Source code for csbdeep.models.config

from __future__ import print_function, unicode_literals, absolute_import, division
from six.moves import range, zip, map, reduce, filter
from six import string_types

import numpy as np
import argparse
import warnings

from distutils.version import LooseVersion
import keras
import keras.backend as K

from ..utils import _raise, axes_check_and_normalize, axes_dict, backend_channels_last


class BaseConfig(argparse.Namespace):

    def __init__(self, axes='YX', n_channel_in=1, n_channel_out=1, allow_new_parameters=False, **kwargs):

        # parse and check axes
        axes = axes_check_and_normalize(axes)
        ax = axes_dict(axes)
        ax = {a: (ax[a] is not None) for a in ax}

        (ax['X'] and ax['Y']) or _raise(ValueError('lateral axes X and Y must be present.'))
        # not (ax['Z'] and ax['T']) or _raise(ValueError('using Z and T axes together not supported.'))

        axes.startswith('S') or (not ax['S']) or _raise(ValueError('sample axis S must be first.'))
        axes = axes.replace('S','') # remove sample axis if it exists

        n_dim = len(axes.replace('C',''))

        # TODO: Config not independent of backend. Problem?
        # could move things around during train/predict as an alternative... good idea?
        # otherwise, users can choose axes of input image anyhow, so doesn't matter if model is fixed to something else
        if backend_channels_last():
            if ax['C']:
                axes[-1] == 'C' or _raise(ValueError('channel axis must be last for backend (%s).' % K.backend()))
            else:
                axes += 'C'
        else:
            if ax['C']:
                axes[0] == 'C' or _raise(ValueError('channel axis must be first for backend (%s).' % K.backend()))
            else:
                axes = 'C'+axes

        self.n_dim                  = n_dim
        self.axes                   = axes
        self.n_channel_in           = int(max(1,n_channel_in))
        self.n_channel_out          = int(max(1,n_channel_out))

        self.train_checkpoint       = 'weights_best.h5'
        self.train_checkpoint_last  = 'weights_last.h5'
        self.train_checkpoint_epoch = 'weights_now.h5'

        self.update_parameters(allow_new_parameters, **kwargs)


    def is_valid(self, return_invalid=False):
        return (True, tuple()) if return_invalid else True


    def update_parameters(self, allow_new=False, **kwargs):
        if not allow_new:
            attr_new = []
            for k in kwargs:
                try:
                    getattr(self, k)
                except AttributeError:
                    attr_new.append(k)
            if len(attr_new) > 0:
                raise AttributeError("Not allowed to add new parameters (%s)" % ', '.join(attr_new))
        for k in kwargs:
            setattr(self, k, kwargs[k])




[docs]class Config(BaseConfig): """Default configuration for a CARE model. This configuration is meant to be used with :class:`CARE` and related models (e.g., :class:`IsotropicCARE`). Parameters ---------- axes : str Axes of the neural network (channel axis optional). n_channel_in : int Number of channels of given input image. n_channel_out : int Number of channels of predicted output image. probabilistic : bool Probabilistic prediction of per-pixel Laplace distributions or typical regression of per-pixel scalar values. allow_new_parameters : bool Allow adding new configuration attributes (i.e. not listed below). kwargs : dict Overwrite (or add) configuration attributes (see below). Example ------- >>> config = Config('YX', probabilistic=True, unet_n_depth=3) Attributes ---------- n_dim : int Dimensionality of input images (2 or 3). unet_residual : bool Parameter `residual` of :func:`csbdeep.nets.common_unet`. Default: ``n_channel_in == n_channel_out`` unet_n_depth : int Parameter `n_depth` of :func:`csbdeep.nets.common_unet`. Default: ``2`` unet_kern_size : int Parameter `kern_size` of :func:`csbdeep.nets.common_unet`. Default: ``5 if n_dim==2 else 3`` unet_n_first : int Parameter `n_first` of :func:`csbdeep.nets.common_unet`. Default: ``32`` unet_last_activation : str Parameter `last_activation` of :func:`csbdeep.nets.common_unet`. Default: ``linear`` train_loss : str Name of training loss. Default: ``'laplace' if probabilistic else 'mae'`` train_epochs : int Number of training epochs. Default: ``100`` train_steps_per_epoch : int Number of parameter update steps per epoch. Default: ``400`` train_learning_rate : float Learning rate for training. Default: ``0.0004`` train_batch_size : int Batch size for training. Default: ``16`` train_tensorboard : bool Enable TensorBoard for monitoring training progress. Default: ``True`` train_checkpoint : str Name of checkpoint file for model weights (only best are saved); set to ``None`` to disable. Default: ``weights_best.h5`` train_reduce_lr : dict Parameter :class:`dict` of ReduceLROnPlateau_ callback; set to ``None`` to disable. Default: ``{'factor': 0.5, 'patience': 10, 'min_delta': 0}`` .. _ReduceLROnPlateau: https://keras.io/callbacks/#reducelronplateau """ def __init__(self, axes='YX', n_channel_in=1, n_channel_out=1, probabilistic=False, allow_new_parameters=False, **kwargs): """See class docstring.""" super(Config, self).__init__(axes, n_channel_in, n_channel_out) not ('Z' in self.axes and 'T' in self.axes) or _raise(ValueError('using Z and T axes together not supported.')) self.probabilistic = bool(probabilistic) # default config (can be overwritten by kwargs below) self.unet_residual = self.n_channel_in == self.n_channel_out self.unet_n_depth = 2 self.unet_kern_size = 5 if self.n_dim==2 else 3 self.unet_n_first = 32 self.unet_last_activation = 'linear' if backend_channels_last(): self.unet_input_shape = self.n_dim*(None,) + (self.n_channel_in,) else: self.unet_input_shape = (self.n_channel_in,) + self.n_dim*(None,) self.train_loss = 'laplace' if self.probabilistic else 'mae' self.train_epochs = 100 self.train_steps_per_epoch = 400 self.train_learning_rate = 0.0004 self.train_batch_size = 16 self.train_tensorboard = True # the parameter 'min_delta' was called 'epsilon' for keras<=2.1.5 min_delta_key = 'epsilon' if LooseVersion(keras.__version__)<=LooseVersion('2.1.5') else 'min_delta' self.train_reduce_lr = {'factor': 0.5, 'patience': 10, min_delta_key: 0} # disallow setting 'n_dim' manually try: del kwargs['n_dim'] # warnings.warn("ignoring parameter 'n_dim'") except: pass self.update_parameters(allow_new_parameters, **kwargs)
[docs] def is_valid(self, return_invalid=False): """Check if configuration is valid. Returns ------- bool Flag that indicates whether the current configuration values are valid. """ def _is_int(v,low=None,high=None): return ( isinstance(v,int) and (True if low is None else low <= v) and (True if high is None else v <= high) ) ok = {} ok['n_dim'] = self.n_dim in (2,3) try: axes_check_and_normalize(self.axes,self.n_dim+1,disallowed='S') ok['axes'] = True except: ok['axes'] = False ok['n_channel_in'] = _is_int(self.n_channel_in,1) ok['n_channel_out'] = _is_int(self.n_channel_out,1) ok['probabilistic'] = isinstance(self.probabilistic,bool) ok['unet_residual'] = ( isinstance(self.unet_residual,bool) and (not self.unet_residual or (self.n_channel_in==self.n_channel_out)) ) ok['unet_n_depth'] = _is_int(self.unet_n_depth,1) ok['unet_kern_size'] = _is_int(self.unet_kern_size,1) ok['unet_n_first'] = _is_int(self.unet_n_first,1) ok['unet_last_activation'] = self.unet_last_activation in ('linear','relu') ok['unet_input_shape'] = ( isinstance(self.unet_input_shape,(list,tuple)) and len(self.unet_input_shape) == self.n_dim+1 and self.unet_input_shape[-1] == self.n_channel_in # and all((d is None or (_is_int(d) and d%(2**self.unet_n_depth)==0) for d in self.unet_input_shape[:-1])) ) ok['train_loss'] = ( ( self.probabilistic and self.train_loss == 'laplace' ) or (not self.probabilistic and self.train_loss in ('mse','mae')) ) ok['train_epochs'] = _is_int(self.train_epochs,1) ok['train_steps_per_epoch'] = _is_int(self.train_steps_per_epoch,1) ok['train_learning_rate'] = np.isscalar(self.train_learning_rate) and self.train_learning_rate > 0 ok['train_batch_size'] = _is_int(self.train_batch_size,1) ok['train_tensorboard'] = isinstance(self.train_tensorboard,bool) ok['train_checkpoint'] = self.train_checkpoint is None or isinstance(self.train_checkpoint,string_types) ok['train_reduce_lr'] = self.train_reduce_lr is None or isinstance(self.train_reduce_lr,dict) if return_invalid: return all(ok.values()), tuple(k for (k,v) in ok.items() if not v) else: return all(ok.values())