def train(
image,
patch_shape=(16, 32, 32),
ratio=0.7,
name="untitled",
model_dir=".",
view_history=True,
):
# create data generator object
datagen = N2V_DataGenerator()
# patch additional axes
image = image[np.newaxis, ..., np.newaxis]
patches = datagen.generate_patches_from_list([image], shape=patch_shape)
logger.info(f"patch shape: {patches.shape}")
n_patches = patches.shape[0]
logger.info(f"{n_patches} patches generated")
# split training set and validation set
i = int(n_patches * ratio)
X, X_val = patches[:i], patches[i:]
# create training config
config = N2VConfig(
X,
unet_kern_size=3,
train_steps_per_epoch=100,
train_epochs=100,
train_loss="mse",
batch_norm=True,
train_batch_size=4,
n2v_perc_pix=1.6,
n2v_patch_shape=patch_shape,
n2v_manipulator="uniform_withCP",
n2v_neighborhood_radius=5,
)
model = N2V(config=config, name=name, basedir=model_dir)
# train and save the model
history = model.train(X, X_val)
model.export_TF()
plot_history(history, ["loss", "val_loss"])
def __prepareData(self):
# split patches from the training images
data = self.dataGen.generate_patches_from_list(
self.getTrainingImages(),
shape=(self.patchSize, self.patchSize),
augment=self.dataAugmentationActivated)
# create a threshold (10 % patches for the validation)
threshold = int(data.shape[0] * (self.percentValidation / 100))
# split the patches into training patches and validation patches
self.trainingData = data[threshold:]
self.validationData = data[:threshold]
if not self.numberOfSteps:
self.numberOfSteps = int(
self.trainingData.shape[0] / self.batchSize) + 1
print(data.shape[0], "patches created.")
print(threshold, "patch images for validation (",
self.percentValidation, "%).")
print(self.trainingData.shape[0] - threshold,
"patch images for training.")
print(self.numberOfSteps)
# noinspection PyTypeChecker
self.config = N2VConfig(self.trainingData,
unet_kern_size=self.kernelSize,
train_steps_per_epoch=self.numberOfSteps,
train_epochs=self.numberOfEpochs,
train_loss='mse',
batch_norm=True,
train_batch_size=self.batchSize,
n2v_patch_shape=(self.patchSize,
self.patchSize),
n2v_perc_pix=self.percentPixel,
n2v_manipulator='uniform_withCP',
unet_n_depth=self.netDepth,
unet_n_first=self.uNetNFirst,
train_learning_rate=self.initialLearningRate,
n2v_neighborhood_radius=5)
print(vars(self.config))
self.model = N2V(self.config, self.name, basedir=self.path)
print("Setup done.")
print(self.config)
def train_predict(n_tiles=(1,4,4), params=params, files=None, headless=False, **unet_config):
"""
These advanced options can be set by keyword arguments:
n_tiles : tuple(int)
Number of tiles to tile the image into, if it is too large for memory.
unet_residual : bool
Parameter `residual` of :func:`n2v_old.nets.common_unet`. Default: ``n_channel_in == n_channel_out``
unet_n_depth : int
Parameter `n_depth` of :func:`n2v_old.nets.common_unet`. Default: ``2``
unet_kern_size : int
Parameter `kern_size` of :func:`n2v_old.nets.common_unet`. Default: ``5 if n_dim==2 else 3``
unet_n_first : int
Parameter `n_first` of :func:`n2v_old.nets.common_unet`. Default: ``32``
batch_norm : bool
Activate batch norm
unet_last_activation : str
Parameter `last_activation` of :func:`n2v_old.nets.common_unet`. Default: ``linear``
train_learning_rate : float
Learning rate for training. Default: ``0.0004``
n2v_patch_shape : tuple
Random patches of this shape are extracted from the given training data. Default: ``(64, 64) if n_dim==2 else (64, 64, 64)``
n2v_manipulator : str
Noise2Void pixel value manipulator. Default: ``uniform_withCP``
train_reduce_lr : dict
Parameter :class:`dict` of ReduceLROnPlateau_ callback; set to ``None`` to disable. Default: ``{'factor': 0.5, 'patience': 10}``
n2v_manipulator : str
Noise2Void pixel value manipulator. Default: ``uniform_withCP``
"""
from n2v.models import N2VConfig, N2V
from n2v.utils.n2v_utils import manipulate_val_data
from n2v.internals.N2V_DataGenerator import N2V_DataGenerator
if not headless:
from csbdeep.utils import plot_history
from matplotlib import pyplot as plt
np = numpy
# Init reader
datagen = BFListReader()
print("Loading images ...")
if files is None:
datagen.from_glob(params["in_dir"], params["glob"])
files = datagen.get_file_names()
else:
datagen.from_file_list(files)
print("Training ...")
for c in params["train_channels"]:
print(" -- Channel {}".format(c))
imgs_for_patches = datagen.load_imgs_generator()
imgs_for_predict = datagen.load_imgs_generator()
img_ch = (im[..., c:c+1] for im in imgs_for_patches)
img_ch_predict = (im[..., c:c+1] for im in imgs_for_predict)
npatches = params["n_patches_per_image"] if params["n_patches_per_image"] > 1 else None
patches = N2V_DataGenerator().generate_patches_from_list(img_ch, num_patches_per_img=npatches, shape=params['patch_size'], augment=params['augment'])
numpy.random.shuffle(patches)
sep = int(len(patches)*0.9)
X = patches[:sep]
X_val = patches[ sep:]
config = N2VConfig(X,
train_steps_per_epoch=params["train_steps_per_epoch"],
train_epochs=params["train_epochs"],
train_loss='mse',
train_batch_size=params["train_batch_size"],
n2v_perc_pix=params["n2v_perc_pix"],
n2v_patch_shape=params['patch_size'],
n2v_manipulator='uniform_withCP',
n2v_neighborhood_radius=params["n2v_neighborhood_radius"], **unet_config)
# a name used to identify the model
model_name = '{}_ch{}'.format(params['name'], c)
# the base directory in which our model will live
basedir = 'models'
# We are now creating our network model.
model = N2V(config=config, name=model_name, basedir=params["in_dir"])
history = model.train(X, X_val)
val_patch = X_val[0,..., 0]
val_patch_pred = model.predict(val_patch, axes=params["axes"])
if "Z" in params["axes"]:
val_patch = val_patch.max(0)
val_patch_pred = val_patch_pred.max(0)
if not headless:
f, ax = plt.subplots(1,2, figsize=(14,7))
ax[0].imshow(val_patch,cmap='gray')
ax[0].set_title('Validation Patch')
ax[1].imshow(val_patch_pred,cmap='gray')
ax[1].set_title('Validation Patch N2V')
plt.figure(figsize=(16,5))
plot_history(history,['loss','val_loss'])
print(" -- Predicting channel {}".format(c))
for f, im in zip(files, img_ch_predict):
print(" -- {}".format(f))
pixel_reso = get_space_time_resolution(str(f))
res_img = []
for t in range(len(im)):
nt = n_tiles if "Z" in params["axes"] else n_tiles[1:]
pred = model.predict(im[t,..., 0], axes=params["axes"], n_tiles=nt)
if "Z" in params["axes"]:
pred = pred[:, None, ...]
res_img.append(pred)
pred = numpy.stack(res_img)
if "Z" not in params["axes"]:
pred = pred[:, None, None, ...]
reso = (1 / pixel_reso.X, 1 / pixel_reso.Y )
spacing = pixel_reso.Z
unit = pixel_reso.Xunit
finterval = pixel_reso.T
tifffile.imsave("{}_n2v_pred_ch{}.tiff".format(str(f)[:-4], c), pred, imagej=True, resolution=reso, metadata={'axes': 'TZCYX',
'finterval': finterval,
'spacing' : spacing,
'unit' : unit})
X = patches[:600]
X_val = patches[600:]
# Let's look at two patches
#plt.figure(figsize=(14,7))
#plt.subplot(1,2,1)
#plt.imshow(X[0,16,...,0],cmap='magma')
#plt.title('Training Patch')
#plt.subplot(1,2,2)
#plt.imshow(X_val[0,16,...,0],cmap='magma')
#plt.title('Validation Patch')
#plt.show()
# You can increase "train_steps_per_epoch" to get even better results at the price of longer computation.
config = N2VConfig(X, unet_kern_size=3,
train_steps_per_epoch=100, train_epochs=10, train_loss='mse', batch_norm=True,
train_batch_size=4, n2v_perc_pix=1.6, n2v_patch_shape=(32, 64, 64),
n2v_manipulator='uniform_withCP', n2v_neighborhood_radius=5)
# Let's look at the parameters stored in the config-object.
vars(config)
# a name used to identify the model
model_name = 'n2v_3D'
# the base directory in which our model will live
basedir = 'models'
# We are now creating our network model
model = N2V(config=config, name=model_name, basedir=basedir)
history = model.train(X, X_val)
print(sorted(list(history.history.keys())))
#plt.figure(figsize=(16,5))
#plot_history(history,['loss','val_loss'])
#plt.subplot(1,2,1)
#plt.imshow(X[0,...])
#plt.title('Training Patch')
#plt.subplot(1,2,2)
#plt.imshow(X_val[0,...])
#plt.title('Validation Patch')
#plt.show()
# You can increase "train_steps_per_epoch" to get even better results at the price of longer computation
config = N2VConfig(X,
unet_kern_size=3,
unet_n_first=64,
unet_n_depth=3,
train_steps_per_epoch=5,
train_epochs=25,
train_loss='mse',
batch_norm=True,
train_batch_size=128,
n2v_perc_pix=5,
n2v_patch_shape=(64, 64),
n2v_manipulator='uniform_withCP',
n2v_neighborhood_radius=5)
vars(config)
# name used to identify the model
model_name = 'n2v_2D_RGB'
# the base directory in which our model will live
basedir = 'models'
# We are now creating our network model
model = N2V(config, model_name, basedir=basedir)
history = model.train(X, X_val)
augment=(not args.noAugment))
# The patches are non-overlapping, so we can split them into train and validation data.
frac = int((len(patches)) * float(args.validationFraction) / 100.0)
print("total no. of patches: " + str(len(patches)) + "\ttraining patches: " +
str(len(patches) - frac) + "\tvalidation patches: " + str(frac))
X = patches[frac:]
X_val = patches[:frac]
config = N2VConfig(X,
unet_kern_size=args.netKernelSize,
train_steps_per_epoch=int(args.stepsPerEpoch),
train_epochs=int(args.epochs),
train_loss='mse',
batch_norm=True,
train_batch_size=args.batchSize,
n2v_perc_pix=args.n2vPercPix,
n2v_patch_shape=pshape,
n2v_manipulator='uniform_withCP',
n2v_neighborhood_radius=5,
train_learning_rate=args.learningRate,
unet_n_depth=args.netDepth,
unet_n_first=args.unet_n_first)
# Let's look at the parameters stored in the config-object.
vars(config)
# a name used to identify the model
model_name = args.name
# the base directory in which our model will live
basedir = args.baseDir
# We are now creating our network model.
X_val = X_val[..., np.newaxis]
print(X_val.shape)
# In[5]:
# IMPORTANT!! I add clip
X = np.clip(X, 0, 255.).astype(np.uint8).astype(np.float32)
X_val = np.clip(X_val, 0, 255.)
config = N2VConfig(X,
unet_kern_size=3,
train_steps_per_epoch=400,
train_epochs=200,
train_loss='mse',
batch_norm=True,
train_batch_size=args.batch_size,
n2v_perc_pix=args.perc_pix,
n2v_patch_shape=(args.patch_size, args.patch_size),
unet_n_first=96,
unet_residual=True,
n2v_manipulator='uniform_withCP',
n2v_neighborhood_radius=2)
vars(config)
model = N2V(config, args.exp_name, basedir=args.ckpt_dir)
model.prepare_for_training(metrics=())
# We are ready to start training now.
history = model.train(X, X_val)
#
#
datagen = N2V_DataGenerator()
imgs = datagen.load_imgs_from_directory(directory=image_path, dims='ZYX')
print(imgs[0].shape)
# default = 32,64,64
patches = datagen.generate_patches_from_list(imgs[:1], shape=(32, 64, 64))
# default = :600
X = patches[:600]
X_val = patches[600:]
numberEpochs = 20
config = N2VConfig(X,
unet_kern_size=3,
train_steps_per_epoch=int(X.shape[0] / 128),
train_epochs=numberEpochs,
train_loss='mse',
batch_norm=True,
train_batch_size=4,
n2v_perc_pix=0.198,
n2v_patch_shape=(32, 64, 64),
n2v_manipulator='uniform_withCP',
n2v_neighborhood_radius=5)
vars(config)
model_name = '20epoch'
model = N2V(config=config, name=model_name, basedir=image_path)
history = model.train(X, X_val)
print(sorted(list(history.history.keys())))
model.export_TF()
# Load the image, and predict the denoised image.
img = imread(os.path.join(image_path, image_name))
pred = model.predict(img, axes='ZYX', n_tiles=(2, 4, 4))
print(X.shape)
X_val = X_val[..., np.newaxis]
print(X_val.shape)
# Let's look at one of our training and validation patches.
plt.figure(figsize=(14,7))
plt.subplot(1,2,1)
plt.imshow(X[0,...,0], cmap='gray')
plt.title('Training Patch');
plt.subplot(1,2,2)
plt.imshow(X_val[0,...,0], cmap='gray')
plt.title('Validation Patch');
plt.show()
config = N2VConfig(X, unet_kern_size=3,
train_steps_per_epoch=200, train_epochs=100, train_loss='mse', batch_norm=True,#400 , 200
train_batch_size=128, n2v_perc_pix=0.198, n2v_patch_shape=(64, 64),
unet_n_first = 96,
unet_residual = True,
n2v_manipulator='uniform_withCP', n2v_neighborhood_radius=2)
# Let's look at the parameters stored in the config-object.
#print(vars(config))
# a name used to identify the model
model_name = 'BSD68_reproducability_5x5'
# the base directory in which our model will live
basedir = 'models'
# We are now creating our network model.
model = N2V(config, model_name, basedir=basedir)
model.prepare_for_training(metrics=())
# We are ready to start training now.
