Problem with WholeSlideDataConfiguration

Problem with WholeSlideDataConfiguration  

  By: antoniosantos on March 30, 2022, 12:51 a.m.

Good night dear. How is everything?

I have a problem to create the batch_iterator of the wholeslidedata library

Error \/


RegistrantNotRegisteredError Traceback (most recent call last)
Input In [5], in <cell line: 1>()
----> 1 with createbatchiterator(mode=mode, userconfig=userconfig, cpus=cpus) as trainingbatchiterator:
2 pprint(trainingbatchiterator.dataset.annotationsperlabelperkey)

File D:\anaconda3\lib\site-packages\wholeslidedata\iterators.py:60, in createbatchiterator(userconfig, mode, batches, update, presets, cpus, context, determinstic, iteratorclass)
45 def createbatchiterator(
46 userconfig,
47 mode,
(...)
54 iterator
class=BatchIterator,
55 ):
56 configbuilder = WholeSlideDataConfiguration.build(
57 user
config=userconfig, modes=(mode,), buildinstances=False, presets=presets
58 )
---> 60 builds = WholeSlideDataConfiguration.build(
61 userconfig=userconfig, modes=(mode,), presets=presets
62 )
64 updatequeue = Queue() if update else None
66 batch
commander = BatchCommander(
67 configbuilder=configbuilder,
68 mode=mode,
69 resetindex=batches,
70 update
queue=update_queue,
71 )

File D:\anaconda3\lib\site-packages\creationism\configuration\config.py:294, in Configuration.build(cls, userconfig, modes, buildinstances, buildkey, presets, externalconfigurations, searchpaths, *args, kwargs)
292 resolve
none(configuration)
293 if buildinstances:
--> 294 return configuration.build
instances(externalconfigurations=externalconfigurations, buildkey=buildkey)
295 return configuration**

File D:\anaconda3\lib\site-packages\creationism\configuration\config.py:320, in Configuration.buildinstances(self, externalconfigurations, buildkey)
317 build
keys = buildkeys[:index]
319 for key in build
keys:
--> 320 build[mode][key] = build[mode][key].build(configurations)
322 build = build.cast()
323 if build_key:

File D:\anaconda3\lib\site-packages\creationism\configuration\config.py:242, in ConfigDict.build(self, configuration)
231 return ConfigObject(
232 buildregistrantobject(
233 self,
(...)
238 )
239 )
241 if module is not None and attribute is not None:
--> 242 return ConfigObject(
build_object(self, module, attribute))
244 return self

File D:\anaconda3\lib\site-packages\creationism\configuration\config.py:348, in buildobject(builds, module, attribute)
346 for attr in attributes:
347 attribute = getattr(attribute, attr)
--> 348 return attribute(builds.cast())

File D:\anaconda3\lib\site-packages\wholeslidedata\dataset.py:132, in WholeSlideDataSet.init(self, mode, associations, labels, renamedlabels, loadimages, copypath)
130 self.
loadimages = loadimages
131 self.copypath = copypath
--> 132 super().init(mode, associations, labels, renamed
labels)

File D:\anaconda3\lib\site-packages\wholeslidedata\dataset.py:40, in DataSet.init(self, mode, associations, labels, renamedlabels)
37 self.
labels = labels
38 self.renamedlabels = renamedlabels
---> 40 self.data = self.
open(self.associations)
41 self.
samplereferences, self.allsamplereferences = self.initsamples(self.data)
42 self.alllabels = Labels.create(list(self.allsample_references.keys()))

File D:\anaconda3\lib\site-packages\wholeslidedata\dataset.py:144, in WholeSlideDataSet.open(self, associations)
137 data[file
key] = {
138 WholeSlideDataSet.IMAGESIDENTIFIER: dict(),
139 WholeSlideDataSet.ANNOTATIONS
IDENTIFIER: dict(),
140 }
141 for wsiindex, wsifile in enumerate(associatedfiles[WholeSlideImageFile]):
142 data[file
key][WholeSlideDataSet.IMAGESIDENTIFIER][
143 wsi
index
--> 144 ] = self.openimage(wsifile)
145 for wsa
index, wsafile in enumerate(
146 associated
files[WholeSlideAnnotationFile]
147 ):
148 data[filekey][WholeSlideDataSet.ANNOTATIONSIDENTIFIER][
149 wsaindex
150 ] = self.
openannotation(wsafile)

File D:\anaconda3\lib\site-packages\wholeslidedata\dataset.py:157, in WholeSlideDataSet.openimage(self, wsifile)
155 wsi
file.copy(self.copypath)
156 if self.loadimages:
--> 157 return wsifile.open()
158 return wsi
file.path

File D:\anaconda3\lib\site-packages\wholeslidedata\source\files.py:86, in WholeSlideImageFile.open(self)
85 def open(self):
---> 86 return WholeSlideImage(self.path, self.imagebackend)

File D:\anaconda3\lib\site-packages\wholeslidedata\image\wholeslideimage.py:19, in WholeSlideImage.init(self, path, backend)
15 def init(
16 self, path: str, backend: WholeSlideImageBackend = 'openslide',
17 ) -> None:
18 self.path = Path(path)
---> 19 self.
backend = WholeSlideImageBackend.create(backend, path=self.path)
20 self.
extension = self.path.suffix
22 self.
shapes = self.backend.init_shapes()

File D:\anaconda3\lib\site-packages\creationism\registration\factory.py:64, in RegistrantFactory.create(cls, registrantname, returntype, args, kwargs)
55 @classmethod
56 def create(
57 cls,
(...)
61 kwargs
62 ):
63 if cls._REGISTER is None:
---> 64 raise RegistrantNotRegisteredError(
65 cls=cls,
66 registrant_name=registrant_name,
67 register=cls._REGISTER,
68 )
70 if issubclass(type(registrant_name), cls):
71 return registrant_name
*

RegistrantNotRegisteredError:
Registrant 'openslide' is not found in the register of class 'WholeSlideImageBackend' with an empty register.

Can anybody help me? I've already installed openslide and I'm using ubuntu as the operating system and put the file path correctly but the error still persists

 Last edited by: antoniosantos on March 30, 2022, 12:52 a.m., edited 1 time in total.

Re: Problem with WholeSlideDataConfiguration  

  By: amickan on March 30, 2022, 7:09 a.m.

Dear Antonio,

This forum is only for technical support around the platform. For questions about data analysis pertaining to algorithms or challenges, please contact the respective organizers directly.

Best,
Anne