Hi @YuniWang2020
thank you for reporting it the problem.
Could you try the following to convert to RTDOSE:
go to the Dicom tab
select an RTDOSE file that it is similar to the USRBIN file
Click on the Import -> USRBIN
It should create an RTDOSE equivalent file embedding the USRBIN as pixel data, and with an instance number 100+InstanceNumber of the original file
Dear @vasilis
Many thanks for your reply, My flair updates to 3.1-3 and I do have CT and RTdose files in my data set:
but still can not convert USRBIN to RT dose:
Started 2020.09.03 13:38:45
Usrbin: /home/fluka/FLUKAwork/DICOM/phatom_99.bnn
RTDOSE: /home/fluka/FLUKAwork/DICOM/Test/RD.dcm
e> ERROR: Cannot open RTDOSE ‘/home/fluka/FLUKAwork/DICOM/Test/RD.dcm’
‘NoneType’ object has no attribute ‘read_file’
It may be my test dicom file is too old? Raystation provided this dicom set for my fluka test, it shows the time is 2009.
@YuniWang2020 I would prefer to fix it no matter if your dicom is old.
Could you try to move the RD.dcm file in the same directory that phantom_99.bnn is located?
@vasilis In the same folder also do not work, as well as copy .bnn to dicom folder. thus I send you these files by email: dicomBnnConvertRD.zip (104.25MB). May help to debug.
Yuni.
BS
Sorry David, still not work. make with no error, but install has same problem. also tried rpm pakage, failed again. I totally set up a new vmware ubuntu 18.04 system to repeat these steps, still not work.
Is the virtual machine cause the problem? but the previous flair version works.
when you are now installing from source you still get the usrbin2dvh: No such file or directory error, or the same with the .rpm package?
If the first, could you try to delete the whole folder of geoviewer, and start over the compilation again?
If the second, that seems to me to be a bug in flair.
@YuniWang2020
the changes I’ve made was mostly on the python part, so for your testing you don’t really need to compile the geoviewer but you can expand the flair…tgz in some directory and copy or symbolic link the files geoviewer.so, usrbin2dvh, fonts/* from the default installation of flair e.g.
Imagine on your home folder
tar xzvf flair-3.1-4a.tgz
cd flair-3.1
ln -sf /usr/local/flair/geoviewer.so .
ln -sf /usr/local/flair/usrbin2dvh .
ln -sf /usr/local/flair/fonts .
When you run you will get some warning on mismatching geoviewer version, but is not a problem for the testing
File “/usr/local/flair/RTViewerTab.py”, line 1517, in roiShow
self._addROI(roi)
File “/usr/local/flair/RTViewerTab.py”, line 1582, in _addROI
array[:,:,iZ] = np.array(img)
ValueError: could not broadcast input array from shape (335,187) into shape (187,335)
Traceback (most recent call last):
File “/usr/local/flair/tkFlair.py”, line 1276, in call
return self.func(*args)
File “/usr/local/flair/RTViewerTab.py”, line 1517, in roiShow
self._addROI(roi)
File “/usr/local/flair/RTViewerTab.py”, line 1582, in _addROI
array[:,:,iZ] = np.array(img)
ValueError: could not broadcast input array from shape (335,187) into shape (187,335)
Usrbin: /home/fluka/FLUKAwork/dicom/fluka/dicom_99.bnn
RTDOSE: /home/fluka/FLUKAwork/dicom/RD1.2.752.243.1.1.20171116154726694.1370.10272.dcm
e> ERROR: Cannot open RTDOSE ‘/home/fluka/FLUKAwork/dicom/RD1.2.752.243.1.1.20171116154726694.1370.10272.dcm’
‘NoneType’ object has no attribute ‘read_file’
so I add anothter link:
ln -sf /usr/local/flair/usrbin2rtdose.py ~/FLUKA4.0/Flair/flair-3.1/usrbin2rtdose.py
but has the same error.
