Posts by jweste

jweste · Aug 21st 2022

Quote from marcelvanherk

How do you deploy the latest OHIF as a single json file with Yarn? I can then test it easier on my development machine.

Thanks, Marcel

Sorry, Marcel

I didn´t see your post.

Here we have instructions to build and deploy:

https://docs.ohif.org/deployme…build-for-production.html

I never did it. I am not a OHIF user.

I am testing OHIF because it will be cool have it working with conquest node API.

Although I am not a PHP user, it will be easy others users make a Laravel API from node API sample.

Luiz

jweste · Aug 20th 2022

Quote from marcelvanherk

I got the RTSTRUCT working too in php! I'll have a look at the coding error.

Code

function getinstance($st,$se,$sop) {
include 'config.php';
ob_start();
passthru($exe.' "--dolua:dofile([[rquery.lua]]);getinstance([[CONQUESTSRV1]],[['.$st.']],[['.$se.']],[['.$sop.']])"');
$var = ob_get_contents();
ob_end_clean();
header('Access-Control-Allow-Headers: *');
header('Access-Control-Allow-Origin: *');
header('Content-Type: multipart/related; boundary=simpleconquestqidobridge3141592654');

echo("--simpleconquestqidobridge3141592654\r\n");
echo("Content-Type: application/dicom\r\n");
echo("Content-Transfer-Encoding: binary\r\n\r\n");
echo $var;
echo("--simpleconquestqidobridge3141592654--\r\n\r\n");
}

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Are you using it instead of wadouri endpoint in ohif?

jweste · Aug 20th 2022

Quote from marcelvanherk

Hi,

389: I think not, your function returns a dicom object, mine just binary pixel data

388: Ok, so it is a different bug; can you post the dicom object?

Marcel

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Here is: https://www.dropbox.com/s/rki0…pleDicomSR_RT.tar.gz?dl=0

jweste · Aug 20th 2022

Quote from marcelvanherk

I got the RTSTRUCT working too in php! I'll have a look at the coding error.

Code

function getinstance($st,$se,$sop) {
include 'config.php';
ob_start();
passthru($exe.' "--dolua:dofile([[rquery.lua]]);getinstance([[CONQUESTSRV1]],[['.$st.']],[['.$se.']],[['.$sop.']])"');
$var = ob_get_contents();
ob_end_clean();
header('Access-Control-Allow-Headers: *');
header('Access-Control-Allow-Origin: *');
header('Content-Type: multipart/related; boundary=simpleconquestqidobridge3141592654');

echo("--simpleconquestqidobridge3141592654\r\n");
echo("Content-Type: application/dicom\r\n");
echo("Content-Transfer-Encoding: binary\r\n\r\n");
echo $var;
echo("--simpleconquestqidobridge3141592654--\r\n\r\n");
}

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Where OHIF is calling this endpoint?

jweste · Aug 20th 2022

Quote from marcelvanherk

And a working getframe(). Returns binary information without header, tested on old OHIF with wadors.

Code

function getframe(ae, st, se, sop, fr)
  local remotecode = 
[[
  local ae=']]..(ae or servercommand('get_param:MyACRNema'))..[[';
  local q2=DicomObject:new();
  q2.QueryRetrieveLevel='IMAGE'
  q2.StudyInstanceUID=']]..st..[['
  q2.SeriesInstanceUID=']]..(se or '')..[['
  q2.SOPInstanceUID=']]..(sop or '')..[['
  local fr=]]..(fr or 1)..[[
  local r = dicomget(ae, 'IMAGE', q2)
  local s=tempfile('.txt') 
  f = io.open(s, 'wb')
  f:write(r[0]:GetImage(tonumber(fr)-1));
  f:close()
  returnfile=s
]]
 local f = servercommand('lua:'..remotecode, 'binary')
 io.write(f)
end

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I had done this function in lua api.

Isn´t ok?

Code

function readframe(studyInstanceUid,seriesInstanceUid,sopInstanceUid,frame)
  local imagelocation = studyInstanceUid..'\\\\'..seriesInstanceUid..'\\\\'..sopInstanceUid
  local remotecode =
[[
  local x=newdicomobject(); 
  local outfile = tempfile('.dcm')
  local oframe=']]..frame..[['
  x:Read("]]..imagelocation..[[");
 
  x:Script('save frame '..oframe..' to '..outfile)
  returnfile = outfile
  ]]
  b=servercommand('lua:'..remotecode,'binary')
  io.write(b or '')
end

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jweste · Aug 20th 2022

Hi Marcel,

I just tested with the latest version and I still have the problem.

jweste · Aug 20th 2022

Quote from marcelvanherk

Can you post the full incorrect json file?

Marcel

Hi, Marcel

This is the json with problem:

Parse error on line 1:

...vr": "SQ", "Value":[}]}}]},"00700080": {

-----------------------^

Expecting 'STRING', 'NUMBER', 'NULL', 'TRUE', 'FALSE', '{', '[', ']', got '}'

json.zip

jweste · Aug 20th 2022

The json error is in:

Parse error on line 1:

...vr": "SQ", "Value":[}]}}]},"00700080": {

-----------------------^

Expecting 'STRING', 'NUMBER', 'NULL', 'TRUE', 'FALSE', '{', '[', ']', got '}'

jweste · Aug 20th 2022

Hi, Marcel

I just load a rt struct without errors while loading.

But if I click on SR or Seg I get this message(in red).

The metadata function still have a bad json format

jweste · Aug 20th 2022

Quote from marcelvanherk

Luiz,

Does your api work with the old OHIF (just posted on Git).? My php one does.

In mine I have a wado-rs instance endpoint, but it is not accepted by the new OHIF.

Marcel

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Hi, Marcel

>>In mine I have a wado-rs instance endpoint, but it is not accepted by the new OHIF.

Could you post the wado-rs endpoint code?

jweste · Aug 20th 2022

>>I think the only OHIF error is that we are not yet able to serve dicom-rs instances in the correct format- that is used by OHIF to load RTSTRUCTS therefore I have not been able to display RTSTRUCTS. 1.03 does not give any errors, I do not think it supports RTSTRUCT at all.

I agree.

I am searching for wado-rs sample response in the web. But, no look until now.

jweste · Aug 20th 2022

Hi, Marcel

I don´t know if this is usefull for you, but with orthanc and conquest using the same dicom file the struct tags are something as below.

The orthanc tags is not a json file. I copied the metadata from browse. Some tags I collapsed to make easier the copy.

Attached is the same metadata generated by conquest.

I see some tags in orthanc file, not presents in conquest.

I attached the conquest equivalent json metadata generated.

conquest: json.txt

orthanc: orthanc.txt

orthanc: orthanc_main.txt

Code

0008,0000 (GenericGroupLength): 282
0008,0005 (SpecificCharacterSet): ISO_IR 192
0008,0012 (InstanceCreationDate): 20190225
....
»Item 0
0008,0100 (CodeValue): 113100
0008,0102 (CodingSchemeDesignator): DCM
0008,0104 (CodeMeaning): Basic Application Confidentiality Profile
0013,0000 (PrivateGroupLength): 52
0013,0010 (PrivateCreator): CTP
0013,1010 (Unknown Tag & Data): Null
0013,1013 (Unknown Tag & Data): Null
0018,0000 (GenericGroupLength): 16
...
0020,0000 (GenericGroupLength): 164
... 
3006,00a4 (RTROIInterpretedType): ORGAN
3006,00a6 (ROIInterpreter):
»Item 1
3006,0082 (ObservationNumber): 6
3006,0084 (ReferencedROINumber): 6
3006,0085 (ROIObservationLabel): Spinal-Cord
3006,00a4 (RTROIInterpretedType): ORGAN
3006,00a6 (ROIInterpreter):
»Item 2
»Item 3
300e,0000 (GenericGroupLength): 18
300e,0002 (ApprovalStatus): UNAPPROVED

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jweste · Aug 20th 2022

Are you able to render at least one rtstruct file from conquest using ohif?

jweste · Aug 20th 2022

Quote from marcelvanherk

Metadata works for all files, but the old OHIF 1.03 viewer does not attempt to load RTSTRUCTs so it does not need the instance loader.

Marcel

Yes, I see

jweste · Aug 20th 2022

I see no differences between old and new ohif using the API except the error with rtstruct files.

with struct files:

1. The old ohif(you posted) doesn't throw an error, but it doesn´t render the image. Probably, it catches the error.

2. The latest dev ohif throw an error, and it doesn´t render the image as well

I imported the same struct dicom to orthanc.

But It didn´t able to render it.

I'm afraid I haven´t a decent rtstruct file to test.

jweste · Aug 20th 2022

Hi, Marcel

>>Does your api work with the old OHIF (just posted on Git).? My php one does.

Are you talking about dicom files with RTSTRUCT?

jweste · Aug 19th 2022

Quote from marcelvanherk

Hi Luiz,

Thanks! I have added extra processing in dgate for DS and IS tags - now the the metadata is well accepted. Just posted to Git.

The next issue is that RTSTRUCT is not accessed with wadouri but with rs (seems like an error in OHIF to me).

So the instance route must work as well . I have trouble forming the output with php as it requires multipart output, but almost there!

Marcel

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I have structured wado-rs api endpoints in the sources.

But, it´s not operational yet.

Luiz

jweste · Aug 19th 2022

Quote from marcelvanherk

Update on Git.

If you do Serialize(true, true, true) OB, OW and OF are written as an array of numbers

If you do Serialize(true, false, true) OB, OW and OF are not written at all

Getting closer all the time!

Marcel

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Great work.

Sorry for I don´t able to help you in this DICOM API part.

My skills in that area isn´t enough.

Luiz

jweste · Aug 19th 2022

Hi, Marcel,

The metadata still has problem:

other dicom rtstruct: https://www.dropbox.com/s/avt5tqmfm2tewv0/dicomrt2.zip?dl=0

json.zip

Code

Parse error on line 1:
...vr": "OB", "Value":["aڒ�'8MO駖����_�D3SN\
-----------------------^
Expecting 'STRING', 'NUMBER', 'NULL', 'TRUE', 'FALSE', '{', '[', ']', got 'undefined'

jweste · Aug 19th 2022

Hi, Marcel,

I am using now your latest metadata function.

I saw two problems:

1. With this metadata function version the pat id "0009703828" - Head Exp2 doesn´t show in OHIF. The version prior to this works.

2.The json generated with metadata function is not well formed when tested with dicom RTSTRUCT file.

And many value tags aren´t trimmed the extra spaces.

The dicom file is https://www.dropbox.com/s/cfya74vjmebdhet/LUNG1-001.zip?dl=0

Here is the json file

json.txt

If you put the file content into https://jsonformatter.org/ and validate you get:

Code

Parse error on line 1:
...vr": "AT", "Value":["b\u0000\6\u0000"]},
-----------------------^
Expecting 'STRING', 'NUMBER', 'NULL', 'TRUE', 'FALSE', '{', '[', ']', got 'undefined'

Here is my latest lua script:

pasted-from-clipboard.zip

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