Remove private _add_tiles

pathml/core/h5managers.py

@@ -254,9 +254,10 @@ def remove_tile(self, key):
  """
  if not isinstance(key, (str, tuple)):
  raise KeyError(f"key must be str or tuple, check valid keys in repr")
- if str(key) not in self.h5["tiles"].keys():
- raise KeyError(f"key {key} is not in Tiles")
- del self.h5["tiles"][str(key)]
+ if str(key) in self.h5["tiles"].keys():
+ del self.h5["tiles"][str(key)]
+ else:
+ logger.info((f"key {key} is not in Tiles")
 
  def add_mask(self, key, mask):
  """

pathml/core/slide_data.py

@@ -176,19 +176,19 @@ def __init__(
  _load_from_h5path = True
 
  if backend.lower() == "openslide":
- backend_obj = pathml.core.OpenSlideBackend(filepath)
+ slide = pathml.core.OpenSlideBackend(filepath)
  elif backend.lower() == "bioformats":
- backend_obj = pathml.core.BioFormatsBackend(filepath, dtype)
+ slide = pathml.core.BioFormatsBackend(filepath, dtype)
  elif backend.lower() == "dicom":
- backend_obj = pathml.core.DICOMBackend(filepath)
+ slide = pathml.core.DICOMBackend(filepath)
  elif backend.lower() == "h5path":
- backend_obj = None
+ slide = None
  else:
  raise ValueError(f"invalid backend: {repr(backend)}.")
 
  self._filepath = filepath if filepath else None
  self.backend = backend
- self.slide = backend_obj if backend_obj else None
+ self.slide = slide
  self.name = name
  self.labels = labels
  self.slide_type = slide_type
@@ -223,8 +223,8 @@ def __init__(
 
  self.masks = pathml.core.Masks(h5manager=self.h5manager, masks=masks)
  self.tiles = pathml.core.Tiles(h5manager=self.h5manager, tiles=tiles)
- self._add_tiles = tiles is None and not _load_from_h5path
 
+ self._generated_tiles = False
  self.tile_size = tile_size
  self._tile_stride = tile_stride
  self.tile_level = tile_level
@@ -245,7 +245,8 @@ def tile_stride(self, value):
  self._tile_stride = value
 
  def get_tiles(self):
- if self._add_tiles:
+ if self.slide is None and not self._generated_tiles:
+ self._generated_tiles = True
  for tile in self._generate_tiles():
  yield tile
  else:
@@ -307,9 +308,6 @@ def run(
  assert isinstance(
  pipeline, pathml.preprocessing.pipeline.Pipeline
  ), f"pipeline is of type {type(pipeline)} but must be of type pathml.preprocessing.pipeline.Pipeline"
- assert (
- self.slide is not None or not self._add_tiles
- ), "cannot run pipeline because self.slide is None and no tiles already exist"
 
  shutdown_after = False
 
@@ -329,13 +327,13 @@ def run(
  futures, with_results=True, raise_errors=False
  ):
  if future.status == "finished":
- if self._add_tiles:
- self.tiles.add(result)
+ self.tiles.add(result)
  if future.status == "error":
  typ, exc, tb = result
  if typ is DropTileException:
- # TODO: remove tile if it already is in Tiles
- # TODO: figure out how to access tile.coords; need to get input that led to exception...
+ # TODO: remove existing tiles
+ # figure out how to access tile.coords from input tile
+ # self.tiles.remove(tile.coords)
  pass
  else:
  raise exc.with_traceback(tb)
@@ -362,15 +360,11 @@ def run(
  try:
  pipeline.apply(tile)
  except DropTileException:
- if not self._add_tiles:
- self.tiles.remove(tile.coords)
- if self._add_tiles:
- self.tiles.add(tile)
+ self.tiles.remove(tile.coords)
+ self.tiles.add(tile)
 
  if write_dir:
  self.write(Path(write_dir) / f"{self.name}.h5path")
- # Tiles generated after pipeline run
- self._add_tiles = False
 
  @property
  def shape(self):