def __call__(self, parameterized, plots=[], **params):
self.p = param.ParamOverrides(self, params)
if self.p.initializer:
self.p.initializer(parameterized)
self._id = uuid.uuid4().hex
self._widgets = {}
self.parameterized = parameterized
widgets, views = self.widgets()
layout = ipywidgets.Layout(display='flex', flex_flow=self.p.layout)
if self.p.close_button:
layout.border = 'solid 1px'
widget_box = ipywidgets.VBox(children=widgets, layout=layout)
plot_outputs = tuple(Output() for p in plots)
if views or plots:
outputs = tuple(views.values()) + plot_outputs
view_box = ipywidgets.VBox(children=outputs, layout=layout)
layout = self.p.view_position
if layout in ['below', 'right']:
children = [widget_box, view_box]
else:
children = [view_box, widget_box]
box = ipywidgets.VBox if layout in ['below', 'above'
] else ipywidgets.HBox
widget_box = box(children=children)
display(widget_box)
self._widget_box = widget_box
self._display_handles = {}
# Render defined View parameters
for pname, view in views.items():
p_obj = self.parameterized.params(pname)
value = getattr(self.parameterized, pname)
if value is None:
continue
handle = self._update_trait(pname, p_obj.renderer(value))
if handle:
self._display_handles[pname] = handle
# Render supplied plots
for p, o in zip(plots, plot_outputs):
with o:
display(p)
# Keeps track of changes between button presses
self._changed = {}
if self.p.on_init:
self.execute()
def __call__(self, data, **params):
p = param.ParamOverrides(self, params)
if isinstance(data, HoloMap):
ranges = {d.name: data.range(d) for d in data.dimensions()}
data = data.clone({k: GridMatrix(self._process(p, v, ranges))
for k, v in data.items()}).collate()
if p.overlay_dims:
data = data.map(lambda x: x.overlay(p.overlay_dims), (HoloMap,))
return data
elif isinstance(data, Element):
data = self._process(p, data)
return GridMatrix(data)
def __call__(self, map_obj, **params):
watch = params.pop('watch', True)
self.p = param.ParamOverrides(self, params)
callback = self._dynamic_operation(map_obj)
streams = self._get_streams(map_obj, watch)
if isinstance(map_obj, DynamicMap):
dmap = map_obj.clone(callback=callback, shared_data=self.p.shared_data,
streams=streams)
if self.p.shared_data:
dmap.data = OrderedDict([(k, callback.callable(*k))
for k, v in dmap.data])
else:
dmap = self._make_dynamic(map_obj, callback, streams)
return dmap
def __call__(self, nodes, edges, **params):
p = param.ParamOverrides(self,params)
# Convert graph into list of edge segments
edges = _convert_graph_to_edge_segments(nodes, edges)
# This is simply to let the work split out over multiple cores
edge_batches = list(batches(edges, p.batch_size))
# This gets the edges split into lots of small segments
# Doing this inside a delayed function lowers the transmission overhead
edge_segments = [resample_edges(batch, p.min_segment_length, p.max_segment_length) for batch in edge_batches]
for i in range(p.iterations):
# Each step, the size of the 'blur' shrinks
bandwidth = p.initial_bandwidth * p.decay**(i + 1) * p.accuracy
# If it's this small, there won't be a change anyway
if bandwidth < 2:
break
# Draw the density maps and combine them
images = [draw_to_surface(segment, bandwidth, p.accuracy) for segment in edge_segments]
overall_image = sum(images)
gradients = get_gradients(overall_image)
# Move edges along the gradients and resample when necessary
# This could include smoothing to adjust the amount a graph can change
edge_segments = [advect_resample_all(gradients, segment, p.advect_iterations, p.accuracy, p.min_segment_length, p.max_segment_length)
for segment in edge_segments]
# Do a final resample to a smaller size for nicer rendering
edge_segments = [resample_edges(segment, p.min_segment_length, p.max_segment_length) for segment in edge_segments]
# Finally things can be sent for computation
edge_segments = compute(*edge_segments)
# Smooth out the graph
for i in range(10):
for batch in edge_segments:
smooth(batch, p.tension)
# Flatten things
new_segs = []
for batch in edge_segments:
new_segs.extend(batch)
# Convert list of edge segments to Pandas dataframe
return _convert_edge_segments_to_dataframe(new_segs)
def download(self, catalog_id, file_path, dataset, **kwargs):
p = param.ParamOverrides(self, kwargs)
self.parameter = p.parameter
self.end = pd.to_datetime(p.end)
self.start = pd.to_datetime(p.start)
self._catalog_id = catalog_id
if dataset is None:
dataset = 'station-' + catalog_id
try:
url = self.url
logger.info('downloading data from %s' % url)
data = pd.read_csv(url)
if data.empty:
raise ValueError('No Data Available')
rename = {x: x.split()[0] for x in data.columns.tolist()}
units = {x.split()[0]: x.split()[-1].strip('()').lower() for x in data.columns.tolist()}
data.rename(columns=rename, inplace=True)
data = data.set_index('time')
data.index = pd.to_datetime(data.index)
data.rename(columns={self.parameter_code: self.parameter})
file_path = os.path.join(file_path, self.BASE_PATH, self.service_name, dataset, '{0}.h5'.format(dataset))
metadata = {
'file_path': file_path,
'file_format': 'timeseries-hdf5',
'datatype': 'timeseries',
'parameter': p.parameter,
'unit': units[self.parameter_code],
'service_id': 'svc://noaa:{}/{}'.format(self.service_name, catalog_id)
}
# save data to disk
io = load_plugins('io', 'timeseries-hdf5')['timeseries-hdf5']
io.write(file_path, data, metadata)
del metadata['service_id']
return metadata
except HTTPError as error:
if error.code == 500:
raise ValueError('No Data Available')
elif error.code == 400:
raise ValueError('Bad Request')
else:
raise error
def __call__(self, nodes, edges, **params):
"""
Convert a graph data structure into a path structure for plotting
Given a set of nodes (as a dataframe with a unique ID for each
node) and a set of edges (as a dataframe with with columns for the
source and destination IDs for each edge), returns a dataframe
with with one path for each edge suitable for use with
Datashader. The returned dataframe has columns for x and y
location, with paths represented as successive points separated by
a point with NaN as the x or y value.
"""
p = param.ParamOverrides(self, params)
edges, segment_class = _convert_graph_to_edge_segments(nodes, edges, p)
return _convert_edge_segments_to_dataframe(edges, segment_class, p)
def __call__(self, nodes, edges=None, **params):
p = param.ParamOverrides(self, params)
np.random.seed(p.seed)
df = nodes.copy()
points = np.asarray(
np.random.uniform(low=-115, high=-105, size=(len(df), 1)))
pointsy = np.asarray(
np.random.uniform(low=30, high=40, size=(len(df), 1)))
df[p.x] = points[:, 0]
df[p.y] = pointsy[:, 0]
return df
def __call__(self, *args, **params):
# Abort if IPython not found
try:
ip = params.pop('ip', None) or get_ipython() # noqa (get_ipython)
except:
return
p = param.ParamOverrides(self, params)
if hasattr(ip, 'kernel') and not self._loaded:
# TODO: JLab extension and pyviz_comms should be changed
# to allow multiple cleanup comms to be registered
JupyterCommManager.get_client_comm(self._process_comm_msg,
"hv-extension-comm")
_load_nb(p.inline)
self._loaded = True
Viewable._comm_manager = JupyterCommManager
def process_element(self, element, key, **params):
"""
The process_element method allows a single element to be
operated on given an externally supplied key.
"""
if hasattr(self, 'p'):
if self._allow_extra_keywords:
extras = self.p._extract_extra_keywords(params)
self.p._extra_keywords.update(extras)
params = {k: v for k, v in params.items() if k not in self.p._extra_keywords}
self.p.update(params)
self.p._check_params(params)
else:
self.p = param.ParamOverrides(self, params,
allow_extra_keywords=self._allow_extra_keywords)
return self._apply(element, key)
def __call__(self, **params):
# Generates all channels, then returns the default channel
p = param.ParamOverrides(self, params)
params['xdensity'] = p.xdensity
params['ydensity'] = p.ydensity
params['bounds'] = p.bounds
# (not **p)
for i in range(len(p.generators)):
self._channel_data[i] = p.generators[i](**params)
for c in self.channel_transforms:
self._channel_data = c(self._channel_data)
return sum(act for act in self._channel_data) / len(self._channel_data)
def __call__(self, skyplots, **params):
self.p = param.ParamOverrides(self, params)
pointer = hv.streams.PointerXY(x=0, y=0)
cross_opts = dict(style={'line_width': 1, 'color': 'black'})
cross_dmap = hv.DynamicMap(lambda x, y: (hv.VLine(x).opts(**cross_opts) *
hv.HLine(y).opts(**cross_opts)), streams=[pointer])
plots = []
for s in skyplots:
if self.p.crosshair:
plot = (s*cross_dmap).relabel(s.label)
else:
plot = s
plots.append(plot)
return hv.Layout(plots)
def __call__(self, *args, **params):
resources = self._get_resources(args, params)
ip = params.pop('ip', None)
p = param.ParamOverrides(self, params)
Store.display_formats = p.display_formats
if 'html' not in p.display_formats and len(p.display_formats) > 1:
msg = ('Output magic unable to control displayed format '
'as IPython notebook uses fixed precedence '
'between %r' % p.display_formats)
display(HTML('<b>Warning</b>: %s' % msg))
if notebook_extension._loaded == False:
ip = get_ipython() if ip is None else ip # noqa (get_ipython)
param_ext.load_ipython_extension(ip, verbose=False)
load_magics(ip)
OutputMagic.initialize()
set_display_hooks(ip)
notebook_extension._loaded = True
css = ''
if p.width is not None:
css += '<style>div.container { width: %s%% }</style>' % p.width
if p.css:
css += '<style>%s</style>' % p.css
if css:
display(HTML(css))
resources = list(resources)
if len(resources) == 0: return
# Create a message for the logo (if shown)
js_names = {'holoviews': 'HoloViewsJS'} # resource : displayed name
loaded = ', '.join(js_names[r] if r in js_names else r.capitalize() +
'JS' for r in resources)
load_hvjs(logo=p.logo,
JS=('holoviews' in resources),
message='%s successfully loaded in this cell.' % loaded)
for r in [r for r in resources if r != 'holoviews']:
Store.renderers[r].load_nb(inline=p.inline)
if resources[-1] != 'holoviews':
get_ipython().magic(u"output backend=%r" %
resources[-1]) # noqa (get_ipython))
def __call__(self, **params_to_override):
# Cache image to avoid channel_data being deleted before channel-specific processing completes.
p = param.ParamOverrides(self, params_to_override)
if not (p.cache_image and (p._image is not None)):
self._cached_average = super(FileImage,
self).__call__(**params_to_override)
self._channel_data = self._process_channels(
p, **params_to_override)
for c in self.channel_transforms:
self._channel_data = c(self._channel_data)
if p.cache_image is False:
self._image = None
return self._cached_average
def download(self, catalog_id, file_path, dataset, **kwargs):
p = param.ParamOverrides(self, kwargs)
bbox = listify(p.bbox)
tile_indices = self._get_indices_from_bbox(*bbox,
zoom_level=p.zoom_level)
pixel_indices = self._get_indices_from_bbox(*bbox,
zoom_level=p.zoom_level,
as_pixels=True)
tile_bbox = self._get_bbox_from_indices(*tile_indices,
zoom_level=p.zoom_level)
pixel_bbox = self._get_bbox_from_indices(*pixel_indices,
zoom_level=p.zoom_level,
from_pixels=True)
if p.crop_to_bbox:
upper_left_corner = tile_bbox[0], tile_bbox[3]
crop_bbox = self._get_crop_bbox(pixel_indices,
*upper_left_corner,
zoom_level=p.zoom_level)
adjusted_bbox = pixel_bbox
else:
crop_bbox = None
adjusted_bbox = tile_bbox
image_array = self._download_and_stitch_tiles(p.url, tile_indices,
crop_bbox, p.zoom_level,
p.max_tiles)
file_path = os.path.join(file_path, dataset + '.tiff')
self._write_image_to_tif(image_array, adjusted_bbox, file_path)
metadata = {
'metadata': {
'bbox': adjusted_bbox
},
'file_path': file_path,
'file_format': 'raster-gdal',
'datatype': 'image',
}
return metadata
def publish(self, **kwargs):
try:
p = param.ParamOverrides(self, kwargs)
params = {'name': p.title, 'description': p.collection_description}
resource_information_dict = self.gc.createResource(
path='collection', params=params)
folder_creation_dict = self.gc.createFolder(
parentId=resource_information_dict['_id'],
name=p.folder_name,
description=p.folder_description,
parentType='collection')
for dataset in p.dataset:
dataset_metadata = get_metadata(dataset)[dataset]
fpath = dataset_metadata['file_path']
self.gc.uploadFileToFolder(folder_creation_dict['_id'], fpath)
except Exception as e:
raise e
return resource_information_dict['_id']
def _build_specs(self, specs, kwargs, fp_precision):
"""
Returns the specs, the remaining kwargs and whether or not the
constructor was called with kwarg or explicit specs.
"""
if specs is None:
overrides = param.ParamOverrides(self,
kwargs,
allow_extra_keywords=True)
extra_kwargs = overrides.extra_keywords()
kwargs = dict([(k, v) for (k, v) in kwargs.items()
if k not in extra_kwargs])
rounded_specs = list(
self.round_floats([extra_kwargs], fp_precision))
if extra_kwargs == {}: return [], kwargs, True
else: return rounded_specs, kwargs, False
return list(self.round_floats(specs, fp_precision)), kwargs, True
def __call__(self, nodes, edges=None, **params):
p = param.ParamOverrides(self, params)
np.random.seed(p.seed)
r = 0.5 # radius
x0, y0 = 0.5, 0.5 # center of unit circle
circumference = 2 * np.pi
df = nodes.copy()
if p.uniform:
thetas = np.arange(circumference, step=circumference/len(df))
else:
thetas = np.asarray(np.random.random((len(df),))) * circumference
df[p.x] = x0 + r * np.cos(thetas)
df[p.y] = y0 + r * np.sin(thetas)
return df
def __call__(self, src, **params):
self.p = param.ParamOverrides(self, params)
dims, keys = unique_dimkeys(src)
if isinstance(src, Layout) and not src.uniform:
raise Exception("TreeOperation can only process uniform Layouts")
if not dims:
return self.process_element(src, None)
else:
dim_names = [d.name for d in dims]
values = {}
for key in keys:
selection = src.select(**dict(zip(dim_names, key)))
if not isinstance(selection, Layout):
selection = Layout.from_values([selection])
processed = self._process(selection, key)
if isinstance(processed, list):
processed = Layout.from_values(processed)
values[key] = processed
return Collator(values, kdims=dims)()
def __call__(self, element, **kwargs):
params = dict(kwargs)
for k, v in kwargs.items():
if util.is_param_method(v, has_deps=True):
params[k] = v()
elif isinstance(v, param.Parameter) and isinstance(
v.owner, param.Parameterized):
params[k] = getattr(v.owner, v.name)
self.p = param.ParamOverrides(self, params)
if not self.p.dynamic:
kwargs['dynamic'] = False
if isinstance(element, HoloMap):
# Backwards compatibility for key argument
return element.clone([(k, self._apply(el, key=k))
for k, el in element.items()])
elif isinstance(element, ViewableElement):
return self._apply(element)
elif 'streams' not in kwargs:
kwargs['streams'] = self.p.streams
return element.apply(self, **kwargs)
def __call__(self, nodes, edges, **params):
p = param.ParamOverrides(self, params)
# Convert graph into sparse adjacency matrix and array of points
points = _extract_points_from_nodes(nodes)
matrix = _convert_edges_to_sparse_matrix(edges)
if p.k is None:
p.k = np.sqrt(1.0 / len(points))
# the initial "temperature" is about .1 of domain area (=1x1)
# this is the largest step allowed in the dynamics.
temperature = 0.1
# simple cooling scheme.
# linearly step down by dt on each iteration so last iteration is size dt.
cooling(matrix, points, temperature, p)
# Return the nodes with updated positions
return _merge_points_with_nodes(nodes, points)
def __call__(self, element, **params):
self.p = param.ParamOverrides(self, params)
if isinstance(element, ViewableElement):
processed = self._process(element)
elif isinstance(element, GridSpace):
# Initialize an empty axis layout
processed = GridSpace(None, label=element.label)
# Populate the axis layout
for pos, cell in element.items():
processed[pos] = self(cell, **params)
elif isinstance(element, HoloMap):
mapped_items = [(k, self._process(el, key=k))
for k, el in element.items()]
refval = mapped_items[0][1]
processed = element.clone(mapped_items,
group=refval.group,
label=refval.label)
else:
raise ValueError("Cannot process type %r" % type(element).__name__)
return processed
def __call__(self, parameterized, **params):
self.p = param.ParamOverrides(self, params)
if self.p.initializer:
self.p.initializer(parameterized)
self._widgets = {}
self.parameterized = parameterized
widgets, views = self.widgets()
layout = ipywidgets.Layout(display='flex', flex_flow=self.p.layout)
if self.p.close_button:
layout.border = 'solid 1px'
widget_box = ipywidgets.VBox(children=widgets, layout=layout)
if views:
view_box = ipywidgets.VBox(children=views, layout=layout)
layout = self.p.view_position
if layout in ['below', 'right']:
children = [widget_box, view_box]
else:
children = [view_box, widget_box]
box = ipywidgets.VBox if layout in ['below', 'above'] else ipywidgets.HBox
widget_box = box(children=children)
display(Javascript(WIDGET_JS))
display(widget_box)
self._widget_box = widget_box
for view in views:
p_obj = self.parameterized.params(view.name)
value = getattr(self.parameterized, view.name)
if value is not None:
self._update_trait(view.name, p_obj.renderer(value))
# Keeps track of changes between button presses
self._changed = {}
if self.p.on_init:
self.execute()
def __call__(self, paths=[], **params_to_override):
"""
Takes a single path string or a list of path strings and
returns the corresponing version control information.
"""
p=param.ParamOverrides(self, dict(params_to_override, paths=paths))
if p.paths == []:
raise Exception("No paths to version controlled repositories given.")
paths = [p.paths] if isinstance(p.paths, str) else p.paths
def _desc(path, ind):
for vcs in p.commands.keys():
if os.path.exists(os.path.join(path, vcs)):
proc = subprocess.Popen(p.commands[vcs][ind],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE, cwd=path)
return str(proc.communicate()[0].decode()).strip()
abspaths = [os.path.abspath(path) for path in paths]
return {'vcs_versions' : dict((path, _desc(path,0)) for path in abspaths),
'vcs_messages': dict((path, _desc(path,1)) for path in abspaths),
'vcs_diffs': dict((path, _desc(path,2)) for path in abspaths)}
def __call__(self, element, **params):
self.p = param.ParamOverrides(self, params)
dynamic = ((self.p.dynamic == 'default'
and isinstance(element, DynamicMap))
or self.p.dynamic is True)
if isinstance(element, GridSpace):
# Initialize an empty axis layout
grid_data = ((pos, self(cell, **params))
for pos, cell in element.items())
processed = GridSpace(grid_data,
label=element.label,
kdims=element.kdims)
elif dynamic:
from ..util import Dynamic
streams = getattr(self.p, 'streams', [])
processed = Dynamic(element,
streams=streams,
operation=self,
kwargs=params)
elif isinstance(element, ViewableElement):
processed = self._process(element)
elif isinstance(element, DynamicMap):
if any((not d.values) for d in element.kdims):
raise ValueError('Applying a non-dynamic operation requires '
'all DynamicMap key dimensions to define '
'the sampling by specifying values.')
samples = tuple(d.values for d in element.kdims)
processed = self(element[samples], **params)
elif isinstance(element, HoloMap):
mapped_items = [(k, self._process(el, key=k))
for k, el in element.items()]
processed = element.clone(mapped_items)
else:
raise ValueError("Cannot process type %r" % type(element).__name__)
return processed
def download(self, catalog_id, file_path, dataset, **kwargs):
p = param.ParamOverrides(self, kwargs)
self.parameter = p.parameter
self.end = pd.to_datetime(p.end)
self.start = pd.to_datetime(p.start)
self._catalog_entry = catalog_id
if dataset is None:
dataset = 'station-' + catalog_id
# if end is None:
# end = pd.datetime.now().strftime('%Y-%m-%d')
#
# if start is None:
# start = pd.to_datetime(end) - pd.datetools.timedelta(days=30)
# start = start.strftime('%Y-%m-%d')
file_path = os.path.join(file_path, BASE_PATH, self.service_name,
dataset, '{0}.h5'.format(dataset))
metadata = {
'file_path': file_path,
'file_format': 'timeseries-hdf5',
'datatype': DataType.TIMESERIES,
'parameter': self.parameter,
'unit': self._unit_map[self.parameter],
'service_id': 'svc://ncdc:{}/{}'.format(self.service_name,
catalog_id)
}
# save data to disk
io = load_plugins('io', 'timeseries-hdf5')['timeseries-hdf5']
io.write(file_path, self.data, metadata)
del metadata['service_id']
return metadata
def layout(self, element, **params):
self.p = param.ParamOverrides(self, params)
graph = {'nodes': [], 'links': []}
self.computeNodeLinks(element, graph)
self.computeNodeValues(graph)
self.computeNodeDepths(graph)
self.computeNodeBreadths(graph)
self.computeLinkBreadths(graph)
paths = self.computePaths(graph)
node_data = []
for node in graph['nodes']:
node_data.append((np.mean([node['x0'], node['x1']]),
np.mean([node['y0'], node['y1']]),
node['index'])+tuple(node['values']))
if element.nodes.ndims == 3:
kdims = element.nodes.kdims
elif element.nodes.ndims:
kdims = element.node_type.kdims[:2] + element.nodes.kdims[-1:]
else:
kdims = element.node_type.kdims
nodes = element.node_type(node_data, kdims=kdims, vdims=element.nodes.vdims)
edges = element.edge_type(paths)
return nodes, edges, graph
def __call__(self, *args, **params):
imports = [(name, b) for name, b in self._backends.items()
if name in args or params.get(name, False)]
if not imports or 'matplotlib' not in Store.renderers:
imports = imports + [('matplotlib', 'mpl')]
args = list(args)
for backend, imp in imports:
try:
__import__('holoviews.plotting.%s' % imp)
except ImportError:
if backend in args:
args.pop(args.index(backend))
if backend in params:
params.pop(backend)
self.warning("HoloViews %s backend could not be imported, "
"ensure %s is installed." % (backend, backend))
finally:
if backend == 'matplotlib' and not notebook_extension._loaded:
svg_exporter = Store.renderers['matplotlib'].instance(
holomap=None, fig='svg')
holoviews.archive.exporters = [svg_exporter] +\
holoviews.archive.exporters
OutputMagic.allowed['backend'] = list_backends()
OutputMagic.allowed['fig'] = list_formats('fig', backend)
OutputMagic.allowed['holomap'] = list_formats(
'holomap', backend)
resources = self._get_resources(args, params)
ip = params.pop('ip', None)
p = param.ParamOverrides(self, params)
Store.display_formats = p.display_formats
if 'html' not in p.display_formats and len(p.display_formats) > 1:
msg = ('Output magic unable to control displayed format '
'as IPython notebook uses fixed precedence '
'between %r' % p.display_formats)
display(HTML('<b>Warning</b>: %s' % msg))
if notebook_extension._loaded == False:
ip = get_ipython() if ip is None else ip # noqa (get_ipython)
param_ext.load_ipython_extension(ip, verbose=False)
load_magics(ip)
OutputMagic.initialize(list(self._backends.keys()))
set_display_hooks(ip)
notebook_extension._loaded = True
css = ''
if p.width is not None:
css += '<style>div.container { width: %s%% }</style>' % p.width
if p.css:
css += '<style>%s</style>' % p.css
if css:
display(HTML(css))
resources = list(resources)
if len(resources) == 0: return
# Create a message for the logo (if shown)
js_names = {'holoviews': 'HoloViewsJS'} # resource : displayed name
loaded = ', '.join(js_names[r] if r in js_names else r.capitalize() +
'JS' for r in resources)
load_hvjs(logo=p.logo,
JS=('holoviews' in resources),
message='%s successfully loaded in this cell.' % loaded)
for r in [r for r in resources if r != 'holoviews']:
Store.renderers[r].load_nb(inline=p.inline)
if resources[-1] != 'holoviews':
get_ipython().magic(u"output backend=%r" %
resources[-1]) # noqa (get_ipython))
def __call__(self, *args, **params):
super(notebook_extension, self).__call__(*args, **params)
# Abort if IPython not found
try:
ip = params.pop('ip', None) or get_ipython() # noqa (get_ipython)
except:
return
# Notebook archive relies on display hooks being set to work.
try:
if version_info[0] >= 4:
import nbformat # noqa (ensures availability)
else:
from IPython import nbformat # noqa (ensures availability)
from .archive import notebook_archive
holoviews.archive = notebook_archive
except ImportError:
pass
# Not quite right, should be set when switching backends
if 'matplotlib' in Store.renderers and not notebook_extension._loaded:
svg_exporter = Store.renderers['matplotlib'].instance(holomap=None,
fig='svg')
holoviews.archive.exporters = [svg_exporter
] + holoviews.archive.exporters
p = param.ParamOverrides(
self, {k: v
for k, v in params.items() if k != 'config'})
if p.case_sensitive_completion:
from IPython.core import completer
completer.completions_sorting_key = self.completions_sorting_key
resources = self._get_resources(args, params)
Store.display_formats = p.display_formats
if 'html' not in p.display_formats and len(p.display_formats) > 1:
msg = ('Output magic unable to control displayed format '
'as IPython notebook uses fixed precedence '
'between %r' % p.display_formats)
display(HTML('<b>Warning</b>: %s' % msg))
loaded = notebook_extension._loaded
if loaded == False:
param_ext.load_ipython_extension(ip, verbose=False)
load_magics(ip)
Store.output_settings.initialize(list(Store.renderers.keys()))
Store.set_display_hook('html+js', LabelledData, pprint_display)
Store.set_display_hook('png', LabelledData, png_display)
Store.set_display_hook('svg', LabelledData, svg_display)
notebook_extension._loaded = True
css = ''
if p.width is not None:
css += '<style>div.container { width: %s%% }</style>' % p.width
if p.css:
css += '<style>%s</style>' % p.css
if css:
display(HTML(css))
resources = list(resources)
if len(resources) == 0: return
Renderer.load_nb()
for r in [r for r in resources if r != 'holoviews']:
Store.renderers[r].load_nb(inline=p.inline)
if hasattr(ip, 'kernel') and not loaded:
Renderer.comm_manager.get_client_comm(
notebook_extension._process_comm_msg, "hv-extension-comm")
# Create a message for the logo (if shown)
self.load_hvjs(
logo=p.logo,
bokeh_logo=p.logo and ('bokeh' in resources),
mpl_logo=p.logo
and (('matplotlib' in resources) or resources == ['holoviews']),
plotly_logo=p.logo and ('plotly' in resources),
JS=('holoviews' in resources))
def download(self, catalog_id, file_path, dataset, **kwargs):
p = param.ParamOverrides(self, kwargs)
parameter = p.parameter
start = p.start
end = p.end
period = p.period
if dataset is None:
dataset = 'station-' + catalog_id
if start and end:
period = None
pmap = self.parameter_map(invert=True)
parameter_code, statistic_code = (pmap[parameter].split(':') +
[None])[:2]
data = nwis.get_site_data(catalog_id,
parameter_code=parameter_code,
statistic_code=statistic_code,
start=start,
end=end,
period=period,
service=self.service_name)
# dict contains only one key since only one parameter/statistic was
# downloaded, this would need to be changed if multiple
# parameter/stat were downloaded together
if not data:
raise ValueError('No Data Available')
data = list(data.values())[0]
# convert to dataframe and cleanup bad data
df = pd.DataFrame(data['values'])
if df.empty:
raise ValueError('No Data Available')
df = df.set_index('datetime')
df.value = df.value.astype(float)
if statistic_code in ['00001', '00002', '00003']:
df.index = pd.to_datetime(df.index).to_period('D')
else:
df.index = pd.to_datetime(df.index) # this is in UTC
df[df.values == -999999] = pd.np.nan
df.rename(columns={'value': parameter}, inplace=True)
file_path = os.path.join(file_path, BASE_PATH, self.service_name,
dataset, '{0}.h5'.format(dataset))
del data['values']
metadata = {
'name':
dataset,
'metadata':
data,
'file_path':
file_path,
'file_format':
'timeseries-hdf5',
'datatype':
'timeseries',
'parameter':
parameter,
'unit':
data['variable']['units']['code'],
'service_id':
'svc://usgs-nwis:{}/{}'.format(self.service_name, catalog_id)
}
# save data to disk
io = load_plugins('io', 'timeseries-hdf5')['timeseries-hdf5']
io.write(file_path, df, metadata)
del metadata['service_id']
return metadata
def __call__(self, nodes, edges, **params):
if skimage is None:
raise ImportError(
"hammer_bundle operation requires scikit-image. "
"Ensure you install the dependency before applying "
"bundling.")
p = param.ParamOverrides(self, params)
# Calculate min/max for coordinates
xmin, xmax = np.min(nodes[p.x]), np.max(nodes[p.x])
ymin, ymax = np.min(nodes[p.y]), np.max(nodes[p.y])
# Normalize coordinates
nodes = nodes.copy()
nodes[p.x] = minmax_normalize(nodes[p.x], xmin, xmax)
nodes[p.y] = minmax_normalize(nodes[p.y], ymin, ymax)
# Convert graph into list of edge segments
edges, segment_class = _convert_graph_to_edge_segments(nodes, edges, p)
# This is simply to let the work split out over multiple cores
edge_batches = list(batches(edges, p.batch_size))
# This gets the edges split into lots of small segments
# Doing this inside a delayed function lowers the transmission overhead
edge_segments = [
resample_edges(batch, p.min_segment_length, p.max_segment_length,
segment_class.ndims) for batch in edge_batches
]
for i in range(p.iterations):
# Each step, the size of the 'blur' shrinks
bandwidth = p.initial_bandwidth * p.decay**(i + 1) * p.accuracy
# If it's this small, there won't be a change anyway
if bandwidth < 2:
break
# Draw the density maps and combine them
images = [
draw_to_surface(segment, bandwidth, p.accuracy,
segment_class.accumulate)
for segment in edge_segments
]
overall_image = sum(images)
gradients = get_gradients(overall_image)
# Move edges along the gradients and resample when necessary
# This could include smoothing to adjust the amount a graph can change
edge_segments = [
advect_resample_all(gradients, segment, p.advect_iterations,
p.accuracy, p.min_segment_length,
p.max_segment_length, segment_class)
for segment in edge_segments
]
# Do a final resample to a smaller size for nicer rendering
edge_segments = [
resample_edges(segment, p.min_segment_length, p.max_segment_length,
segment_class.ndims) for segment in edge_segments
]
# Finally things can be sent for computation
edge_segments = compute(*edge_segments)
# Smooth out the graph
for i in range(10):
for batch in edge_segments:
smooth(batch, p.tension, segment_class.idx, segment_class.idy)
# Flatten things
new_segs = []
for batch in edge_segments:
new_segs.extend(batch)
# Convert list of edge segments to Pandas dataframe
df = _convert_edge_segments_to_dataframe(new_segs, segment_class, p)
# Denormalize coordinates
df[p.x] = minmax_denormalize(df[p.x], xmin, xmax)
df[p.y] = minmax_denormalize(df[p.y], ymin, ymax)
return df