Merge pull request #37 from sentinel-hub/develop

Add resunet-a architecture used for field delineation

README.md

@@ -60,6 +60,7 @@ Project also contains other folders:
 Segmentation models for land cover semantic segmentation:
 * **Fully-Convolutional-Network (FCN, a.k.a. U-net)**, vanilla implementation of method described in this [paper](https://arxiv.org/abs/1505.04597). This network expects 2D MSI images as inputs and predicts 2D label maps as output.
 * **Temporal FCN**, where the whole time-series is considered as a 3D MSI volume and convolutions are performed along the temporal dimension as well spatial dimension. The output of the network is a 2D label map as in previous cases. More details can be found in this [paper](https://www.researchgate.net/publication/333262625_Spatio-Temporal_Deep_Learning_An_Application_to_Land_Cover_Classification).
+* **ResUNet-a**, architecture proposed in Diakogiannis et al. ["ResUNet-a: A deep learning framework for semantic segmetnation of remotely sensed data"](https://www.sciencedirect.com/science/article/abs/pii/S0924271620300149). Original `mxnet` implementation can be found [here](https://github.com/feevos/resuneta).
 
 Classification models for crop classification using time-series:
 * **TCN**: Implementation of the TCN network taken from the [keras-TCN implementation by Philippe Remy](https://github.com/philipperemy/keras-tcn).

eoflow/models/metrics.py

@@ -1,5 +1,13 @@
+import warnings
+
+from typing import Any, Callable, List
+
+from skimage import measure
+from scipy import ndimage
+
 import tensorflow as tf
 import tensorflow_addons as tfa
+import numpy as np
 
 
 class InitializableMetric(tf.keras.metrics.Metric):
@@ -156,3 +164,144 @@ def get_config(self):
         self.assert_initialized()
 
         return self.metric.get_config()
+
+
+class GeometricMetrics(InitializableMetric):
+    """"
+    Implementation of Geometric error metrics. Oversegmentation, Undersegmentation, Border, Fragmentation errors.
+
+    The error metrics are based on a paper by C. Persello, A Novel Protocol for Accuracy Assessment in Classification of
+    Very High Resolution Images (https://ieeexplore.ieee.org/document/5282610)
+    """
+
+    @staticmethod
+    def _detect_edges(im: np.ndarray, thr: float = 0) -> np.ndarray:
+        """ Edge detection function using the sobel operator. """
+        sx = ndimage.sobel(im, axis=0, mode='constant')
+        sy = ndimage.sobel(im, axis=1, mode='constant')
+        sob = np.hypot(sx, sy)
+        return sob > thr
+
+    @staticmethod
+    def _segmentation_error(intersection_area: float, object_area: float) -> float:
+        return 1. - intersection_area / object_area
+
+    @staticmethod
+    def _intersection(mask1: np.ndarray, mask2: np.ndarray) -> float:
+        return np.sum(np.logical_and(mask1, mask2))
+
+    def _border_err(self, border_ref_edge: np.ndarray, border_meas_edge: np.ndarray) -> float:
+        ref_edge_size = np.sum(border_ref_edge)
+        intersection = self._intersection(border_ref_edge, border_meas_edge)
+        err = intersection / ref_edge_size if ref_edge_size != 0 else 0
+        be = 1. - err
+        return be
+
+    def _fragmentation_err(self, r: int, reference_mask: np.ndarray) -> float:
+        if r <= 1:
+            return 0
+        den = np.sum(reference_mask) - self.pixel_size
+        err = (r - 1.) / den if den > 0 else 0
+        return err
+
+    @staticmethod
+    def _validate_input(reference, measurement):
+        if np.ndim(reference) != np.ndim(measurement):
+            raise ValueError("Reference and measurement input shapes must match.")
+
+    def __init__(self, pixel_size: int = 1, edge_func: Callable = None, **edge_func_params: Any):
+
+        super().__init__(name='geometric_metrics', dtype=tf.float64)
+
+        self.oversegmentation_error = []
+        self.undersegmentation_error = []
+        self.border_error = []
+        self.fragmentation_error = []
+
+        self.edge_func = self._detect_edges if edge_func is None else edge_func
+        self.edge_func_params = edge_func_params
+        self.pixel_size = pixel_size
+
+    def update_state(self, reference: np.ndarray, measurement: np.ndarray, encode_reference: bool = True,
+                     background_value: int = 0) -> None:
+        """ Calculate the error metrics for a measurement and reference arrays. For each .
+
+        If encode_reference is set to True, connected components will be used to label objects in the reference and
+        measurements.
+        """
+
+        if not tf.executing_eagerly():
+            warnings.warn("Geometric metrics must be run with eager execution. If running as a compiled Keras model, "
+                          "enable eager execution with model.run_eagerly = True")
+
+        reference = reference.numpy() if isinstance(reference, tf.Tensor) else reference
+        measurement = measurement.numpy() if isinstance(reference, tf.Tensor) else measurement
+
+        self._validate_input(reference, measurement)
+
+        for ref, meas in zip(reference, measurement):
+            ref = ref
+            meas = meas
+
+            if encode_reference:
+                cc_reference = measure.label(ref, background=background_value)
+            else:
+                cc_reference = ref
+
+            cc_measurement = measure.label(meas, background=background_value)
+            components_reference = set(np.unique(cc_reference)).difference([background_value])
+
+            ref_edges = self.edge_func(cc_reference)
+            meas_edges = self.edge_func(cc_measurement)
+            for component in components_reference:
+                reference_mask = cc_reference == component
+
+                uniq, count = np.unique(cc_measurement[reference_mask & (cc_measurement != background_value)],
+                                        return_counts=True)
+                ref_area = np.sum(reference_mask)
+
+                max_interecting_measurement = uniq[count.argmax()] if len(count) > 0 else background_value
+                meas_mask = cc_measurement == max_interecting_measurement
+                meas_area = np.count_nonzero(cc_measurement == max_interecting_measurement)
+                intersection_area = count.max() if len(count) > 0 else 0
+
+                self.oversegmentation_error.append(self._segmentation_error(intersection_area, ref_area))
+                self.undersegmentation_error.append(self._segmentation_error(intersection_area, meas_area))
+                border_ref_edge = ref_edges.squeeze() & reference_mask.squeeze()
+                border_meas_edge = meas_edges.squeeze() & meas_mask.squeeze()
+
+                self.border_error.append(self._border_err(border_ref_edge, border_meas_edge))
+                self.fragmentation_error.append(self._fragmentation_err(len(uniq), reference_mask))
+
+    def get_oversegmentation_error(self) -> float:
+        """ Return oversegmentation error. """
+        return np.array(self.oversegmentation_error).mean()
+
+    def get_undersegmentation_error(self) -> float:
+        """ Return undersegmentation error. """
+
+        return np.array(self.undersegmentation_error).mean()
+
+    def get_border_error(self) -> float:
+        """ Return border error. """
+
+        return np.array(self.border_error).mean()
+
+    def get_fragmentation_error(self) -> float:
+        """ Return fragmentation error. """
+
+        return np.array(self.fragmentation_error).mean()
+
+    def result(self) -> List[float]:
+        """ Return a list  of values representing oversegmentation, undersegmentation, border, fragmentation errors. """
+
+        return [self.get_oversegmentation_error(),
+                self.get_undersegmentation_error(),
+                self.get_border_error(), self.get_fragmentation_error()]
+
+    def reset_states(self) -> None:
+        """ Empty all the error arrays. """
+        self.oversegmentation_error = []
+        self.undersegmentation_error = []
+        self.border_error = []
+        self.fragmentation_error = []