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DataAnalyzer enhancements #6131

Merged
merged 9 commits into from
Mar 16, 2023
Merged

DataAnalyzer enhancements #6131

merged 9 commits into from
Mar 16, 2023

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myron
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@myron myron commented Mar 11, 2023 •
edited by wyli
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Adds several improvements to DataAnalyzer, including

  • Calculates image sizes in mm and their summaries (in additional to shapes and spacing)
  • Saves the datastats.yaml file as 2 files, the summary and the statistics by case. The datastats.yaml will have only summaries, to be able to load it faster. Otherwise for a large datasets (with many labels) YAML loading takes over 2minutes.

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • 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.
  • Documentation updated, tested make html command in the docs/ folder.

myron added 2 commits March 10, 2023 19:19
@myron
data_analyser improv
ef67254 
Signed-off-by: myron <amyronenko@nvidia.com>
@myron
black
739f66b 
Signed-off-by: myron <amyronenko@nvidia.com>
@myron myron added the enhancement New feature or request label Mar 11, 2023
@myron myron added this to the Auto3DSeg enhancement [P0 v1.2] milestone Mar 11, 2023
wyli added 2 commits March 11, 2023 12:58
@wyli
fixes typing
7bc04a7 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
Merge remote-tracking branch 'upstream/dev' into stats
9164062 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
wyli
wyli approved these changes Mar 11, 2023
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looks good to me, I added a few lines to fix the typing error monai/apps/auto3dseg/transforms.py:64:26: error: "Tensor" has no attribute "meta" [attr-defined]

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wyli commented Mar 11, 2023

/build

@wyli wyli enabled auto-merge (squash) March 11, 2023 13:08
@wyli wyli disabled auto-merge March 11, 2023 14:10
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wyli commented Mar 13, 2023

/build

@wyli wyli enabled auto-merge (squash) March 13, 2023 22:45
@wyli wyli disabled auto-merge March 14, 2023 10:21
myron added 2 commits March 15, 2023 17:20
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Merge remote-tracking branch 'upstream/dev' into stats
d07b4e2
@myron
hmm
906afad 
Signed-off-by: myron <amyronenko@nvidia.com>
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wyli commented Mar 16, 2023

/build

@wyli wyli enabled auto-merge (squash) March 16, 2023 06:48
@wyli
larger tol for pixel diff rotate Project-MONAI#6149
e88edf7 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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wyli commented Mar 16, 2023

/build

@wyli wyli merged commit 678b512 into Project-MONAI:dev Mar 16, 2023
@mingxin-zheng mingxin-zheng mentioned this pull request Mar 18, 2023
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@myron myron mentioned this pull request Mar 21, 2023
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@wyli wyli wyli approved these changes

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Auto3DSeg enhancement [P0 v1.2]
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