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frankkramer-lab / MIScnn

A framework for Medical Image Segmentation with Convolutional Neural Networks and Deep Learning
GNU General Public License v3.0
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Resolving grayscale image handling & conversions #91

Closed jumutc closed 2 years ago

jumutc commented 3 years ago

For some datasets like Fluo-N2DL-HeLa after loading by Image_interface we get blank images because of img_raw.convert("LA") conversion. This breaks down training and execution of subfunctions.

muellerdo commented 3 years ago

Hey @jumutc,

thank you for finding this bug and providing a solution! :) Sorry for the inconvenience, that Continuous Integration is currently disabled due to travis-ci.org has moved to travis-ci.com, which requires permissions and setup again (already on my to-do list before my vacation).

When running pytest locally, I got the following exception for this pull request:

============================= test session starts ==============================
platform linux -- Python 3.6.9, pytest-5.4.3, py-1.8.1, pluggy-0.13.1 -- /usr/bin/python
cachedir: .pytest_cache
rootdir: /home/mudomini/projects/MIScnn
plugins: cov-2.10.0, typeguard-2.12.1
collected 136 items                                                            

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=================================== FAILURES ===================================
___________________ IO_interfacesTEST.test_IOI_IMAGE_loading ___________________

self = <tests.test_iointerfaces.IO_interfacesTEST testMethod=test_IOI_IMAGE_loading>

    def test_IOI_IMAGE_loading(self):
        interface = Image_interface(pattern="image_\\d+")
        sample_list = interface.initialize(self.tmp_data.name)
        img_01 = interface.load_image(sample_list[0])
        seg_01 = interface.load_segmentation(sample_list[0])
        true_img_01 = np.array(Image.fromarray(self.img[:, :, :3]).convert('LA'))
>       self.assertTrue(np.array_equal(img_01[0], true_img_01[:,:,0]))
E       AssertionError: False is not true

tests/test_iointerfaces.py:97: AssertionError
jumutc commented 3 years ago

Hi @muellerdo,

This exception is strange as I was running all tests locally and all was green! I will investigate. My Python version is higher so maybe there are some diffs coming from this fact.

jumutc commented 3 years ago

@muellerdo tests are fixed!