def extract_image(self, input_path, output_path, supplements_path, image_nb, save=True):
current = Image.open(os.path.join(input_path, "in{0:06d}.jpg".format(image_nb)))
new_data = MosaicImage(current, self.image_parameters)
self.som.set_data(new_data.get_data())
winners = self.som.get_all_winners()
diff_winners = np.zeros(winners.shape)
for j in range(len(winners)):
diff_winners[j] = manhattan_distance(np.asarray(winners[j]), np.asarray(self.initial_map[j]))
diff_winners = diff_winners.reshape(new_data.nb_pictures)
diff_winners = np.kron(diff_winners, np.ones((self.pictures_dim[0], self.pictures_dim[1])))
# diff_winners *= 30 # Use this parameter ?
diff_winners = ImageOps.autocontrast(Image.fromarray(diff_winners).convert('L'))
reconstructed = Image.fromarray(new_data.reconstruct(self.som.get_reconstructed_data(winners)))
som_difference = ImageOps.autocontrast(ImageChops.difference(reconstructed, current).convert('L'))
som_difference_modulated = ImageChops.multiply(som_difference, diff_winners)
# Binarizing
fn = lambda x: 255 if x > self.threshold else 0
thresholded = som_difference_modulated.convert('L').point(fn, mode='1')
result = ImageChops.multiply(thresholded, self.mask)
# Saving
if save:
som_difference.save(os.path.join(supplements_path, "difference", "dif{0:06d}.png".format(image_nb)))
diff_winners.save(os.path.join(supplements_path, "diff_winners", "win{0:06d}.png".format(image_nb)))
som_difference_modulated.save(os.path.join(supplements_path, "saliency", "sal{0:06d}.png".format(image_nb)))
thresholded.save(os.path.join(supplements_path, "thresholded", "thr{0:06d}.png".format(image_nb)))
result.save(os.path.join(output_path, "bin{0:06d}.png".format(image_nb)))
def learning(self, bkg_image):
# PARAMETERS
self.image_parameters = Parameters({"pictures_dim": self.pictures_dim})
data = MosaicImage(bkg_image, self.image_parameters)
inputs_SOM = Parameters({"alpha": Variable(start=self.alpha_start, end=self.alpha_end, nb_steps=self.nb_epochs),
"sigma": Variable(start=self.sigma_start, end=self.sigma_end, nb_steps=self.nb_epochs),
"data": data.get_data(),
"neurons_nbr": self.neurons_nb,
"epochs_nbr": self.nb_epochs})
self.som = SOM(inputs_SOM)
# RUN
for i in range(self.nb_epochs):
# print('Epoch', i)
self.som.run_epoch()
self.initial_map = self.som.get_all_winners()
def regenerate_database():
global data_types
data_types = {
"spokenDigits":
SpokenDigitsDataset(
"/users/yabernar/workspace/watSOM/Data/FSDD/recordings",
1000).get_data(),
"images":
MosaicImage(
Image.open(
"/users/yabernar/workspace/watSOM/Code/fast_som/Elijah.png"),
Parameters({"pictures_dim": [10, 10]})).get_data(),
"uniform3D":
uniform(1000, 3),
"pixel_colors":
PixelsFromImage(
Image.open(
"/users/yabernar/workspace/watSOM/Code/fast_som/Elijah.png"),
1000).get_data(),
"catShape":
GenerateFromShape(
Image.open(
"/users/yabernar/workspace/watSOM/Code/fast_som/cat-silhouette.png"
), 1000).get_data(),
"uniform2D":
uniform(1000, 2)
}
def load_dataset(self):
if self.dataset["type"] == "image":
path = os.path.join("Data", "images", self.dataset["file"])
img = Image.open(path)
parameters = Parameters({
"pictures_dim":
[self.dataset["width"], self.dataset["height"]]
})
self.data = MosaicImage(img, parameters)
elif self.dataset["type"] == "random_image":
path = os.path.join("Data", "images", self.dataset["file"])
img = Image.open(path)
parameters = Parameters({
"pictures_dim":
[self.dataset["width"], self.dataset["height"]]
})
self.data = MosaicImage(img, parameters)
self.training_data = RandomImage(img, parameters)
elif self.dataset["type"] == "tracking":
path = os.path.join("Data", "tracking", "dataset",
self.dataset["file"], "back.jpg")
#if self.metadata["seed"] % 2 == 1:
# path = os.path.join("Data", "tracking", "dataset", self.dataset["file"], "input", "bkg.jpg")
#else:
# path = os.path.join("Data", "tracking", "dataset", self.dataset["file"], "input", "bkg2.jpg")
img = Image.open(path)
parameters = Parameters({
"pictures_dim":
[self.dataset["width"], self.dataset["height"]]
})
self.data = MosaicImage(img, parameters)
else:
print("Error : No dataset type specified !")
# global_error += spatial.distance.euclidean(observation, self.network.nodes[s_1]['vector'])**2
# return global_error
def square_error(self, winners=None):
if winners is None:
winners = self.get_all_winners()
error = np.zeros(winners.shape)
for i in np.ndindex(winners.shape):
error[i] = np.mean(
(self.data[i] - self.network.nodes[winners[i]]['vector'])**2)
return np.mean(error)
if __name__ == '__main__':
bkg = MosaicImage(
Image.open(
os.path.join("Data", "tracking", "dataset", "baseline", "office",
"bkg.jpg")), Parameters({"pictures_dim": [16, 16]}))
image = MosaicImage(
Image.open(
os.path.join("Data", "tracking", "dataset", "baseline", "office",
"input", "in001010.jpg")),
Parameters({"pictures_dim": [16, 16]}))
nb_epochs = 100
inputs = Parameters({
"epsilon_winner": 0.1,
"epsilon_neighbour": 0.006,
"maximum_age": 10,
"error_decrease_new_unit": 0.5,
"error_decrease_global": 0.995,
"data": bkg.get_data(),
return np.mean(error)
if __name__ == '__main__':
for n in range(10, 61, 2):
start = time.time()
nb_epochs = 10
inputs = Parameters({
"alpha":
Variable(start=0.6, end=0.05, nb_steps=nb_epochs),
"sigma":
Variable(start=0.5, end=0.2, nb_steps=nb_epochs),
"data":
MosaicImage(
Image.open(
"/users/yabernar/workspace/watSOM/Code/fast_som/Elijah.png"
), Parameters({"pictures_dim": [10, 10]})).get_data(),
"neurons_nbr": (n, n),
"epochs_nbr":
nb_epochs
})
som = FastSOM(inputs)
som.run()
end = time.time()
print("Executed in " + str(end - start) + " seconds.", n, "neurons")
print("MSQE :", som.mean_square_quantization_error(), "MSDtN :",
som.mean_square_distance_to_neighbour())
class Execution:
def __init__(self):
self.metadata = {}
self.dataset = {}
self.model = {}
self.codebooks = {}
self.metrics = {}
self.data = None
self.training_data = None
self.map = None
def open(self, path):
txt = codecs.open(path, 'r', encoding='utf-8').read()
data = json.loads(txt)
self.metadata = data["metadata"]
self.dataset = data["dataset"]
self.model = data["model"]
self.codebooks = data["codebooks"]
self.metrics = data["metrics"]
def light_open(self, path):
txt = codecs.open(path, 'r', encoding='utf-8').read()
data = json.loads(txt)
self.metadata = data["metadata"]
self.dataset = data["dataset"]
self.model = data["model"]
self.metrics = data["metrics"]
def save(self, path):
data = {
"metadata": self.metadata,
"dataset": self.dataset,
"model": self.model,
"metrics": self.metrics,
"codebooks": self.codebooks
}
json.dump(data,
codecs.open(os.path.join(path,
self.metadata["name"] + ".json"),
'w',
encoding='utf-8'),
indent=2)
def load_dataset(self):
if self.dataset["type"] == "image":
path = os.path.join("Data", "images", self.dataset["file"])
img = Image.open(path)
parameters = Parameters({
"pictures_dim":
[self.dataset["width"], self.dataset["height"]]
})
self.data = MosaicImage(img, parameters)
elif self.dataset["type"] == "random_image":
path = os.path.join("Data", "images", self.dataset["file"])
img = Image.open(path)
parameters = Parameters({
"pictures_dim":
[self.dataset["width"], self.dataset["height"]]
})
self.data = MosaicImage(img, parameters)
self.training_data = RandomImage(img, parameters)
elif self.dataset["type"] == "tracking":
path = os.path.join("Data", "tracking", "dataset",
self.dataset["file"], "back.jpg")
#if self.metadata["seed"] % 2 == 1:
# path = os.path.join("Data", "tracking", "dataset", self.dataset["file"], "input", "bkg.jpg")
#else:
# path = os.path.join("Data", "tracking", "dataset", self.dataset["file"], "input", "bkg2.jpg")
img = Image.open(path)
parameters = Parameters({
"pictures_dim":
[self.dataset["width"], self.dataset["height"]]
})
self.data = MosaicImage(img, parameters)
else:
print("Error : No dataset type specified !")
def run(self):
#if self.metadata["seed"] % 2 == 1:
np.random.seed(self.metadata["seed"])
#else:
# np.random.seed(self.metadata["seed"]-1)
if self.model["model"] == "gng":
self.runGNG()
else:
self.runSOM()
def runGNG(self):
if self.data is None:
self.load_dataset()
inputs = Parameters({
"epsilon_winner":
self.model["epsilon_winner"], # 0.1,
"epsilon_neighbour":
self.model["epsilon_neighbour"], # 0.006,
"maximum_age":
self.model["maximum_age"], # 10,
"error_decrease_new_unit":
self.model["error_decrease_new_unit"], # 0.5,
"error_decrease_global":
self.model["error_decrease_global"], # 0.995,
"data":
self.data.get_data(),
"neurons_nbr":
self.model["nb_neurons"],
"epochs_nbr":
self.model["nb_epochs"]
})
self.map = GrowingNeuralGas(inputs)
self.map.run()
def runSOM(self):
if self.data is None:
self.load_dataset()
nb_epochs = self.model["nb_epochs"]
if "alpha_start" not in self.model: self.model["alpha_start"] = 0.2
if "alpha_end" not in self.model: self.model["alpha_end"] = 0.05
if "sigma_start" not in self.model: self.model["sigma_start"] = 0.7
if "sigma_end" not in self.model: self.model["sigma_end"] = 0.015
if "nb_images_evals" not in self.dataset:
self.dataset["nb_images_evals"] = 75
parameters = Parameters({
"alpha":
Variable(start=self.model["alpha_start"],
end=self.model["alpha_end"],
nb_steps=nb_epochs),
"sigma":
Variable(start=self.model["sigma_start"],
end=self.model["sigma_end"],
nb_steps=nb_epochs),
"data":
self.data.get_data(),
"neurons_nbr": (self.model["width"], self.model["height"]),
"epochs_nbr":
nb_epochs
})
if self.model["model"] == "standard":
self.map = SOM(parameters)
elif self.model["model"] == "fast":
self.map = FastSOM(parameters)
elif self.model["model"] == "recursive":
self.map = RecursiveSOM(parameters)
else:
print("Error : Unknown model !")
# if "initialisation" not in self.codebooks:
# self.codebooks["initialisation"] = self.som.neurons.tolist()
if "final" in self.codebooks:
self.map.neurons = np.asarray(self.codebooks["final"])
else:
self.map.run()
#for i in range(nb_epochs):
# self.map.run_epoch()
#self.codebooks["final"] = copy.deepcopy(self.map.neurons.tolist())
# for i in range(nb_epochs):
# print("Epoch "+str(i+1))
# if "Epoch "+str(i + 1) not in self.codebooks:
# if self.training_data is not None:
# self.som.data = self.training_data.get_data(self.som.data.shape[0])
# self.som.run_epoch()
# # self.codebooks["Epoch " + str(i + 1)] = copy.deepcopy(self.som.neurons.tolist())
# self.som.run_epoch()
self.map.data = self.data.get_data()
def compute_metrics(self):
self.metrics["Square_error"] = self.map.square_error()
if self.model["model"] == "gng":
self.metrics["Neurons"] = len(self.map.network.nodes())
self.metrics["Connections"] = len(self.map.network.edges())
if self.dataset["type"] == "tracking":
current_path = os.path.join("Data", "tracking", "dataset",
self.dataset["file"])
input_path = os.path.join(current_path, "input")
roi_file = open(os.path.join(current_path, "temporalROI.txt"),
"r").readline().split()
temporal_roi = (int(roi_file[0]), int(roi_file[1]))
mask_roi = Image.open(os.path.join(current_path, "ROI.png"))
nb_img_gen = self.dataset["nb_images_evals"]
step = 1
if nb_img_gen > 0:
step = (temporal_roi[1] + 1 - temporal_roi[0]) // nb_img_gen
base = os.path.join("Results", "GNGopti", self.metadata["name"],
"results")
output_path = os.path.join(base, self.dataset["file"])
supplements_path = os.path.join(base, "supplements")
parameters = Parameters({
"pictures_dim":
[self.dataset["width"], self.dataset["height"]],
"step":
step
})
trackingMetric = TrackingMetrics(input_path,
output_path,
supplements_path,
temporal_roi,
mask_roi,
parameters=parameters)
trackingMetric.compute(self.map)
cmp = Comparator()
fmeasure, precision, recall = cmp.evaluate__folder_c(
current_path, output_path, step)
# print(fitness)
self.metrics["fmeasure"] = fmeasure
self.metrics["precision"] = precision
self.metrics["recall"] = recall
def compute_varying_threshold_metric(self):
if self.dataset["type"] == "tracking":
current_path = os.path.join("Data", "tracking", "dataset",
self.dataset["file"])
roi_file = open(os.path.join(current_path, "temporalROI.txt"),
"r").readline().split()
temporal_roi = (int(roi_file[0]), int(roi_file[1]))
base = os.path.join("Results", "Sizing", self.metadata["name"],
"results")
output_path = os.path.join(base, self.dataset["file"])
supplements_path = os.path.join(base, "supplements")
difference_path = os.path.join(supplements_path, "saliency")
nb_img_gen = self.dataset["nb_images_evals"]
step = 1
if nb_img_gen > 0:
step = (temporal_roi[1] + 1 - temporal_roi[0]) // nb_img_gen
res = []
ranges = list(range(1, 20)) + list(range(20, 101, 5))
for threshold in ranges:
for img in os.listdir(difference_path):
som_difference = Image.open(
os.path.join(difference_path, img))
# Binarizing
fn = lambda x: 255 if x > threshold else 0
thresholded = som_difference.convert('L').point(fn,
mode='1')
result = Image.new("L", som_difference.size)
result.paste(thresholded, (0, 0))
result.save(os.path.join(output_path, "bin" + img[3:]))
cmp = Comparator()
fitness = cmp.evaluate__folder_c(current_path, output_path,
step)
# print(fitness)
res.append(fitness)
#self.metrics["fmeasure-t" + str(threshold)] = fitness
self.metrics["fmeasure_threshold"] = res
def compute_steps_metrics(self):
# self.metrics["Square_error"] = self.som.square_error()
# self.metrics["Neurons"] = len(self.som.network.nodes())
# self.metrics["Connections"] = len(self.som.network.edges())
if self.dataset["type"] == "tracking":
current_path = os.path.join("Data", "tracking", "dataset",
self.dataset["file"])
input_path = os.path.join(current_path, "input")
roi_file = open(os.path.join(current_path, "temporalROI.txt"),
"r").readline().split()
temporal_roi = (int(roi_file[0]), int(roi_file[1]))
mask_roi = Image.open(os.path.join(current_path, "ROI.png"))
base = os.path.join("Results", "GNGoptimisation",
self.metadata["name"], "results")
output_path = os.path.join(base, self.dataset["file"])
supplements_path = os.path.join(base, "supplements")
parameters = Parameters({
"pictures_dim":
[self.dataset["width"], self.dataset["height"]]
})
# ranges = list(range(1, 5)) + list(range(5, 101, 5))
#res = []
#ranges = range(1,201)
#for i in ranges:
# cmp = Comparator()
# fitness = cmp.evaluate__folder_c(current_path, output_path, i)
# res.append(fitness)
#self.metrics["fmeasure-steps"] = res
res = []
nb_image_ranges = range(5, 201)
for i in nb_image_ranges:
step = (temporal_roi[1] + 1 - temporal_roi[0]) // i
cmp = Comparator()
fitness = cmp.evaluate__folder_c(current_path, output_path,
step)
res.append(fitness)
self.metrics["fmeasure-nbimgs"] = res
def full_threshold_evaluation(self, path):
self.compute_varying_threshold_metric()
self.save(path)
print("Simulation", self.metadata["name"], "ended")
def full_step_evaluation(self, path):
self.compute_steps_metrics()
self.save(path)
print("Simulation", self.metadata["name"], "ended")
def full_simulation(self, path):
if "fmeasure" not in self.metrics:
self.run()
self.compute_metrics()
self.save(path)
for i in diff:
error.append(np.mean(np.abs(i)))
return np.mean(error)
def square_error(self):
rec = self.get_reconstructed_data()
diff = rec - self.data
error = []
for i in diff:
error.append(np.mean(i**2))
return np.mean(error)
if __name__ == '__main__':
start = time.time()
img = MosaicImage(Image.open("Data/images/Elijah.png"),
Parameters({"pictures_dim": [10, 10]}))
nb_epochs = 100
inputs = Parameters({
"alpha":
Variable(start=0.6, end=0.05, nb_steps=nb_epochs),
"sigma":
Variable(start=0.5, end=0.001, nb_steps=nb_epochs),
"data":
img.get_data(),
"neurons_nbr": (8, 8),
"epochs_nbr":
nb_epochs
})
som = RecursiveSOM(inputs)
som.run()
import os
import numpy as np
from PIL import Image, ImageOps, ImageChops
from Code.Parameters import Parameters, Variable
from Code.SOM import SOM
from Data.Mosaic_Image import MosaicImage
pictures_dim = [10, 10]
name = "office"
path = os.path.join("Data", "spikes", "office", "src")
bkg = Image.open(os.path.join(path, name + "0.png"))
img_parameters = Parameters({"pictures_dim": pictures_dim})
data = MosaicImage(bkg, img_parameters)
nb_epochs = 100
parameters = Parameters({
"alpha":
Variable(start=0.6, end=0.05, nb_steps=nb_epochs),
"sigma":
Variable(start=0.5, end=0.001, nb_steps=nb_epochs),
"data":
data.get_data(),
"neurons_nbr": (10, 10),
"epochs_nbr":
nb_epochs
})
map = SOM(parameters)
for i in range(nb_epochs):
print("Epoch " + str(i + 1))
map.run_epoch()
map.data = data.get_data()
print(categories)
print(elements)
chosen_path = path + "/dataset/" + categories[11] + "/" + elements[0]
temporal_ROI = (1, 200)
plot = None
bkg = Image.open(chosen_path + "/input/" + 'bkg.jpg')
# bkg = Image.open(path2 + video + '{0:05d}.png'.format(1))
# bkg = Image.open(path3 + "example_base.png")
############
# LEARNING #
############
pictures_dim = [10, 10]
parameters = Parameters({"pictures_dim": pictures_dim})
data = MosaicImage(bkg, parameters)
nb_epochs = 50
inputs_SOM = Parameters({
"alpha":
Variable(start=0.5, end=0.25, nb_steps=nb_epochs),
"sigma":
Variable(start=0.1, end=0.03, nb_steps=nb_epochs),
"data":
data.get_data(),
"neurons_nbr": (10, 10),
"epochs_nbr":
nb_epochs
})
som = SOM(inputs_SOM)
for i in range(nb_epochs):
print('Epoch ', i)
vector - self.network.nodes[i]['vector'])
def fully_random_vector(self):
return np.random.randint(np.shape(self.data)[0])
def unique_random_vector(self):
self.current_vector_index = self.vector_list.pop(0)
return self.current_vector_index
def generate_random_list(self):
self.vector_list = list(range(len(self.data)))
np.random.shuffle(self.vector_list)
if __name__ == '__main__':
img = MosaicImage(Image.open(os.path.join("Data", "Images", "Lenna.png")),
Parameters({"pictures_dim": [20, 20]}))
data = img.get_data()
start = time.time()
nb_epochs = 20
inputs = Parameters({
"alpha":
Variable(start=0.6, end=0.05, nb_steps=nb_epochs),
"sigma":
Variable(start=0.5, end=0.001, nb_steps=nb_epochs),
"data":
img.get_data(),
"neurons_nbr": (5, 5),
"epochs_nbr":
nb_epochs
print(elements)
chosen_path = path + "/dataset/" + categories[1] + "/" + elements[0]
temporal_ROI = (400, 1700)
plot = None
bkg = Image.open(chosen_path + "/input/" + 'in{0:06d}.jpg'.format(472))
# bkg = Image.open(path + 'ducks{0:05d}.png'.format(1))
# bkg = Image.open("/users/yabernar/workspace/watSOM/Data/color_test.png")
############
# LEARNING #
############
pictures_dim = [10, 10]
parameters = Parameters({"pictures_dim": pictures_dim})
data = SlidingWindow(bkg, parameters)
mosaic = MosaicImage(bkg, parameters)
nb_epochs = 5
inputs_SOM = Parameters({
"alpha":
Variable(start=0.5, end=0.25, nb_steps=nb_epochs),
"sigma":
Variable(start=0.1, end=0.03, nb_steps=nb_epochs),
"data":
data.get_data(),
"neurons_nbr": (10, 10),
"epochs_nbr":
nb_epochs
})
som = SOM(inputs_SOM)
for i in range(nb_epochs):
print('Epoch ', i)
for i in np.ndindex(winners.shape):
error[i] = np.mean((self.working_data[i] - self.network.nodes[winners[i]]['vector'])**2)
return np.mean(error)
def display(self):
reconstructed = self.img.reconstruct(self.get_reconstructed_data())
# som_image = mosaic.reconstruct(gng.get_neural_list(), size=som.neurons_nbr)
print("Error : ", self.square_error())
print("Neurons : ", len(self.network.nodes()))
print("Connections : ", len(self.network.edges()))
plt.imshow(reconstructed)
plt.show()
if __name__ == '__main__':
img = MosaicImage(Image.open(os.path.join("Data", "Tracking", "Dataset", "baseline", "highway", "bkg.jpg")), Parameters({"pictures_dim": [16, 16]}))
data = img.get_data()
gng = GrowingNeuralGas(data)
gng.img = img
gng.fit_network(e_b=0.1, e_n=0.006, a_max=10, l=200, a=0.5, d=0.995, passes=100, plot_evolution=False)
reconstructed = img.reconstruct(gng.get_reconstructed_data())
# som_image = mosaic.reconstruct(gng.get_neural_list(), size=som.neurons_nbr)
# print(gng.get_all_winners())
plt.imshow(reconstructed)
plt.show()
print(len(gng.network.nodes))
img2 = MosaicImage(Image.open(os.path.join("Data", "Tracking", "Dataset", "baseline", "highway", "input", "in001010.jpg")), Parameters({"pictures_dim": [16, 16]}))
data2 = img2.get_data()
old_winners = gng.get_all_winners()
gng.data = data2
categories = sorted(os.listdir(path + "/dataset"), key=str.lower)
elements = sorted(os.listdir(path + "/dataset/" + categories[1]), key=str.lower)
print(categories)
print(elements)
chosen_path = path + "/dataset/" + categories[1] + "/" + elements[1] + "/input/"
temporal_ROI = (570, 2050)
images_list = []
parameters = Parameters({"pictures_dim": pictures_dim})
plot = None
img = Image.open(chosen_path + 'in{0:06d}.jpg'.format(1)).convert('L')
bkg = Image.open(chosen_path + 'in{0:06d}.jpg'.format(60)).convert('L')
difference = ImageChops.difference(img, bkg)
data = MosaicImage(difference, parameters)
nb_epochs = 50
inputs_SOM = Parameters({"alpha": Variable(start=0.6, end=0.05, nb_steps=nb_epochs),
"sigma": Variable(start=0.5, end=0.001, nb_steps=nb_epochs),
"data": data.get_data(),
"neurons_nbr": (10, 10),
"epochs_nbr": nb_epochs})
som = SOM(inputs_SOM)
for i in range(nb_epochs):
print('Epoch ', i)
som.run_epoch()
original = data.image
reconstructed = data.reconstruct(som.get_reconstructed_data())
som_image = data.reconstruct(som.get_neural_list(), size=som.neurons_nbr)
difference = ImageChops.difference(original, Image.fromarray(reconstructed))