Editing RT structures ROI names in lua

toskrip · Dec 10th 2015

Hey,

I was writing a simple lua script, that should allow to do modifications on RTSTRUCT ROINames of already existing data within conquest (I don't need this as converter, because this functionality will be accessible from different webapp calling it as web service).

I have troubles saving the modified RTSTRUCT back to conquest. I was thinking to save it to incoming and let it be reimported, but the Write method does not seem to do the job. Am I missing something?

One additional question... is there a better way of getting the MAGDevice0 path from lua rather than hardcoding it into a script?

My script is here:

Code

-- This script is querying ConQuest PACS in order to retrieve
-- DICOM RTSTRUCT instance restricted via QueryString parameters
-- and update specified ROIName with provided new value


local patientid = CGI('patientidmatch');
local studyuid = CGI('studyUID');
local seriesuid = CGI('seriesUID');
local instanceuid = CGI('instanceUID');
local modality = CGI('modality');
local roiname = CGI('roiname')
local value = CGI('value');


-- Functions declaration


function queryinstance()
  local images, imaget, b, s


  if source == '(local)' then
    s = servercommand('get_param:MyACRNema')
  else
    s = source;
  end


  b = DicomObject:new()
  b.PatientID = patientid
  b.StudyInstanceUID = studyuid
  b.SeriesInstanceUID = seriesuid
  b.SOPInstanceUID = instanceuid
  b.Modality = modality


  rtstructs = dicomquery(s, 'IMAGE', b)


  for i = 0, #rtstructs-1 do


   sop = rtstructs[i].SOPInstanceUID
   local objectfile = dbquery("dicomimages", "objectfile", "sopinstanc = '"..sop.."'")[1][1]


   structs = DicomObject:new()
   structs:Read('/mnt/data1/'..objectfile)


   local roinumber, index
   for i = 0, #structs.StructureSetROISequence-1 do


    if structs.StructureSetROISequence[i].ROIName == roiname then
     structs.StructureSetROISequence[i].ROIName = value;
    end;


   end;


   --structs:Write('/mnt/data1/incoming/'..rtstructs[i].SOPInstanceUID)
   structs:Write('skuska-rt-change.dcm')


  end;
end


-- RESPONSE


HTML('Content-type: application/json\n');
queryinstance()

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I would be glad if somebody can point me to the correct direction for saving data back to conquest.

best

Tomas

marcelvanherk · Dec 10th 2015

Hi,

you can call x:AddImage() -- or addimage(x)

all commands are shown in overview.lua

To query dicom.ini use gpps:

print('----- Read any dicom.ini item -----')
section = 'sscscp'; item = 'MAGDevice0'; default='';
print(gpps(section, item, default))

Marcel

toskrip · Dec 11th 2015

Thanks for prompt response,

I was actually running older version of conquest that did not seem to have AddImage method implemented. So I migrated to 14-17d now but I am getting an error on AddImage:

Code

Removed file: [MAG0:DD-L036D0E1/233412335242842699416507238827857724766_0003_000002_139382758702b5.v2]
***Could not remove IOD /mnt/data1/DD-L036D0E1/233412335242842699416507238827857724766_0003_000002_139382758702b5.v2
***Error writing file: /mnt/data1/DD-L036D0E1/233412335242842699416507238827857724766_0003_000002_14498299920000.dcm
***[lua addimage] Error entering object into serverlocalhost

Also now it removes the instance from DB but it does not delete the dcm file. Just an idea... do I need some additional configuration in web dicom.ini file to make use of AddImage method?

Tomas

marcelvanherk · Dec 11th 2015

Hi Tomas,

do you know why it wants to remove the file? Normally it just overwrites. Or are you now using .dcm file extension.

Marcel

toskrip · Dec 11th 2015

I was missing some of DB configurations in my web dicom.ini. Now the error is gone, it says:

Code

Lua script rewritten file: /mnt/data1/DD-L036D0E1/233412335242842699416507238827857724766_0003_000002_139382758702b5.v2

however the ROIName is unmodified... is modification of tag within sequences supported?

BTW my script now looks like this:

Code

-- This script is querying ConQuest PACS in order to retrieve
-- DICOM RTSTRUCT instance restricted via QueryString parameters
-- and update specified ROIName with provided new value


local patientid = CGI('patientidmatch');
local studyuid = CGI('studyUID');
local seriesuid = CGI('seriesUID');
local instanceuid = CGI('instanceUID');
local roiname = CGI('roiname');
local roinumber = CGI('roinumber');
local value = CGI('value');


-- Functions declaration


function queryinstance()
  local rtstructs, b, s


  if source == '(local)' then
    s = servercommand('get_param:MyACRNema')
  else
    s = source;
  end


  b = DicomObject:new()
  b.PatientID = patientid
  b.StudyInstanceUID = studyuid
  b.SeriesInstanceUID = seriesuid
  b.SOPInstanceUID = instanceuid


  rtstructs = dicomquery(s, 'IMAGE', b)


  section = 'sscscp';
  item = 'MAGDevice0';
  mag0 = gpps(section, item, '');


  for i = 0, #rtstructs-1 do


   modified = false;


   sop = rtstructs[i].SOPInstanceUID
   local objectfile = dbquery("dicomimages", "objectfile", "sopinstanc = '"..sop.."'")[1][1]


   structs = DicomObject:new()
   structs:Read(mag0..objectfile)


   if (structs.Modality == 'RTSTRUCT') then


    for i = 0, #structs.StructureSetROISequence-1 do


     if (structs.StructureSetROISequence[i].ROIName == roiname and structs.StructureSetROISequence[i].ROINumber == roinumber) then
      structs.StructureSetROISequence[i].ROIName = value;
      print(structs.StructureSetROISequence[i].ROIName);
      modified = true;
     end;


    end;


    -- Persist changes in RTSTRUCT
    if modified == true then
     structs:AddImage();
    end;
   end;
  end;
end


-- RESPONSE


HTML('Content-type: application/json\n');
queryinstance()

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T

toskrip · Dec 11th 2015

If I try to change some other tag e.g. PatientName it change the value in SQL database but does not apply it on DICOM lvl, when I dump the file nothing changed there. I have a feeling that I am still missing something in web dicom.ini configuration to allow lua persisting modification on dicom level.

T

marcelvanherk · Dec 12th 2015

Hi,

if you change the image and rewrite is this is the same as resending an image to conquest. The fact that the database changes suggests that the image is correctly reloaded (it reads it to fill the database). You can change tags in a sequence but .v2 file extensions (implicit coding) and sequences are a bad match. Can you save the image with struct:Save and or struct:Dump to see what is going on?

Marcel

toskrip · Dec 14th 2015

I will try to track down, what is happening there. I am using the default 3 as FileNameSyntax property in my conquest instance. You say that v2 are bad match... do you think it would be wise to switch to the option 4 when I am planning to have more lua scripts modifying DICOM data in a long term?

T

toskrip · Dec 14th 2015

Hmm at the end I got it running but it is a little bit ugly. Seems like when lua script is executed as web service it does not have permission to do certain operations (write, dump, ...). However if I use servercommand('lua:'..script), given that the modification (write logic) is within the composed script string, this is executed with conquest user permission and the file is properly modified.

The working script is here:

Code

-- This script is querying ConQuest PACS in order to retrieve
-- DICOM RTSTRUCT instance restricted via QueryString parameters
-- and update specified ROIName with provided new value


local patientid = CGI('patientidmatch');
local studyuid = CGI('studyUID');
local seriesuid = CGI('seriesUID');
local instanceuid = CGI('instanceUID');
local roiname = CGI('roiname');
local roinumber = CGI('roinumber');
local value = CGI('value');


-- Functions declaration


function queryinstance()
  local rtstructs, b, s

  if source == '(local)' then
    s = servercommand('get_param:MyACRNema')
  else
    s = source;
  end

  b = DicomObject:new()
  b.PatientID = patientid
  b.StudyInstanceUID = studyuid
  b.SeriesInstanceUID = seriesuid
  b.SOPInstanceUID = instanceuid

  rtstructs = dicomquery(s, 'IMAGE', b)

  for i = 0, #rtstructs-1 do

   local sop = rtstructs[i].SOPInstanceUID
   local imagelocation = patientid..':'..sop

   servercommand('lua:'.."modified = false; structs=DicomObject:new(); structs:Read('"..imagelocation.."'); if (structs.Modality == 'RTSTRUCT') then for i = 0, #structs.StructureSetROISequence-1 do if (structs.StructureSetROISequence[i].ROIName == '"..roiname.."' and structs.StructureSetROISequence[i].ROINumber == '"..roinumber.."') then structs.StructureSetROISequence[i].ROIName = '"..value.."'; modified=true; end; end; if modified == true then structs:AddImage(); end; end;");

  end;
end;


-- RESPONSE


HTML('Content-type: application/json\n');
queryinstance()

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Tomas

marcelvanherk · Dec 15th 2015

Hi Tomas,

Ah, I can see that. The web service can indeed instruct the dicom server to do its jobs for it. A web service has no access to the local file system.

Regards,

Marcel

Editing RT structures ROI names in lua

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