Improves get_channels

src/spatialdata_plot/pp/basic.py

@@ -2,6 +2,8 @@
 
 import spatialdata as sd
 from anndata import AnnData
+import pandas as pd
+
 
 from ..accessor import register_spatial_data_accessor
 from .colorize import _colorize
@@ -23,12 +25,12 @@ def _copy(
  shapes: Union[None, dict] = None,
  table: Union[dict, AnnData] = None,
  ) -> sd.SpatialData:
-
+
  """
  Helper function to copies the references from the original SpatialData
  object to the subsetted SpatialData object.
  """
-
+
  return sd.SpatialData(
  images=self._sdata.images if images is None else images,
  labels=self._sdata.labels if labels is None else labels,
@@ -39,76 +41,74 @@ def _copy(
  )
 
  def get_region_key(self) -> str:
-
+
  "Quick access to the data's region key."
-
+
  return self._sdata.table.uns["spatialdata_attrs"]["region_key"]
 
  def get_bb(self, x: Union[slice, list, tuple], y: Union[slice, list, tuple]) -> sd.SpatialData:
-
+
  """Get bounding box around a point.
 
  Parameters
  ----------
  x : Union[slice, list, tuple]
- x range of the bounding box
+ x range of the bounding box. Stepsize will be ignored if slice
  y : Union[slice, list, tuple]
- y range of the bounding box
+ y range of the bounding box. Stepsize will be ignored if slice
 
  Returns
  -------
  sd.SpatialData
  subsetted SpatialData object
  """
-
+
  if not isinstance(x, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'x' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(x, (list, tuple)):
-
+
  if len(x) != 2:
-
+
  raise ValueError("Parameter 'x' must be of length 2.")
-
+
  if x[1] <= x[0]:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
+
  # x is clean
  x = slice(x[0], x[1])
-
+
  elif isinstance(x, slice):
-
+
  if x.stop <= x.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  if not isinstance(y, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'y' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(y, (list, tuple)):
-
+
  if len(y) != 2:
-
+
  raise ValueError("Parameter 'y' must be of length 2.")
-
+
  if y[1] <= y[0]:
-
+
  raise ValueError("The current choice of 'y' would result in an empty slice.")
-
+
  # y is clean
  y = slice(y[0], y[1])
-
+
  elif isinstance(y, slice):
-
+
  if y.stop <= y.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  selection = dict(x=x, y=y) # makes use of xarray sel method
 
  # TODO: error handling if selection is out of bounds
@@ -138,26 +138,26 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  # TODO: error handling if keys are not in images
 
  if not isinstance(keys, (list, str)):
-
+
  raise TypeError("Parameter 'keys' must either be of type 'str' or 'list'.")
 
- if isinstance(keys, list):
-
+ if isinstance(keys, list):
+
  if not all([isinstance(key, str) for key in keys]):
-
+
  raise TypeError("All elements in 'keys' must be of type 'str'.")
 
  if isinstance(keys, str):
  keys = [keys]
-
+
  assert all([isinstance(key, str) for key in keys])
-
+
  valid_keys = list(self._sdata.images.keys())
-
+
  for key in keys:
-
+
  if key not in valid_keys:
-
+
  raise ValueError(f"Key '{key}' is not a valid key. Valid choices are: " + ", ".join(valid_keys))
 
  selected_images = {key: img for key, img in self._sdata.images.items() if key in keys}
@@ -168,35 +168,67 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  new_table = None
  # make sure that table exists
  if hasattr(self._sdata, "table"):
-
+
  if hasattr(self._sdata.table, "obs"):
-
+
  # create mask of used keys
  mask = self._sdata.table.obs[self._sdata.pp.get_region_key()]
  mask = list(mask.str.contains("|".join(keys)))
  # print(mask)
-
+
  new_table = self._sdata.table[mask, :]
-
 
  return self._copy(images=selected_images, labels=selected_labels, table=new_table)
 
- def get_channels(self, keys: Union[list, slice]) -> sd.SpatialData:
- """Get channels from a list of keys.
+ def get_channels(self, channels: Union[list, slice]) -> sd.SpatialData:
+ """Subset a spatialdata object to the selected channels.
 
- Parameters
- ----------
- keys : list
- list of keys to select
+ Images that don't have the selected channels will be dropped.
 
- Returns
- -------
- sd.SpatialData
- subsetted SpatialData object
  """
- selection = dict(c=keys)
- # TODO: error handling if selection is out of bounds
- channels_images = {key: img.sel(selection) for key, img in self._sdata.images.items()}
+
+ if not isinstance(channels, (list, slice)):
+
+ raise TypeError("Parameter 'channels' must either be of type 'list' or 'slice'.")
+
+ if isinstance(channels, list):
+
+ if not all([isinstance(channel, int) for channel in channels]):
+
+ raise TypeError("All elements in 'channels' must be of type 'int'.")
+
+ if isinstance(channels, list):
+
+ if not len(channels) > 0:
+
+ raise ValueError("The list of channels cannot be empty.")
+
+ # validate that selection is within bounds
+ # 1) parse slice into list, respecting stepsize
+ if isinstance(channels, slice):
+
+ channels = [x for x in range(start=channels.start, stop=channels.stop, step=channels.step or 1)]
+
+ # 2) check which images have how many channels
+ image_names = []
+ n_channels = []
+ for image_name, image in self._sdata.images.items():
+ image_names.append(image_name)
+ n_channels.append(image.shape[0])
+
+ channels_in_image = pd.DataFrame({"image_name": image_names, "n_channels": n_channels})
+
+ # 3) drop images that don't have enough channels for the selection
+ channels_in_image = channels_in_image[channels_in_image.n_channels - 1 >= max(channels)]
+ valid_images = channels_in_image.image_name.values.tolist()
+ sdata_with_valid_images = self._sdata.pp.get_images(keys=valid_images)
+
+ if len(sdata_with_valid_images.images.keys()) < 1:
+
+ raise ValueError("The choice of channels results in an empty selection.")
+
+ selected_channels = dict(c=channels)
+ channels_images = {key: img.sel(selected_channels) for key, img in self._sdata.images.items()}
 
  return self._copy(images=channels_images)
 

src/spatialdata_plot/pp/basic.py

@@ -2,6 +2,8 @@
 
 import spatialdata as sd
 from anndata import AnnData
+import pandas as pd
+
 
 from ..accessor import register_spatial_data_accessor
 from .colorize import _colorize
@@ -23,12 +25,12 @@ def _copy(
  shapes: Union[None, dict] = None,
  table: Union[dict, AnnData] = None,
  ) -> sd.SpatialData:
-
+
  """
  Helper function to copies the references from the original SpatialData
  object to the subsetted SpatialData object.
  """
-
+
  return sd.SpatialData(
  images=self._sdata.images if images is None else images,
  labels=self._sdata.labels if labels is None else labels,
@@ -39,76 +41,74 @@ def _copy(
  )
 
  def get_region_key(self) -> str:
-
+
  "Quick access to the data's region key."
-
+
  return self._sdata.table.uns["spatialdata_attrs"]["region_key"]
 
  def get_bb(self, x: Union[slice, list, tuple], y: Union[slice, list, tuple]) -> sd.SpatialData:
-
+
  """Get bounding box around a point.
 
  Parameters
  ----------
  x : Union[slice, list, tuple]
- x range of the bounding box
+ x range of the bounding box. Stepsize will be ignored if slice
  y : Union[slice, list, tuple]
- y range of the bounding box
+ y range of the bounding box. Stepsize will be ignored if slice
 
  Returns
  -------
  sd.SpatialData
  subsetted SpatialData object
  """
-
+
  if not isinstance(x, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'x' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(x, (list, tuple)):
-
+
  if len(x) != 2:
-
+
  raise ValueError("Parameter 'x' must be of length 2.")
-
+
  if x[1] <= x[0]:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
+
  # x is clean
  x = slice(x[0], x[1])
-
+
  elif isinstance(x, slice):
-
+
  if x.stop <= x.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  if not isinstance(y, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'y' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(y, (list, tuple)):
-
+
  if len(y) != 2:
-
+
  raise ValueError("Parameter 'y' must be of length 2.")
-
+
  if y[1] <= y[0]:
-
+
  raise ValueError("The current choice of 'y' would result in an empty slice.")
-
+
  # y is clean
  y = slice(y[0], y[1])
-
+
  elif isinstance(y, slice):
-
+
  if y.stop <= y.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  selection = dict(x=x, y=y) # makes use of xarray sel method
 
  # TODO: error handling if selection is out of bounds
@@ -138,26 +138,26 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  # TODO: error handling if keys are not in images
 
  if not isinstance(keys, (list, str)):
-
+
  raise TypeError("Parameter 'keys' must either be of type 'str' or 'list'.")
 
- if isinstance(keys, list):
-
+ if isinstance(keys, list):
+
  if not all([isinstance(key, str) for key in keys]):
-
+
  raise TypeError("All elements in 'keys' must be of type 'str'.")
 
  if isinstance(keys, str):
  keys = [keys]
-
+
  assert all([isinstance(key, str) for key in keys])
-
+
  valid_keys = list(self._sdata.images.keys())
-
+
  for key in keys:
-
+
  if key not in valid_keys:
-
+
  raise ValueError(f"Key '{key}' is not a valid key. Valid choices are: " + ", ".join(valid_keys))
 
  selected_images = {key: img for key, img in self._sdata.images.items() if key in keys}
@@ -168,35 +168,67 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  new_table = None
  # make sure that table exists
  if hasattr(self._sdata, "table"):
-
+
  if hasattr(self._sdata.table, "obs"):
-
+
  # create mask of used keys
  mask = self._sdata.table.obs[self._sdata.pp.get_region_key()]
  mask = list(mask.str.contains("|".join(keys)))
  # print(mask)
-
+
  new_table = self._sdata.table[mask, :]
-
 
  return self._copy(images=selected_images, labels=selected_labels, table=new_table)
 
- def get_channels(self, keys: Union[list, slice]) -> sd.SpatialData:
- """Get channels from a list of keys.
+ def get_channels(self, channels: Union[list, slice]) -> sd.SpatialData:
+ """Subset a spatialdata object to the selected channels.
 
- Parameters
- ----------
- keys : list
- list of keys to select
+ Images that don't have the selected channels will be dropped.
 
- Returns
- -------
- sd.SpatialData
- subsetted SpatialData object
  """
- selection = dict(c=keys)
- # TODO: error handling if selection is out of bounds
- channels_images = {key: img.sel(selection) for key, img in self._sdata.images.items()}
+
+ if not isinstance(channels, (list, slice)):
+
+ raise TypeError("Parameter 'channels' must either be of type 'list' or 'slice'.")
+
+ if isinstance(channels, list):
+
+ if not all([isinstance(channel, int) for channel in channels]):
+
+ raise TypeError("All elements in 'channels' must be of type 'int'.")
+
+ if isinstance(channels, list):
+
+ if not len(channels) > 0:
+
+ raise ValueError("The list of channels cannot be empty.")
+
+ # validate that selection is within bounds
+ # 1) parse slice into list, respecting stepsize
+ if isinstance(channels, slice):
+
+ channels = [x for x in range(start=channels.start, stop=channels.stop, step=channels.step or 1)]
+
+ # 2) check which images have how many channels
+ image_names = []
+ n_channels = []
+ for image_name, image in self._sdata.images.items():
+ image_names.append(image_name)
+ n_channels.append(image.shape[0])
+
+ channels_in_image = pd.DataFrame({"image_name": image_names, "n_channels": n_channels})
+
+ # 3) drop images that don't have enough channels for the selection
+ channels_in_image = channels_in_image[channels_in_image.n_channels - 1 >= max(channels)]
+ valid_images = channels_in_image.image_name.values.tolist()
+ sdata_with_valid_images = self._sdata.pp.get_images(keys=valid_images)
+
+ if len(sdata_with_valid_images.images.keys()) < 1:
+
+ raise ValueError("The choice of channels results in an empty selection.")
+
+ selected_channels = dict(c=channels)
+ channels_images = {key: img.sel(selected_channels) for key, img in self._sdata.images.items()}
 
  return self._copy(images=channels_images)
 

src/spatialdata_plot/pp/basic.py

@@ -2,6 +2,8 @@
 
 import spatialdata as sd
 from anndata import AnnData
+import pandas as pd
+
 
 from ..accessor import register_spatial_data_accessor
 from .colorize import _colorize
@@ -23,12 +25,12 @@ def _copy(
  shapes: Union[None, dict] = None,
  table: Union[dict, AnnData] = None,
  ) -> sd.SpatialData:
-
+
  """
  Helper function to copies the references from the original SpatialData
  object to the subsetted SpatialData object.
  """
-
+
  return sd.SpatialData(
  images=self._sdata.images if images is None else images,
  labels=self._sdata.labels if labels is None else labels,
@@ -39,76 +41,74 @@ def _copy(
  )
 
  def get_region_key(self) -> str:
-
+
  "Quick access to the data's region key."
-
+
  return self._sdata.table.uns["spatialdata_attrs"]["region_key"]
 
  def get_bb(self, x: Union[slice, list, tuple], y: Union[slice, list, tuple]) -> sd.SpatialData:
-
+
  """Get bounding box around a point.
 
  Parameters
  ----------
  x : Union[slice, list, tuple]
- x range of the bounding box
+ x range of the bounding box. Stepsize will be ignored if slice
  y : Union[slice, list, tuple]
- y range of the bounding box
+ y range of the bounding box. Stepsize will be ignored if slice
 
  Returns
  -------
  sd.SpatialData
  subsetted SpatialData object
  """
-
+
  if not isinstance(x, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'x' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(x, (list, tuple)):
-
+
  if len(x) != 2:
-
+
  raise ValueError("Parameter 'x' must be of length 2.")
-
+
  if x[1] <= x[0]:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
+
  # x is clean
  x = slice(x[0], x[1])
-
+
  elif isinstance(x, slice):
-
+
  if x.stop <= x.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  if not isinstance(y, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'y' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(y, (list, tuple)):
-
+
  if len(y) != 2:
-
+
  raise ValueError("Parameter 'y' must be of length 2.")
-
+
  if y[1] <= y[0]:
-
+
  raise ValueError("The current choice of 'y' would result in an empty slice.")
-
+
  # y is clean
  y = slice(y[0], y[1])
-
+
  elif isinstance(y, slice):
-
+
  if y.stop <= y.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  selection = dict(x=x, y=y) # makes use of xarray sel method
 
  # TODO: error handling if selection is out of bounds
@@ -138,26 +138,26 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  # TODO: error handling if keys are not in images
 
  if not isinstance(keys, (list, str)):
-
+
  raise TypeError("Parameter 'keys' must either be of type 'str' or 'list'.")
 
- if isinstance(keys, list):
-
+ if isinstance(keys, list):
+
  if not all([isinstance(key, str) for key in keys]):
-
+
  raise TypeError("All elements in 'keys' must be of type 'str'.")
 
  if isinstance(keys, str):
  keys = [keys]
-
+
  assert all([isinstance(key, str) for key in keys])
-
+
  valid_keys = list(self._sdata.images.keys())
-
+
  for key in keys:
-
+
  if key not in valid_keys:
-
+
  raise ValueError(f"Key '{key}' is not a valid key. Valid choices are: " + ", ".join(valid_keys))
 
  selected_images = {key: img for key, img in self._sdata.images.items() if key in keys}
@@ -168,35 +168,67 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  new_table = None
  # make sure that table exists
  if hasattr(self._sdata, "table"):
-
+
  if hasattr(self._sdata.table, "obs"):
-
+
  # create mask of used keys
  mask = self._sdata.table.obs[self._sdata.pp.get_region_key()]
  mask = list(mask.str.contains("|".join(keys)))
  # print(mask)
-
+
  new_table = self._sdata.table[mask, :]
-
 
  return self._copy(images=selected_images, labels=selected_labels, table=new_table)
 
- def get_channels(self, keys: Union[list, slice]) -> sd.SpatialData:
- """Get channels from a list of keys.
+ def get_channels(self, channels: Union[list, slice]) -> sd.SpatialData:
+ """Subset a spatialdata object to the selected channels.
 
- Parameters
- ----------
- keys : list
- list of keys to select
+ Images that don't have the selected channels will be dropped.
 
- Returns
- -------
- sd.SpatialData
- subsetted SpatialData object
  """
- selection = dict(c=keys)
- # TODO: error handling if selection is out of bounds
- channels_images = {key: img.sel(selection) for key, img in self._sdata.images.items()}
+
+ if not isinstance(channels, (list, slice)):
+
+ raise TypeError("Parameter 'channels' must either be of type 'list' or 'slice'.")
+
+ if isinstance(channels, list):
+
+ if not all([isinstance(channel, int) for channel in channels]):
+
+ raise TypeError("All elements in 'channels' must be of type 'int'.")
+
+ if isinstance(channels, list):
+
+ if not len(channels) > 0:
+
+ raise ValueError("The list of channels cannot be empty.")
+
+ # validate that selection is within bounds
+ # 1) parse slice into list, respecting stepsize
+ if isinstance(channels, slice):
+
+ channels = [x for x in range(start=channels.start, stop=channels.stop, step=channels.step or 1)]
+
+ # 2) check which images have how many channels
+ image_names = []
+ n_channels = []
+ for image_name, image in self._sdata.images.items():
+ image_names.append(image_name)
+ n_channels.append(image.shape[0])
+
+ channels_in_image = pd.DataFrame({"image_name": image_names, "n_channels": n_channels})
+
+ # 3) drop images that don't have enough channels for the selection
+ channels_in_image = channels_in_image[channels_in_image.n_channels - 1 >= max(channels)]
+ valid_images = channels_in_image.image_name.values.tolist()
+ sdata_with_valid_images = self._sdata.pp.get_images(keys=valid_images)
+
+ if len(sdata_with_valid_images.images.keys()) < 1:
+
+ raise ValueError("The choice of channels results in an empty selection.")
+
+ selected_channels = dict(c=channels)
+ channels_images = {key: img.sel(selected_channels) for key, img in self._sdata.images.items()}
 
  return self._copy(images=channels_images)
 

src/spatialdata_plot/pp/basic.py

@@ -2,6 +2,8 @@
 
 import spatialdata as sd
 from anndata import AnnData
+import pandas as pd
+
 
 from ..accessor import register_spatial_data_accessor
 from .colorize import _colorize
@@ -23,12 +25,12 @@ def _copy(
  shapes: Union[None, dict] = None,
  table: Union[dict, AnnData] = None,
  ) -> sd.SpatialData:
-
+
  """
  Helper function to copies the references from the original SpatialData
  object to the subsetted SpatialData object.
  """
-
+
  return sd.SpatialData(
  images=self._sdata.images if images is None else images,
  labels=self._sdata.labels if labels is None else labels,
@@ -39,76 +41,74 @@ def _copy(
  )
 
  def get_region_key(self) -> str:
-
+
  "Quick access to the data's region key."
-
+
  return self._sdata.table.uns["spatialdata_attrs"]["region_key"]
 
  def get_bb(self, x: Union[slice, list, tuple], y: Union[slice, list, tuple]) -> sd.SpatialData:
-
+
  """Get bounding box around a point.
 
  Parameters
  ----------
  x : Union[slice, list, tuple]
- x range of the bounding box
+ x range of the bounding box. Stepsize will be ignored if slice
  y : Union[slice, list, tuple]
- y range of the bounding box
+ y range of the bounding box. Stepsize will be ignored if slice
 
  Returns
  -------
  sd.SpatialData
  subsetted SpatialData object
  """
-
+
  if not isinstance(x, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'x' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(x, (list, tuple)):
-
+
  if len(x) != 2:
-
+
  raise ValueError("Parameter 'x' must be of length 2.")
-
+
  if x[1] <= x[0]:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
+
  # x is clean
  x = slice(x[0], x[1])
-
+
  elif isinstance(x, slice):
-
+
  if x.stop <= x.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  if not isinstance(y, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'y' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(y, (list, tuple)):
-
+
  if len(y) != 2:
-
+
  raise ValueError("Parameter 'y' must be of length 2.")
-
+
  if y[1] <= y[0]:
-
+
  raise ValueError("The current choice of 'y' would result in an empty slice.")
-
+
  # y is clean
  y = slice(y[0], y[1])
-
+
  elif isinstance(y, slice):
-
+
  if y.stop <= y.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  selection = dict(x=x, y=y) # makes use of xarray sel method
 
  # TODO: error handling if selection is out of bounds
@@ -138,26 +138,26 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  # TODO: error handling if keys are not in images
 
  if not isinstance(keys, (list, str)):
-
+
  raise TypeError("Parameter 'keys' must either be of type 'str' or 'list'.")
 
- if isinstance(keys, list):
-
+ if isinstance(keys, list):
+
  if not all([isinstance(key, str) for key in keys]):
-
+
  raise TypeError("All elements in 'keys' must be of type 'str'.")
 
  if isinstance(keys, str):
  keys = [keys]
-
+
  assert all([isinstance(key, str) for key in keys])
-
+
  valid_keys = list(self._sdata.images.keys())
-
+
  for key in keys:
-
+
  if key not in valid_keys:
-
+
  raise ValueError(f"Key '{key}' is not a valid key. Valid choices are: " + ", ".join(valid_keys))
 
  selected_images = {key: img for key, img in self._sdata.images.items() if key in keys}
@@ -168,35 +168,67 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  new_table = None
  # make sure that table exists
  if hasattr(self._sdata, "table"):
-
+
  if hasattr(self._sdata.table, "obs"):
-
+
  # create mask of used keys
  mask = self._sdata.table.obs[self._sdata.pp.get_region_key()]
  mask = list(mask.str.contains("|".join(keys)))
  # print(mask)
-
+
  new_table = self._sdata.table[mask, :]
-
 
  return self._copy(images=selected_images, labels=selected_labels, table=new_table)
 
- def get_channels(self, keys: Union[list, slice]) -> sd.SpatialData:
- """Get channels from a list of keys.
+ def get_channels(self, channels: Union[list, slice]) -> sd.SpatialData:
+ """Subset a spatialdata object to the selected channels.
 
- Parameters
- ----------
- keys : list
- list of keys to select
+ Images that don't have the selected channels will be dropped.
 
- Returns
- -------
- sd.SpatialData
- subsetted SpatialData object
  """
- selection = dict(c=keys)
- # TODO: error handling if selection is out of bounds
- channels_images = {key: img.sel(selection) for key, img in self._sdata.images.items()}
+
+ if not isinstance(channels, (list, slice)):
+
+ raise TypeError("Parameter 'channels' must either be of type 'list' or 'slice'.")
+
+ if isinstance(channels, list):
+
+ if not all([isinstance(channel, int) for channel in channels]):
+
+ raise TypeError("All elements in 'channels' must be of type 'int'.")
+
+ if isinstance(channels, list):
+
+ if not len(channels) > 0:
+
+ raise ValueError("The list of channels cannot be empty.")
+
+ # validate that selection is within bounds
+ # 1) parse slice into list, respecting stepsize
+ if isinstance(channels, slice):
+
+ channels = [x for x in range(start=channels.start, stop=channels.stop, step=channels.step or 1)]
+
+ # 2) check which images have how many channels
+ image_names = []
+ n_channels = []
+ for image_name, image in self._sdata.images.items():
+ image_names.append(image_name)
+ n_channels.append(image.shape[0])
+
+ channels_in_image = pd.DataFrame({"image_name": image_names, "n_channels": n_channels})
+
+ # 3) drop images that don't have enough channels for the selection
+ channels_in_image = channels_in_image[channels_in_image.n_channels - 1 >= max(channels)]
+ valid_images = channels_in_image.image_name.values.tolist()
+ sdata_with_valid_images = self._sdata.pp.get_images(keys=valid_images)
+
+ if len(sdata_with_valid_images.images.keys()) < 1:
+
+ raise ValueError("The choice of channels results in an empty selection.")
+
+ selected_channels = dict(c=channels)
+ channels_images = {key: img.sel(selected_channels) for key, img in self._sdata.images.items()}
 
  return self._copy(images=channels_images)
 

src/spatialdata_plot/pp/basic.py

@@ -2,6 +2,8 @@
 
 import spatialdata as sd
 from anndata import AnnData
+import pandas as pd
+
 
 from ..accessor import register_spatial_data_accessor
 from .colorize import _colorize
@@ -23,12 +25,12 @@ def _copy(
  shapes: Union[None, dict] = None,
  table: Union[dict, AnnData] = None,
  ) -> sd.SpatialData:
-
+
  """
  Helper function to copies the references from the original SpatialData
  object to the subsetted SpatialData object.
  """
-
+
  return sd.SpatialData(
  images=self._sdata.images if images is None else images,
  labels=self._sdata.labels if labels is None else labels,
@@ -39,76 +41,74 @@ def _copy(
  )
 
  def get_region_key(self) -> str:
-
+
  "Quick access to the data's region key."
-
+
  return self._sdata.table.uns["spatialdata_attrs"]["region_key"]
 
  def get_bb(self, x: Union[slice, list, tuple], y: Union[slice, list, tuple]) -> sd.SpatialData:
-
+
  """Get bounding box around a point.
 
  Parameters
  ----------
  x : Union[slice, list, tuple]
- x range of the bounding box
+ x range of the bounding box. Stepsize will be ignored if slice
  y : Union[slice, list, tuple]
- y range of the bounding box
+ y range of the bounding box. Stepsize will be ignored if slice
 
  Returns
  -------
  sd.SpatialData
  subsetted SpatialData object
  """
-
+
  if not isinstance(x, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'x' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(x, (list, tuple)):
-
+
  if len(x) != 2:
-
+
  raise ValueError("Parameter 'x' must be of length 2.")
-
+
  if x[1] <= x[0]:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
+
  # x is clean
  x = slice(x[0], x[1])
-
+
  elif isinstance(x, slice):
-
+
  if x.stop <= x.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  if not isinstance(y, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'y' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(y, (list, tuple)):
-
+
  if len(y) != 2:
-
+
  raise ValueError("Parameter 'y' must be of length 2.")
-
+
  if y[1] <= y[0]:
-
+
  raise ValueError("The current choice of 'y' would result in an empty slice.")
-
+
  # y is clean
  y = slice(y[0], y[1])
-
+
  elif isinstance(y, slice):
-
+
  if y.stop <= y.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  selection = dict(x=x, y=y) # makes use of xarray sel method
 
  # TODO: error handling if selection is out of bounds
@@ -138,26 +138,26 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  # TODO: error handling if keys are not in images
 
  if not isinstance(keys, (list, str)):
-
+
  raise TypeError("Parameter 'keys' must either be of type 'str' or 'list'.")
 
- if isinstance(keys, list):
-
+ if isinstance(keys, list):
+
  if not all([isinstance(key, str) for key in keys]):
-
+
  raise TypeError("All elements in 'keys' must be of type 'str'.")
 
  if isinstance(keys, str):
  keys = [keys]
-
+
  assert all([isinstance(key, str) for key in keys])
-
+
  valid_keys = list(self._sdata.images.keys())
-
+
  for key in keys:
-
+
  if key not in valid_keys:
-
+
  raise ValueError(f"Key '{key}' is not a valid key. Valid choices are: " + ", ".join(valid_keys))
 
  selected_images = {key: img for key, img in self._sdata.images.items() if key in keys}
@@ -168,35 +168,67 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  new_table = None
  # make sure that table exists
  if hasattr(self._sdata, "table"):
-
+
  if hasattr(self._sdata.table, "obs"):
-
+
  # create mask of used keys
  mask = self._sdata.table.obs[self._sdata.pp.get_region_key()]
  mask = list(mask.str.contains("|".join(keys)))
  # print(mask)
-
+
  new_table = self._sdata.table[mask, :]
-
 
  return self._copy(images=selected_images, labels=selected_labels, table=new_table)
 
- def get_channels(self, keys: Union[list, slice]) -> sd.SpatialData:
- """Get channels from a list of keys.
+ def get_channels(self, channels: Union[list, slice]) -> sd.SpatialData:
+ """Subset a spatialdata object to the selected channels.
 
- Parameters
- ----------
- keys : list
- list of keys to select
+ Images that don't have the selected channels will be dropped.
 
- Returns
- -------
- sd.SpatialData
- subsetted SpatialData object
  """
- selection = dict(c=keys)
- # TODO: error handling if selection is out of bounds
- channels_images = {key: img.sel(selection) for key, img in self._sdata.images.items()}
+
+ if not isinstance(channels, (list, slice)):
+
+ raise TypeError("Parameter 'channels' must either be of type 'list' or 'slice'.")
+
+ if isinstance(channels, list):
+
+ if not all([isinstance(channel, int) for channel in channels]):
+
+ raise TypeError("All elements in 'channels' must be of type 'int'.")
+
+ if isinstance(channels, list):
+
+ if not len(channels) > 0:
+
+ raise ValueError("The list of channels cannot be empty.")
+
+ # validate that selection is within bounds
+ # 1) parse slice into list, respecting stepsize
+ if isinstance(channels, slice):
+
+ channels = [x for x in range(start=channels.start, stop=channels.stop, step=channels.step or 1)]
+
+ # 2) check which images have how many channels
+ image_names = []
+ n_channels = []
+ for image_name, image in self._sdata.images.items():
+ image_names.append(image_name)
+ n_channels.append(image.shape[0])
+
+ channels_in_image = pd.DataFrame({"image_name": image_names, "n_channels": n_channels})
+
+ # 3) drop images that don't have enough channels for the selection
+ channels_in_image = channels_in_image[channels_in_image.n_channels - 1 >= max(channels)]
+ valid_images = channels_in_image.image_name.values.tolist()
+ sdata_with_valid_images = self._sdata.pp.get_images(keys=valid_images)
+
+ if len(sdata_with_valid_images.images.keys()) < 1:
+
+ raise ValueError("The choice of channels results in an empty selection.")
+
+ selected_channels = dict(c=channels)
+ channels_images = {key: img.sel(selected_channels) for key, img in self._sdata.images.items()}
 
  return self._copy(images=channels_images)
 

src/spatialdata_plot/pp/basic.py

@@ -2,6 +2,8 @@
 
 import spatialdata as sd
 from anndata import AnnData
+import pandas as pd
+
 
 from ..accessor import register_spatial_data_accessor
 from .colorize import _colorize
@@ -23,12 +25,12 @@ def _copy(
  shapes: Union[None, dict] = None,
  table: Union[dict, AnnData] = None,
  ) -> sd.SpatialData:
-
+
  """
  Helper function to copies the references from the original SpatialData
  object to the subsetted SpatialData object.
  """
-
+
  return sd.SpatialData(
  images=self._sdata.images if images is None else images,
  labels=self._sdata.labels if labels is None else labels,
@@ -39,76 +41,74 @@ def _copy(
  )
 
  def get_region_key(self) -> str:
-
+
  "Quick access to the data's region key."
-
+
  return self._sdata.table.uns["spatialdata_attrs"]["region_key"]
 
  def get_bb(self, x: Union[slice, list, tuple], y: Union[slice, list, tuple]) -> sd.SpatialData:
-
+
  """Get bounding box around a point.
 
  Parameters
  ----------
  x : Union[slice, list, tuple]
- x range of the bounding box
+ x range of the bounding box. Stepsize will be ignored if slice
  y : Union[slice, list, tuple]
- y range of the bounding box
+ y range of the bounding box. Stepsize will be ignored if slice
 
  Returns
  -------
  sd.SpatialData
  subsetted SpatialData object
  """
-
+
  if not isinstance(x, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'x' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(x, (list, tuple)):
-
+
  if len(x) != 2:
-
+
  raise ValueError("Parameter 'x' must be of length 2.")
-
+
  if x[1] <= x[0]:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
+
  # x is clean
  x = slice(x[0], x[1])
-
+
  elif isinstance(x, slice):
-
+
  if x.stop <= x.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  if not isinstance(y, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'y' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(y, (list, tuple)):
-
+
  if len(y) != 2:
-
+
  raise ValueError("Parameter 'y' must be of length 2.")
-
+
  if y[1] <= y[0]:
-
+
  raise ValueError("The current choice of 'y' would result in an empty slice.")
-
+
  # y is clean
  y = slice(y[0], y[1])
-
+
  elif isinstance(y, slice):
-
+
  if y.stop <= y.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  selection = dict(x=x, y=y) # makes use of xarray sel method
 
  # TODO: error handling if selection is out of bounds
@@ -138,26 +138,26 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  # TODO: error handling if keys are not in images
 
  if not isinstance(keys, (list, str)):
-
+
  raise TypeError("Parameter 'keys' must either be of type 'str' or 'list'.")
 
- if isinstance(keys, list):
-
+ if isinstance(keys, list):
+
  if not all([isinstance(key, str) for key in keys]):
-
+
  raise TypeError("All elements in 'keys' must be of type 'str'.")
 
  if isinstance(keys, str):
  keys = [keys]
-
+
  assert all([isinstance(key, str) for key in keys])
-
+
  valid_keys = list(self._sdata.images.keys())
-
+
  for key in keys:
-
+
  if key not in valid_keys:
-
+
  raise ValueError(f"Key '{key}' is not a valid key. Valid choices are: " + ", ".join(valid_keys))
 
  selected_images = {key: img for key, img in self._sdata.images.items() if key in keys}
@@ -168,35 +168,67 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  new_table = None
  # make sure that table exists
  if hasattr(self._sdata, "table"):
-
+
  if hasattr(self._sdata.table, "obs"):
-
+
  # create mask of used keys
  mask = self._sdata.table.obs[self._sdata.pp.get_region_key()]
  mask = list(mask.str.contains("|".join(keys)))
  # print(mask)
-
+
  new_table = self._sdata.table[mask, :]
-
 
  return self._copy(images=selected_images, labels=selected_labels, table=new_table)
 
- def get_channels(self, keys: Union[list, slice]) -> sd.SpatialData:
- """Get channels from a list of keys.
+ def get_channels(self, channels: Union[list, slice]) -> sd.SpatialData:
+ """Subset a spatialdata object to the selected channels.
 
- Parameters
- ----------
- keys : list
- list of keys to select
+ Images that don't have the selected channels will be dropped.
 
- Returns
- -------
- sd.SpatialData
- subsetted SpatialData object
  """
- selection = dict(c=keys)
- # TODO: error handling if selection is out of bounds
- channels_images = {key: img.sel(selection) for key, img in self._sdata.images.items()}
+
+ if not isinstance(channels, (list, slice)):
+
+ raise TypeError("Parameter 'channels' must either be of type 'list' or 'slice'.")
+
+ if isinstance(channels, list):
+
+ if not all([isinstance(channel, int) for channel in channels]):
+
+ raise TypeError("All elements in 'channels' must be of type 'int'.")
+
+ if isinstance(channels, list):
+
+ if not len(channels) > 0:
+
+ raise ValueError("The list of channels cannot be empty.")
+
+ # validate that selection is within bounds
+ # 1) parse slice into list, respecting stepsize
+ if isinstance(channels, slice):
+
+ channels = [x for x in range(start=channels.start, stop=channels.stop, step=channels.step or 1)]
+
+ # 2) check which images have how many channels
+ image_names = []
+ n_channels = []
+ for image_name, image in self._sdata.images.items():
+ image_names.append(image_name)
+ n_channels.append(image.shape[0])
+
+ channels_in_image = pd.DataFrame({"image_name": image_names, "n_channels": n_channels})
+
+ # 3) drop images that don't have enough channels for the selection
+ channels_in_image = channels_in_image[channels_in_image.n_channels - 1 >= max(channels)]
+ valid_images = channels_in_image.image_name.values.tolist()
+ sdata_with_valid_images = self._sdata.pp.get_images(keys=valid_images)
+
+ if len(sdata_with_valid_images.images.keys()) < 1:
+
+ raise ValueError("The choice of channels results in an empty selection.")
+
+ selected_channels = dict(c=channels)
+ channels_images = {key: img.sel(selected_channels) for key, img in self._sdata.images.items()}
 
  return self._copy(images=channels_images)
 

src/spatialdata_plot/pp/basic.py

@@ -2,6 +2,8 @@
 
 import spatialdata as sd
 from anndata import AnnData
+import pandas as pd
+
 
 from ..accessor import register_spatial_data_accessor
 from .colorize import _colorize
@@ -23,12 +25,12 @@ def _copy(
  shapes: Union[None, dict] = None,
  table: Union[dict, AnnData] = None,
  ) -> sd.SpatialData:
-
+
  """
  Helper function to copies the references from the original SpatialData
  object to the subsetted SpatialData object.
  """
-
+
  return sd.SpatialData(
  images=self._sdata.images if images is None else images,
  labels=self._sdata.labels if labels is None else labels,
@@ -39,76 +41,74 @@ def _copy(
  )
 
  def get_region_key(self) -> str:
-
+
  "Quick access to the data's region key."
-
+
  return self._sdata.table.uns["spatialdata_attrs"]["region_key"]
 
  def get_bb(self, x: Union[slice, list, tuple], y: Union[slice, list, tuple]) -> sd.SpatialData:
-
+
  """Get bounding box around a point.
 
  Parameters
  ----------
  x : Union[slice, list, tuple]
- x range of the bounding box
+ x range of the bounding box. Stepsize will be ignored if slice
  y : Union[slice, list, tuple]
- y range of the bounding box
+ y range of the bounding box. Stepsize will be ignored if slice
 
  Returns
  -------
  sd.SpatialData
  subsetted SpatialData object
  """
-
+
  if not isinstance(x, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'x' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(x, (list, tuple)):
-
+
  if len(x) != 2:
-
+
  raise ValueError("Parameter 'x' must be of length 2.")
-
+
  if x[1] <= x[0]:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
+
  # x is clean
  x = slice(x[0], x[1])
-
+
  elif isinstance(x, slice):
-
+
  if x.stop <= x.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  if not isinstance(y, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'y' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(y, (list, tuple)):
-
+
  if len(y) != 2:
-
+
  raise ValueError("Parameter 'y' must be of length 2.")
-
+
  if y[1] <= y[0]:
-
+
  raise ValueError("The current choice of 'y' would result in an empty slice.")
-
+
  # y is clean
  y = slice(y[0], y[1])
-
+
  elif isinstance(y, slice):
-
+
  if y.stop <= y.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  selection = dict(x=x, y=y) # makes use of xarray sel method
 
  # TODO: error handling if selection is out of bounds
@@ -138,26 +138,26 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  # TODO: error handling if keys are not in images
 
  if not isinstance(keys, (list, str)):
-
+
  raise TypeError("Parameter 'keys' must either be of type 'str' or 'list'.")
 
- if isinstance(keys, list):
-
+ if isinstance(keys, list):
+
  if not all([isinstance(key, str) for key in keys]):
-
+
  raise TypeError("All elements in 'keys' must be of type 'str'.")
 
  if isinstance(keys, str):
  keys = [keys]
-
+
  assert all([isinstance(key, str) for key in keys])
-
+
  valid_keys = list(self._sdata.images.keys())
-
+
  for key in keys:
-
+
  if key not in valid_keys:
-
+
  raise ValueError(f"Key '{key}' is not a valid key. Valid choices are: " + ", ".join(valid_keys))
 
  selected_images = {key: img for key, img in self._sdata.images.items() if key in keys}
@@ -168,35 +168,67 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  new_table = None
  # make sure that table exists
  if hasattr(self._sdata, "table"):
-
+
  if hasattr(self._sdata.table, "obs"):
-
+
  # create mask of used keys
  mask = self._sdata.table.obs[self._sdata.pp.get_region_key()]
  mask = list(mask.str.contains("|".join(keys)))
  # print(mask)
-
+
  new_table = self._sdata.table[mask, :]
-
 
  return self._copy(images=selected_images, labels=selected_labels, table=new_table)
 
- def get_channels(self, keys: Union[list, slice]) -> sd.SpatialData:
- """Get channels from a list of keys.
+ def get_channels(self, channels: Union[list, slice]) -> sd.SpatialData:
+ """Subset a spatialdata object to the selected channels.
 
- Parameters
- ----------
- keys : list
- list of keys to select
+ Images that don't have the selected channels will be dropped.
 
- Returns
- -------
- sd.SpatialData
- subsetted SpatialData object
  """
- selection = dict(c=keys)
- # TODO: error handling if selection is out of bounds
- channels_images = {key: img.sel(selection) for key, img in self._sdata.images.items()}
+
+ if not isinstance(channels, (list, slice)):
+
+ raise TypeError("Parameter 'channels' must either be of type 'list' or 'slice'.")
+
+ if isinstance(channels, list):
+
+ if not all([isinstance(channel, int) for channel in channels]):
+
+ raise TypeError("All elements in 'channels' must be of type 'int'.")
+
+ if isinstance(channels, list):
+
+ if not len(channels) > 0:
+
+ raise ValueError("The list of channels cannot be empty.")
+
+ # validate that selection is within bounds
+ # 1) parse slice into list, respecting stepsize
+ if isinstance(channels, slice):
+
+ channels = [x for x in range(start=channels.start, stop=channels.stop, step=channels.step or 1)]
+
+ # 2) check which images have how many channels
+ image_names = []
+ n_channels = []
+ for image_name, image in self._sdata.images.items():
+ image_names.append(image_name)
+ n_channels.append(image.shape[0])
+
+ channels_in_image = pd.DataFrame({"image_name": image_names, "n_channels": n_channels})
+
+ # 3) drop images that don't have enough channels for the selection
+ channels_in_image = channels_in_image[channels_in_image.n_channels - 1 >= max(channels)]
+ valid_images = channels_in_image.image_name.values.tolist()
+ sdata_with_valid_images = self._sdata.pp.get_images(keys=valid_images)
+
+ if len(sdata_with_valid_images.images.keys()) < 1:
+
+ raise ValueError("The choice of channels results in an empty selection.")
+
+ selected_channels = dict(c=channels)
+ channels_images = {key: img.sel(selected_channels) for key, img in self._sdata.images.items()}
 
  return self._copy(images=channels_images)
 

src/spatialdata_plot/pp/basic.py

@@ -2,6 +2,8 @@
 
 import spatialdata as sd
 from anndata import AnnData
+import pandas as pd
+
 
 from ..accessor import register_spatial_data_accessor
 from .colorize import _colorize
@@ -23,12 +25,12 @@ def _copy(
  shapes: Union[None, dict] = None,
  table: Union[dict, AnnData] = None,
  ) -> sd.SpatialData:
-
+
  """
  Helper function to copies the references from the original SpatialData
  object to the subsetted SpatialData object.
  """
-
+
  return sd.SpatialData(
  images=self._sdata.images if images is None else images,
  labels=self._sdata.labels if labels is None else labels,
@@ -39,76 +41,74 @@ def _copy(
  )
 
  def get_region_key(self) -> str:
-
+
  "Quick access to the data's region key."
-
+
  return self._sdata.table.uns["spatialdata_attrs"]["region_key"]
 
  def get_bb(self, x: Union[slice, list, tuple], y: Union[slice, list, tuple]) -> sd.SpatialData:
-
+
  """Get bounding box around a point.
 
  Parameters
  ----------
  x : Union[slice, list, tuple]
- x range of the bounding box
+ x range of the bounding box. Stepsize will be ignored if slice
  y : Union[slice, list, tuple]
- y range of the bounding box
+ y range of the bounding box. Stepsize will be ignored if slice
 
  Returns
  -------
  sd.SpatialData
  subsetted SpatialData object
  """
-
+
  if not isinstance(x, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'x' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(x, (list, tuple)):
-
+
  if len(x) != 2:
-
+
  raise ValueError("Parameter 'x' must be of length 2.")
-
+
  if x[1] <= x[0]:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
+
  # x is clean
  x = slice(x[0], x[1])
-
+
  elif isinstance(x, slice):
-
+
  if x.stop <= x.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  if not isinstance(y, (slice, list, tuple)):
-
+
  raise TypeError("Parameter 'y' must be one of 'slice', 'list', 'tuple'.")
-
+
  if isinstance(y, (list, tuple)):
-
+
  if len(y) != 2:
-
+
  raise ValueError("Parameter 'y' must be of length 2.")
-
+
  if y[1] <= y[0]:
-
+
  raise ValueError("The current choice of 'y' would result in an empty slice.")
-
+
  # y is clean
  y = slice(y[0], y[1])
-
+
  elif isinstance(y, slice):
-
+
  if y.stop <= y.start:
-
+
  raise ValueError("The current choice of 'x' would result in an empty slice.")
-
-
+
  selection = dict(x=x, y=y) # makes use of xarray sel method
 
  # TODO: error handling if selection is out of bounds
@@ -138,26 +138,26 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  # TODO: error handling if keys are not in images
 
  if not isinstance(keys, (list, str)):
-
+
  raise TypeError("Parameter 'keys' must either be of type 'str' or 'list'.")
 
- if isinstance(keys, list):
-
+ if isinstance(keys, list):
+
  if not all([isinstance(key, str) for key in keys]):
-
+
  raise TypeError("All elements in 'keys' must be of type 'str'.")
 
  if isinstance(keys, str):
  keys = [keys]
-
+
  assert all([isinstance(key, str) for key in keys])
-
+
  valid_keys = list(self._sdata.images.keys())
-
+
  for key in keys:
-
+
  if key not in valid_keys:
-
+
  raise ValueError(f"Key '{key}' is not a valid key. Valid choices are: " + ", ".join(valid_keys))
 
  selected_images = {key: img for key, img in self._sdata.images.items() if key in keys}
@@ -168,35 +168,67 @@ def get_images(self, keys: Union[list, str], label_func: Callable = lambda x: x)
  new_table = None
  # make sure that table exists
  if hasattr(self._sdata, "table"):
-
+
  if hasattr(self._sdata.table, "obs"):
-
+
  # create mask of used keys
  mask = self._sdata.table.obs[self._sdata.pp.get_region_key()]
  mask = list(mask.str.contains("|".join(keys)))
  # print(mask)
-
+
  new_table = self._sdata.table[mask, :]
-
 
  return self._copy(images=selected_images, labels=selected_labels, table=new_table)
 
- def get_channels(self, keys: Union[list, slice]) -> sd.SpatialData:
- """Get channels from a list of keys.
+ def get_channels(self, channels: Union[list, slice]) -> sd.SpatialData:
+ """Subset a spatialdata object to the selected channels.
 
- Parameters
- ----------
- keys : list
- list of keys to select
+ Images that don't have the selected channels will be dropped.
 
- Returns
- -------
- sd.SpatialData
- subsetted SpatialData object
  """
- selection = dict(c=keys)
- # TODO: error handling if selection is out of bounds
- channels_images = {key: img.sel(selection) for key, img in self._sdata.images.items()}
+
+ if not isinstance(channels, (list, slice)):
+
+ raise TypeError("Parameter 'channels' must either be of type 'list' or 'slice'.")
+
+ if isinstance(channels, list):
+
+ if not all([isinstance(channel, int) for channel in channels]):
+
+ raise TypeError("All elements in 'channels' must be of type 'int'.")
+
+ if isinstance(channels, list):
+
+ if not len(channels) > 0:
+
+ raise ValueError("The list of channels cannot be empty.")
+
+ # validate that selection is within bounds
+ # 1) parse slice into list, respecting stepsize
+ if isinstance(channels, slice):
+
+ channels = [x for x in range(start=channels.start, stop=channels.stop, step=channels.step or 1)]
+
+ # 2) check which images have how many channels
+ image_names = []
+ n_channels = []
+ for image_name, image in self._sdata.images.items():
+ image_names.append(image_name)
+ n_channels.append(image.shape[0])
+
+ channels_in_image = pd.DataFrame({"image_name": image_names, "n_channels": n_channels})
+
+ # 3) drop images that don't have enough channels for the selection
+ channels_in_image = channels_in_image[channels_in_image.n_channels - 1 >= max(channels)]
+ valid_images = channels_in_image.image_name.values.tolist()
+ sdata_with_valid_images = self._sdata.pp.get_images(keys=valid_images)
+
+ if len(sdata_with_valid_images.images.keys()) < 1:
+
+ raise ValueError("The choice of channels results in an empty selection.")
+
+ selected_channels = dict(c=channels)
+ channels_images = {key: img.sel(selected_channels) for key, img in self._sdata.images.items()}
 
  return self._copy(images=channels_images)