WSIReader defaults and tensor conversion #6058

drbeh · 2023-02-23T23:37:44Z

Description

This PR enable to instantiate WSIReader classes with default values for mode and dtype. It also accepts torch.dtype as dtype and if torch.dtype is provided, the output will be a torch.Tensor to avoid additional step to convert the output for inference.

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
New tests added to cover the changes.
Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
In-line docstrings updated.

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

…ireader-defaults

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

…ireader-defaults

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

monai/data/wsi_reader.py

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

Nic-Ma · 2023-03-07T23:59:55Z

/black

Nic-Ma · 2023-03-08T00:00:03Z

/build

drbeh · 2023-03-08T15:14:44Z

@Nic-Ma it seems that blossom test has failed but I cannot see what has happened. How can I get the visibility on that? Thanks

Nic-Ma · 2023-03-08T15:20:34Z

Hi @drbeh ,

I think the error is as below:

2023-03-08T02:13:10.5286648Z [2023-03-08T02:12:42.239Z] ======================================================================
2023-03-08T02:13:10.5287076Z [2023-03-08T02:12:42.239Z] FAIL: test_read_region_device_1__home_jenkins_agent_workspace_MONAI_premerge_monai_tests_testing_data_temp_CMU_1_tiff_tiff (tests.test_wsireader.TestCuCIM)
2023-03-08T02:13:10.5287345Z [2023-03-08T02:12:42.239Z] ----------------------------------------------------------------------
2023-03-08T02:13:10.5287547Z [2023-03-08T02:12:42.239Z] Traceback (most recent call last):
2023-03-08T02:13:10.5287895Z [2023-03-08T02:12:42.239Z]   File "/opt/conda/lib/python3.8/site-packages/parameterized/parameterized.py", line 533, in standalone_func
2023-03-08T02:13:10.5288106Z [2023-03-08T02:12:42.239Z]     return func(*(a + p.args), **p.kwargs)
2023-03-08T02:13:10.5288467Z [2023-03-08T02:12:42.239Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_wsireader.py", line 562, in test_read_region_device
2023-03-08T02:13:10.5288715Z [2023-03-08T02:12:42.239Z]     self.assertEqual(img.device, torch.device(device))
2023-03-08T02:13:10.5289093Z [2023-03-08T02:12:42.239Z] AssertionError: device(type='cuda', index=0) != device(type='cuda')
2023-03-08T02:13:10.5289226Z [2023-03-08T02:12:42.239Z] 
2023-03-08T02:13:10.5289452Z [2023-03-08T02:12:42.239Z] ======================================================================
2023-03-08T02:13:10.5289868Z [2023-03-08T02:12:42.239Z] FAIL: test_read_region_device_3__home_jenkins_agent_workspace_MONAI_premerge_monai_tests_testing_data_temp_CMU_1_tiff_tiff (tests.test_wsireader.TestCuCIM)
2023-03-08T02:13:10.5290134Z [2023-03-08T02:12:42.239Z] ----------------------------------------------------------------------
2023-03-08T02:13:10.5290336Z [2023-03-08T02:12:42.239Z] Traceback (most recent call last):
2023-03-08T02:13:10.5290683Z [2023-03-08T02:12:42.239Z]   File "/opt/conda/lib/python3.8/site-packages/parameterized/parameterized.py", line 533, in standalone_func
2023-03-08T02:13:10.5290898Z [2023-03-08T02:12:42.239Z]     return func(*(a + p.args), **p.kwargs)
2023-03-08T02:13:10.5291260Z [2023-03-08T02:12:42.239Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_wsireader.py", line 559, in test_read_region_device
2023-03-08T02:13:10.5291465Z [2023-03-08T02:12:42.239Z]     assert_allclose(img, expected_img)
2023-03-08T02:13:10.5291790Z [2023-03-08T02:12:42.239Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/utils.py", line 124, in assert_allclose
2023-03-08T02:13:10.5292123Z [2023-03-08T02:12:42.239Z]     np.testing.assert_equal(isinstance(actual, np.ndarray), isinstance(desired, np.ndarray), "numpy type")
2023-03-08T02:13:10.5292448Z [2023-03-08T02:12:42.239Z]   File "/opt/conda/lib/python3.8/site-packages/numpy/testing/_private/utils.py", line 425, in assert_equal
2023-03-08T02:13:10.5292642Z [2023-03-08T02:12:42.239Z]     raise AssertionError(msg)
2023-03-08T02:13:10.5292811Z [2023-03-08T02:12:42.239Z] AssertionError: 
2023-03-08T02:13:10.5293009Z [2023-03-08T02:12:42.239Z] Items are not equal: numpy type
2023-03-08T02:13:10.5293226Z [2023-03-08T02:12:42.239Z]  ACTUAL: True
2023-03-08T02:13:10.5293378Z [2023-03-08T02:12:42.239Z]  DESIRED: False
2023-03-08T02:13:10.5293508Z [2023-03-08T02:12:42.239Z] 
2023-03-08T02:13:10.5293734Z [2023-03-08T02:12:42.239Z] ======================================================================
2023-03-08T02:13:10.5294158Z [2023-03-08T02:12:42.239Z] FAIL: test_read_region_device_5__home_jenkins_agent_workspace_MONAI_premerge_monai_tests_testing_data_temp_CMU_1_tiff_tiff (tests.test_wsireader.TestCuCIM)
2023-03-08T02:13:10.5294426Z [2023-03-08T02:12:42.239Z] ----------------------------------------------------------------------
2023-03-08T02:13:10.5294627Z [2023-03-08T02:12:42.239Z] Traceback (most recent call last):
2023-03-08T02:13:10.5294973Z [2023-03-08T02:12:42.239Z]   File "/opt/conda/lib/python3.8/site-packages/parameterized/parameterized.py", line 533, in standalone_func
2023-03-08T02:13:10.5295222Z [2023-03-08T02:12:42.239Z]     return func(*(a + p.args), **p.kwargs)
2023-03-08T02:13:10.5295583Z [2023-03-08T02:12:42.239Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_wsireader.py", line 559, in test_read_region_device
2023-03-08T02:13:10.5295788Z [2023-03-08T02:12:42.239Z]     assert_allclose(img, expected_img)
2023-03-08T02:13:10.5296115Z [2023-03-08T02:12:42.239Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/utils.py", line 124, in assert_allclose
2023-03-08T02:13:10.5296447Z [2023-03-08T02:12:42.239Z]     np.testing.assert_equal(isinstance(actual, np.ndarray), isinstance(desired, np.ndarray), "numpy type")
2023-03-08T02:13:10.5296772Z [2023-03-08T02:12:42.239Z]   File "/opt/conda/lib/python3.8/site-packages/numpy/testing/_private/utils.py", line 425, in assert_equal
2023-03-08T02:13:10.5296954Z [2023-03-08T02:12:42.239Z]     raise AssertionError(msg)
2023-03-08T02:13:10.5297121Z [2023-03-08T02:12:42.239Z] AssertionError: 
2023-03-08T02:13:10.5297316Z [2023-03-08T02:12:42.239Z] Items are not equal: numpy type
2023-03-08T02:13:10.5297469Z [2023-03-08T02:12:42.239Z]  ACTUAL: True
2023-03-08T02:13:10.5297632Z [2023-03-08T02:12:42.239Z]  DESIRED: False
2023-03-08T02:13:10.5297764Z [2023-03-08T02:12:42.239Z] 
2023-03-08T02:13:10.5297991Z [2023-03-08T02:12:42.239Z] ======================================================================
2023-03-08T02:13:10.5298418Z [2023-03-08T02:12:42.239Z] FAIL: test_read_region_device_1__home_jenkins_agent_workspace_MONAI_premerge_monai_tests_testing_data_temp_CMU_1_tiff_tiff (tests.test_wsireader.TestTiffFile)
2023-03-08T02:13:10.5298686Z [2023-03-08T02:12:42.239Z] ----------------------------------------------------------------------
2023-03-08T02:13:10.5298884Z [2023-03-08T02:12:42.239Z] Traceback (most recent call last):
2023-03-08T02:13:10.5299224Z [2023-03-08T02:12:42.239Z]   File "/opt/conda/lib/python3.8/site-packages/parameterized/parameterized.py", line 533, in standalone_func
2023-03-08T02:13:10.5299437Z [2023-03-08T02:12:42.239Z]     return func(*(a + p.args), **p.kwargs)
2023-03-08T02:13:10.5299787Z [2023-03-08T02:12:42.239Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_wsireader.py", line 562, in test_read_region_device
2023-03-08T02:13:10.5300030Z [2023-03-08T02:12:42.239Z]     self.assertEqual(img.device, torch.device(device))
2023-03-08T02:13:10.5300291Z [2023-03-08T02:12:42.239Z] AssertionError: device(type='cuda', index=0) != device(type='cuda')
2023-03-08T02:13:10.5300423Z [2023-03-08T02:12:42.239Z] 
2023-03-08T02:13:10.5300648Z [2023-03-08T02:12:42.239Z] ======================================================================
2023-03-08T02:13:10.5301075Z [2023-03-08T02:12:42.239Z] FAIL: test_read_region_device_3__home_jenkins_agent_workspace_MONAI_premerge_monai_tests_testing_data_temp_CMU_1_tiff_tiff (tests.test_wsireader.TestTiffFile)
2023-03-08T02:13:10.5301337Z [2023-03-08T02:12:42.239Z] ----------------------------------------------------------------------
2023-03-08T02:13:10.5301540Z [2023-03-08T02:12:42.239Z] Traceback (most recent call last):
2023-03-08T02:13:10.5301928Z [2023-03-08T02:12:42.239Z]   File "/opt/conda/lib/python3.8/site-packages/parameterized/parameterized.py", line 533, in standalone_func
2023-03-08T02:13:10.5302136Z [2023-03-08T02:12:42.239Z]     return func(*(a + p.args), **p.kwargs)
2023-03-08T02:13:10.5302494Z [2023-03-08T02:12:42.239Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_wsireader.py", line 559, in test_read_region_device
2023-03-08T02:13:10.5302698Z [2023-03-08T02:12:42.239Z]     assert_allclose(img, expected_img)
2023-03-08T02:13:10.5303022Z [2023-03-08T02:12:42.239Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/utils.py", line 124, in assert_allclose
2023-03-08T02:13:10.5303354Z [2023-03-08T02:12:42.239Z]     np.testing.assert_equal(isinstance(actual, np.ndarray), isinstance(desired, np.ndarray), "numpy type")
2023-03-08T02:13:10.5303711Z [2023-03-08T02:12:42.239Z]   File "/opt/conda/lib/python3.8/site-packages/numpy/testing/_private/utils.py", line 425, in assert_equal
2023-03-08T02:13:10.5303910Z [2023-03-08T02:12:42.239Z]     raise AssertionError(msg)
2023-03-08T02:13:10.5304076Z [2023-03-08T02:12:42.239Z] AssertionError: 
2023-03-08T02:13:10.5304273Z [2023-03-08T02:12:42.239Z] Items are not equal: numpy type
2023-03-08T02:13:10.5304428Z [2023-03-08T02:12:42.239Z]  ACTUAL: True
2023-03-08T02:13:10.5304588Z [2023-03-08T02:12:42.239Z]  DESIRED: False
2023-03-08T02:13:10.5304718Z [2023-03-08T02:12:42.239Z] 
2023-03-08T02:13:10.5304942Z [2023-03-08T02:12:42.239Z] ======================================================================
2023-03-08T02:13:10.5305369Z [2023-03-08T02:12:42.239Z] FAIL: test_read_region_device_5__home_jenkins_agent_workspace_MONAI_premerge_monai_tests_testing_data_temp_CMU_1_tiff_tiff (tests.test_wsireader.TestTiffFile)
2023-03-08T02:13:10.5305632Z [2023-03-08T02:12:42.239Z] ----------------------------------------------------------------------
2023-03-08T02:13:10.5305832Z [2023-03-08T02:12:42.239Z] Traceback (most recent call last):
2023-03-08T02:13:10.5306178Z [2023-03-08T02:12:42.239Z]   File "/opt/conda/lib/python3.8/site-packages/parameterized/parameterized.py", line 533, in standalone_func
2023-03-08T02:13:10.5306382Z [2023-03-08T02:12:42.239Z]     return func(*(a + p.args), **p.kwargs)
2023-03-08T02:13:10.5306737Z [2023-03-08T02:12:42.239Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_wsireader.py", line 559, in test_read_region_device
2023-03-08T02:13:10.5306941Z [2023-03-08T02:12:42.239Z]     assert_allclose(img, expected_img)
2023-03-08T02:13:10.5307272Z [2023-03-08T02:12:42.239Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/utils.py", line 124, in assert_allclose
2023-03-08T02:13:10.5307602Z [2023-03-08T02:12:42.239Z]     np.testing.assert_equal(isinstance(actual, np.ndarray), isinstance(desired, np.ndarray), "numpy type")
2023-03-08T02:13:10.5307925Z [2023-03-08T02:12:42.239Z]   File "/opt/conda/lib/python3.8/site-packages/numpy/testing/_private/utils.py", line 425, in assert_equal
2023-03-08T02:13:10.5308117Z [2023-03-08T02:12:42.239Z]     raise AssertionError(msg)
2023-03-08T02:13:10.5308286Z [2023-03-08T02:12:42.239Z] AssertionError: 
2023-03-08T02:13:10.5308477Z [2023-03-08T02:12:42.239Z] Items are not equal: numpy type
2023-03-08T02:13:10.5308632Z [2023-03-08T02:12:42.239Z]  ACTUAL: True
2023-03-08T02:13:10.5308791Z [2023-03-08T02:12:42.239Z]  DESIRED: False
2023-03-08T02:13:10.5308922Z [2023-03-08T02:12:42.239Z] 
2023-03-08T02:13:10.5309182Z [2023-03-08T02:12:42.239Z] ----------------------------------------------------------------------
2023-03-08T02:13:10.5309366Z [2023-03-08T02:12:42.239Z] Ran 12302 tests in 1393.784s
2023-03-08T02:13:10.5309496Z [2023-03-08T02:12:42.239Z] 
2023-03-08T02:13:10.5309693Z [2023-03-08T02:12:42.239Z] FAILED (failures=6, skipped=521)

Thanks.

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

Nic-Ma · 2023-03-08T15:55:24Z

/build

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

drbeh · 2023-03-08T21:33:05Z

@Nic-Ma I am making few changes. Please hold on a bit. Thanks

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

drbeh · 2023-03-09T15:14:40Z

@Nic-Ma it is ready, and has passed all the tests locally. Thanks

Nic-Ma · 2023-03-09T15:40:08Z

/build

drbeh · 2023-03-10T18:09:45Z

@Nic-Ma @wyli it seems that the issue with blossom has fixed. Can we run blossom tests again here?

wyli · 2023-03-10T19:16:16Z

/build

drbeh · 2023-03-13T15:56:33Z

@Nic-Ma @wyli @ericspod do you have any idea why quick-py3 (ubuntu-latest) are getting cancelled?
https://github.com/Project-MONAI/MONAI/actions/runs/4406004944/jobs/7717649759#step:12:17631

The only thing that I can think of is memory limit since TiffFile loads the entire image unlike other backends (cucim and openslide).

However, the same test are going well on Mac quick-py3 (macOS-latest):
https://github.com/Project-MONAI/MONAI/actions/runs/4406004944/jobs/7717649413#step:12:17755

Do we have different memory limits on the instances that Mac and Ubuntu quick tests are running?

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

monai/data/wsi_reader.py

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

drbeh · 2023-03-13T19:06:49Z

@Nic-Ma @wyli the issue with quick tests on ubuntu is resolved. As I expected, it was due to memory limitation and reducing the image size for that test case helped not to face that issue again.
Please let's finally merge this if you don't have any other comments.

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

wyli · 2023-03-14T16:28:12Z

/build

wyli · 2023-03-14T18:04:33Z

it seems the memory issue is still here https://github.com/Project-MONAI/MONAI/actions/runs/4418529796/jobs/7745780000 could you please have a look soon @drbeh it might block 1.2rc releases... cc @Nic-Ma @KumoLiu

drbeh · 2023-03-14T18:12:37Z

@wyli I'll make a PR to make all the test to use the lowest resolution so we can save memory and time.

drbeh added 7 commits February 22, 2023 12:51

Update wsi reader to have object defaults for mode and dtype

bce46a5

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

update comments

d0c0318

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

add device

12a353f

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

add unittests

fe57e79

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

Merge branch 'dev' into fix-6056-wsireader-defaults

5ae1822

Merge branch 'dev' of github.com:Project-MONAI/MONAI into fix-6056-ws…

0f73d95

…ireader-defaults

add supported backends

d48d3c9

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

drbeh force-pushed the fix-6056-wsireader-defaults branch from 5fc3b15 to d48d3c9 Compare March 1, 2023 21:56

drbeh added 3 commits March 2, 2023 15:26

Merge branch 'dev' of github.com:Project-MONAI/MONAI into fix-6056-ws…

d0748cc

…ireader-defaults

Merge branch 'dev' of github.com:Project-MONAI/MONAI into fix-6056-ws…

153b14c

…ireader-defaults

formatting

0ae2536

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

drbeh marked this pull request as ready for review March 6, 2023 17:05

drbeh requested review from wyli, KumoLiu and Nic-Ma March 6, 2023 17:06

KumoLiu approved these changes Mar 7, 2023

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drbeh added 2 commits March 7, 2023 10:52

Merge branch 'dev' into fix-6056-wsireader-defaults

cf1f93b

device conversion for numpy dtype and added tests

e4702d7

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

Nic-Ma approved these changes Mar 7, 2023

View reviewed changes

fix device comparison

a36fb63

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

drbeh added 4 commits March 8, 2023 11:26

remove redundant type

ddb9fdc

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

remove redundant type

0f3355b

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

change from not cpu to cuda

9e17c01

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

torch dtype

e242b65

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

drbeh added 6 commits March 9, 2023 09:47

simplify get_data args, cleanup and update docstring

c4acdc5

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

typing

a06f95d

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

Merge branch 'dev' into fix-6056-wsireader-defaults

3a7baff

add unittests for none device and dtype

8b85a10

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

update dtype float32

762e6a3

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

correct numpy default for None

6effd94

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

wyli enabled auto-merge (squash) March 10, 2023 19:16

wyli disabled auto-merge March 10, 2023 20:53

Merge branch 'dev' into fix-6056-wsireader-defaults

fec192f

drbeh enabled auto-merge (squash) March 13, 2023 14:24

drbeh disabled auto-merge March 13, 2023 15:43

remove test case 0 to check on ubuntu quick test

0d0d6c1

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

wyli reviewed Mar 13, 2023

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monai/data/wsi_reader.py Outdated Show resolved Hide resolved

read at level=8 for test case 0 to save memory

e51fe48

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

drbeh and others added 2 commits March 14, 2023 10:39

remove default conversion of None device

dab7c41

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

Merge branch 'dev' into fix-6056-wsireader-defaults

bf37fda

wyli merged commit 01b6d70 into Project-MONAI:dev Mar 14, 2023

drbeh deleted the fix-6056-wsireader-defaults branch March 14, 2023 18:12

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WSIReader defaults and tensor conversion #6058

WSIReader defaults and tensor conversion #6058

drbeh commented Feb 23, 2023 •

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drbeh commented Mar 14, 2023

WSIReader defaults and tensor conversion #6058

WSIReader defaults and tensor conversion #6058

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drbeh commented Feb 23, 2023 • edited Loading

Description

Types of changes

Nic-Ma commented Mar 7, 2023

Nic-Ma commented Mar 8, 2023

drbeh commented Mar 8, 2023

Nic-Ma commented Mar 8, 2023

Nic-Ma commented Mar 8, 2023

drbeh commented Mar 8, 2023

drbeh commented Mar 9, 2023

Nic-Ma commented Mar 9, 2023

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wyli commented Mar 10, 2023

drbeh commented Mar 13, 2023 • edited Loading

drbeh commented Mar 13, 2023 • edited Loading

wyli commented Mar 14, 2023

wyli commented Mar 14, 2023

drbeh commented Mar 14, 2023

drbeh commented Feb 23, 2023 •

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drbeh commented Mar 13, 2023 •

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drbeh commented Mar 13, 2023 •

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