[vtkusers] Set window/level and convert image DICOM

Fri Jan 22 16:53:21 EST 2016

Hi Pedro,

I've given you all of the information that you need.  At the very most, all
you have left to do is a little bit of mathematics.

 - David

On Fri, Jan 22, 2016 at 2:44 PM, Pedro Paulo <pedropaulobmjr at hotmail.com>
wrote:

> Yeah, I used with version 6 and functioned normally, thank you, do you
> know how I could do these operations of window/level using my code?
> It is the last feature of my software and I have no idea how to do it.
>
>
>
> ------------------------------
> *De:* David Gobbi <david.gobbi at gmail.com>
> *Enviado:* sexta-feira, 22 de janeiro de 2016 19:22
>
> *Para:* Pedro Paulo
> *Cc:* vtkusers at vtk.org
> *Assunto:* Re: [vtkusers] Set window/level and convert image DICOM
>
> 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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