[vtkusers] Set window/level and convert image DICOM

Pedro Paulo pedropaulobmjr at hotmail.com
Mon Jan 25 19:43:54 EST 2016 

Oops, indeed, it was the hurry, I was leaving work ...


________________________________
De: David Gobbi <david.gobbi at gmail.com>
Enviado: segunda-feira, 25 de janeiro de 2016 22:27
Para: Pedro Paulo
Cc: vtkusers at vtk.org
Assunto: Re: [vtkusers] Set window/level and convert image DICOM

Hi Pedro,

In your code, I suspect the vtkImageShiftScale is redundant. You can remove it and get the same result.

 - David

On Mon, Jan 25, 2016 at 2:31 PM, Pedro Paulo <pedropaulobmjr at hotmail.com<mailto:pedropaulobmjr at hotmail.com>> wrote:

I would like to thank David Gobbi for support and to all who have read but couldn't somehow help, I managed to apply the window/level and convert the image correctly, below is my code, which may be useful to someone in the future, and I believe it will:


from vtk import *

reader = vtkDICOMImageReader()
reader.SetFileName("input.dcm")
reader.Update()
image = reader.GetOutput()


windowlevel = vtkImageMapToWindowLevelColors()
windowlevel.SetInput(reader.GetOutput())

windowlevel.SetWindow(2500)
windowlevel.SetLevel(200)
windowlevel.Update()


shiftScaleFilter = vtkImageShiftScale()
shiftScaleFilter.SetOutputScalarTypeToUnsignedChar()
shiftScaleFilter.SetInputConnection(windowlevel.GetOutputPort())

shiftScaleFilter.SetShift(-1.0*windowlevel.GetOutput().GetScalarRange()[0])
oldRange = windowlevel.GetOutput().GetScalarRange()[1] - windowlevel.GetOutput().GetScalarRange()[0]
newRange = 255

shiftScaleFilter.SetScale(newRange/oldRange)
shiftScaleFilter.Update()


writer = vtkPNGWriter()
writer.SetFileName("out.png")
writer.SetInputConnection(windowlevel.GetOutputPort())
writer.Write()


________________________________
De: Pedro Paulo <pedropaulobmjr at hotmail.com<mailto:pedropaulobmjr at hotmail.com>>
Enviado: domingo, 24 de janeiro de 2016 07:39

Para: Pedro Paulo
Cc: vtkusers at vtk.org<mailto:vtkusers at vtk.org>
Assunto: Re: [vtkusers] Set window/level and convert image DICOM


Now I'm beginning to understand, I was not understanding some things about DICOM, now my question is, do you know how I can access the value of each pixel in the image? And if possible, change these values, for now, only access is sufficient.


________________________________
De: Pedro Paulo <pedropaulobmjr at hotmail.com<mailto:pedropaulobmjr at hotmail.com>>
Enviado: sábado, 23 de janeiro de 2016 06:58
Para: David Gobbi
Assunto: Re: [vtkusers] Set window/level and convert image DICOM


That's the point, I did not understand the steps I need to take to make this calculation of w/l and convert the image to png. I do not ask you to do the implementation, only tell me the steps I need to do, because I did not understand completely, the rest I try to do.


________________________________
De: David Gobbi <david.gobbi at gmail.com<mailto:david.gobbi at gmail.com>>
Enviado: sexta-feira, 22 de janeiro de 2016 21:53
Para: Pedro Paulo
Cc: vtkusers at vtk.org<mailto:vtkusers at vtk.org>
Assunto: Re: [vtkusers] Set window/level and convert image DICOM

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<mailto: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<mailto:david.gobbi at gmail.com>>
Enviado: sexta-feira, 22 de janeiro de 2016 19:22

Para: Pedro Paulo
Cc: vtkusers at vtk.org<mailto: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<mailto: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<mailto:david.gobbi at gmail.com>>
Enviado: sexta-feira, 22 de janeiro de 2016 18:40

Para: Pedro Paulo
Cc: vtkusers at vtk.org<mailto: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<mailto: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. [&#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<mailto:david.gobbi at gmail.com>>
Enviado: quinta-feira, 21 de janeiro de 2016 22:00
Para: Pedro Paulo
Cc: vtkusers at vtk.org<mailto: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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