[vtkusers] Changing level/window in LUT for ImageSlice: Unwanted clipping effects
Sophonet
vtk12af6bc42 at kant.sophonet.de
Thu Feb 2 17:56:41 EST 2017
David, do you have a test program / test code that works on your end
(preferrably with an external array similar to my setup)? I could try
here and further trace down the problem I have. Python code would be
fine as well.
Thanks,
Sophonet
Am 2017-02-02 20:12, schrieb David Gobbi:
> Hi Sophonet,
>
> This code looks very fishy to me:
>
> colorMap_->GetTableValue(255, aboveColor);
>
> colorMap_->GetTableValue(0, belowColor);
>
> You shouldn't call GetTableValue() before you have built the table.
> If you haven't built the table, how do you know what colors are stored
> at positions 0 and 255? They could be (0,0,0,0).
>
> - David
>
> On Thu, Feb 2, 2017 at 11:51 AM, Sophonet
> <vtk12af6bc42 at kant.sophonet.de> wrote:
>
>> Hi David,
>>
>> here it is (needed to copy a few lines since the functionality is
>> part of a class). Note that it contains your work-around twice,
>> once, when setting an external colormap, and the second time when
>> changing window/level.
>>
>> Oh, after pasting, it came into my mind that using an external
>> color table might be the reason? In this case, I recall, Build() is
>> not really needed anyway...
>>
>> Hope this helps. Thanks for looking into this so quickly,
>>
>> Sophonet
>>
>> // Initialization
>> vtkSmartPointer<vtkLookupTable> colorMap_ =
>> vtkSmartPointer<vtkLookupTable>::New();
>> vtkSmartPointer<vtkImageProperty> imageProperty_ =
>> vtkSmartPointer<vtkImageProperty>::New();
>> colorMap_->SetNumberOfTableValues(256);
>> colorMap_->SetRange(0, 1);
>>
>> imageProperty_->SetLookupTable(colorMap_);
>> imageProperty_->UseLookupTableScalarRangeOn();
>>
>> imageSlice_->SetProperty(imageProperty_);
>>
>> // Setting color map from external RGBA array
>> colorMap_->SetTable(colorArray); // please see below how I have set
>> up the array...
>> double aboveColor[4];
>> double belowColor[4];
>> colorMap_->GetTableValue(255, aboveColor);
>> colorMap_->SetAboveRangeColor(aboveColor);
>> colorMap_->UseAboveRangeColorOn();
>> colorMap_->GetTableValue(0, belowColor);
>> colorMap_->SetBelowRangeColor(belowColor);
>> colorMap_->UseBelowRangeColorOn();
>> colorMap_->SetNumberOfTableValues(256);
>> colorMap_->Build();
>>
>> // Callback for level / window
>> double minmax[2];
>> minmax[0] = windowLevel_[1] - 0.5*windowLevel_[0];
>> minmax[1] = windowLevel_[1] + 0.5*windowLevel_[0];
>> colorMap_->SetRange(minmax);
>> double aboveColor[4];
>> double belowColor[4];
>> colorMap_->GetTableValue(255, aboveColor);
>> colorMap_->SetAboveRangeColor(aboveColor);
>> colorMap_->UseAboveRangeColorOn();
>> colorMap_->GetTableValue(0, belowColor);
>> colorMap_->SetBelowRangeColor(belowColor);
>> colorMap_->UseBelowRangeColorOn();
>> colorMap_->SetNumberOfTableValues(256);
>> colorMap_->Build();
>>
>> //////////////////////////////////////
>> const unsigned char grayscale[4*256] = {
>> 0, 0, 0, 255, 1, 1, 1, 255,
>> // you can imagine how things continue. I have other more useful
>> arrays for other color scales as well
>> // ...
>> };
>>
>> vtkSmartPointer<vtkUnsignedCharArray> colorArray =
>> vtkSmartPointer<vtkUnsignedCharArray>::New();
>> newMap->SetNumberOfValues(256);
>> newMap->SetNumberOfComponents(4);
>> newMap->SetArray(const_cast<unsigned char *>(grayscale), 4 * 256,
>> 1);
>>
>> Am 2017-02-02 18:51, schrieb David Gobbi:
>> Hi Sophonet,
>>
>> Can you send the exact code that you use to set up the lookup
>> table,
>> including the call to Build(), so that I can check locally?
>>
>> - David
>>
>> On Thu, Feb 2, 2017 at 10:42 AM, Sophonet
>> <vtk12af6bc42 at kant.sophonet.de> wrote:
>>
>> Well, on my system your proposed change did not work, I still see
>> transparent color when LUT clipping occurs, exactly as before. I
>> have even copied your lines of your previous posting plus the
>> Build() call below the SetRange() callback, in which I am doing
>> level/windowing. Not sure why though - I might check again using
>> the
>> HEAD (I am on 7.1.0 release)
>>
>> - Sophonet
>>
>> Am 2017-02-02 18:08, schrieb David Gobbi:
>> Okay, here is a very simple work-around for this issue: Just call
>> Build() on the table after you have set all the other table
>> parameters. Please let me know if this fixes the issue.
>>
>> I've submitted a fix for mapper so that it will call Build()
>> automatically. I'm not sure why it didn't do this before.
>>
>> - David
>>
>> On Thu, Feb 2, 2017 at 8:41 AM, David Gobbi <david.gobbi at gmail.com>
>> wrote:
>>
>> I've discovered more about this issue. The Above/Below colors
>> will
>> work if you call SetNumberOfColors after turning them on:
>>
>> table->SetBelowRangeColor(1,0,0,1);
>> table->SetAboveRangeColor(0,1,0,1);
>> table->UseAboveRangeColorOn();
>> table->UseBelowRangeColorOn();
>> table->SetNumberOfColors(256);
>>
>> I'm still investigating to see why this happens.
>>
>> - David
>>
>> On Thu, Feb 2, 2017 at 7:20 AM, David Gobbi <david.gobbi at gmail.com>
>> wrote:
>>
>> Hi Sophonet,
>>
>> I have confirmed that what you report is true: the
>> vtkImageResliceMapper (and vtkImageSliceMapper) seem to ignore the
>> AboveRangeColor and the BelowRangeColor. This is also true for
>> the
>> current VTK master branch. My current theory is that the mapper
>> clamps the scalars to the range before they go through the lookup
>> table. Hopefully I'll have a fix for this soon.
>>
>> As a workaround (a inefficient workaround), you can use
>> vtkImageMapToColors to apply the lookup table to the image before
>> it
>> goes to the mapper.
>>
>> - David
>>
>>
>> On Thu, Feb 2, 2017 at 5:10 AM, Sophonet
>> <vtk12af6bc42 at kant.sophonet.de> wrote:
>> Dear list,
>>
>> for displaying images, I am using vtkImageResliceMapper. For
>> changing the colormap, I set a dedicated color map to the
>> imageSlice's property (which is a vtkLookupTable) and tell to use
>> its scalar range:
>>
>> colorMap_->SetNumberOfTableValues(256);
>> colorMap_->SetRange(0, 1);
>>
>> imageProperty_->SetLookupTable(colorMap_);
>> imageProperty_->UseLookupTableScalarRangeOn();
>>
>> Now, when changing level/window interactively with the mouse, I am
>> setting the range in the colorMap via
>>
>> double minmax[2];
>> // set values of minmax correctly
>> colorMap_->SetRange(minmax);
>>
>> The changes are displayed correctly - however, areas in which
>> original scalars of the image are clipped, the resulting color is
>> displayed as transparent. However, I would like to display the
>> maximum / minimum value in the color table.
>>
>> I have tried using colorMap_->SetAboveRangeColor() and
>> colorMap_->SetAboveRangeColorOn() (likewise for ...BelowRange...),
>> with no apparent effect.
>>
>> Any advice?
>>
>> I am using VTK 7.1.0.
>>
>> Thanks,
>>
>> Sophonet
>>
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