Merge pull request #916 from keflavich/issue915

fix for 915: account for different use cases of median

spectral_cube/dask_spectral_cube.py

@@ -287,15 +287,6 @@ def __exit__(self, *args):
  def _compute(self, array):
  return array.compute(**self._scheduler_kwargs)
 
- def _warn_slow(self, funcname):
- if self._is_huge and not self.allow_huge_operations:
- raise ValueError("This function ({0}) requires loading the entire "
- "cube into memory, and the cube is large ({1} "
- "pixels), so by default we disable this operation. "
- "To enable the operation, set "
- "`cube.allow_huge_operations=True` and try again."
- .format(funcname, self.size))
-
  def _get_filled_data(self, view=(), fill=np.nan, check_endian=None, use_memmap=None):
 
  if check_endian:

spectral_cube/spectral_cube.py

@@ -1191,6 +1191,17 @@ def median(self, axis=None, iterate_rays=False, **kwargs):
  except ImportError:
  bnok = False
 
+ how = kwargs.pop('how', None)
+ if how == 'slice' and (not isinstance(axis, (list, tuple)) or len(axis) != 2):
+ raise ValueError("Cannot compute median slicewise unless you're compressing over two axes.")
+ elif how == 'ray':
+ if axis not in (0, 1, 2):
+ raise ValueError("Cannot compute median raywise unless you're compressing over one axis.")
+ else:
+ if not iterate_rays:
+ iterate_rays = True
+ warnings.warn("how='ray' was specified in call to median; this is setting iterate_rays=True")
+
  # slicewise median is nonsense, must force how = 'cube'
  # bottleneck.nanmedian does not allow axis to be a list or tuple
  if bnok and not iterate_rays and not isinstance(axis, (list, tuple)):
@@ -1203,7 +1214,12 @@ def median(self, axis=None, iterate_rays=False, **kwargs):
  log.debug("Using numpy nanmedian")
  result = self.apply_numpy_function(np.nanmedian, axis=axis,
  projection=True, unit=self.unit,
- how='cube',**kwargs)
+ how='cube', **kwargs)
+ elif iterate_rays:
+ result = self.apply_numpy_function(
+ nanmedian if bnok else np.nanmedian if hasattr(np, 'nanmedian') else np.median,
+ axis=axis, projection=True, unit=self.unit, how='ray',
+ check_endian=True, **kwargs)
  else:
  log.debug("Using numpy median iterating over rays")
  result = self.apply_function(np.median, projection=True, axis=axis,

spectral_cube/utils.py

@@ -1,4 +1,5 @@
 import warnings
+import inspect
 
 from functools import wraps
 
@@ -33,19 +34,26 @@ def warn_slow(function):
  @wraps(function)
  def wrapper(self, *args, **kwargs):
  # if the function accepts a 'how', the 'cube' approach requires the whole cube in memory
- warn_how = (kwargs.get('how') == 'cube') or 'how' not in kwargs
- if self._is_huge and not self.allow_huge_operations and warn_how:
- raise ValueError("This function ({0}) requires loading the entire "
- "cube into memory, and the cube is large ({1} "
- "pixels), so by default we disable this operation. "
- "To enable the operation, set "
- "`cube.allow_huge_operations=True` and try again. "
- "Alternatively, you may want to consider using an "
- "approach that does not load the whole cube into "
- "memory by specifying how='slice' or how='ray'. "
- "See {bigdataurl} for details."
- .format(str(function), self.size,
- bigdataurl=bigdataurl))
+ argspec = inspect.getfullargspec(function)
+ accepts_how_keyword = 'how' in argspec.args or argspec.varkw == 'how'
+
+ warn_how = accepts_how_keyword and ((kwargs.get('how') == 'cube') or 'how' not in kwargs)
+
+ if self._is_huge and not self.allow_huge_operations:
+ warn_message = ("This function ({0}) requires loading the entire "
+ "cube into memory, and the cube is large ({1} "
+ "pixels), so by default we disable this operation. "
+ "To enable the operation, set "
+ "`cube.allow_huge_operations=True` and try again. ").format(str(function), self.size)
+
+ if warn_how:
+ warn_message += ("Alternatively, you may want to consider using an "
+ "approach that does not load the whole cube into "
+ "memory by specifying how='slice' or how='ray'. ")
+
+ warn_message += ("See {bigdataurl} for details.".format(bigdataurl=bigdataurl))
+
+ raise ValueError(warn_message)
  elif warn_how and not self._is_huge:
  # TODO: add check for whether cube has been loaded into memory
  warnings.warn("This function ({0}) requires loading the entire cube into "