[vtkusers] Changing level/window in LUT for ImageSlice: Unwanted clipping effects

[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
>>>
>>
>>  _______________________________________________
>>  Powered by www.kitware.com [1]
>>
>>  Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html [2]
>>
>>  Please keep messages on-topic and check the VTK FAQ at:
>> http://www.vtk.org/Wiki/VTK_FAQ [3]
>>
>>  Search the list archives at: http://markmail.org/search/?q=vtkusers
>> [4]
>>
>>  Follow this link to subscribe/unsubscribe:
>>  http://public.kitware.com/mailman/listinfo/vtkusers [5]
>>
>>
>>
>> Links:
>> ------
>> [1] http://www.kitware.com
>> [2] http://www.kitware.com/opensource/opensource.html
>> [3] http://www.vtk.org/Wiki/VTK_FAQ
>> [4] http://markmail.org/search/?q=vtkusers
>> [5] http://public.kitware.com/mailman/listinfo/vtkusers
>>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/opensou
> rce/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/vtkusers
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/vtkusers/attachments/20170202/61d9364a/attachment.html>