deepmicroscopy / midog_reference_docker Goto Github PK

Reference implementation of domain-adversarial training on a RetinaNet (to use as template in the MIDOG challenge)

Dockerfile 6.11% Batchfile 2.93% Shell 3.79% Python 87.16%

midog_reference_docker's Issues

Error in Transforming coordinates

Hi,

When implementing this docker locally my code fails in the final stage of prediction on transforming the coordinates. E.g.:

world_coords = image_data.TransformContinuousIndexToPhysicalPoint(
  [c for c in coord]
)

The following error is then given:

Traceback (most recent call last):
  File "process.py", line 121, in <module>
    Mitosisdetection().process()
  File "/home/adams/anaconda3/envs/tf23/lib/python3.8/site-packages/evalutils/evalutils.py", line 183, in process
    self.process_cases()
  File "/home/adams/anaconda3/envs/tf23/lib/python3.8/site-packages/evalutils/evalutils.py", line 191, in process_cases
    self._case_results.append(self.process_case(idx=idx, case=case))
  File "process.py", line 74, in process_case
    scored_candidates = self.predict(input_image=input_image)
  File "process.py", line 105, in predict
    world_coords = input_image.TransformContinuousIndexToPhysicalPoint(
  File "/home/adams/anaconda3/envs/tf23/lib/python3.8/site-packages/SimpleITK/SimpleITK.py", line 3264, in TransformContinuousIndexToPhysicalPoint
    return _SimpleITK.Image_TransformContinuousIndexToPhysicalPoint(self, index)
TypeError: in method 'Image_TransformContinuousIndexToPhysicalPoint', argument 2 of type 'std::vector< double,std::allocator< double > > const &'

Please can someone advise? Thanks for your help.

Bets wishes,
Adam Shephard

training script

Hi, will the training code be provided ? I am wondering whether the original training data is processed the same as the test data (in this repository, create overlapping patches for the whole image). Or directly resize to 512*512

`No such file or directory` error when running test.sh

I have tested process.py successfully out of the docker.
But when I run test.sh,
As seen in the image, there is no such file called mitotic-figures.json.

Did I miss something?
How to deal with this problem?

Question about test set

Hi,
Is the test set of MIDOG 2021 available now that the challenge is over? How can I access it?
Or how can I test my model on the test set?
Thanks

deepmicroscopy / midog_reference_docker Goto Github PK

midog_reference_docker's People

Contributors

Stargazers

Watchers

Forkers

midog_reference_docker's Issues

Error in Transforming coordinates

training script

`No such file or directory` error when running test.sh

Question about test set

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent