keras-eval

Evaluation abstraction for Keras models. Example Notebook

Requires keras-model-specs. We support python 3+.

Example Evaluation

probs, labels = evaluator.evaluate(data_dir=data_dir, top_k=2, confusion_matrix=True, save_confusion_matrix_path='cm.png')

evaluator.show_results('average')

model	f1_score	fdr	positives	sensitivity	specificity	auroc	negatives	precision	accuracy
mobilenet_v1.h5	0.934	0.064	1869	0.934	0.934	0.807	131	0.936	0.934

evaluator.show_results('individual')

class	sensitivity	precision	f1_score	specificity	FDR	AUROC	TP	FP	FN	% of samples
cats	0.907	0.960	0.933	0.962	0.040	1.0	907	38	93	50.0
dogs	0.962	0.912	0.936	0.907	0.088	1.0	962	93	38	50.0

mean, lower, upper = evaluator.plot_confidence_interval('accuracy', confidence_value=0.95)

Plot the Classifier Confidence Interval:

Plot the errors in which the classifier was more confident:

evaluator.plot_most_confident('errors', n_images=20)

And many more functions to evaluate and visualize results in the following lines and in the Example Notebook and Report Template

Use the code

Clone the repository

git clone https://github.com/triagemd/keras-eval.git

To install project dependencies, inside the root folder run

script/up

To create an IPython kernel do the following in the virtual environment:

source .venv/bin/activate

pip install ipykernel

ipython kernel install --user --name=keras-eval.venv

Evaluator Class

Easy predictions and evaluations for a single model or an ensemble of many models.

The format to load models is the following:

For a single model

# The input is the model path
model_path = '/model_folder/resnet_50/model.h5'

# Inside model folder, there should be a '/model_folder/resnet_50/model_spec.json' file

with the following format as example:

{
 "name": "your_name",
 "preprocess_args": [
  156.2336961908687,
  122.03200584422879,
  109.9825961313363
 ],
 "preprocess_func": "mean_subtraction",
 "target_size": [
  299,
  299,
  3
 ]
}

For an ensemble of models

# The input is the parent folder
ensemble_models_dir = '/model_folder'

# That folder must contain several folders containing the models we want to load with their respective specs
# e.g. '/model_folder/resnet_50/model.h5', '/model_folder/resnet_50/model_spec.json', '/model_folder/densenet201/model.h5', '/model_folder/densenet201/model_spec.json'

Apply Data Augmentation at Test time

We include the addition of data_augmentation as an argument in evaluate(). It is a dictionary consisting of 3 elements:

'scale_sizes': 'default' (4 similar scales to Original paper) or a list of sizes. Each scaled image then will be cropped into three square parts. For each square, we then take the 4 corners and the center "target_size" crop as well as the square resized to "target_size".
'transforms': list of transforms to apply to these crops in addition to not applying any transform ('horizontal_flip', 'vertical_flip', 'rotate_90', 'rotate_180', 'rotate_270' are supported now).
'crop_original': 'center_crop' mode allows to center crop the original image prior do the rest of transforms, scalings + croppings.

If 'scale_sizes' is None the image will be resized to "target_size" and transforms will be applied over that image.

For instance: data_augmentation={'scale_sizes':'default', 'transforms':['horizontal_flip', 'rotate_180'], 'crop_original':'center_crop'}

For 144 crops as the GoogleNet paper, select data_augmentation={'scale_sizes':'default', 'transforms':['horizontal_flip']}. This results in 4x3x6x2 = 144 crops per image.

probs, labels = evaluator.evaluate(data_dir=data_dir, top_k=2, confusion_matrix=True, data_augmentation={'scale_sizes': [356, 284], 'transforms': ['horizontal_flip'], 'crop_original': 'center_crop'})

To evaluate on coarse classes after training on granular classes

Given a model trained on M classes and test set based on N classes (M > N), allow the evaluation on sets of classes by providing a concept dictionary.

Case 1: Regular evaluation

E.g. Training scenario:

[class_0]
[class_1]
[class_2]
[class_3]

Regular evaluation scenario:

[class_0]
[class_1]
[class_2]
[class_3]

Results for regular evaluation:

model	accuracy	precision	f1_score	number_of_samples	number_of_classes
animals_combine_classes.hdf5	0.733	0.876	0.744	15	5

Case 2: Class consolidated evaluation Evaluate on classes grouped on sets of training classes. Class consolidated evaluation scenario:

[test_set_0] class_0 or class_1
[test_set_1] class_2 or class_3

The probability changes during class consolidation as seen below:

probability(test_set_0) =  probability(class_0) + probability(class_1)
probability(test_set_1) = probability(class_2) + probability(class_3)

For this purpose, the mapping between the training and testing dictionary must be provided as a .json file with the following format:

[
  {
    "class_index": 0,
    "class_name": "00000_cat",
    "group": "00000_domestic"
  },
  {
    "class_index": 1,
    "class_name": "00001_dog",
    "group": "00000_domestic"
  },
  {
    "class_index": 2,
    "class_name": "00002_goose",
    "group": "00001_water"
  },
  {
    "class_index": 3,
    "class_name": "00003_turtle",
    "group": "00001_water"
  },
  {
    "class_index": 4,
    "class_name": "00004_elephant",
    "group": "00002_wild"
  }
]

Results for class consolidated evaluation:

model	accuracy	precision	f1_score	number_of_samples	number_of_classes
animals_combine_classes.hdf5	0.733	0.841	0.729	15	3

You can specify all the following options.

Evaluator

from keras_eval.eval import Evaluator

evaluator = Evaluator(
                data_dir=None,
                concepts=None,
                concept_dictionary_path=None,
                ensemble_models_dir=None,
                model_path=model_path,
                loss_function='categorical_crossentropy',
                metrics=['accuracy'],
                batch_size=32,
                verbose=0)

Evaluation Functions

Evaluate a set of images.

Each sub-folder under 'data_dir/' will be considered as a different class. E.g. 'data_dir/class_1/dog.jpg' , 'data_dir/class_2/cat.jpg' If you are evaluating an ensemble of models, we currently allow for these probability combination modes: 'maximum', 'arithmetic', 'geometric', 'harmonic'

evaluate

data_dir = 'tests/files/catdog/test/'
probabilities, labels = evaluator.evaluate(data_dir=None, top_k=2, filter_indices=None, confusion_matrix=False, save_confusion_matrix_path=None, verbose=1)
# probabilities.shape = [n_models, n_samples, n_classes]
# labels.shape = [n_samples, n_classes]

Predict class probabilities of a set of images from a folder.

predict

folder_path = 'tests/files/catdog/test/cat/'
probs = evaluator.predict(folder_path)

Predict class probabilities of a single image

predict

image_path = 'tests/files/catdog/test/cat/cat-1.jpg'
probs = evaluator.predict(image_path)

Evaluator attributes

After making predictions you can access to evaluator.image_paths to get a list of the files forwarded.

Additional options

You can also add more options once the Evaluator object has been created, like loading more models or setting class names and abbreviations to show in the confusion matrix.

add_model

model_path = '/your_model_path/model.h5
# Also supports model custom objects
custom_objects = None
evaluator.add_model(model_path, custom_objects)

add_model_ensemble

model_path = '/your_model_ensemble_path/'
evaluator.add_model_ensemble(model_path)

set_concepts

concepts = [{'label':'Cat', 'id': 'cats'},
            {'label':'Dog', 'id': 'dogs'},]

evaluator.set_concepts(concepts)

Extra

For more information check the Example Notebook and the source code.

Contact

This library is mantained by @triagemd. To report any problem or issue, please use the Issues section.