Setting marker colors yields error

[rcpeene]

I'm attempting to render neuropixel probes with ccfwidgets and set the marker colors within a jupyter notebook. This yields an error an itk widgets.

Here is my code;

colors = [(1.00, 0, 0.5) for i in range(len(points))]
ccf = CCFWidget(markers=[points])
ccf.marker_colors = colors

where points is a numpy array with shape (2304, 3)

Here is the traceback;

IndexError                                Traceback (most recent call last)
Cell In [49], line 2
      1 ccf = CCFWidget(markers=[points])
----> 2 ccf.marker_colors = colors

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traitlets\traitlets.py:715, in TraitType.__set__(self, obj, value)
    713     raise TraitError('The "%s" trait is read-only.' % self.name)
    714 else:
--> 715     self.set(obj, value)

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traitlets\traitlets.py:2865, in List.set(self, obj, value)
   2863     return super().set(obj, [value])
   2864 else:
-> 2865     return super().set(obj, value)

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traitlets\traitlets.py:689, in TraitType.set(self, obj, value)
    688 def set(self, obj, value):
--> 689     new_value = self._validate(obj, value)
    690     try:
    691         old_value = obj._trait_values[self.name]

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traitlets\traitlets.py:723, in TraitType._validate(self, obj, value)
    721     value = self.validate(obj, value)  # type:ignore[attr-defined]
    722 if obj._cross_validation_lock is False:
--> 723     value = self._cross_validate(obj, value)
    724 return value

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traitlets\traitlets.py:729, in TraitType._cross_validate(self, obj, value)
    727 if self.name in obj._trait_validators:
    728     proposal = Bunch({"trait": self, "value": value, "owner": obj})
--> 729     value = obj._trait_validators[self.name](obj, proposal)
    730 elif hasattr(obj, "_%s_validate" % self.name):
    731     meth_name = "_%s_validate" % self.name

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traitlets\traitlets.py:1132, in EventHandler.__call__(self, *args, **kwargs)
   1130 """Pass `*args` and `**kwargs` to the handler's function if it exists."""
   1131 if hasattr(self, "func"):
-> 1132     return self.func(*args, **kwargs)
   1133 else:
   1134     return self._init_call(*args, **kwargs)

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\ccfwidget\widget_ccf.py:289, in CCFWidget._validate_marker_colors(self, proposal)
    286 @validate('marker_colors')
    287 def _validate_marker_colors(self, proposal):
    288     value = proposal['value']
--> 289     self.itk_viewer.point_set_colors = [(1.0, 0.0, 0.0),]*len(self.swc_point_sets) + value
    290     return value

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traitlets\traitlets.py:715, in TraitType.__set__(self, obj, value)
    713     raise TraitError('The "%s" trait is read-only.' % self.name)
    714 else:
--> 715     self.set(obj, value)

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traittypes\traittypes.py:108, in Array.set(self, obj, value)
    107 def set(self, obj, value):
--> 108     new_value = self._validate(obj, value)
    109     old_value = obj._trait_values.get(self.name, self.default_value)
    110     obj._trait_values[self.name] = new_value

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traitlets\traitlets.py:723, in TraitType._validate(self, obj, value)
    721     value = self.validate(obj, value)  # type:ignore[attr-defined]
    722 if obj._cross_validation_lock is False:
--> 723     value = self._cross_validate(obj, value)
    724 return value

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traitlets\traitlets.py:729, in TraitType._cross_validate(self, obj, value)
    727 if self.name in obj._trait_validators:
    728     proposal = Bunch({"trait": self, "value": value, "owner": obj})
--> 729     value = obj._trait_validators[self.name](obj, proposal)
    730 elif hasattr(obj, "_%s_validate" % self.name):
    731     meth_name = "_%s_validate" % self.name

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\traitlets\traitlets.py:1132, in EventHandler.__call__(self, *args, **kwargs)
   1130 """Pass `*args` and `**kwargs` to the handler's function if it exists."""
   1131 if hasattr(self, "func"):
-> 1132     return self.func(*args, **kwargs)
   1133 else:
   1134     return self._init_call(*args, **kwargs)

File ~\AppData\Local\Programs\Python\Python39\lib\site-packages\itkwidgets\widget_viewer.py:633, in Viewer._validate_point_set_colors(self, proposal)
    631 result = np.zeros((n_colors, 3), dtype=np.float32)
    632 for index, color in enumerate(value):
--> 633     result[index, :] = matplotlib.colors.to_rgb(color)
    634 if len(value) < n_colors:
    635     for index in range(len(value), n_colors):

IndexError: index 1 is out of bounds for axis 0 with size 1

I looked in the examples and found no documentation about the usage of setting marker_colors, so I'm not 100% my usage is correct. The same error is given when passing marker_colors in the ccf constructor. Is this a problem with itkwidgets?

[rcpeene]

Any insight would be useful here so I can add colored points.

[bendichter]

@rpeene can you try using either the keys or the values of this dict?

{'tab:blue': '#1f77b4',
'tab:orange': '#ff7f0e',
'tab:green': '#2ca02c',
'tab:red': '#d62728',
'tab:purple': '#9467bd',
'tab:brown': '#8c564b',
'tab:pink': '#e377c2',
'tab:gray': '#7f7f7f',
'tab:olive': '#bcbd22',
'tab:cyan': '#17becf'}

[rcpeene]

TraitError: could not convert string to float: '#1f77b4'
This error for both keys and values.
It was my understanding that marker_colors ought to be an n x 3 array of floats where n is the number of points.

[rcpeene]

Any updates here? Would love to have this feature working for the databook.

[bendichter]

@thewtex , any idea what might be going on here?

[arjunsridhar12345]

hello, are there any updates on this? would very much like to add colored points to the widget. I am able to pass in a list of colors but the colors do not appear on the widget (all the points are the same color)

[bendichter]

Sorry I am not really able to support this feature myself as I am not that familiar with the itkwidgets package. I think this would rest on @thewtex to fix.