[vtkusers] Set window/level and convert image DICOM

[Pedro Paulo]

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. [&#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<mailto: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<mailto: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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