[vtkusers] Set window/level and convert image DICOM

[David Gobbi]

Hi Pedro,

If you get that error with vtkScalarsToColors, then your VTK is very old!
To use vtkScalarsToColors like this, you must use vtk 5.10, vtk 6, or vtk 7.

Maybe you should keep your original code, with vtkImageShiftScale.
The math to convert from "range" to "shift/scale" is shown on this page:
http://www.cognitive-antics.net/mw/index.php?title=Data_range_remapping

 - David



On Fri, Jan 22, 2016 at 12:11 PM, Pedro Paulo <pedropaulobmjr at hotmail.com>
wrote:

> I would like to set the WindowCenter and WindowWidth with which the image
> is converted to png, when I do the conversion using the program I sent, it
> makes the window and level automatically, which I do not want it to do.
> For your second question, yes, I want to calculate my own window and level
> when I convert the image.
> For example, I want to make a conversion with the values ww=2000, wl=250
> and at another time to make a conversion into the same image with the
> values ww=3000, wl=150.
>
>
> I tried using your code like this:
>
>
> from vtk import *
>
> reader = vtkDICOMImageReader()
> reader.SetFileName("img.dcm")
> reader.Update()
> image = reader.GetOutput()
>
> ###########################################################
> ww = 2500
> wl = 200
>
> greymap = vtkScalarsToColors()
> greymap.SetRange(wl-0.5*ww, wl+0.5*ww)
>
> applymap = vtkImageMapToColors()
> applymap.SetInputConnection(reader.GetOutputPort())
> applymap.SetLookupTable(greymap)
>
> applymap.SetOutputFormatToRGB()
> applymap.Update()
> ###########################################################
>
> and I got the following error:
>
> Traceback (most recent call last):
>   File "ff.py", line 12, in <module>
>     greymap = vtkScalarsToColors ()
> TypeError: this is an abstract class and can not be instantiated
>
>
>
> ------------------------------
> *De:* David Gobbi <david.gobbi at gmail.com>
> *Enviado:* sexta-feira, 22 de janeiro de 2016 18:40
>
> *Para:* Pedro Paulo
> *Cc:* vtkusers at vtk.org
> *Assunto:* Re: [vtkusers] Set window/level and convert image DICOM
>
> Hi Pedro,
>
> I think that I misunderstood your question.  Do you want to apply the
> preset
> WindowCenter and WindowWidth that are stored in the DICOM meta data?
> Or do you want to compute your own window and level?
>
>  - David
>
>
> On Thu, Jan 21, 2016 at 11:46 PM, Pedro Paulo <pedropaulobmjr at hotmail.com>
> wrote:
>
>> I'm using python to do this, my code is below, how do I add your code in
>> mine to give right?
>>
>> Does your vtk-dicom package set the parameters ww/wl and do the
>> conversion?
>>
>> Sorry my bad english. [image: &#X1f60a]
>>
>>
>>
>> from vtk import *
>>
>> reader = vtkDICOMImageReader()
>> reader.SetFileName('image.dcm')
>> reader.Update()
>> image = reader.GetOutput()
>>
>> shiftScaleFilter = vtkImageShiftScale()
>> shiftScaleFilter.SetOutputScalarTypeToUnsignedChar()
>> shiftScaleFilter.SetInputConnection(reader.GetOutputPort())
>>
>> shiftScaleFilter.SetShift(-1.0*image.GetScalarRange()[0])
>> oldRange = image.GetScalarRange()[1] - image.GetScalarRange()[0]
>> newRange = 255
>>
>> shiftScaleFilter.SetScale(newRange/oldRange)
>> shiftScaleFilter.Update()
>>
>> writer = vtkPNGWriter()
>> writer.SetFileName('output.jpg')
>> writer.SetInputConnection(shiftScaleFilter.GetOutputPort())
>> writer.Write()
>>
>>
>>
>> ------------------------------
>> *De:* David Gobbi <david.gobbi at gmail.com>
>> *Enviado:* quinta-feira, 21 de janeiro de 2016 22:00
>> *Para:* Pedro Paulo
>> *Cc:* vtkusers at vtk.org
>> *Assunto:* Re: [vtkusers] Set window/level and convert image DICOM
>>
>> Just to clarify my previous email, all CT and PET DICOM images have
>> RescaleIntercept/RescaleSlope, but for CT, it is not uncommon to have
>> RescaleIntercept = 0 and RescaleSlope = 1.  In any case, these fields
>> cannot be ignored if you plan to use WindowCenter and WindowWidth.
>>
>> On Thu, Jan 21, 2016 at 2:47 PM, David Gobbi <david.gobbi at gmail.com>
>> wrote:
>>
>>> Hi Pedro,
>>>
>>> I recommend using vtkImageMapToColors to apply a greyscale lookup table.
>>> In python, for example, it would look like this:
>>>
>>> from vtk import *
>>>
>>> greymap = vtkScalarsToColors()
>>> greymap.SetRange(wl - 0.5*ww, wl + 0.5*ww)
>>>
>>> applymap = vtkImageMapToColors()
>>> applymap.SetInputConnection(...)
>>> applymap.SetLookupTable(greymap)
>>> applymap.SetOutputFormatToRGB() # or use SetOutputFormatToLuminance()
>>> applymap.Update()
>>>
>>> Be careful, though, because according to the DICOM standard the
>>> VOI LUT (i.e. window/level) should only be applied after the Modality LUT
>>> (i.e. the RescaleIntercept/RescaleSlope).  Probably around half of the
>>> CT images and nearly all PET images have RescaleIntercept/RescaleSlope,
>>> so if you do not take these into account, you'll get an incorrect
>>> result.  You'd
>>> be safe with MRI, which does not have RescaleIntercept/Slope.
>>>
>>> So, of course, I'd suggest that you use my vtk-dicom package ;-)
>>> https://github.com/dgobbi/vtk-dicom
>>> It has a filter called vtkDICOMApplyRescale that will correctly apply the
>>> rescale information.
>>>
>>>  - David
>>>
>>>
>>> On Thu, Jan 21, 2016 at 2:22 PM, Pedro Paulo <pedropaulobmjr at hotmail.com
>>> > wrote:
>>>
>>>> Hi people, I want to convert a DICOM image to a png, but, before
>>>> converting, I would like to set the parameters of Window Width and Window
>>>> Center, to that the png image looks like if the parameters of ww/wl were
>>>> seen in a viewer, does anyone know how could I do this?
>>>> Thanks!
>>>>
>>>
>>>
>>
>
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