):
#print(image_path)
img = io.imread('charts/%s' % image_path, as_grey=True)
# io.imshow(img)
# io.show()
img = img.reshape([128, 128, 1])
all_images.append(img)
counter += 1
data = np.array(all_images)
validation_size = int(data.__len__()*validation_percent/100)
return data[:data.__len__()-validation_size], labels[:data.__len__()-validation_size], \
data[data.__len__()-validation_size:], labels[data.__len__()-validation_size:]
def load_image_files(container_path, dimension=(64, 64)):
"""
Load image files with categories as subfolder names
which performs like scikit-learn sample dataset
Parameters
----------
container_path : string or unicode
Path to the main folder holding one subfolder per category
dimension : tuple
size to which image are adjusted to
Returns
-------
Bunch
"""
image_dir = Path(container_path)
folders = [
directory for directory in image_dir.iterdir() if directory.is_dir()
]
categories = [fo.name for fo in folders]
descr = "A image classification dataset"
images = []
flat_data = []
target = []
for i, direc in enumerate(folders):
for file in direc.iterdir():
img = io.imread(file)
img_resized = resize(img,
dimension,
anti_aliasing=True,
mode='reflect')
flat_data.append(img_resized.flatten())
images.append(img_resized)
target.append(i)
flat_data = np.array(flat_data)
target = np.array(target)
images = np.array(images)
return Bunch(data=flat_data,
target=target,
target_names=categories,
images=images,
DESCR=descr)
def draw_edge_dir(detector, predictor, source_dir, target_dir,
add_face_keypoints):
if not os.path.exists(target_dir):
os.makedirs(target_dir)
img_paths = glob.glob(os.path.join(source_dir, '*.jpg'))
face_edger = FaceEdge()
en = 0
for img_path in img_paths:
if en % 1000 == 0 and en != 0:
print("The number of processed images is", en)
img = io.imread(img_path)
dets = detector(img, 1)
if len(dets) > 0:
shape = predictor(img, dets[0])
points = np.empty([68, 2], dtype=int)
for b in range(68):
points[b, 0] = shape.part(b).x
points[b, 1] = shape.part(b).y
img_ = Image.open(img_path)
img_size = img_.size
face_edger.get_crop_coords(points, img_size)
B_crop = face_edger.crop(img_)
params = get_img_params(B_crop.size)
transform_scale = get_transform(params,
method=Image.BILINEAR,
normalize=False)
edge_image = face_edger.get_face_image(points, transform_scale,
img_size, img_,
add_face_keypoints)
save_path = os.path.join(target_dir, os.path.basename(img_path))
torchvision.utils.save_image(edge_image, filename=(save_path))
en += 1
print("The total number of edge images is ", en)
def __getitem__(self, n):
"""Return image n in the collection.
Loading is done on demand.
Parameters
----------
n : int
The image number to be returned.
Returns
-------
img : ndarray
The `n`-th image in the collection.
"""
n = self._check_imgnum(n)
idx = n % len(self.data)
if (self.conserve_memory and n != self._cached) or (self.data[idx] is None):
self.data[idx] = imread(self.files[n], self.as_grey, dtype=self._dtype)
self._cached = n
return self.data[idx]
import numpy as np
import os
import subprocess
from PIL import Image
from matplotlib import pyplot
from skimage import io, transform
######################################################################
# First, let's load the image, pre-process it using standard skimage
# python library. Note that this preprocessing is the standard practice of
# processing data for training/testing neural networks.
#
# load the image
img_in = io.imread("./_static/img/cat.jpg")
# resize the image to dimensions 224x224
img = transform.resize(img_in, [224, 224])
# save this resized image to be used as input to the model
io.imsave("./_static/img/cat_224x224.jpg", img)
######################################################################
# Now, as a next step, let's take the resized cat image and run the
# super-resolution model in Caffe2 backend and save the output image. The
# image processing steps below have been adopted from PyTorch
# implementation of super-resolution model
# `here <https://github.com/pytorch/examples/blob/master/super_resolution/super_resolve.py>`__
#