Merge a0a1d83 into 48aba7d

doc/user_guide/index.rst

@@ -105,6 +105,9 @@ These guides provide detail about specific additional features in HoloViews:
 `Working with renderers and plots <Plots_and_Renderers.html>`_
  Using the ``Renderer`` and ``Plot`` classes for access to the plotting machinery.
 
+`Using linked brushing to cross-filter complex datasets <Linked_Brushing.html>`_
+ Explains how to use the `link_selections` helper to cross-filter multiple elements.
+
 `Using Annotators to edit and label data <Annotators.html>`_
  Explains how to use the `annotate` helper to edit and annotate elements with the help of drawing tools and editable tables.
 
@@ -148,6 +151,7 @@ These guides provide detail about specific additional features in HoloViews:
     Plotting with matplotlib <Plotting_with_Matplotlib>
     Plotting with plotly <Plotting_with_Plotly>
     Working with Plot and Renderers <Plots_and_Renderers>
+    Linked Brushing <Linked_Brushing>
     Annotators <Annotators>
     Exporting and Archiving <Exporting_and_Archiving>
     Continuous Coordinates <Continuous_Coordinates>

holoviews/core/accessors.py

@@ -97,7 +97,8 @@ class Apply(object):
     def __init__(self, obj, mode=None):
         self._obj = obj
 
-    def __call__(self, function, streams=[], link_inputs=True, dynamic=None, **kwargs):
+    def __call__(self, function, streams=[], link_inputs=True, dynamic=None,
+                 per_element=False, **kwargs):
         """Applies a function to all (Nd)Overlay or Element objects.
 
         Any keyword arguments are passed through to the function. If
@@ -122,6 +123,10 @@ def __call__(self, function, streams=[], link_inputs=True, dynamic=None, **kwarg
                 supplied, an instance parameter is supplied as a
                 keyword argument, or the supplied function is a
                 parameterized method.
+            per_element (bool, optional): Whether to apply per element
+                By default apply works on the leaf nodes, which
+                includes both elements and overlays. If set it will
+                apply directly to elements.
             kwargs (dict, optional): Additional keyword arguments
                 Keyword arguments which will be supplied to the
                 function.
@@ -131,6 +136,7 @@ def __call__(self, function, streams=[], link_inputs=True, dynamic=None, **kwarg
             contained (Nd)Overlay or Element objects.
         """
         from .dimension import ViewableElement
+        from .element import Element
         from .spaces import HoloMap, DynamicMap
         from ..util import Dynamic
 
@@ -164,7 +170,8 @@ def function(object, **kwargs):
             kwargs = {k: v.param.value if isinstance(v, Widget) else v
                       for k, v in kwargs.items()}
 
-        applies = isinstance(self._obj, ViewableElement)
+        spec = Element if per_element else ViewableElement
+        applies = isinstance(self._obj, spec)
         params = {p: val for p, val in kwargs.items()
                   if isinstance(val, param.Parameter)
                   and isinstance(val.owner, param.Parameterized)}
@@ -299,6 +306,46 @@ def _filter_cache(self, dmap, kdims):
                 filtered.append((key, value))
         return filtered
 
+    def _transform_dimension(self, kdims, vdims, dimension):
+        if dimension in kdims:
+            idx = kdims.index(dimension)
+            dimension = self._obj.kdims[idx]
+        elif dimension in vdims:
+            idx = vdims.index(dimension)
+            dimension = self._obj.vdims[idx]
+        return dimension
+
+    def _create_expression_transform(self, kdims, vdims, exclude=[]):
+        from .dimension import dimension_name
+        from ..util.transform import dim
+
+        def _transform_expression(expression):
+            if dimension_name(expression.dimension) in exclude:
+                dimension = expression.dimension
+            else:
+                dimension = self._transform_dimension(
+                    kdims, vdims, expression.dimension
+                )
+            expression = expression.clone(dimension)
+            ops = []
+            for op in expression.ops:
+                new_op = dict(op)
+                new_args = []
+                for arg in op['args']:
+                    if isinstance(arg, dim):
+                        arg = _transform_expression(arg)
+                    new_args.append(arg)
+                new_op['args'] = tuple(new_args)
+                new_kwargs = {}
+                for kw, kwarg in op['kwargs'].items():
+                    if isinstance(kwarg, dim):
+                        kwarg = _transform_expression(kwarg)
+                    new_kwargs[kw] = kwarg
+                new_op['kwargs'] = new_kwargs
+                ops.append(new_op)
+            expression.ops = ops
+            return expression
+        return _transform_expression
 
     def __call__(self, specs=None, **dimensions):
         """
@@ -324,13 +371,15 @@ def __call__(self, specs=None, **dimensions):
         kdims = self.replace_dimensions(obj.kdims, dimensions)
         vdims = self.replace_dimensions(obj.vdims, dimensions)
         zipped_dims = zip(obj.kdims+obj.vdims, kdims+vdims)
-        renames = {pk.name: nk for pk, nk in zipped_dims if pk != nk}
+        renames = {pk.name: nk for pk, nk in zipped_dims if pk.name != nk.name}
 
         if self.mode == 'dataset':
             data = obj.data
             if renames:
                 data = obj.interface.redim(obj, renames)
-            clone = obj.clone(data, kdims=kdims, vdims=vdims)
+            transform = self._create_expression_transform(kdims, vdims, list(renames.values()))
+            transforms = obj._transforms + [transform]
+            clone = obj.clone(data, kdims=kdims, vdims=vdims, transforms=transforms)
             if self._obj.dimensions(label='name') == clone.dimensions(label='name'):
                 # Ensure that plot_id is inherited as long as dimension
                 # name does not change

holoviews/core/data/__init__.py

@@ -283,14 +283,21 @@ def __init__(self, data, kdims=None, vdims=None, **kwargs):
         input_data = data
         dataset_provided = 'dataset' in kwargs
         input_dataset = kwargs.pop('dataset', None)
-        input_pipeline = kwargs.pop(
-            'pipeline', None
-        )
+        input_pipeline = kwargs.pop('pipeline', None)
+        input_transforms = kwargs.pop('transforms', None)
 
         if isinstance(data, Element):
             pvals = util.get_param_values(data)
             kwargs.update([(l, pvals[l]) for l in ['group', 'label']
                            if l in pvals and l not in kwargs])
+        if isinstance(data, Dataset):
+            if not dataset_provided and data._dataset is not None:
+                input_dataset = data._dataset
+            if input_pipeline is None:
+                input_pipeline = data.pipeline
+            if input_transforms is None:
+                input_transforms = data._transforms
+
         kwargs.update(process_dimensions(kdims, vdims))
         kdims, vdims = kwargs.get('kdims'), kwargs.get('vdims')
 
@@ -316,6 +323,7 @@ def __init__(self, data, kdims=None, vdims=None, **kwargs):
             operations=input_pipeline.operations + [init_op],
             output_type=type(self),
         )
+        self._transforms = input_transforms or []
 
         # Handle initializing the dataset property.
         self._dataset = None
@@ -331,7 +339,6 @@ def dataset(self):
         """
         The Dataset that this object was created from
         """
-        from . import Dataset
         if self._dataset is None:
             datatype = list(util.unique_iterator(self.datatype+Dataset.datatype))
             dataset = Dataset(self, _validate_vdims=False, datatype=datatype)
@@ -526,7 +533,7 @@ def select(self, selection_expr=None, selection_specs=None, **selection):
         selection = {dim_name: sel for dim_name, sel in selection.items()
                      if dim_name in self.dimensions()+['selection_mask']}
         if (selection_specs and not any(self.matches(sp) for sp in selection_specs)
-                or (not selection and not selection_expr)):
+            or (not selection and not selection_expr)):
             return self
 
         # Handle selection dim expression

holoviews/core/data/array.py

@@ -18,6 +18,8 @@ class ArrayInterface(Interface):
 
     datatype = 'array'
 
+    named = False
+
     @classmethod
     def dimension_type(cls, dataset, dim):
         return dataset.data.dtype.type
@@ -123,9 +125,7 @@ def sort(cls, dataset, by=[], reverse=False):
 
 
     @classmethod
-    def values(
-            cls, dataset, dim, expanded=True, flat=True, compute=True, keep_index=False
-    ):
+    def values(cls, dataset, dim, expanded=True, flat=True, compute=True, keep_index=False):
         data = dataset.data
         dim_idx = dataset.get_dimension_index(dim)
         if data.ndim == 1:
@@ -136,6 +136,13 @@ def values(
         return values
 
 
+    @classmethod
+    def mask(cls, dataset, mask, mask_value=np.nan):
+        masked = np.copy(dataset.data)
+        masked[mask] = mask_value
+        return masked
+
+
     @classmethod
     def reindex(cls, dataset, kdims=None, vdims=None):
         # DataFrame based tables don't need to be reindexed

holoviews/core/data/dask.py

@@ -90,15 +90,7 @@ def sort(cls, dataset, by=[], reverse=False):
         return dataset.data
 
     @classmethod
-    def values(
-            cls,
-            dataset,
-            dim,
-            expanded=True,
-            flat=True,
-            compute=True,
-            keep_index=False,
-    ):
+    def values(cls, dataset, dim, expanded=True, flat=True, compute=True, keep_index=False):
         dim = dataset.get_dimension(dim)
         data = dataset.data[dim.name]
         if not expanded:

holoviews/core/data/dictionary.py

@@ -224,6 +224,16 @@ def concat(cls, datasets, dimensions, vdims):
         return OrderedDict([(d.name, np.concatenate(columns[d.name])) for d in dims])
 
 
+    @classmethod
+    def mask(cls, dataset, mask, mask_value=np.nan):
+        masked = OrderedDict()
+        for k, v in dataset.data.items():
+            new_array = np.copy(dataset.data[k])
+            new_array[mask] = mask_value
+            masked[k] = new_array
+        return masked
+
+
     @classmethod
     def sort(cls, dataset, by=[], reverse=False):
         by = [dataset.get_dimension(d).name for d in by]
@@ -246,10 +256,8 @@ def range(cls, dataset, dimension):
 
 
     @classmethod
-    def values(
-            cls, dataset, dim, expanded=True, flat=True, compute=True, keep_index=False
-    ):
-        dim = dataset.get_dimension(dim).name
+    def values(cls, dataset, dim, expanded=True, flat=True, compute=True, keep_index=False):
+        dim = dataset.get_dimension(dim, strict=True).name
         values = dataset.data.get(dim)
         if isscalar(values):
             if not expanded:

holoviews/core/data/grid.py

@@ -58,6 +58,7 @@ def init(cls, eltype, data, kdims, vdims):
         ndims = len(kdims)
         dimensions = [dimension_name(d) for d in kdims+vdims]
         vdim_tuple = tuple(dimension_name(vd) for vd in vdims)
+
         if isinstance(data, tuple):
             if (len(data) != len(dimensions) and len(data) == (ndims+1) and
                 len(data[-1].shape) == (ndims+1)):
@@ -66,18 +67,34 @@ def init(cls, eltype, data, kdims, vdims):
                 data[vdim_tuple] = value_array
             else:
                 data = {d: v for d, v in zip(dimensions, data)}
-        elif isinstance(data, list) and data == []:
-            data = OrderedDict([(d, []) for d in dimensions])
+        elif (isinstance(data, list) and data == []):
+            if len(kdims) == 1:
+                data = OrderedDict([(d, []) for d in dimensions])
+            else:
+                data = OrderedDict([(d.name, np.array([])) for d in kdims])
+                if len(vdims) == 1:
+                    data[vdims[0].name] = np.zeros((0, 0))
+                else:
+                    data[vdim_tuple] = np.zeros((0, 0, len(vdims)))
         elif not any(isinstance(data, tuple(t for t in interface.types if t is not None))
                      for interface in cls.interfaces.values()):
             data = {k: v for k, v in zip(dimensions, zip(*data))}
         elif isinstance(data, np.ndarray):
-            if data.ndim == 1:
-                if eltype._auto_indexable_1d and len(kdims)+len(vdims)>1:
-                    data = np.column_stack([np.arange(len(data)), data])
-                else:
-                    data = np.atleast_2d(data).T
-            data = {k: data[:,i] for i,k in enumerate(dimensions)}
+            if data.shape == (0, 0) and len(vdims) == 1:
+                array = data
+                data = OrderedDict([(d.name, np.array([])) for d in kdims])
+                data[vdims[0].name] = array
+            elif data.shape == (0, 0, len(vdims)):
+                array = data
+                data = OrderedDict([(d.name, np.array([])) for d in kdims])
+                data[vdim_tuple] = array
+            else:
+                if data.ndim == 1:
+                    if eltype._auto_indexable_1d and len(kdims)+len(vdims)>1:
+                        data = np.column_stack([np.arange(len(data)), data])
+                    else:
+                        data = np.atleast_2d(data).T
+                data = {k: data[:, i] for i, k in enumerate(dimensions)}
         elif isinstance(data, list) and data == []:
             data = {d: np.array([]) for d in dimensions[:ndims]}
             data.update({d: np.empty((0,) * ndims) for d in dimensions[ndims:]})
@@ -245,9 +262,9 @@ def _infer_interval_breaks(cls, coord, axis=0):
         if sys.version_info.major == 2 and len(coord) and isinstance(coord[0], (dt.datetime, dt.date)):
             # np.diff does not work on datetimes in python 2
             coord = coord.astype('datetime64')
-        if len(coord) == 0:
+        if coord.shape[axis] == 0:
             return np.array([], dtype=coord.dtype)
-        if len(coord) > 1:
+        if coord.shape[axis] > 1:
             deltas = 0.5 * np.diff(coord, axis=axis)
         else:
             deltas = np.array([0.5])
@@ -393,9 +410,7 @@ def ndloc(cls, dataset, indices):
 
 
     @classmethod
-    def values(
-            cls, dataset, dim, expanded=True, flat=True, compute=True, keep_index=False
-    ):
+    def values(cls, dataset, dim, expanded=True, flat=True, compute=True, keep_index=False):
         dim = dataset.get_dimension(dim, strict=True)
         if dim in dataset.vdims or dataset.data[dim.name].ndim > 1:
             vdim_tuple = cls.packed(dataset)
@@ -598,6 +613,29 @@ def select(cls, dataset, selection_mask=None, **selection):
         return data
 
 
+    @classmethod
+    def mask(cls, dataset, mask, mask_val=np.nan):
+        mask = cls.canonicalize(dataset, mask)
+        packed = cls.packed(dataset)
+        masked = OrderedDict(dataset.data)
+        if packed:
+            masked = dataset.data[packed].copy()
+            try:
+                masked[mask] = mask_val
+            except ValueError:
+                masked = masked.astype('float')
+                masked[mask] = mask_val
+        else:
+            for vd in dataset.vdims:
+                masked[vd.name] = marr = masked[vd.name].copy()
+                try:
+                    marr[mask] = mask_val
+                except ValueError:
+                    masked[vd.name] = marr = marr.astype('float')
+                    marr[mask] = mask_val
+        return masked
+
+
     @classmethod
     def sample(cls, dataset, samples=[]):
         """

holoviews/core/data/image.py

@@ -20,6 +20,8 @@ class ImageInterface(GridInterface):
 
     datatype = 'image'
 
+    named = False
+
     @classmethod
     def init(cls, eltype, data, kdims, vdims):
         if kdims is None:
@@ -199,6 +201,13 @@ def values(
             return None
 
 
+    @classmethod
+    def mask(cls, dataset, mask, mask_val=np.nan):
+        masked = dataset.data.copy().astype('float')
+        masked[np.flipud(mask)] = mask_val
+        return masked
+
+
     @classmethod
     def select(cls, dataset, selection_mask=None, **selection):
         """

holoviews/core/data/interface.py

@@ -158,6 +158,9 @@ class Interface(param.Parameterized):
     # Denotes whether the interface expects ragged data
     multi = False
 
+    # Whether the interface stores the names of the underlying dimensions
+    named = True
+
     @classmethod
     def loaded(cls):
         """
@@ -229,7 +232,7 @@ def initialize(cls, eltype, data, kdims, vdims, datatype=None):
                     datatype = eltype.datatype
 
             interface = data.interface
-            if interface.datatype in datatype and interface.datatype in eltype.datatype:
+            if interface.datatype in datatype and interface.datatype in eltype.datatype and interface.named:
                 data = data.data
             elif interface.multi and any(cls.interfaces[dt].multi for dt in datatype if dt in cls.interfaces):
                 data = [d for d in data.interface.split(data, None, None, 'columns')]