Detect and select: attaching nodule centroid marker to current slice #250

Serhiy-Shekhovtsov · 2017-11-25T17:52:37Z

Implemented slice switching for candidate list, and a way for user to see when slice differs and attach the marker to current slice.

Description

Following features has been implemented:

switching the viewer to candidate's slice when selecting a candidate
showing to user that marker is on an other slice
clicking on a marker attaches it to current slice

On back-end I have added a method for loading candidates with cases and series. Series object will also have list of DICOM files in the folder saved in uri property.

Reference to official issue

It's an improvement of #148

Screenshot:

full size image

CLA

I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well

lamby · 2017-11-26T02:37:33Z

interface/backend/api/views.py

+        series = candidate['case']['series']
+
+        if 'files' not in series:
+            series['files'] = glob.glob1(series['uri'], '*.dcm')


Can you document why glob1 and not regular glob?

I have put a comment. Btw, this entire piece should be moved from here. We should discover and save list of files only once - when creating a case. So as soon as #145 is done(PR #233 is pending), we will move it.

reubano · 2017-11-26T04:36:46Z

Ran this on aws and am getting a few errors:

...
interface_1   |   File "/usr/local/lib/python3.6/dist-packages/django/views/generic/base.py", line 68, in view
interface_1   |     return self.dispatch(request, *args, **kwargs)
interface_1   |   File "/usr/local/lib/python3.6/dist-packages/rest_framework/views.py", line 489, in dispatch
interface_1   |     response = self.handle_exception(exc)
interface_1   |   File "/usr/local/lib/python3.6/dist-packages/rest_framework/views.py", line 449, in handle_exception
interface_1   |     self.raise_uncaught_exception(exc)
interface_1   |   File "/usr/local/lib/python3.6/dist-packages/rest_framework/views.py", line 486, in dispatch
interface_1   |     response = handler(request, *args, **kwargs)
interface_1   |   File "/app/backend/api/views.py", line 70, in get
interface_1   |     ds = dicom.read_file(path, force=True)
interface_1   |   File "/usr/local/lib/python3.6/dist-packages/dicom/filereader.py", line 614, in read_file
interface_1   |     force=force)
interface_1   |   File "/usr/local/lib/python3.6/dist-packages/dicom/filereader.py", line 553, in read_partial
interface_1   |     stop_when=stop_when, defer_size=defer_size)
interface_1   |   File "/usr/local/lib/python3.6/dist-packages/dicom/filereader.py", line 305, in read_dataset
interface_1   |     raw_data_element = next(de_gen)
interface_1   |   File "/usr/local/lib/python3.6/dist-packages/dicom/filereader.py", line 219, in data_element_generator
interface_1   |     value = fp_read(length)
interface_1   | MemoryError
...
vue_1         | [HPM] Proxy created: /  ->  http://interface:8000
vue_1         | > Starting dev server...
vue_1         |  ERROR  Failed to compile with 1 errors04:30:22
vue_1         | 
vue_1         |  error  in ./src/components/open-image/OpenDICOM.vue
vue_1         | 
vue_1         | 
vue_1         |   ✘  http://eslint.org/docs/rules/indent  Expected indentation of 8 spaces but found 6  
vue_1         |   src/components/open-image/OpenDICOM.vue:76:9
vue_1         |           this.stack.currentImageIdIndex = this.view.paths.indexOf(this.view.state)
vue_1         |            ^
vue_1         | 
vue_1         |   ✘  http://eslint.org/docs/rules/indent  Expected indentation of 8 spaces but found 6  
vue_1         |   src/components/open-image/OpenDICOM.vue:77:9
vue_1         |           if (this.stack.currentImageIdIndex < 0) this.stack.currentImageIdIndex = 0
vue_1         |            ^
vue_1         | 
vue_1         | 
vue_1         | ✘ 2 problems (2 errors, 0 warnings)
vue_1         | 
vue_1         | 
vue_1         | Errors:
vue_1         |   2  http://eslint.org/docs/rules/indent
vue_1         | 
vue_1         |  @ ./~/babel-loader/lib!./~/vue-loader/lib/selector.js?type=script&index=0&bustCache!./src/components/detect-and-select/CandidateList.vue 49:0-48
vue_1         |  @ ./src/components/detect-and-select/CandidateList.vue
vue_1         |  @ ./~/babel-loader/lib!./~/vue-loader/lib/selector.js?type=script&index=0&bustCache!./src/views/DetectAndSelect.vue
vue_1         |  @ ./src/views/DetectAndSelect.vue
vue_1         |  @ ./src/routes.js
vue_1         |  @ ./src/main.js
vue_1         |  @ multi ./build/dev-client ./src/main.js
vue_1         | 
vue_1         | > Listening at http://0.0.0.0:8080
...

And navigating to port 8080 returns a 404 error with Cannot GET /.

Serhiy-Shekhovtsov · 2017-11-26T19:49:23Z

@reubano I have fixed mentioned issues.

lamby · 2017-11-27T23:22:51Z

Build seems to be failing though? :)

reubano · 2017-11-27T23:24:49Z

I also noticed port 8080 was still erroring. I ran git bisect and it seems the failure is from a previous commit. Gimme a sec to find it.

reubano · 2017-11-28T05:49:59Z

So according to git bisect, this commit is the first bad one.

reubano · 2017-11-28T17:52:08Z

So this is the error from travis

=================================== FAILURES ===================================
____________________________ test_lung_segmentation ____________________________
self = (0002, 0001), other = (65534, 57357)
    def __eq__(self, other):
        # Check if comparing with another Tag object; if not, create a temp one
        if not isinstance(other, BaseTag):
            try:
>               other = Tag(other)
/usr/local/lib/python3.6/dist-packages/dicom/tag.py:62: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
arg = (65534, 57357), arg2 = None
    def Tag(arg, arg2=None):
        """General function for creating a Tag in any of the standard forms:
        e.g.  Tag(0x00100010), Tag(0x10,0x10), Tag((0x10, 0x10))
        """
        if arg2 is not None:
            arg = (arg, arg2)  # act as if was passed a single tuple
>       if isinstance(arg, (tuple, list)):
/usr/local/lib/python3.6/dist-packages/dicom/tag.py:21: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
signum = 14, frame = <frame object at 0x7faadaf79cf8>
    def _timeout(signum, frame):
>       raise TimeoutExit("Runner timeout is reached, runner is terminating.")
E       app.src.tests.conftest.TimeoutExit: Runner timeout is reached, runner is terminating.
src/tests/conftest.py:96: TimeoutExit
During handling of the above exception, another exception occurred:
dicom_paths = ['/images_full/LIDC-IDRI-0001/1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178/1.3.6.1.4.1.14519.5.2.1...14519.5.2.1.6279.6001.490157381160200744295382098329/1.3.6.1.4.1.14519.5.2.1.6279.6001.619372068417051974713149104919']
    @pytest.mark.stop_timeout
    def test_lung_segmentation(dicom_paths):
        """Test whether the annotations of the LIDC images are inside the segmented lung masks.
        Iterate over all local LIDC images, fetch the annotations, compute their positions within the masks and check that
        at this point the lung masks are set to 255."""
    
        for path in dicom_paths:
            min_z, max_z = get_z_range(path)
            directories = path.split('/')
            lidc_id = directories[2]
            patient_id = directories[-1]
>           original, mask = save_lung_segments(path, patient_id)
src/tests/test_segmentation.py:49: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
src/preprocess/lung_segmentation.py:61: in save_lung_segments
    slices = load_patient(dicom_path)
src/preprocess/lung_segmentation.py:95: in load_patient
    dicom_slice = dicom.read_file(os.path.join(src_dir, s))
/usr/local/lib/python3.6/dist-packages/dicom/filereader.py:614: in read_file
    force=force)
/usr/local/lib/python3.6/dist-packages/dicom/filereader.py:521: in read_partial
    file_meta_dataset = _read_file_meta_info(fileobj)
/usr/local/lib/python3.6/dist-packages/dicom/filereader.py:447: in _read_file_meta_info
    is_little_endian=True, stop_when=not_group2)
/usr/local/lib/python3.6/dist-packages/dicom/filereader.py:309: in read_dataset
    if tag == (0xFFFE, 0xE00D):
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
self = (0002, 0001), other = (65534, 57357)
    def __eq__(self, other):
        # Check if comparing with another Tag object; if not, create a temp one
        if not isinstance(other, BaseTag):
            try:
                other = Tag(other)
            except:
>               raise TypeError("Cannot compare Tag with non-Tag item")
E               TypeError: Cannot compare Tag with non-Tag item
/usr/local/lib/python3.6/dist-packages/dicom/tag.py:64: TypeError
----------------------------- Captured stderr call -----------------------------
ERROR:root:69.xml is no valid DICOM
=============================== warnings summary ===============================
src/tests/test_endpoints.py::test_identify
  /app/src/tests/../../src/preprocess/extract_lungs.py:34: RuntimeWarning: invalid value encountered in less
    truncate=2.0) < intensity_th
src/tests/test_identification.py::test_identify_nodules_001
  /app/src/tests/../../src/preprocess/extract_lungs.py:34: RuntimeWarning: invalid value encountered in less
    truncate=2.0) < intensity_th
src/tests/test_identification.py::test_identify_nodules_003
  /app/src/tests/../../src/preprocess/extract_lungs.py:34: RuntimeWarning: invalid value encountered in less
    truncate=2.0) < intensity_th
-- Docs: http://doc.pytest.org/en/latest/warnings.html
========= 1 failed, 47 passed, 4 xfailed, 3 warnings in 820.90 seconds =========
The command "sh tests/test_docker.sh" exited with 1.
Done. Your build exited with 1.

I also rebuilt it, and port 8080 loads now, but clicking 'Detect and Select' doesn't do anything.

…t slice, added slice index to saving properties

Serhiy-Shekhovtsov · 2017-11-28T19:30:10Z

@reubano, @lamby PR has been fixed by rebasing it of top of last commit that actually fixed the issue.

but clicking 'Detect and Select' doesn't do anything.

This is because of the Router Guard(#239) implementation :) You should click the green bar to make it let you access the next screen:

reubano · 2017-11-28T21:26:31Z

What i see now...

Serhiy-Shekhovtsov · 2017-11-28T21:45:17Z

This is because of bad dummy data. Unfortunately #145 is still not closed, so the proper way to start the case doesn't work.

reubano · 2017-11-28T21:47:44Z

Hmmm, how did you get your screenshots then? The image shows up for me on the master branch.

Serhiy-Shekhovtsov · 2017-11-28T21:50:31Z

I had the Start case feature implemented and working on my end. So I had the data with proper series.uri values. But we had conflicting Pull Requests for the same feature and I closed mine one if favor of an other.

Serhiy-Shekhovtsov · 2017-11-28T22:17:38Z

@reubano this will give you correct data:

    from backend.cases.factories import *
    from backend.cases.models import *
    from backend.images.models import *

    # drop existing case(s) with candidates and nodules
    Case.objects.all().delete()

    # drop imported images
    ImageSeries.objects.all().delete()

    # import a new image and start a new case
    new_image, created = ImageSeries.get_or_create('/images/LIDC-IDRI-0003/1.3.6.1.4.1.14519.5.2.1.6279.6001.101370605276577556143013894866/1.3.6.1.4.1.14519.5.2.1.6279.6001.170706757615202213033480003264')
    new_case = CaseFactory(series=new_image)

    # dummy candidates
    candidates = CandidateFactory.create_batch(5, case=new_case)
    NoduleFactory(candidate=candidates[0], case=new_case)
    NoduleFactory(candidate=candidates[1], case=new_case)
    NoduleFactory(candidate=candidates[4], case=new_case)

reubano · 2017-11-28T22:38:35Z

Thanks, that worked! But the image only appears after moving the slider to a new slice.

Serhiy-Shekhovtsov · 2017-11-28T22:42:34Z

That's because dummy candidates are located on random and often missing slices. Opening a candidate will try to open that slice.

reubano · 2017-11-28T22:57:51Z

Gotcha. Nice work! Well, LGTM.

Serhiy-Shekhovtsov force-pushed the features/detect-and-select-z branch 2 times, most recently from 1ebaad5 to 6ee62df Compare November 25, 2017 20:22

lamby reviewed Nov 26, 2017

View reviewed changes

Serhiy-Shekhovtsov force-pushed the features/detect-and-select-z branch 3 times, most recently from 79235b2 to b97dd9c Compare November 26, 2017 12:06

Serhiy-Shekhovtsov added 4 commits November 28, 2017 20:44

added method that returns candidates with DICOM slices file names

a19918d

updated NoduleMarker to show when marker position differs from curren…

e7cb3cb

…t slice, added slice index to saving properties

added sliceIndex property to DICOM viewer

ba0392d

added slices loading and switching to CandidatesList component

3fd27e9

Serhiy-Shekhovtsov force-pushed the features/detect-and-select-z branch from b97dd9c to 3fd27e9 Compare November 28, 2017 18:45

Serhiy-Shekhovtsov mentioned this pull request Nov 28, 2017

Detect and select: mark\dismiss candidates #254

Merged

1 task

drivendataorg deleted a comment from Serhiy-Shekhovtsov Nov 28, 2017

reubano merged commit 120e5df into drivendataorg:master Nov 29, 2017

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Detect and select: attaching nodule centroid marker to current slice #250

Detect and select: attaching nodule centroid marker to current slice #250

Serhiy-Shekhovtsov commented Nov 25, 2017 •

edited

lamby Nov 26, 2017

Serhiy-Shekhovtsov Nov 26, 2017 •

edited

reubano commented Nov 26, 2017 •

edited

Serhiy-Shekhovtsov commented Nov 26, 2017

lamby commented Nov 27, 2017

reubano commented Nov 27, 2017

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reubano commented Nov 28, 2017

Serhiy-Shekhovtsov commented Nov 28, 2017 •

edited

reubano commented Nov 28, 2017 •

edited

Serhiy-Shekhovtsov commented Nov 28, 2017

reubano commented Nov 28, 2017

Serhiy-Shekhovtsov commented Nov 28, 2017

Serhiy-Shekhovtsov commented Nov 28, 2017 •

edited

reubano commented Nov 28, 2017

Serhiy-Shekhovtsov commented Nov 28, 2017

reubano commented Nov 28, 2017

Detect and select: attaching nodule centroid marker to current slice #250

Detect and select: attaching nodule centroid marker to current slice #250

Conversation

Serhiy-Shekhovtsov commented Nov 25, 2017 • edited

Description

Reference to official issue

Screenshot:

CLA

lamby Nov 26, 2017

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reubano commented Nov 26, 2017 • edited

Serhiy-Shekhovtsov commented Nov 26, 2017

lamby commented Nov 27, 2017

reubano commented Nov 27, 2017

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reubano commented Nov 28, 2017

Serhiy-Shekhovtsov commented Nov 28, 2017 • edited

reubano commented Nov 28, 2017 • edited

Serhiy-Shekhovtsov commented Nov 28, 2017

reubano commented Nov 28, 2017

Serhiy-Shekhovtsov commented Nov 28, 2017

Serhiy-Shekhovtsov commented Nov 28, 2017 • edited

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reubano commented Nov 28, 2017

Serhiy-Shekhovtsov commented Nov 25, 2017 •

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Serhiy-Shekhovtsov Nov 26, 2017 •

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reubano commented Nov 26, 2017 •

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Serhiy-Shekhovtsov commented Nov 28, 2017 •

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Serhiy-Shekhovtsov commented Nov 28, 2017 •

edited