Investigate jupyter itk-widgets for multi-volume rendering #155
Comments
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Just tried it with a 4D array from itkwidgets import view
view(arr_4d)Error traceback:: ---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
/srv/conda/envs/notebook/lib/python3.6/site-packages/itkTemplate.py in __getitem__(self, parameters)
265 try:
--> 266 return(self.__template__[tuple(cleanParameters)])
267 except:
KeyError: (<itkCType signed short>, 4)
During handling of the above exception, another exception occurred:
KeyError Traceback (most recent call last)
/srv/conda/envs/notebook/lib/python3.6/site-packages/itkTemplate.py in __getitem__(self, parameters)
269 try:
--> 270 return(self.__template__[tuple(cleanParameters)])
271 except:
KeyError: (<itkCType signed short>, 4)
During handling of the above exception, another exception occurred:
KeyError Traceback (most recent call last)
<ipython-input-37-f9ba020a412d> in <module>
----> 1 view(multidim_arr)
/srv/conda/envs/notebook/lib/python3.6/site-packages/itkwidgets/widget_viewer.py in view(image, ui_collapsed, annotations, interpolation, cmap, mode, shadow, slicing_planes, gradient_opacity, **kwargs)
448 annotations=annotations, interpolation=interpolation, cmap=cmap,
449 mode=mode, shadow=shadow, slicing_planes=slicing_planes,
--> 450 gradient_opacity=gradient_opacity, **kwargs)
451 return viewer
/srv/conda/envs/notebook/lib/python3.6/site-packages/itkwidgets/widget_viewer.py in __init__(self, **kwargs)
206
207 def __init__(self, **kwargs):
--> 208 super(Viewer, self).__init__(**kwargs)
209 dimension = self.image.GetImageDimension()
210 largest_region = self.image.GetLargestPossibleRegion()
/srv/conda/envs/notebook/lib/python3.6/site-packages/ipywidgets/widgets/widget.py in __init__(self, **kwargs)
409 """Public constructor"""
410 self._model_id = kwargs.pop('model_id', None)
--> 411 super(Widget, self).__init__(**kwargs)
412
413 Widget._call_widget_constructed(self)
/srv/conda/envs/notebook/lib/python3.6/site-packages/traitlets/traitlets.py in __init__(self, *args, **kwargs)
995 for key, value in kwargs.items():
996 if self.has_trait(key):
--> 997 setattr(self, key, value)
998 else:
999 # passthrough args that don't set traits to super
/srv/conda/envs/notebook/lib/python3.6/site-packages/traitlets/traitlets.py in __set__(self, obj, value)
583 raise TraitError('The "%s" trait is read-only.' % self.name)
584 else:
--> 585 self.set(obj, value)
586
587 def _validate(self, obj, value):
/srv/conda/envs/notebook/lib/python3.6/site-packages/traitlets/traitlets.py in set(self, obj, value)
557
558 def set(self, obj, value):
--> 559 new_value = self._validate(obj, value)
560 try:
561 old_value = obj._trait_values[self.name]
/srv/conda/envs/notebook/lib/python3.6/site-packages/traitlets/traitlets.py in _validate(self, obj, value)
589 return value
590 if hasattr(self, 'validate'):
--> 591 value = self.validate(obj, value)
592 if obj._cross_validation_lock is False:
593 value = self._cross_validate(obj, value)
/srv/conda/envs/notebook/lib/python3.6/site-packages/itkwidgets/trait_types.py in validate(self, obj, value)
28 self._source_object = value
29
---> 30 image_from_array = to_itk_image(value)
31 if image_from_array:
32 return image_from_array
/srv/conda/envs/notebook/lib/python3.6/site-packages/itkwidgets/_to_itk.py in to_itk_image(other_image_datatype)
36 case_use_view = False
37 if case_use_view:
---> 38 image_from_array = itk.GetImageViewFromArray(array)
39 else:
40 image_from_array = itk.GetImageFromArray(array)
/srv/conda/envs/notebook/lib/python3.6/site-packages/itkExtras.py in GetImageViewFromArray(arr, isVector)
284 """Get an ITK image view from a Python array.
285 """
--> 286 return _GetImageFromArray(arr, "GetImageViewFromArray", isVector)
287
288 def _GetArrayFromVnlObject(vnlObject, function):
/srv/conda/envs/notebook/lib/python3.6/site-packages/itkExtras.py in _GetImageFromArray(arr, function, isVector)
272 else:
273 Dimension = arr.ndim
--> 274 ImageType = itk.Image[PixelType, Dimension]
275 templatedFunction = getattr(itk.PyBuffer[ImageType], function)
276 return templatedFunction(arr, isVector)
/srv/conda/envs/notebook/lib/python3.6/site-packages/itkTemplate.py in __getitem__(self, parameters)
272 raise KeyError(
273 'itkTemplate : No template %s for the %s class' %
--> 274 (str(parameters), self.__name__))
275
276 def __repr__(self):
KeyError: 'itkTemplate : No template (<itkCType signed short>, 4) for the itk::Image class'
In contrast, this is the output for a grayscale 3D array from itkwidgets import view
view(arr_3d)
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How to reproduce: # Imports
import os
from urllib.request import urlretrieve
import scipy.misc
import numpy as np
import itk
from itkwidgets import view
# Download data
file_name = '005_32months_T2_RegT1_Reg2Atlas_ManualBrainMask_Stripped.nrrd'
if not os.path.exists(file_name):
url = 'https://data.kitware.com/api/v1/file/564a5b078d777f7522dbfaa6/download'
urlretrieve(url, file_name)
# Create image arrays
itk_image = itk.imread(file_name)
arr_3d = itk.GetArrayViewFromImage(itk_image)
arr_4d = np.stack([arr_3d, np.flip(arr_3d), np.flip(arr_3d, axis=1)], axis=-1)
# Visualize
view(arr_3d)
view(arr_4d) |
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Hi @GenevieveBuckley, I was wondering if you ever figured out a nice way to display multiple volumes / 4d data? :) |
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I didn't pursue this further, I switched teams at work & moved focus into other projects. It's worth seeing whether there's been changes to ITK in the meantime. Maybe @thewtex has more insight? |
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IT's not clear what the best way to
Currently we've been using ipyvolume
But itk jupyter widgets has also been improving their support in this area too.
Recently multivolume support was merged into the vtk-js master branch
Later on it might be possible to view multi-dimensional data with the volume renderer widget
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