Deleting of RT structures in lua

kholubyev2 · Nov 20th 2014

Dear Conquest&Lua users!

I want to use lua scripting with conquest to process patient datasets (CT/RTDOSE/RTSTRUC/RTPLAN) exported from TPS before they are imported in R&V. E.g. I want to delete some help structures used during the planning. I take deletebody.lua as example and do the following:

Code

x = DicomObject:new()x.PatientName = ''x.PatientID = ''x.QueryRetrieveLevel = 'STUDY'x.StudyInstanceUID = '' -- you want these returned for the loopx.ModalitiesInStudy = ''b=dicomquery('CONQUESTSRV1', 'STUDY', x)for i=0, #b-1 do  StudyUID = b[i].StudyInstanceUID  Modality = b[i].Modality  Modalities = b[i].ModalitiesInStudy  print('Found ', b[i].PatientName, ' ', StudyUID, ' Modalities: ', Modalities,     ' Modality: ', Modality)  -- try to extract RTS  if string.find(Modalities, "RTSTRUCT")~=NIL then    local SeriesInst = dbquery('DICOMSeries', 'SeriesInst', 'StudyInsta = "'..StudyUID..'" and Modality = "RTSTRUCT"')[1][1]    local StructSOP = dbquery('DICOMImages', 'SOPInstanc', 'SeriesInst = "'..SeriesInst..'"')[1][1]    strucs = newdicomobject()    strucs:Read(b[i].PatientID..':'..StructSOP);    strucs:Dump('J:\\strucs0.txt')    print('         strucs modality: ', strucs.Modality)     -- loop over RTS    print('#Structures:', #strucs.StructureSetROISequence)    local roinumber, index    for istruc=0, #strucs.StructureSetROISequence-1 do      print(strucs.StructureSetROISequence[istruc].ROINumber, ' ',         strucs.StructureSetROISequence[istruc].ROIName);      -- find help contour      if strucs.StructureSetROISequence[istruc].ROIName=='HC_Rektum' then        roinumber = strucs.StructureSetROISequence[istruc].ROINumber        index = istruc        print('  Found ', strucs.StructureSetROISequence[istruc].ROIName,          ' roi# ', roinumber, ' index ', index)      end; -- if HC found    end; -- istruc        -- try to delete help contour    print('  deleting in StructureSetROISequence')    print('    before StructureSetROISequence[', index, ']:',       strucs.StructureSetROISequence[index])    strucs.StructureSetROISequence[index]=nil    print('    after StructureSetROISequence[', index, ']:',       strucs.StructureSetROISequence[index])    print('    after StructureSetROISequence[', index, ']:',       strucs.StructureSetROISequence[index])    print('    after StructureSetROISequence[', index, ']:',       strucs.StructureSetROISequence[index])    for istruc=0, #strucs.ROIContourSequence-1 do      if strucs.ROIContourSequence[istruc].ReferencedROINumber==roinumber then        index = istruc        print('  Found roi# ', roinumber, ' in ROIContourSequence, index ', index)      end;    end;    print('  deleting in ROIContourSequence, index: ', index)    strucs.ROIContourSequence[index]=0    for istruc=0, #strucs.RTROIObservationsSequence-1 do      if strucs.RTROIObservationsSequence[istruc].ReferencedROINumber==roinumber then        index = istruc        print('  Found roi# ', roinumber, ' in RTROIObservationsSequence, index ', index)      end;    end;    print('  deleting in RTROIObservationsSequence, index: ', index)    strucs.RTROIObservationsSequence[index]=0    strucs:Dump('J:\\strucs1.txt')  end; -- if RTSTRUCTend

Here's the output from CONQUESTSRV1 (1.4.17d):

Code

[CONQUESTSRV1] UPACS THREAD 41: STARTED AT: Tue Nov 18 08:57:43 2014[CONQUESTSRV1]  Calling Application Title : "CONQUESTSRV1    "[CONQUESTSRV1]  Called Application Title : "CONQUESTSRV1    "[CONQUESTSRV1]  Application Context : "1.2.840.10008.3.1.1.1", PDU length: 16384[CONQUESTSRV1]  Presentation Context 0 "1.2.840.10008.5.1.4.1.2.2.1" 1[CONQUESTSRV1] (StudyRootQuery) search level: STUDY [CONQUESTSRV1] C-Find (StudyRoot) located 2 records[CONQUESTSRV1] UPACS THREAD 41: ENDED AT: Tue Nov 18 08:57:43 2014[CONQUESTSRV1] UPACS THREAD 41: TOTAL RUNNING TIME: 0 SECONDS[CONQUESTSRV1] Found  HEAD EXP2   1.3.46.670589.5.2.10.2156913941.892665384.993397  Modalities:  CT  Modality:  nil[CONQUESTSRV1] Found  XXXX   1.3.12.2.1107.5.8.9.1010144715133114222.1008359  Modalities:  RTSTRUCT\RTPLAN\RTDOSE\CT  Modality:  nil[CONQUESTSRV1]          strucs modality:  RTSTRUCT[CONQUESTSRV1] #Structures: 31[CONQUESTSRV1] 1   REF[CONQUESTSRV1] 2   1ISO[CONQUESTSRV1] 3   NORM[CONQUESTSRV1] 4   Rektum[CONQUESTSRV1] 5   Bladder[CONQUESTSRV1] 6   Hueftkopf li[CONQUESTSRV1] 7   Hueftkopf re[CONQUESTSRV1] 8   Prostatabett[CONQUESTSRV1] 9   Boost[CONQUESTSRV1] 10   PTV[CONQUESTSRV1] 11   TischModell_10mm[CONQUESTSRV1] 12   RV sine PTV[CONQUESTSRV1] 13   RV cum PTV[CONQUESTSRV1] 14   Blase-PTV[CONQUESTSRV1] 15   HC_Deckelung[CONQUESTSRV1] 16   HC_Rektum[CONQUESTSRV1]   Found  HC_Rektum  roi#  16  index  15[CONQUESTSRV1] 17   h[CONQUESTSRV1] 18   HC_PTV_1-0[CONQUESTSRV1] 19   HC_PTV_2-1[CONQUESTSRV1] 20   Outline[CONQUESTSRV1] 21   Outline-0.5[CONQUESTSRV1] 22   Outline-(PTV+2)[CONQUESTSRV1] 23   _Boost-0.5[CONQUESTSRV1] 24   _Boost+0.5[CONQUESTSRV1] 25   _PTV-Boost[CONQUESTSRV1] 26   _(PTV-Boost)-0.5[CONQUESTSRV1] 27   _PTV-(Boost+0.5)[CONQUESTSRV1] 28   Grad[CONQUESTSRV1] 29   Boost-0.5[CONQUESTSRV1] 30   (PTV-Boost)-0.5[CONQUESTSRV1] 31   PTV-Boost[CONQUESTSRV1]   deleting in StructureSetROISequence[CONQUESTSRV1]     before StructureSetROISequence[ 15 ]: userdata:0253F8A0[CONQUESTSRV1]     after StructureSetROISequence[ 15 ]: userdata:02542D10[CONQUESTSRV1]     after StructureSetROISequence[ 15 ]: userdata:01278400[CONQUESTSRV1]     after StructureSetROISequence[ 15 ]: userdata:0128E258[CONQUESTSRV1]   Found roi#  16  in ROIContourSequence, index  15[CONQUESTSRV1]   deleting in ROIContourSequence, index:  15[CONQUESTSRV1]   Found roi#  16  in RTROIObservationsSequence, index  15[CONQUESTSRV1]   deleting in RTROIObservationsSequence, index:  15

Questions:
1) The dumps in strucs0.txt and strucs1.txt are completely identical. The assignments of the kind:

Code

strucs.StructureSetROISequence[index]=nil

do not seem to delete objects from memory. What am I doing wrong?

2) I don't understand the result of consequtive print statements:

Code

[CONQUESTSRV1]   deleting in StructureSetROISequence
[CONQUESTSRV1]     before StructureSetROISequence[ 15 ]: userdata:0253F8A0
[CONQUESTSRV1]     after StructureSetROISequence[ 15 ]: userdata:02542D10
[CONQUESTSRV1]     after StructureSetROISequence[ 15 ]: userdata:01278400
[CONQUESTSRV1]     after StructureSetROISequence[ 15 ]: userdata:0128E258

What is "02542D10" in "userdata:02542D10"? If this is an object address, why does it differ from print statement to print statement?

Any help and advice is highly appreciated!

Kostya

marcelvanherk · Nov 21st 2014

Hi,

I believe deleting sequence items is not implemented. You can delete items inside a sequence I think.

The address chanegs every time because the lua wrapper around the dicom objects is created new everry time. The underlying data remains the same.

Marcel

kholubyev2 · Nov 24th 2014

Hi Marcel,

thank you very much for the reply. I was using deletebody.lua from the lua folder as an example, here is the original listing:

Code

-- This script delete the 'BODY' contour in RTSTRUCT--[[ To test; r-click evaluate in console after project-run:readdicom('c:\\data\\rtstruct.dcm')Data.Dump('c:\\data\\rtstruct_in.txt')dofile('deletebody.lua')Data.Dump('c:\\data\\rtstruct_out.txt')]]local roinumber, index, ifor i=0, #Data.StructureSetROISequence-1 do  print('Found ', Data.StructureSetROISequence[i].ROINumber, ' ', Data.StructureSetROISequence[i].ROIName);  if Data.StructureSetROISequence[i].ROIName=='BODY' then    --print('Trying to delete ', Data.StructureSetROISequence[i].ROIName)    roinumber = Data.StructureSetROISequence[i].ROINumber    index = i  endendData.StructureSetROISequence[index]=nilfor i=0, #Data.ROIContourSequence-1 do  if Data.ROIContourSequence[i].ReferencedROINumber==roinumber then    index = i  endendData.ROIContourSequence[index]=nilfor i=0, #Data.RTROIObservationsSequence-1 do  if Data.RTROIObservationsSequence[i].ReferencedROINumber==roinumber then    index = i  endendData.RTROIObservationsSequence[index]=nil

It seems deleting sequence items should work, isn't it? Maybe there is special way this script should be called, smth like

Code

FileNameSyntax = lua:dofile('deletebody.lua')

Kostya

Quote from marcelvanherk

Hi,

I believe deleting sequence items is not implemented. You can delete items inside a sequence I think.

The address chanegs every time because the lua wrapper around the dicom objects is created new everry time. The underlying data remains the same.

Marcel

Display More

marcelvanherk · Nov 24th 2014

Hi,

the file should be called as:

ImportConverter0 = deletebody.lua

or

[lua]
ImportConverter0 = dofile('deletebody.lua')

It then triggers on incoming data. I cannot remember the history of deletebody - it may not have been tested.

Marcel

kholubyev2 · Dec 1st 2014

Marcel, thank you!

I've put "ImportConverter0 = dofile('deletebody.lua')" in dicom.ini,
istalled MIPAV 7.1.1 and tried to send RTS dicom to Conquest. The RTS file landed in Conquest withput changes:

Code

[CONQUESTSRV1] UPACS THREAD 7: STARTED AT: Mon Dec 01 15:07:41 2014
[CONQUESTSRV1]  Calling Application Title : "SampleStorage   "
[CONQUESTSRV1]  Called Application Title : " CONQUESTSRV1   "
[CONQUESTSRV1]  Application Context : "1.2.840.10008.3.1.1.1", PDU length: 1024
[CONQUESTSRV1]  Presentation Context 0 "1.2.840.10008.5.1.4.1.1.481.3" 1
[CONQUESTSRV1] No image number
[CONQUESTSRV1] Written file: J:\soft\conquest\dicomserver1417d\data\2000195478\2.16.840.1.113669.2.931128.398608374.20141110102010.326622_0001_000000_14174428620003.dcm
[CONQUESTSRV1] UPACS THREAD 7: ENDED AT: Mon Dec 01 15:07:42 2014
[CONQUESTSRV1] UPACS THREAD 7: TOTAL RUNNING TIME: 1 SECONDS

HC_Rektum contour is still there - I checked the dumps, and there were no printout messages from lua like "Found HC_Rektum", "Trying to delete HC_Rektum". Is dicom.ini a correct place to put [lua] code?

Quote from marcelvanherk

Hi,

the file should be called as:

ImportConverter0 = deletebody.lua

or

[lua]
ImportConverter0 = dofile('deletebody.lua')

It then triggers on incoming data. I cannot remember the history of deletebody - it may not have been tested.

Marcel

Display More

kholubyev2 · Dec 2nd 2014

Hi Marcel,

I can sent images/structures to conquest from MIPAV 7.1.1: the connection with conquest works and deletebody.lua gets called (I'm trying to delete HC_Rektum in this case):

Code

[CONQUESTSRV1] UPACS THREAD 3: STARTED AT: Tue Dec 02 08:21:56 2014[CONQUESTSRV1]  Calling Application Title : "SampleStorage   "[CONQUESTSRV1]  Called Application Title : " CONQUESTSRV1   "[CONQUESTSRV1]  Application Context : "1.2.840.10008.3.1.1.1", PDU length: 1024[CONQUESTSRV1]  Presentation Context 0 "1.2.840.10008.5.1.4.1.1.481.3" 1[CONQUESTSRV1] Found  1   REF[CONQUESTSRV1] Found  2   1ISO[CONQUESTSRV1] Found  3   NORM[CONQUESTSRV1] Found  4   Rektum[CONQUESTSRV1] Found  5   Bladder[CONQUESTSRV1] Found  6   Hueftkopf li[CONQUESTSRV1] Found  7   Hueftkopf re[CONQUESTSRV1] Found  8   Prostatabett[CONQUESTSRV1] Found  9   Boost[CONQUESTSRV1] Found  10   PTV[CONQUESTSRV1] Found  11   TischModell_10mm[CONQUESTSRV1] Found  12   RV sine PTV[CONQUESTSRV1] Found  13   RV cum PTV[CONQUESTSRV1] Found  14   Blase-PTV[CONQUESTSRV1] Found  15   HC_Deckelung[CONQUESTSRV1] Found  16   HC_Rektum[CONQUESTSRV1] Trying to delete  HC_Rektum[CONQUESTSRV1] Found  17   h[CONQUESTSRV1] Found  18   HC_PTV_1-0[CONQUESTSRV1] Found  19   HC_PTV_2-1[CONQUESTSRV1] Found  20   Outline[CONQUESTSRV1] Found  21   Outline-0.5[CONQUESTSRV1] Found  22   Outline-(PTV+2)[CONQUESTSRV1] Found  23   _Boost-0.5[CONQUESTSRV1] Found  24   _Boost+0.5[CONQUESTSRV1] Found  25   _PTV-Boost[CONQUESTSRV1] Found  26   _(PTV-Boost)-0.5[CONQUESTSRV1] Found  27   _PTV-(Boost+0.5)[CONQUESTSRV1] Found  28   Grad[CONQUESTSRV1] Found  29   Boost-0.5[CONQUESTSRV1] Found  30   (PTV-Boost)-0.5[CONQUESTSRV1] Found  31   PTV-Boost[CONQUESTSRV1] Rewritten file: J:\soft\conquest\dicomserver1417d\Data\2000195478\2.16.840.1.113669.2.931128.398608374.20141110102010.326622_0001_000000_14174428620003.dcm[CONQUESTSRV1] UPACS THREAD 3: ENDED AT: Tue Dec 02 08:21:58 2014[CONQUESTSRV1] UPACS THREAD 3: TOTAL RUNNING TIME: 2 SECONDS

Here's once again the lua script I'm calling:

Code

local roinumber, index, i
for i=0, #Data.StructureSetROISequence-1 do
  print('Found ', Data.StructureSetROISequence[i].ROINumber, ' ', Data.StructureSetROISequence[i].ROIName);
  if Data.StructureSetROISequence[i].ROIName=='HC_Rektum' then
    print('Trying to delete ', Data.StructureSetROISequence[i].ROIName)
    roinumber = Data.StructureSetROISequence[i].ROINumber
    index = i
  end
end
Data.StructureSetROISequence[index]=nil

for i=0, #Data.ROIContourSequence-1 do
  if Data.ROIContourSequence[i].ReferencedROINumber==roinumber then
    index = i
  end
end
Data.ROIContourSequence[index]=nil


for i=0, #Data.RTROIObservationsSequence-1 do
  if Data.RTROIObservationsSequence[i].ReferencedROINumber==roinumber then
    index = i
  end
end
Data.RTROIObservationsSequence[index]=nil

Display More

Unfortunately HC_Rektum is still there at server side - I checked the dump. Are there plans to properly implement deleting sequence items? It could provide elegant solutions for some use cases.

Thank you once again for the advices!

Kostya

Quote from marcelvanherk

Hi,

the file should be called as:

ImportConverter0 = deletebody.lua

or

[lua]
ImportConverter0 = dofile('deletebody.lua')

It then triggers on incoming data. I cannot remember the history of deletebody - it may not have been tested.

Marcel

Display More

kholubyev2 · Dec 4th 2014

Hi Marcel and other Conquest users,

were it possible to run python scripts on incoming data at server side?

Thx
Kostya

Quote from marcelvanherk

Hi,

the file should be called as:

ImportConverter0 = deletebody.lua

or

[lua]
ImportConverter0 = dofile('deletebody.lua')

It then triggers on incoming data. I cannot remember the history of deletebody - it may not have been tested.

Marcel

Display More

marcelvanherk · Dec 8th 2014

Hi,

I was travelling. You can delete an entire sequence but not an item in a sequence I think (the script I posted was untested).

Can you delete some stuff inside the sequence item to make it invalid?

There is no way to call python.

Marcel

kholubyev2 · Oct 27th 2015

Hy Marcel and others,

I just wonder what's the present status: can lua delete sequence items now? And it seems one can now call python on server side? (http://forum.image-systems.biz/viewtopic.php?f=33&t=43580)

Thanks in advance,
Kostya

Quote from marcelvanherk

Hi,

I was travelling. You can delete an entire sequence but not an item in a sequence I think (the script I posted was untested).

Can you delete some stuff inside the sequence item to make it invalid?

There is no way to call python.

Marcel

Display More

marcelvanherk · Oct 27th 2015

Hi,

I will add it to the bug list and fix it in due time.

Marcel

Deleting of RT structures in lua

Participate now!

Share