Getting error in SCCOR image visualization #2
Description
This is the visualization of /pghbio/dbmi/batmanlab/yuke/PythonProject/R3Pipeline/R3/20_Batmanghelich/10/Patient_0111259663/Study_CT_CHEST_WITHOUT_CONTRAST_41209592/Series_2_CHEST_WITHOUT/RAW/Series_2_CHEST_WITHOUT.nii.gz nifti image.
but if I try to visualize /pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0075-2/Date_20071215/001/001.nii.gz
I am getting the below error:
`/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/util.py:1993: RuntimeWarning: invalid value encountered in long_scalars
return length/diff
WARNING:param.load_subset: Callable raised "ValueError('cannot convert float NaN to integer')".
Invoked as load_subset('RANDOM', 0)
WARNING:param.dynamic_operation: Callable raised "ValueError('cannot convert float NaN to integer')".
Invoked as dynamic_operation('RANDOM', 0)
WARNING:param.dynamic_operation: Callable raised "ValueError('cannot convert float NaN to integer')".
Invoked as dynamic_operation('RANDOM', 0, clim=(0, 800))
ValueError Traceback (most recent call last)
/pylon5/ac5616p/debdas/anaconda3/lib/python3.8/site-packages/IPython/core/formatters.py in call(self, obj, include, exclude)
968
969 if method is not None:
--> 970 return method(include=include, exclude=exclude)
971 return None
972 else:
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/panel/viewable.py in repr_mimebundle(self, include, exclude)
467
468 doc = _Document()
--> 469 model = self._render_model(doc, comm)
470 ref = model.ref['id']
471 manager = CommManager(comm_id=comm.id, plot_id=ref)
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/panel/viewable.py in _render_model(self, doc, comm)
415 if comm is None:
416 comm = state._comm_manager.get_server_comm()
--> 417 model = self.get_root(doc, comm)
418
419 if config.embed:
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/panel/viewable.py in get_root(self, doc, comm)
640 """
641 doc = doc or _curdoc()
--> 642 root = self._get_model(doc, comm=comm)
643 self._preprocess(root)
644 ref = root.ref['id']
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/panel/layout.py in _get_model(self, doc, root, parent, comm)
118 if root is None:
119 root = model
--> 120 objects = self._get_objects(model, [], doc, root, comm)
121 props = dict(self._init_properties(), objects=objects)
122 model.update(**self._process_param_change(props))
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/panel/layout.py in _get_objects(self, model, old_objects, doc, root, comm)
108 else:
109 try:
--> 110 child = pane._get_model(doc, root, model, comm)
111 except RerenderError:
112 return self._get_objects(model, current_objects[:i], doc, root, comm)
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/panel/pane/holoviews.py in _get_model(self, doc, root, parent, comm)
225 plot = self.object
226 else:
--> 227 plot = self._render(doc, comm, root)
228
229 plot.pane = self
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/panel/pane/holoviews.py in _render(self, doc, comm, root)
284 kwargs = {}
285
--> 286 return renderer.get_plot(self.object, **kwargs)
287
288 def _cleanup(self, root):
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/plotting/bokeh/renderer.py in get_plot(self_or_cls, obj, doc, renderer, **kwargs)
71 combining the bokeh model with another plot.
72 """
---> 73 plot = super(BokehRenderer, self_or_cls).get_plot(obj, doc, renderer, **kwargs)
74 if plot.document is None:
75 plot.document = Document() if self_or_cls.notebook_context else curdoc()
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/plotting/renderer.py in get_plot(self_or_cls, obj, doc, renderer, comm, **kwargs)
209
210 # Initialize DynamicMaps with first data item
--> 211 initialize_dynamic(obj)
212
213 if not renderer:
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/plotting/util.py in initialize_dynamic(obj)
249 continue
250 if not len(dmap):
--> 251 dmap[dmap._initial_key()]
252
253
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/spaces.py in getitem(self, key)
1278 # Not a cross product and nothing cached so compute element.
1279 if cache is not None: return cache
-> 1280 val = self._execute_callback(*tuple_key)
1281 if data_slice:
1282 val = self._dataslice(val, data_slice)
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/spaces.py in _execute_callback(self, *args)
1052
1053 with dynamicmap_memoization(self.callback, self.streams):
-> 1054 retval = self.callback(*args, **kwargs)
1055 return self._style(retval)
1056
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/spaces.py in call(self, *args, **kwargs)
691
692 try:
--> 693 ret = self.callable(*args, **kwargs)
694 except KeyError:
695 # KeyError is caught separately because it is used to signal
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/util/init.py in dynamic_operation(*key, **kwargs)
983
984 def dynamic_operation(*key, **kwargs):
--> 985 key, obj = resolve(key, kwargs)
986 return apply(obj, *key, **kwargs)
987
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/util/init.py in resolve(key, kwargs)
976 elif isinstance(map_obj, DynamicMap) and map_obj._posarg_keys and not key:
977 key = tuple(kwargs[k] for k in map_obj._posarg_keys)
--> 978 return key, map_obj[key]
979
980 def apply(element, *key, **kwargs):
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/spaces.py in getitem(self, key)
1278 # Not a cross product and nothing cached so compute element.
1279 if cache is not None: return cache
-> 1280 val = self._execute_callback(*tuple_key)
1281 if data_slice:
1282 val = self._dataslice(val, data_slice)
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/spaces.py in _execute_callback(self, *args)
1052
1053 with dynamicmap_memoization(self.callback, self.streams):
-> 1054 retval = self.callback(*args, **kwargs)
1055 return self._style(retval)
1056
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/spaces.py in call(self, *args, **kwargs)
691
692 try:
--> 693 ret = self.callable(*args, **kwargs)
694 except KeyError:
695 # KeyError is caught separately because it is used to signal
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/util/init.py in dynamic_operation(*key, **kwargs)
983
984 def dynamic_operation(*key, **kwargs):
--> 985 key, obj = resolve(key, kwargs)
986 return apply(obj, *key, **kwargs)
987
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/util/init.py in resolve(key, kwargs)
976 elif isinstance(map_obj, DynamicMap) and map_obj._posarg_keys and not key:
977 key = tuple(kwargs[k] for k in map_obj._posarg_keys)
--> 978 return key, map_obj[key]
979
980 def apply(element, *key, **kwargs):
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/spaces.py in getitem(self, key)
1278 # Not a cross product and nothing cached so compute element.
1279 if cache is not None: return cache
-> 1280 val = self._execute_callback(*tuple_key)
1281 if data_slice:
1282 val = self._dataslice(val, data_slice)
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/spaces.py in _execute_callback(self, *args)
1052
1053 with dynamicmap_memoization(self.callback, self.streams):
-> 1054 retval = self.callback(*args, **kwargs)
1055 return self._style(retval)
1056
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/spaces.py in call(self, *args, **kwargs)
691
692 try:
--> 693 ret = self.callable(*args, **kwargs)
694 except KeyError:
695 # KeyError is caught separately because it is used to signal
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/data/init.py in load_subset(*args)
940 if drop_dim and self.interface.gridded:
941 data = data.columns()
--> 942 return group_type(data, **group_kwargs)
943 dynamic_dims = [d.clone(values=list(self.interface.values(self, d.name, False)))
944 for d in dimensions]
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/element/raster.py in init(self, data, kdims, vdims, bounds, extents, xdensity, ydensity, rtol, **params)
323 xdensity = xdensity if xdensity else util.compute_density(l, r, dim1, self._time_unit)
324 ydensity = ydensity if ydensity else util.compute_density(b, t, dim2, self._time_unit)
--> 325 SheetCoordinateSystem.init(self, bounds, xdensity, ydensity)
326 if non_finite:
327 self.bounds = BoundingBox(points=((np.nan, np.nan), (np.nan, np.nan)))
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/sheetcoords.py in init(self, bounds, xdensity, ydensity)
164 self.lbrt = np.array(bounds.lbrt())
165
--> 166 r1,r2,c1,c2 = Slice._boundsspec2slicespec(self.lbrt,self)
167 self.__shape = (r2-r1,c2-c1)
168
/pylon5/ac5616p/debdas/anaconda3/envs/debdas_python/lib/python3.8/site-packages/holoviews/core/sheetcoords.py in _boundsspec2slicespec(boundsspec, scs)
517
518 l_idx = int(np.ceil(l_m-0.5))
--> 519 t_idx = int(np.ceil(t_m-0.5))
520 # CBENHANCEMENT: Python 2.6's math.trunc()?
521 r_idx = int(np.floor(r_m+0.5))
ValueError: cannot convert float NaN to integer
Row
[0] WidgetBox
[0] Select(margin=(20, 20, 5, 20), name='subject_id', options=['RANDOM'], value='RANDOM', width=250)
[1] Select(margin=(0, 20, 5, 20), name='z', options=[0], value=0, width=250)
[2] DiscreteSlider(formatter='%d', margin=(0, 20, 5, 20), name='y', options=OrderedDict([('0', ...]), value=0, width=250)
[3] DiscreteSlider(formatter='%d', margin=(5, 20, 20, 20), name='x', options=OrderedDict([('0', ...]), value=0, width=250)
[4] RangeSlider(end=3000, name='contrast', start=-3000, step=1, value=(0, 800))
[1] HoloViews(GridSpace)`