Posts by toskrip

toskrip · Sep 10th 2014

ok thanks for pointing me to that feature,
just to make sure, does it mean that if I encounter error:
[AddImageFile] ./data/incoming/something.dcm -FAILED: Error on Load

RejectedImageConverter0 can catch it?

Tomas

toskrip · Sep 8th 2014

Hi,

I am using the incoming folder of Conquest to automatically import new DICOM data which are coming from external application. From time to time it happened that some files fail to import (they are corrupted, no compliant and need to be fixed manually). Right now such files are not imported and deleted from incoming folder. I would like to keep them in external folder so I can try to fix them manually and import them afterwards.

I was just wondering it there is a possibility to configure Conquest to archive non imported files for later analysis?

best

Tomas

toskrip · Mar 31st 2014

Hi,

Actually I thought that the fact that it is not returning 0 after quitting is not a cause but a symptom that something went wrong during closing of the program.

Currently it is not a big issue, because operating system will clean up and after cca 1 minute and it is possible to start conquest again. However it prevents to fully use conquest-pacs.sh because the restart option will never work properly (unless we introduce quite a log sleep to give OS time to clean up).

I just thought that we should document this bug (I have it reproduced on multiple linux environments).

best

Tomas

toskrip · Mar 28th 2014

Hi Marcel,

we have currently found one bug. In a linux environment when we want to use provided conquest-pacs.sh script using the start option is just fine. However problem starts when you want to stop it and start it again (or restart). It somehow does not release resources because we are getting:

Failed to listen() - bind error

And this is not just a problem with the script but with conquest termination itself. When I run it directly with dgate -v & and then try to quit it dgate --quit:

Try to start again will give me the same Failed to listen() error. It seems like during quitting something went wrong and it does not return standard exit code 0.

any ideas?

best Tomas

toskrip · Nov 8th 2013

Hi,

Can you please specify in more details what the error says. Because we can only guess, when we do not have more precise information.

From what I see:
- your url should look like this at the first place:
http://[URL[/viewer/index.html?input=http://[URL]/viewer/data/cta2.dcm

The other thing to check is if you have reading permission to the data folder, in other words, if you type:
http://[URL]/viewer/data/cta2.dcm

can you download the dcm file?

Tomas

toskrip · Oct 28th 2013

Hallo Yves,

ok I tested it, so far it seems to work fine. One small issue I have, the progress bar is not displayed while loading the slices.

I did a little bit testing with some testing DICOM studies I have in ConQuest:
- CT modality seems to work ok
- MR modality also fine
- PET modality - there is some issue here the image is completely white
- RT DOSE - sometimes not displayed, sometimes throwing index is out of range
- RT Image - throws "cannot append a slice with different number of columns" (seems like number of images does not match)

anyway very nice work, thanks for that. I am really looking forward to the future of this project. When I find some more time I will have a detailed look on the code and maybe I can help you to implement some additional functionality (especially for the ConQuest integration). What could be nice idea for the future is some kind of UI component faster scrolling between slices (I think scrollbar in image toolbar could work). Also DICOM study viewer which will load DICOM series in the study and provide user option to select one or more (multiple series at once) to display could be done.

Actually I seen some nice videos of HTML 5 DICOM viewer here (good source for inspiration)
http://www.youtube.com/user/pacs2u

best

Tomas

toskrip · Oct 8th 2013

Hi,

I will try it hopefully next week, I only loaded the the trunk from your website with multi slice example. I see that it is loading at once but I just see one slice. I thought that I load them and than e.g. the thumbnails of will be displayed in a special panel. Is it there or do you plan this type of functionality?

best

Tomas

toskrip · Aug 21st 2013

Small bugfix and more optional searching parameters via URL query strings.

Code

-- This script is querying ConQuest PACS in order to retrieve 
-- DICOM patient/study/series data restricted via QueryString parameters
-- the data is reported in JSON format


local patientid = CGI('patientidmatch');
local studyuid = CGI('studyUID');
local studydate = CGI('studyDate');
local seriesuid = CGI('seriesUID');
local modality = CGI('modality');
local seriestime = CGI('seriesTime');


-- Functions declaration


function queryallseries()
  local series, seriest, b, s;


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


  b=newdicomobject();
  b.PatientID = patientid
  b.StudyDate        = studydate;
  b.StudyInstanceUID = studyuid;
  b.StudyDescription = '';
  b.SeriesInstanceUID= seriesuid;
  b.SeriesDescription= '';
  b.Modality         = modality;
  b.SeriesTime       = seriestime;


  series=dicomquery(s, 'SERIES', b);


  -- convert returned DDO (userdata) to table; needed to allow table.sort
  seriest={}
  for k1=0,#series-1 do
    seriest[k1+1]={}
    seriest[k1+1].StudyDate        = series[k1].StudyDate
    seriest[k1+1].PatientID        = series[k1].PatientID
    seriest[k1+1].StudyDate        = series[k1].StudyDate
    seriest[k1+1].SeriesTime       = series[k1].SeriesTime
    seriest[k1+1].StudyInstanceUID = series[k1].StudyInstanceUID
    seriest[k1+1].SeriesDescription= series[k1].SeriesDescription
    seriest[k1+1].StudyDescription = series[k1].StudyDescription
    seriest[k1+1].SeriesInstanceUID= series[k1].SeriesInstanceUID
    seriest[k1+1].Modality         = series[k1].Modality
  end
  return seriest
end


-- RESPONSE


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


local series = queryallseries()
table.sort(series, function(a,b) return a.StudyInstanceUID<b.StudyInstanceUID end)


jsonstring = [[ { "Studies": [ ]] -- start of json obj, start of studies collection


for i=1,#series do
  if series[i].StudyDate == '' then series[i].StudyDate = series[i].SeriesDate end
  if series[i].StudyDate == '' or series[i].StudyDate == nil then series[i].StudyDate = 'Unknown' end

  -- If it is first study study or next study in a list
  local split = (i==1) or (series[i-1].StudyInstanceUID ~= series[i].StudyInstanceUID)


  -- If it is a next study
  if split and i~=1 then
    jsonstring = jsonstring .. [[ ] ]] -- end of series collection if next exist
    jsonstring = jsonstring .. [[ } ]] -- end of study object if next exist
    jsonstring = jsonstring .. [[, ]] -- next study can be created
  end


  -- If  it is first study or next study in a list
  if split then
    --DICOM study json object
    jsonstring = jsonstring .. [[ { ]] -- begin of study object
    jsonstring = jsonstring .. [[ "StudyInstanceUID": "]] .. series[i].StudyInstanceUID .. [[", ]]
    jsonstring = jsonstring .. [[ "StudyDate": "]] .. series[i].StudyDate .. [[", ]]
    if series[i].StudyDescription ~= '' and series[i].StudyDescription ~= nil then
      jsonstring = jsonstring .. [[ "StudyDescription": "]] .. series[i].StudyDescription .. [[", ]]  
    end
    jsonstring = jsonstring .. [[ "Series" : [ ]] -- begin of series collection
  end

  -- DICOM series json collection
  jsonstring = jsonstring .. [[ { ]] -- begin of series object
  jsonstring = jsonstring .. [[ "SeriesInstanceUID" : "]] ..series[i].SeriesInstanceUID .. [[", ]]
  if series[i].SeriesDescription ~= '' and series[i].SeriesDescription ~= nil then
    jsonstring = jsonstring .. [[ "SeriesDescription": "]] .. series[i].SeriesDescription .. [[", ]]
  end
  if series[i].SeriesTime ~= '' and series[i].SeriesTime ~= nil then
    jsonstring = jsonstring .. [[ "SeriesTime": "]] .. series[i].SeriesTime .. [[", ]]
  end
  jsonstring = jsonstring .. [[ "Modality": "]] .. series[i].Modality .. [[ " ]]
  jsonstring = jsonstring .. [[ } ]] -- end of series object


  if i ~= #series then
   if series[i+1].StudyInstanceUID == series[i].StudyInstanceUID then
    jsonstring = jsonstring .. [[, ]] -- there will be nex series object
   end
  end  
end


if #series > 0 then
  jsonstring = jsonstring .. [[ ] ]] -- end of series collection
  jsonstring = jsonstring .. [[ } ]] -- end of study object
end
jsonstring = jsonstring .. [[ ] ]] -- end of studies collection
jsonstring = jsonstring .. [[ } ]] -- end of json obj


HTML(jsonstring)

Display More

Tomas

toskrip · Aug 6th 2013

Hallo,

I have a need to create web application where one of the feature should allow to access DICOM study and series data from Conquest. For this purpose I wrote a small lua script which reports the studies and series hierarchy of specified patient. I just want to share the script, maybe somebody else also find it useful.

Code

local patientid = CGI('patientidmatch');


-- Functions declaration


function queryallseries()
  local series, seriest, b, s;


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


  b=newdicomobject();
  b.PatientID = patientid
  b.StudyDate        = '';
  b.StudyInstanceUID = '';
  b.StudyDescription = '';
  b.SeriesDescription= '';
  b.SeriesInstanceUID= '';
  b.Modality         = '';
  b.SeriesTime       = '';


  series=dicomquery(s, 'SERIES', b);


  -- convert returned DDO (userdata) to table; needed to allow table.sort
  seriest={}
  for k1=0,#series-1 do
    seriest[k1+1]={}
    seriest[k1+1].StudyDate        = series[k1].StudyDate
    seriest[k1+1].PatientID        = series[k1].PatientID
    seriest[k1+1].StudyDate        = series[k1].StudyDate
    seriest[k1+1].SeriesTime       = series[k1].SeriesTime
    seriest[k1+1].StudyInstanceUID = series[k1].StudyInstanceUID
    seriest[k1+1].SeriesDescription= series[k1].SeriesDescription
    seriest[k1+1].StudyDescription = series[k1].StudyDescription
    seriest[k1+1].SeriesInstanceUID= series[k1].SeriesInstanceUID
    seriest[k1+1].Modality         = series[k1].Modality
  end
  return seriest
end


-- RESPONSE


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


local series=queryallseries()
table.sort(series, function(a,b) return a.StudyInstanceUID<b.StudyInstanceUID end)


jsonstring = [[ { "Studies": [ ]] -- start of json obj, start of studies collection


for i=1,#series do
  if series[i].StudyDate == '' then series[i].StudyDate = series[i].SeriesDate end
  if series[i].StudyDate == '' or series[i].StudyDate == nil then series[i].StudyDate = 'Unknown' end

  -- If it is first study study or next study in a list
  local split = (i==1) or (series[i-1].StudyInstanceUID ~= series[i].StudyInstanceUID)


  -- If it is a next study
  if split and i~=1 then
    jsonstring = jsonstring .. [[ ] ]] -- end of series collection if next exist
    jsonstring = jsonstring .. [[ } ]] -- end of study object if next exist
    jsonstring = jsonstring .. [[, ]] -- next study can be created
  end


  -- If  it is first study or next study in a list
  if split then
    --DICOM study json object
    jsonstring = jsonstring .. [[ { ]] -- begin of study object
    jsonstring = jsonstring .. [[ "StudyInstanceUID": "]] .. series[i].StudyInstanceUID .. [[", ]]
    jsonstring = jsonstring .. [[ "StudyDate": "]] .. series[i].StudyDate .. [[", ]]
    if series[i].StudyDescription ~= '' and series[i].StudyDescription ~= nil then
      jsonstring = jsonstring .. [[ "StudyDescription": "]] .. series[i].StudyDescription .. [[", ]]  
    end
    jsonstring = jsonstring .. [[ "Series" : [ ]] -- begin of series collection
  end

  -- DICOM series json collection
  jsonstring = jsonstring .. [[ { ]] -- begin of series object
  jsonstring = jsonstring .. [[ "SeriesInstanceUID" : "]] ..series[i].SeriesInstanceUID .. [[", ]]
  if series[i].SeriesDescription ~= '' and series[i].SeriesDescription ~= nil then
    jsonstring = jsonstring .. [[ "SeriesDescription": "]] .. series[i].SeriesDescription .. [[", ]]
  end
  if series[i].SeriesTime ~= '' and series[i].SeriesTime ~= nil then
    jsonstring = jsonstring .. [[ "SeriesTime": "]] .. series[i].SeriesTime .. [[", ]]
  end
  jsonstring = jsonstring .. [[ "Modality": "]] .. series[i].Modality .. [[ " ]]
  jsonstring = jsonstring .. [[ } ]] -- end of series object


  if i ~= #series then
   if series[i+1].StudyInstanceUID == series[i].StudyInstanceUID then
    jsonstring = jsonstring .. [[, ]] -- there will be nex series object
   end
  end  
end


jsonstring = jsonstring .. [[ ] ]] -- end of series collection
jsonstring = jsonstring .. [[ } ]] -- end of study object
jsonstring = jsonstring .. [[ ] ]] -- end of studies collection
jsonstring = jsonstring .. [[ } ]] -- end of json obj


HTML(jsonstring)

Display More

best

Tomas

toskrip · Jun 21st 2013

Ok, now it is querying the values, but still have a problem to use them:

Code

images[k]["9999,0800"]

seems to return null,

actually it would be nice to know exactly how the userstructure returned from dicomquery fucntion looks like. I am new to lua and this is not apparent to me.

thanks a lot

Tomas

toskrip · Jun 20th 2013

Hi marcel

I checked the samples, but I was unable to find there how it is possible to query the private items 0x9999, 0x0800 for the filename etc. so I can copy them afterwards. I would be grateful if you can elaborate this process in more details.

I also found one problem script('rm ' .. directoryname) does not work for the directory... is there another command how I can delete created directory to clean up.

tnx

this is the script so far...

Code

-- For testing only
patientids = {'176490801738950795192257927136423779330'}


-- Functions


function getImagesForPatient(patientid)
  local images, imaget, b, s
  s = servercommand('get_param:MyACRNema')

  -- When running from command line have to specify it directly
  -- For testing only
  s = 'CONQUESTSRV1'

  b = DicomObject:new()
  b.PatientID = patientid
  b.StudyInstanceUID = '*'
  b.SeriesInstanceUID = '*'
  b.SOPInstanceUID = ''
  images = dicomquery(s, 'IMAGE', b)

  imaget={}
  for k=0,#images-1 do
    imaget[k+1]={}
    imaget[k+1].SOPInstanceUID = images[k].SOPInstanceUID
  end
  table.sort(imaget, function(a,b) return a.SOPInstanceUID < b.SOPInstanceUID end)

  return imaget
end


-- Main


-- for all specified patients
for key, patientid in ipairs(patientids) do


  -- create a folder for patient data
  script('mkdir ' .. patientid)

  print('Looking for dicom data for patient with ID: ' .. patientid)

  -- create table of images
  local images = getImagesForPatient(patientid)
  print('Images count for files: ', #images)


  -- now copy for each  dicom data
  -- script('copy testfile to testcopy')
end


-- now zip all


-- now generate html page with zip as download (also some progress bar)


-- now cleanup
for key, patientid in ipairs(patientids) do
 script('rm ' .. patientid)
end

Display More

best
Tomas

toskrip · Jun 14th 2013

Hi Marcel,

I would like to have one functionality, but I am not sure if it is supported so I rather ask you directly. I would like to provide a users a function where they can select patients which they are interested in and ConQuest will create a zip from the dicom files for selected patients that way that the hierarchy of files keeps the same as it is on the server. Basically the zip will have bunch of subfolders named with patient ids and in each subfolder there will the dicom data.

Is there a possibility to do this in a lua script? Can you give me a hint what API I need to call to accomplish this. My idea is to have a script which will read patients ids from querystring and that it locates the data on ConQuest, zip them a provide to download.

I would be grateful if you could point me to the good direction.

best

Tomas

toskrip · Jun 13th 2013

Hi all,

Just a small update. I was able to integrate conquest DICOM zip download functionality directly into OpenClinica CRF from. It is possible to accomplish this, the same way as the viewer integration. Basically I have a new function in javascript file which is included into CRF which is looking like following:

Code

function downloadStudyData(divDICOMPatientID, divDICOMStudyID) {  var patientIdValue = getFieldInput(divDICOMPatientID);  var studyIdValue = getFieldInput(divDICOMStudyID);  if (patientIdValue != "" && studyIdValue != "") {  var url = "myproxyportal/pacs/dicomStudyDownload.faces?" + "&study=" + patientIdValue + ":" + studyIdValue;  window.open(url, "_blank", "width=1100,height=600,scrollbars=1"); } else {  alert("Warning: patientId and studyId must be specified in order to locate DICOM data on PACS server.")

I redirect to my own java based web app, which is working as a proxy to ConQuest web server. (I dont want to expose ConQuest web directly). But for people who does not need this abstraction they can directly invoke link.lua mode of conqest web server (as it is already described in this thread). In that case the following a snapshot of code which can be added to link.lua to generate a download links:

Code

print([[<a href=# onclick="javascript:PopupCenter(
      ']]..script_name..[[?mode=zipstudy&study=]]..
       series[i].PatientID..':'..series[i].StudyInstanceUID..'&dum=.zip'..
      [[', 'Download', 400, 500)">[download DICOM study]</a>]])


print([[<a href=# onclick="javascript:PopupCenter(
      ']]..script_name..[[?mode=zipseries&series=]]..
       series[i].PatientID..':'..series[i].SeriesInstanceUID..'&dum=.zip'..
      [[', 'Download', 400, 500)">[download DICOM series]</a>]])

best

Tomas

toskrip · Jun 4th 2013

Hi,

My colleague actually located the source of the problem. It is in the DumpVR(VR *vr, FILE *f, int iDepth) function in dgate.cpp file.

There is a declaration for array of chars for dicom object printing and the size of char array is only 256. This is not sufficient especially for RTStruct which can have contour points included and and also RTPlan wiith LeafPositionBoundaries element. After increasing the array size to 2048 it is working again. Maybe it would be wise to have some sort of string size checking on this place.

best

Tomas

toskrip · Jun 4th 2013

dicom server process crashes.

Tomas

toskrip · Jun 3rd 2013

Hi,

My feeling is that the bug is still related to the network communication layer. We tested the 1.4.17 on older linux with 2.* kernel and there it works fine. So the bug is showing up only on newer linux versions with kernel version 3.*

Tomas

toskrip · Jun 3rd 2013

Hi Marcel,

I have found one bug in the 1.4.17 release which is, according to my testing, also present in the alpha and beta versions. I have a DICOM data with CT, RTDOSE, RTPLAN and RTSTRUCT modalities.

When I try to view headers for RTSTRUCT and RTPLAN via the web interface I am getting segmentation fault error.
Headers in CT and RTDOSE modalities are shown properly.

Any idea what can cause this problem? Can somebody reproduce it?
Running environment: 64bit Linux (Debian Wheezy), Postgres database

best

Tomas

toskrip · May 3rd 2013

Hallo,

I just give it a try and it is working like a charm.

thank you

Tomas

toskrip · May 2nd 2013

Hi,

I do not see any real danger in it. This setup is kind of standard in cross site scripting. However if you can make it configurable, than it will be definitely safe. Even more you can let the user specify the origin server which their trust. And the cross site scripting will be available only for this server.

trustServer = http://locahost or xxxx

Access-Control-Allow-Origin: trustServer

Tomas

toskrip · May 2nd 2013

Hi Marcel,

The WADO request which is generated is correct. I think the problem is how the HTTP response of WADO request link is formulated. In the header of the HTTP response there should be the following information and CORS should work after that:

Access-Control-Allow-Origin: *

Marcel, is it possible to change WADO response to include this information in the header?

best

Tomas

Posts by toskrip

Archiving files which failed to import for manual fixing

Archiving files which failed to import for manual fixing

Update 1.4.17d released

Update 1.4.17d released

Conquest and html5+js DICOM viewer (DWV), dwv025 below

Conquest and html5+js DICOM viewer (DWV), dwv025 below

Conquest and html5+js DICOM viewer (DWV), dwv025 below

LUA script for accessing DICOM study data in JSON format

LUA script for accessing DICOM study data in JSON format

Create a zip of dicom files for selection of patients

Create a zip of dicom files for selection of patients

Create a zip of dicom files for selection of patients

Openclinica integration

1.4.17 release out

1.4.17 release out

1.4.17 release out

1.4.17 release out

Conquest and html5+js DICOM viewer (DWV), dwv025 below

Conquest and html5+js DICOM viewer (DWV), dwv025 below

Conquest and html5+js DICOM viewer (DWV), dwv025 below