Migrate filter_oob into inputs.py

PiperOrigin-RevId: 655319877

ffn/training/inputs.py

@@ -22,6 +22,7 @@
 from connectomics.common import bounding_box
 from connectomics.common import box_generator
 from connectomics.segmentation import labels as label_utils
+from connectomics.volume import metadata
 from ffn.training import augmentation
 from ffn.training import variables
 import numpy as np
@@ -33,13 +34,11 @@ def create_filename_queue(coordinates_file_pattern, shuffle=True):
   """Creates a queue for reading coordinates from coordinate file.
 
   Args:
-    coordinates_file_pattern: File pattern for TFRecords of
-                              input examples of the form of a glob
-                              pattern or path@shards
-                              or comma-separated file patterns.
+    coordinates_file_pattern: File pattern for TFRecords of input examples of
+      the form of a glob pattern or path@shards or comma-separated file
+      patterns.
     shuffle: Whether to shuffle the coordinate file list. Note that the expanded
-             coordinates_file_pattern is not guaranteed to be sorted
-             alphabetically.
+      coordinates_file_pattern is not guaranteed to be sorted alphabetically.
 
   Returns:
     Tensorflow queue with coordinate filenames
@@ -702,3 +701,91 @@ def sample(
   if repeat:
     sampled_dataset = sampled_dataset.repeat()
   return sampled_dataset
+
+
+def coordinates_in_bounds(
+    coordinates: tf.Tensor,
+    volname: tf.Tensor,
+    radius: Sequence[int],
+    volinfo_map_string: str,
+    use_bboxes: bool = True,
+    name: str = 'coordinates_in_bounds',
+) -> tf.Tensor:
+  """Tensorflow Python Op returning boolean whether coordinates are in bounds.
+
+  Args:
+    coordinates: int64 Tensor of shape `[1, 3]` representing center coordinates
+      from which to retrieve patches.
+    volname: string Tensor of shape `[1]` giving volume from which patch should
+      be retrieved.
+    radius: length 3 sequence indicating the radius of the patches to be
+      retrieved around each coordinates (xyz).
+    volinfo_map_string: comma delimited string mapping volname:volinfo_path,
+      where volinfo_path points to the metadata of the volume from which 
+      patches should be extracted.
+    use_bboxes: whether to use the bounding boxes declared in the volume; if
+      False, the physical size of the volume is used as the bounding box.
+    name: passed to name_scope.
+
+  Returns:
+    Boolean scalar Tensor indicating whether the patch specified by coordinates
+    and radius fits within the volume specified by volname and
+    volinfo_map_string.  This can be passed to tf.cond to select either
+    coordinates or an empty constant of shape `[0, 3]`, which can then be
+    passed to batching (e.g. see tests).
+  """
+  boxes_by_volname = {}
+  for mapping in volinfo_map_string.split(','):
+    k, volinfo_path = mapping.split(':')
+    k = k.encode('utf-8')
+    assert k not in boxes_by_volname
+
+    if volinfo_path.endswith('metadata.json'):
+      f = open(volinfo_path, 'r')
+      meta = metadata.VolumeMetadata.from_json(f.read())
+      if use_bboxes:
+        bboxes = meta.bounding_boxes
+      else:
+        bboxes = [
+            bounding_box.BoundingBox(
+                (0, 0, 0),
+                (meta.volume_size.x, meta.volume_size.y, meta.volume_size.z),
+            )
+        ]
+      boxes_by_volname[k] = bboxes
+
+  if not boxes_by_volname:
+    raise ValueError('boxes_by_volname is empty.')
+
+  def _in_bounds_fn(coordinates, volname):
+    boxes = boxes_by_volname[volname[0]]
+    patch_start = np.array(coordinates) - radius
+    patch_back = np.array(coordinates) + radius
+    for box in boxes:
+      if (box.start <= patch_start).all() and (box.end > patch_back).all():
+        return True
+    return False
+
+  with tf.name_scope(name, values=[coordinates, volname]) as scope:
+    assert coordinates.shape_as_list() == [1, 3]
+    assert volname.shape_as_list() == [1]
+    in_bounds = tf.py_func(
+        _in_bounds_fn,
+        [coordinates, volname],
+        [tf.bool],
+        name=scope,
+        stateful=False,
+    )[0]
+    in_bounds.set_shape([])
+    return in_bounds
+
+
+def filter_oob(
+    item: dict[str, tf.Tensor], volinfo_map_string: str, patch_size: list[int],
+    use_bboxes: bool = True
+) -> tf.Tensor:
+  radius = np.floor_divide(patch_size, 2)
+  return coordinates_in_bounds(
+      item['coord'], item['volname'], radius, volinfo_map_string,
+      use_bboxes
+  )