# Headless DICOM, loadSeriesByUID fails

**URL:** <https://discourse.slicer.org/t/headless-dicom-loadseriesbyuid-fails/8831>\
**Category:** Development\
**Tags:** dicom\
**Created:** [October 18, 2019, 2:02pm UTC](https://discourse.slicer.org/t/headless-dicom-loadseriesbyuid-fails/8831 "2019-10-18T14:02:15Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![unnmdnwb3](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/unnmdnwb3/32/4527_2.png) [@unnmdnwb3](https://discourse.slicer.org/u/unnmdnwb3)\
**Post date:** [October 18, 2019, 2:02pm UTC](https://discourse.slicer.org/t/headless-dicom-loadseriesbyuid-fails/8831/1 "2019-10-18T14:02:15Z")

</div>

Hi everyone,

I’m trying to load DICOM files to scene (within a headless CI-pipeline) by using `DICOMUtils.loadSeriesByUID`, as linked [here](https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/DICOMLib/DICOMUtils.py#L120).

However, **trying to load the scene fails** , although **no error is thrown**.

Importing the files to the db works, using `DICOMUtils.importDicom`, as linked [here](https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/DICOMLib/DICOMUtils.py#L302).

```auto
> New patient inserted: 1
> New patient inserted as : 1
> Need to insert new study: "1.2.826.0.1.3680043.2.146.2.20.3103689.1600244093.0"
> Study Added
> Need to insert new series: "1.3.12.2.1107.5.6.1.2013.31330116120712460953700001577"
> Series Added
> "DICOM indexer has successfully processed 130 files [0.95s]"

```

The series can also be retrieved:

```auto
slicer.dicomDatabase.seriesForStudy(studyList[0])
> ('1.3.12.2.1107.5.6.1.2013.31330116120712460953700001577',)

```

To load the series, I use:

```auto
seriesInstanceUID = '1.3.12.2.1107.5.6.1.2013.31330116120712460953700001577'
ok = utils.loadSeriesByUID([seriesInstanceUID])

```

The loading does not throw an error, but shows this warning:

```auto
> Warning in DICOM plugin Scalar Volume when examining loadable <SeriesName>: Images are not equally spaced (a difference of 3 vs 3 in spacings was detected). If loaded image appears distorted, enable 'Acquisition geometry regularization' in Application settings / DICOM / DICOMScalarVolumePlugin. Please use caution.

```

The function returns `True`, although this seems to be the case even if you import a seriesUID with an invalid UID:

```auto
utils.loadSeriesByUID(['1.3.12.2.1107.5.6.1.2013.31330116120712460953700001577'])
> True

utils.loadSeriesByUID(['an invalid seriesUID'])
> True

```

Either way, after the loading, there are **no child items** attached to the scene:

```auto
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
sceneID = shNode.GetSceneItemID()
items = vtk.vtkIdList()
shNode.GetItemChildren(sceneID, items)
items.GetNumberOfIds()
> 0

```

Is this behaviour linked with the newest [announcements](https://discourse.slicer.org/t/new-dicom-browser-is-ready/8819) of decoupling the widget from the logic?  
Does anyone have a clue why my approach does not work?

Thanks in advance for any feedback! 🙂

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [October 18, 2019, 2:27pm UTC](https://discourse.slicer.org/t/headless-dicom-loadseriesbyuid-fails/8831/2 "2019-10-18T14:27:24Z")

</div>

Interesting - this sounds like something that should work. So if you run the same command in the python console with the gui it does load?

---

<div class="post-metadata">

**Author:** ![unnmdnwb3](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/unnmdnwb3/32/4527_2.png) [@unnmdnwb3](https://discourse.slicer.org/u/unnmdnwb3)\
**Post date:** [October 18, 2019, 2:42pm UTC](https://discourse.slicer.org/t/headless-dicom-loadseriesbyuid-fails/8831/3 "2019-10-18T14:42:52Z")

</div>

Hi @pieper,

Yes exactly, this code works perfectly on my local machine (with GUI), but somehow fails in the pipeline.  
Btw. the pipeline uses `nightly-master:b54b2ea` ([link](https://github.com/Slicer/Slicer/commit/12a221105b1810a5fc6aaf82679c85afb424e8d2)).

Do you think this could be the issue?

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [October 18, 2019, 3:00pm UTC](https://discourse.slicer.org/t/headless-dicom-loadseriesbyuid-fails/8831/4 "2019-10-18T15:00:45Z")

</div>

With the DICOM browser rework, GUI classes are no more needed for indexing and loading DICOM files, so it should be easier to do DICOM operations on a headless node (you should not need to set up X server, etc). However, not all possible use cases are checked by automated testing so maybe there are some regressions.

Do you run the same script exactly the same way?  
Do you launch Slicer using --no-main-window?  
Could you provide a minimal example of a complete script that reproduces the issue?

---

<div class="post-metadata">

**Author:** ![unnmdnwb3](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/unnmdnwb3/32/4527_2.png) [@unnmdnwb3](https://discourse.slicer.org/u/unnmdnwb3)\
**Post date:** [October 21, 2019, 6:40am UTC](https://discourse.slicer.org/t/headless-dicom-loadseriesbyuid-fails/8831/5 "2019-10-21T06:40:05Z")

</div>

Hi @lassoan,

1. Yes, the locally run code is also used for our pipeline - and is therefore exactly the same.
2. We don’t specifically run Slicer, we use `ctest` to run the tests for our extension within our `gitlab-ci`.
3. Sure, the example code below is used for loading the scene:

```python
1. import DICOMLib.DICOMUtils as utils
2.
3. databaseFilePath = 'path/to/slicer/database'
4. slicer.dicomDatabase.openDatabase(databaseFilePath)
5. if not slicer.dicomDatabase.isOpen:
6. self.logger.error('Unable to connect to database')
7.        
8. seriesInstanceUID = '1.3.12.2.1107.5.6.1.2013.31330116120712460953700001577'
9. ok = utils.loadSeriesByUID([seriesInstanceUID])
10. if not ok:
11. self.logger.error('Could not load files from database.')
12.
13. shNode = vtkmrmlutils.getSubjectHierarchyNode()
14. studyID = vtkmrmlutils.getStudyIDs()[0]
15. itemID = vtkmrmlutils.getAllFolderChildren(studyID)[0]
16. 
17. return itemID

```

Previous to this function, files already have been successfully written to the database.

The error-logs for testing the database connection and the loading are both not written. As already mentioned, only the following warning is shown:

```auto
Warning in DICOM plugin Scalar Volume when examining loadable 3: CT LU177 3.0 I31s STD: Images are not equally spaced (a difference of 3 vs 3 in spacings was detected). If loaded image appears distorted, enable 'Acquisition geometry regularization' in Application settings / DICOM / DICOMScalarVolumePlugin. Please use caution.

```

But there is an **error thrown at line 14** :

```auto
subjectID = vtkmrmlutils.getSubjectIDs()[0]
> IndexError: list index out of range

```

As an info, our `vtkmrmlutils` basically wraps all functionality dealing with `vtkmrml` elements. `vtkmrmlutils.getStudyIDs()` returns all nodes with `Level:Study` for the first subject found as a child element of the scene.

```auto
shNode = vtkmrmlutils.getSubjectHierarchyNode()
sceneID = shNode.GetSceneItemID()
try:
    subjectID = vtkmrmlutils.getSubjectIDs()[0]
except:
    raise

```

When trying to find any subjects after loading (_with no apparent error thrown by **DICOMUtils** _), there is no subject to be found in the scene. This means, the files are not correctly loaded, otherwise we would find `1 Subject -> 1 Study -> 1 Series`:

Does this help?

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [October 22, 2019, 12:49pm UTC](https://discourse.slicer.org/t/headless-dicom-loadseriesbyuid-fails/8831/6 "2019-10-22T12:49:34Z")

</div>

How do you determine `databaseFilePath`? When you launch Slicer in testing mode the database is set to a temporary location (see [here](https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/DICOM/DICOM.py#L121-L125)).

The database is attempted to be opened on application startup (see [here](https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/DICOM/DICOM.py#L69)). Maybe the database is switched to the temporary one after you open yours? You can print the database folder and filesForSeries from the database after your failed attempts to retrieve subject hierarchy items.

But all these are really just guessing. The best would be if you could give complete example of your test and CMake file that runs it.

---

<div class="post-metadata">

**Author:** ![unnmdnwb3](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/unnmdnwb3/32/4527_2.png) [@unnmdnwb3](https://discourse.slicer.org/u/unnmdnwb3)\
**Post date:** [October 22, 2019, 1:02pm UTC](https://discourse.slicer.org/t/headless-dicom-loadseriesbyuid-fails/8831/7 "2019-10-22T13:02:21Z")

</div>

Hi @lassoan,

Thanks for your input! We didn’t change anything, but updated the version of `nightly-master` that we use to commit [b485c8b](https://github.com/Slicer/Slicer/commit/80338611790baf572bca02c4e3f90d4aeb3f92de) and this fixed the issue that we had!