[Datumaro] Instance polygon-mask conversions in COCO format (#1008)

* Microoptimizations

* Mask conversion functions

* Add mask-polygon conversions

* Add mask-polygon conversions in coco

* Add mask-polygon conversions in coco

* Update requirements

* Option to disable crop

* Fix cli parameter passing

* Fix test

* Fixes in COCO

datumaro/datumaro/components/extractor.py

@@ -159,12 +159,16 @@ def __eq__(self, other):
 
 class MaskObject(Annotation):
     # pylint: disable=redefined-builtin
-    def __init__(self, image=None, label=None,
+    def __init__(self, image=None, label=None, z_order=None,
             id=None, attributes=None, group=None):
         super().__init__(id=id, type=AnnotationType.mask,
             attributes=attributes, group=group)
         self._image = image
         self._label = label
+
+        if z_order is None:
+            z_order = 0
+        self._z_order = z_order
     # pylint: enable=redefined-builtin
 
     @property
@@ -181,22 +185,69 @@ def painted_data(self, colormap):
         raise NotImplementedError()
 
     def area(self):
-        raise NotImplementedError()
+        if self._label is None:
+            raise NotImplementedError()
+        return np.count_nonzero(self.image)
 
     def extract(self, class_id):
         raise NotImplementedError()
 
-    def bbox(self):
-        raise NotImplementedError()
+    def get_bbox(self):
+        if self._label is None:
+            raise NotImplementedError()
+        image = self.image
+        cols = np.any(image, axis=0)
+        rows = np.any(image, axis=1)
+        x0, x1 = np.where(cols)[0][[0, -1]]
+        y0, y1 = np.where(rows)[0][[0, -1]]
+        return [x0, y0, x1 - x0, y1 - y0]
+
+    @property
+    def z_order(self):
+        return self._z_order
 
     def __eq__(self, other):
         if not super().__eq__(other):
             return False
         return \
             (self.label == other.label) and \
+            (self.z_order == other.z_order) and \
             (self.image is not None and other.image is not None and \
                 np.all(self.image == other.image))
 
+class RleMask(MaskObject):
+    # pylint: disable=redefined-builtin
+    def __init__(self, rle=None, label=None, z_order=None,
+            id=None, attributes=None, group=None):
+        lazy_decode = self._lazy_decode(rle)
+        super().__init__(image=lazy_decode, label=label, z_order=z_order,
+            id=id, attributes=attributes, group=group)
+
+        self._rle = rle
+    # pylint: enable=redefined-builtin
+
+    @staticmethod
+    def _lazy_decode(rle):
+        from pycocotools import mask as mask_utils
+        return lambda: mask_utils.decode(rle).astype(np.bool)
+
+    def area(self):
+        from pycocotools import mask as mask_utils
+        return mask_utils.area(self._rle)
+
+    def bbox(self):
+        from pycocotools import mask as mask_utils
+        return mask_utils.toBbox(self._rle)
+
+    @property
+    def rle(self):
+        return self._rle
+
+    def __eq__(self, other):
+        if not isinstance(other, __class__):
+            return super().__eq__(other)
+        return self._rle == other._rle
+
 def compute_iou(bbox_a, bbox_b):
     aX, aY, aW, aH = bbox_a
     bX, bY, bW, bH = bbox_b
@@ -217,12 +268,16 @@ def compute_iou(bbox_a, bbox_b):
 
 class ShapeObject(Annotation):
     # pylint: disable=redefined-builtin
-    def __init__(self, type, points=None, label=None,
+    def __init__(self, type, points=None, label=None, z_order=None,
             id=None, attributes=None, group=None):
         super().__init__(id=id, type=type,
             attributes=attributes, group=group)
         self.points = points
         self.label = label
+
+        if z_order is None:
+            z_order = 0
+        self._z_order = z_order
     # pylint: enable=redefined-builtin
 
     def area(self):
@@ -247,22 +302,24 @@ def get_bbox(self):
     def get_points(self):
         return self.points
 
-    def get_mask(self):
-        raise NotImplementedError()
+    @property
+    def z_order(self):
+        return self._z_order
 
     def __eq__(self, other):
         if not super().__eq__(other):
             return False
         return \
             (self.points == other.points) and \
+            (self.z_order == other.z_order) and \
             (self.label == other.label)
 
 class PolyLineObject(ShapeObject):
     # pylint: disable=redefined-builtin
-    def __init__(self, points=None,
-            label=None, id=None, attributes=None, group=None):
+    def __init__(self, points=None, label=None, z_order=None,
+            id=None, attributes=None, group=None):
         super().__init__(type=AnnotationType.polyline,
-            points=points, label=label,
+            points=points, label=label, z_order=z_order,
             id=id, attributes=attributes, group=group)
     # pylint: enable=redefined-builtin
 
@@ -274,12 +331,12 @@ def area(self):
 
 class PolygonObject(ShapeObject):
     # pylint: disable=redefined-builtin
-    def __init__(self, points=None,
+    def __init__(self, points=None, z_order=None,
             label=None, id=None, attributes=None, group=None):
         if points is not None:
             assert len(points) % 2 == 0 and 3 <= len(points) // 2, "Wrong polygon points: %s" % points
         super().__init__(type=AnnotationType.polygon,
-            points=points, label=label,
+            points=points, label=label, z_order=z_order,
             id=id, attributes=attributes, group=group)
     # pylint: enable=redefined-builtin
 
@@ -291,15 +348,15 @@ def area(self):
 
         _, _, w, h = self.get_bbox()
         rle = mask_utils.frPyObjects([self.get_points()], h, w)
-        area = mask_utils.area(rle)
+        area = mask_utils.area(rle)[0]
         return area
 
 class BboxObject(ShapeObject):
     # pylint: disable=redefined-builtin
-    def __init__(self, x=0, y=0, w=0, h=0,
-            label=None, id=None, attributes=None, group=None):
+    def __init__(self, x=0, y=0, w=0, h=0, label=None, z_order=None,
+            id=None, attributes=None, group=None):
         super().__init__(type=AnnotationType.bbox,
-            points=[x, y, x + w, y + h], label=label,
+            points=[x, y, x + w, y + h], label=label, z_order=z_order,
             id=id, attributes=attributes, group=group)
     # pylint: enable=redefined-builtin
 
@@ -368,7 +425,7 @@ class PointsObject(ShapeObject):
     ])
 
     # pylint: disable=redefined-builtin
-    def __init__(self, points=None, visibility=None, label=None,
+    def __init__(self, points=None, visibility=None, label=None, z_order=None,
             id=None, attributes=None, group=None):
         if points is not None:
             assert len(points) % 2 == 0
@@ -381,10 +438,10 @@ def __init__(self, points=None, visibility=None, label=None,
             else:
                 visibility = []
                 for _ in range(len(points) // 2):
-                    visibility.append(self.Visibility.absent)
+                    visibility.append(self.Visibility.visible)
 
         super().__init__(type=AnnotationType.points,
-            points=points, label=label,
+            points=points, label=label, z_order=z_order,
             id=id, attributes=attributes, group=group)
 
         self.visibility = visibility
@@ -393,6 +450,17 @@ def __init__(self, points=None, visibility=None, label=None,
     def area(self):
         return 0
 
+    def get_bbox(self):
+        xs = [p for p, v in zip(self.points[0::2], self.visibility)
+            if v != __class__.Visibility.absent]
+        ys = [p for p, v in zip(self.points[1::2], self.visibility)
+            if v != __class__.Visibility.absent]
+        x0 = min(xs, default=0)
+        x1 = max(xs, default=0)
+        y0 = min(ys, default=0)
+        y1 = max(ys, default=0)
+        return [x0, y0, x1 - x0, y1 - y0]
+
     def __eq__(self, other):
         if not super().__eq__(other):
             return False

datumaro/datumaro/components/extractors/ms_coco.py

@@ -4,45 +4,21 @@
 # SPDX-License-Identifier: MIT
 
 from collections import OrderedDict
-from itertools import chain
-import numpy as np
 import os.path as osp
 
 from pycocotools.coco import COCO
 import pycocotools.mask as mask_utils
 
 from datumaro.components.extractor import (Extractor, DatasetItem,
     DEFAULT_SUBSET_NAME, AnnotationType,
-    LabelObject, MaskObject, PointsObject, PolygonObject,
+    LabelObject, RleMask, PointsObject, PolygonObject,
     BboxObject, CaptionObject,
     LabelCategories, PointsCategories
 )
 from datumaro.components.formats.ms_coco import CocoTask, CocoPath
 from datumaro.util.image import lazy_image
 
 
-class RleMask(MaskObject):
-    # pylint: disable=redefined-builtin
-    def __init__(self, rle=None, label=None,
-            id=None, attributes=None, group=None):
-        lazy_decode = lambda: mask_utils.decode(rle).astype(np.bool)
-        super().__init__(image=lazy_decode, label=label,
-            id=id, attributes=attributes, group=group)
-
-        self._rle = rle
-    # pylint: enable=redefined-builtin
-
-    def area(self):
-        return mask_utils.area(self._rle)
-
-    def bbox(self):
-        return mask_utils.toBbox(self._rle)
-
-    def __eq__(self, other):
-        if not isinstance(other, __class__):
-            return super().__eq__(other)
-        return self._rle == other._rle
-
 class CocoExtractor(Extractor):
     def __init__(self, path, task, merge_instance_polygons=False):
         super().__init__()
@@ -144,8 +120,7 @@ def _load_items(self, loader):
 
             anns = loader.getAnnIds(imgIds=img_id)
             anns = loader.loadAnns(anns)
-            anns = list(chain(*(
-                self._load_annotations(ann, image_info) for ann in anns)))
+            anns = sum((self._load_annotations(a, image_info) for a in anns), [])
 
             items[img_id] = DatasetItem(id=img_id, subset=self._subset,
                 image=image, annotations=anns)
@@ -167,25 +142,34 @@ def _load_annotations(self, ann, image_info=None):
         if 'score' in ann:
             attributes['score'] = ann['score']
 
-        if self._task is CocoTask.instances:
+        group = ann_id # make sure all tasks' annotations are merged
+
+        if self._task in [CocoTask.instances, CocoTask.person_keypoints]:
             x, y, w, h = ann['bbox']
             label_id = self._get_label_id(ann)
-            group = None
 
             is_crowd = bool(ann['iscrowd'])
             attributes['is_crowd'] = is_crowd
 
+            if self._task is CocoTask.person_keypoints:
+                keypoints = ann['keypoints']
+                points = [p for i, p in enumerate(keypoints) if i % 3 != 2]
+                visibility = keypoints[2::3]
+                parsed_annotations.append(
+                    PointsObject(points, visibility, label=label_id,
+                        id=ann_id, attributes=attributes, group=group)
+                )
+
             segmentation = ann.get('segmentation')
             if segmentation is not None:
-                group = ann_id
                 rle = None
 
                 if isinstance(segmentation, list):
                     # polygon - a single object can consist of multiple parts
                     for polygon_points in segmentation:
                         parsed_annotations.append(PolygonObject(
                             points=polygon_points, label=label_id,
-                            id=ann_id, group=group, attributes=attributes
+                            id=ann_id, attributes=attributes, group=group
                         ))
 
                     if self._merge_instance_polygons:
@@ -204,7 +188,7 @@ def _load_annotations(self, ann, image_info=None):
 
                 if rle is not None:
                     parsed_annotations.append(RleMask(rle=rle, label=label_id,
-                        id=ann_id, group=group, attributes=attributes
+                        id=ann_id, attributes=attributes, group=group
                     ))
 
             parsed_annotations.append(
@@ -214,30 +198,14 @@ def _load_annotations(self, ann, image_info=None):
         elif self._task is CocoTask.labels:
             label_id = self._get_label_id(ann)
             parsed_annotations.append(
-                LabelObject(label=label_id, id=ann_id, attributes=attributes)
-            )
-        elif self._task is CocoTask.person_keypoints:
-            keypoints = ann['keypoints']
-            points = [p for i, p in enumerate(keypoints) if i % 3 != 2]
-            visibility = keypoints[2::3]
-            bbox = ann.get('bbox')
-            label_id = self._get_label_id(ann)
-            group = None
-            if bbox is not None:
-                group = ann_id
-            parsed_annotations.append(
-                PointsObject(points, visibility, label=label_id,
+                LabelObject(label=label_id,
                     id=ann_id, attributes=attributes, group=group)
             )
-            if bbox is not None:
-                parsed_annotations.append(
-                    BboxObject(*bbox, label=label_id, group=group)
-                )
         elif self._task is CocoTask.captions:
             caption = ann['caption']
             parsed_annotations.append(
                 CaptionObject(caption,
-                    id=ann_id, attributes=attributes)
+                    id=ann_id, attributes=attributes, group=group)
             )
         else:
             raise NotImplementedError()