[Rtk-users] ITK ERROR: Geometry is empty error when generating DRRs

[Simon Rit]

Hi,
1) AddProjection with source / detector positions + u/v decomposes the
provided information in a set of 9 parameters (SID, SDD, source / detector
offsets in the u / v directions and 3 angles). Maybe try to retrieve these
parameters and pass them changing the GantryAngle only? The getters are
available here
<https://github.com/SimonRit/RTK/blob/master/include/rtkThreeDCircularProjectionGeometry.h#L152-L212>.
The problem will likely be that the parameters are defined in a given
convention and what you call GantryAngle might not be equal to that of RTK.
2) No, you'll have to play with small tests and find out by yourself.
Simon

On Tue, Dec 13, 2022 at 11:19 AM Suranga W <
isurusuranga.wijesinghe at gmail.com> wrote:

>  MCR.nii.gz
> <https://drive.google.com/file/d/1-fv97l5u0J_-P0CoO7gMVpqJpMHXUOHB/view?usp=drive_web>
> Hi Simon,
>
> 1.) So, if I want to generate different DRRs by changing the gantry angle,
> how can I do so with these configurations?
> For example, if I invoke the other overloaded AddProjection method which
> can pass the gantry angle, I am unable to set the machine parameters as
> expected. In that case, how can I do it?
>
> 2.) How can I change the origin and size of teh input CT image if I only
> have the field-of-view origin at detector ? Could you please elaborate with
> sample codes if possible for these two cases?
> I herewith attached a sample CT volume for your further consideration.
>
> Could you please assist me in resolving these two problems ? Thanks in
> advance for your time and consideration.
>
>
>
> On Mon, Dec 12, 2022 at 3:08 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>
>> Hi,
>> 1) You can't. This method uses another parametrization.
>> 2) You can set the field-of-view parameters by adjusting the origin and
>> size of the input image.
>> Simon
>>
>> On Mon, Dec 12, 2022 at 3:59 PM Suranga W <
>> isurusuranga.wijesinghe at gmail.com> wrote:
>>
>>> Hi Simon,
>>>
>>> Many thanks. I have another few questions though.
>>>
>>> 1.) How can I pass different gantry angles if I use the aforementioned
>>> AddProjection method, which lacks the gantryAngle parameter? What I want is
>>> to generate DRR images for angles 36, 72, 108, and so on.
>>>
>>> 2.) If I have the field of view origin from a corresponding kV X-ray
>>> dicom image (let's say for gantry angle zero Field of View Origin at
>>> detector is [116.853836060, 4.566089153] in pixels see
>>> <https://dicom.innolitics.com/ciods/enhanced-xa-image/enhanced-xa-image-multi-frame-functional-groups/52009229/00189432/00187030>),
>>> how can I use them to produce DRRs with aforementioned machine
>>> configurations in AddProjection method ?
>>>
>>>
>>>
>>> On Mon, Dec 12, 2022 at 8:43 AM Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Hi,
>>>> You might have missed an earlier message
>>>> WARNING: In
>>>> /home/srit/src/itk/itk/Modules/Remote/RTK/src/rtkThreeDCircularProjectionGeometry.cxx,
>>>> line 210
>>>> DataObject (0x55d436d7ee10): Failed to AddProjection
>>>> The problem is that the two vectors describing the projection
>>>> orientation are not unit vector. You can correct this with:
>>>> geometry.AddProjection([-60.0, 59.0 + sid, 34.0],[-60.0 + 115.,
>>>> 59.0+sid-sdd, 34.0],[1./math.sqrt(2.),1./math.sqrt(2.),0.],[0.,0.,1.])
>>>> Simon
>>>>
>>>> On Fri, Dec 9, 2022 at 1:43 PM Suranga W <
>>>> isurusuranga.wijesinghe at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I attempted to generate DRRs by adding the geometry configuration to
>>>>> the ThreeDCircularProjectionGeometry object, as shown in the attached code
>>>>> (python based code). However, I encountered a runtime error as below
>>>>> (please look at the end of the email).
>>>>>
>>>>> On the other hand, how can I pass the relevant gantry angle to it for
>>>>> generating DRRs at different angles if I add geometry configuration using
>>>>> the addProjection method as mentioned in my code?
>>>>>
>>>>> What I mean is that if I use the code below to set machine parameters,
>>>>> I'm not able to add the corresponding gantry angle for generating DRRs.
>>>>>
>>>>> *geometry.AddProjection([-60.0, 59.0 + sid, 34.0],[-60.0 + 115.,
>>>>> 59.0+sid-sdd, 34.0],[1.,1.,0.],[0.,0.,1.])*
>>>>>
>>>>> where [-60.0, 59.0, 34.0] represents the patient's isocenter.
>>>>>
>>>>> However, if I use the code below, I can use the gantry angle but I
>>>>> cannot set the machine geometry configuration.
>>>>>
>>>>> *geometry.AddProjection(sid, sdd, gantryAngle, projOffsetX,
>>>>> projOffsetY, outOfPlaneAngle, inPlaneAngle, sourceOffsetX, sourceOffsetY)*
>>>>>
>>>>> I attached a CT volume for your further reference.
>>>>>
>>>>> Please assist me in resolving this issue.
>>>>>
>>>>> ---------------------------------------------------------------------------RuntimeError                              Traceback (most recent call last)
>>>>> Cell In [29], line 45     43 rei.SetInput(0, constantImageSource.GetOutput())     44 rei.SetInput(1, CT)---> 45 rei.Update()     47 Dimension = 3     48 OutputPixelType = itk.UC
>>>>> RuntimeError: D:\a\im\include\rtkProjectionsRegionConstIteratorRayBased.hxx:88:
>>>>> ITK ERROR: Geometry is empty, cannot determine iterator type.
>>>>>
>>>>>  drr_projection_with_diff_angles.txt
>>>>> <https://drive.google.com/file/d/1Ags89Lpczvrk_rdHpGSqDcBrashzNSZr/view?usp=drive_web>
>>>>>  sample_CT.nii.gz
>>>>> <https://drive.google.com/file/d/1SGh0cjspFwTj2v8qTLXtcCfbUvyUENS5/view?usp=drive_web>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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