Merge pull request #31 from juglab/issue_20

Issue 20

.travis.yml

@@ -13,41 +13,22 @@ env:
 matrix:
   include:
     - os: linux
-      python: 3.5
-    - os: linux
-      python: 3.6
-      ###########
-    - os: linux
-      python: 3.6
-      if: branch = master
-      env: TENSORFLOW='tensorflow<1.12'   KERAS='keras'
-    - os: linux
+      dist: bionic
       python: 3.6
-      if: branch = master
-      env: TENSORFLOW='tensorflow<1.11'   KERAS='keras'
+      env: TENSORFLOW='tensorflow==1.14.0' KERAS='keras==2.2.4'
     - os: linux
+      dist: bionic
       python: 3.6
-      if: branch = master
-      env: TENSORFLOW='tensorflow<1.10'   KERAS='keras==2.2.2'
+      env: TENSORFLOW='tensorflow==1.12.0' KERAS='keras==2.2.4'
     - os: linux
-      python: 3.6
-      if: branch = master
-      # env: TENSORFLOW='tensorflow<1.9'    KERAS='keras==2.2.0' # causes segmentation fault, why?
-      env: TENSORFLOW='tensorflow<1.8'    KERAS='keras==2.2.0'
-    - os: linux
-      python: 3.6
-      if: branch = master
-      env: TENSORFLOW='tensorflow<1.8'    KERAS='keras==2.1.6'
-    - os: linux
-      python: 3.6
-      if: branch = master
-      # lowest supported keras version, last tensorflow release that supports CUDA 8
-      env: TENSORFLOW='tensorflow==1.4.1' KERAS='keras==2.1.6'
-      ###########
+      dist: bionic
+      python: 3.7
+      env: TENSORFLOW='tensorflow==1.14.0' KERAS='keras==2.2.4'
 
 install:
   - pip install $TENSORFLOW $KERAS
   - pip install .
 
 script:
-  - pytest -v --durations=50
+  - cd tests; pytest -v -s test*.py 
+  - cd functional; ./test_training2D_RGB.py; ./test_prediction2D_RGB.py; ./test_training3D.py; ./test_prediction3D.py

README.md

@@ -12,18 +12,18 @@ Our implementation is based on [CSBDEEP](http://csbdeep.bioimagecomputing.com) (
 
 ## Installation
 This implementation requires [Tensorflow](https://www.tensorflow.org/install/).
-We have tested Noise2Void on LinuxMint 18.3 using python 3.6 and tensorflow-gpu 1.12.0.
+We have tested Noise2Void on LinuxMint 19 and Ubuntu 18.0 using python 3.6 and 3.7 and tensorflow-gpu 1.12.0 and 1.14.0.
 
 #### If you start from scratch...
-We recommend using [conda](https://docs.conda.io/en/latest/miniconda.html).
+We recommend using [miniconda](https://docs.conda.io/en/latest/miniconda.html).
 If you do not yet have a strong opinion, just use it too!
 
 After installing Miniconda, the following lines might are likely the easiest way to get Tensorflow and CuDNN installed on your machine (_Note:_ Macs are not supported, and if you sit on a Windows machine all this might also require some modifications.):
 
 ```
 $ conda create -n 'n2v' python=3.6
 $ source activate n2v
-$ conda install tensorflow-gpu==1.12
+$ conda install tensorflow-gpu==1.14
 $ pip install jupyter
 ```
 
@@ -35,11 +35,13 @@ $ pip install n2v
 ```
 
 #### Option 2: Git-Clone and install from sources
-Or clone the repository:
+This option is ideal if you want to edit the code. Clone the repository:
+
 ```
 $ git clone https://github.com/juglab/n2v.git
 ```
 Change into its directory and install it:
+
 ```
 $ cd n2v
 $ pip install -e .

n2v/models/n2v_config.py

@@ -2,11 +2,13 @@
 
 import keras.backend as K
 
+from csbdeep.models import BaseConfig
 from csbdeep.utils import _raise, axes_check_and_normalize, axes_dict, backend_channels_last
 
 from six import string_types
 
 import numpy as np
+from logging.config import BaseConfigurator
 
 # This class is a adapted version of csbdeep.models.config.py.
 class N2VConfig(argparse.Namespace):
@@ -68,83 +70,87 @@ class N2VConfig(argparse.Namespace):
     """
 
     def __init__(self, X, **kwargs):
-        """See class docstring."""
-
-        assert len(X.shape) == 4 or len(X.shape) == 5, "Only 'SZYXC' or 'SYXC' as dimensions is supported."
-
-        n_dim = len(X.shape) - 2
-        n_channel_in = X.shape[-1]
-        n_channel_out = n_channel_in
-        mean = np.mean(X)
-        std = np.std(X)
-
-        if n_dim == 2:
-            axes = 'SYXC'
-        elif n_dim == 3:
-            axes = 'SZYXC'
-
-        # 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
-
-        if backend_channels_last():
-            if ax['C']:
-                axes[-1] == 'C' or _raise(ValueError('channel axis must be last for backend (%s).' % K.backend()))
+
+        # X is empty if config is None
+        if (X.size != 0):
+
+            assert len(X.shape) == 4 or len(X.shape) == 5, "Only 'SZYXC' or 'SYXC' as dimensions is supported."
+
+            n_dim = len(X.shape) - 2
+            n_channel_in = X.shape[-1]
+            n_channel_out = n_channel_in
+            mean = np.mean(X)
+            std = np.std(X)
+
+            if n_dim == 2:
+                axes = 'SYXC'
+            elif n_dim == 3:
+                axes = 'SZYXC'
+
+            # 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
+
+            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:
-                axes += 'C'
-        else:
-            if ax['C']:
-                axes[0] == 'C' or _raise(ValueError('channel axis must be first for backend (%s).' % K.backend()))
+                if ax['C']:
+                    axes[0] == 'C' or _raise(ValueError('channel axis must be first for backend (%s).' % K.backend()))
+                else:
+                    axes = 'C'+axes
+
+            # normalization parameters
+            self.mean                  = str(mean)
+            self.std                   = str(std)
+            # directly set by parameters
+            self.n_dim                 = n_dim
+            self.axes                  = axes
+            self.n_channel_in          = int(n_channel_in)
+            self.n_channel_out         = int(n_channel_out)
+
+            # default config (can be overwritten by kwargs below)
+            self.unet_residual         = False
+            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:
-                axes = 'C'+axes
-
-        # normalization parameters
-        self.mean                  = str(mean)
-        self.std                   = str(std)
-        # directly set by parameters
-        self.n_dim                 = n_dim
-        self.axes                  = axes
-        self.n_channel_in          = int(n_channel_in)
-        self.n_channel_out         = int(n_channel_out)
-
-        # default config (can be overwritten by kwargs below)
-        self.unet_residual         = False
-        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            = '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
-        self.train_checkpoint      = 'weights_best.h5'
-        self.train_reduce_lr       = {'factor': 0.5, 'patience': 10}
-        self.batch_norm            = True
-        self.n2v_perc_pix           = 1.5
-        self.n2v_patch_shape       = (64, 64) if self.n_dim==2 else (64, 64, 64)
-        self.n2v_manipulator       = 'uniform_withCP'
-        self.n2v_neighborhood_radius = 5
-
-        # disallow setting 'n_dim' manually
-        try:
-            del kwargs['n_dim']
-            # warnings.warn("ignoring parameter 'n_dim'")
-        except:
-            pass
+                self.unet_input_shape  = (self.n_channel_in,) + self.n_dim*(None,)
+
+            self.train_loss            = '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
+            self.train_checkpoint      = 'weights_best.h5'
+            self.train_reduce_lr       = {'factor': 0.5, 'patience': 10}
+            self.batch_norm            = True
+            self.n2v_perc_pix           = 1.5
+            self.n2v_patch_shape       = (64, 64) if self.n_dim==2 else (64, 64, 64)
+            self.n2v_manipulator       = 'uniform_withCP'
+            self.n2v_neighborhood_radius = 5
+
+            # disallow setting 'n_dim' manually
+            try:
+                del kwargs['n_dim']
+                # warnings.warn("ignoring parameter 'n_dim'")
+            except:
+                pass
+
+        self.probabilistic         = False
 
         for k in kwargs:
             setattr(self, k, kwargs[k])
@@ -215,3 +221,16 @@ def _is_int(v,low=None,high=None):
             return all(ok.values()), tuple(k for (k,v) in ok.items() if not v)
         else:
             return all(ok.values())
+
+    def update_parameters(self, allow_new=True, **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])

n2v/models/n2v_standard.py

@@ -1,5 +1,5 @@
 from csbdeep.models import CARE
-from csbdeep.utils import _raise, axes_check_and_normalize, axes_dict
+from csbdeep.utils import _raise, axes_check_and_normalize, axes_dict, load_json, save_json
 from csbdeep.internals import nets
 from csbdeep.internals.predict import Progress
 
@@ -64,25 +64,32 @@ class N2V(CARE):
         """
 
     def __init__(self, config, name=None, basedir='.'):
-        """See class docstring"""
-        config is None or isinstance(config, N2VConfig) or _raise(ValueError('Invalid configuration: %s' % str(config)))
+        """See class docstring."""
+
+        config is None or isinstance(config,self._config_class) or _raise (
+            ValueError("Invalid configuration of type '%s', was expecting type '%s'." % (type(config).__name__, self._config_class.__name__))
+        )
         if config is not None and not config.is_valid():
             invalid_attr = config.is_valid(True)[1]
             raise ValueError('Invalid configuration attributes: ' + ', '.join(invalid_attr))
-        (not (config is None and basedir is None)) or _raise(ValueError())
+        (not (config is None and basedir is None)) or _raise(ValueError("No config provided and cannot be loaded from disk since basedir=None."))
 
-        name is None or isinstance(name, string_types) or _raise(ValueError())
-        basedir is None or isinstance(basedir, (string_types, Path)) or _raise(ValueError())
+        name is None or (isinstance(name,string_types) and len(name)>0) or _raise(ValueError("No valid name: '%s'" % str(name)))
+        basedir is None or isinstance(basedir,(string_types,Path)) or _raise(ValueError("No valid basedir: '%s'" % str(basedir)))
         self.config = config
         self.name = name if name is not None else datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S.%f")
         self.basedir = Path(basedir) if basedir is not None else None
+        if config is not None:
+            # config was provided -> update before it is saved to disk
+            self._update_and_check_config()
         self._set_logdir()
+        if config is None:
+            # config was loaded from disk -> update it after loading
+            self._update_and_check_config()
         self._model_prepared = False
         self.keras_model = self._build()
         if config is None:
             self._find_and_load_weights()
-        else:
-            config.probabilistic = False
 
 
     def _build(self):
@@ -205,8 +212,8 @@ def train(self, X, validation_X, epochs=None, steps_per_epoch=None):
                                                     self.config.train_batch_size, int(train_num_pix/100 * self.config.n2v_perc_pix),
                                                     self.config.n2v_patch_shape, manipulator)
 
-        # validation_Y is also validation_X plus a concatinated masking channel.
-        # To speed things up, we precomupte the masking vo the validation data.
+        # validation_Y is also validation_X plus a concatenated masking channel.
+        # To speed things up, we precompute the masking vo the validation data.
         validation_Y = np.concatenate((validation_X, np.zeros(validation_X.shape, dtype=validation_X.dtype)), axis=axes.index('C'))
         n2v_utils.manipulate_val_data(validation_X, validation_Y,
                                                         num_pix=int(val_num_pix/100 * self.config.n2v_perc_pix),
@@ -272,13 +279,16 @@ def on_epoch_end(self, epoch, logs=None):
                             if epoch % self.freq == 0:
                                 # TODO: implement batched calls to sess.run
                                 # (current call will likely go OOM on GPU)
+                                tensors = self.model.inputs + self.gt_outputs + self.model.sample_weights
                                 if self.model.uses_learning_phase:
-                                    cut_v_data = len(self.model.inputs)
-                                    val_data = [self.validation_data[0][:self.n_images]] + [0]
-                                    tensors = self.model.inputs + [K.learning_phase()]
+                                    tensors += [K.learning_phase()]
+                                    val_data = list(v[:self.n_images] for v in self.validation_data[:-1])
+                                    val_data += self.validation_data[-1:]
                                 else:
                                     val_data = list(v[:self.n_images] for v in self.validation_data)
-                                    tensors = self.model.inputs
+                                # GIT issue 20: We need to remove the masking component from the validation data to prevent crash.
+                                end_index = (val_data[1].shape)[-1]//2
+                                val_data[1] = val_data[1][...,:end_index]
                                 feed_dict = dict(zip(tensors, val_data))
                                 result = self.sess.run([self.merged], feed_dict=feed_dict)
                                 summary_str = result[0]
@@ -365,3 +375,26 @@ def predict(self, img, axes, resizer=PadAndCropResizer(), n_tiles=None):
         pred = self._predict_mean_and_scale(normalized, axes=axes, normalizer=None, resizer=resizer, n_tiles=n_tiles)[0]
 
         return self.__denormalize__(pred, mean, std)
+
+    def _set_logdir(self):
+        self.logdir = self.basedir / self.name
+
+        config_file =  self.logdir / 'config.json'
+        if self.config is None:
+            if config_file.exists():
+                config_dict = load_json(str(config_file))
+                self.config = self._config_class(np.array([]), **config_dict)
+                if not self.config.is_valid():
+                    invalid_attr = self.config.is_valid(True)[1]
+                    raise ValueError('Invalid attributes in loaded config: ' + ', '.join(invalid_attr))
+            else:
+                raise FileNotFoundError("config file doesn't exist: %s" % str(config_file.resolve()))
+        else:
+            if self.logdir.exists():
+                warnings.warn('output path for model already exists, files may be overwritten: %s' % str(self.logdir.resolve()))
+            self.logdir.mkdir(parents=True, exist_ok=True)
+            save_json(vars(self.config), str(config_file))
+
+    @property
+    def _config_class(self):
+        return N2VConfig

n2v/version.py

@@ -1 +1 @@
-__version__ = '0.1.6'
+__version__ = '0.1.7'