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WSIReader defaults at initialization #6056

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drbeh opened this issue Feb 23, 2023 · 0 comments · Fixed by #6058
Closed

WSIReader defaults at initialization #6056

drbeh opened this issue Feb 23, 2023 · 0 comments · Fixed by #6058
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@drbeh
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Pathology/Microscopy Digital Pathology and Microscopy related
Milestone
Enhance WSIReader...

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drbeh commented Feb 23, 2023 •
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Many WSIReader defaults are being set at get_data() method but it would be useful to be able to set those default values to be set in __init__ so the WSIReader with defaults can be passed as a reader for wsi datasets and inference.
For instance, this is a required feature for whole slide patch inference to enable users to pass arguments for wsireader to the splitter.
@drbeh drbeh converted this from a draft issue Feb 23, 2023
@drbeh drbeh self-assigned this Feb 23, 2023
@drbeh drbeh added the Pathology/Microscopy Digital Pathology and Microscopy related label Feb 23, 2023
@drbeh drbeh changed the title WSIReader defaults at initialization WSIReader defaults at initialization Feb 23, 2023
@drbeh drbeh moved this from 🌱 Todo to 🌋 In Progress in AI in Pathology🔬 Feb 23, 2023
@drbeh drbeh mentioned this issue Feb 23, 2023
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@drbeh drbeh moved this from 🌋 In Progress to 👍 Approved in AI in Pathology🔬 Mar 9, 2023
wyli pushed a commit that referenced this issue Mar 14, 2023
@drbeh
WSIReader defaults and tensor conversion (#6058)
01b6d70 
Fixes #6056 

### 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
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] New tests added to cover the changes.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.

---------

Signed-off-by: Behrooz <[email protected]>
@github-project-automation github-project-automation bot moved this from 👍 Approved to 💯 Complete in AI in Pathology🔬 Mar 14, 2023
@drbeh drbeh added this to MONAI v1.2 Mar 20, 2023
@drbeh drbeh moved this to Done in MONAI v1.2 Mar 20, 2023
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@drbeh drbeh

Labels
Pathology/Microscopy Digital Pathology and Microscopy related
Projects
AI in Pathology🔬
Status: 💯 Complete
MONAI v1.2
Status: Done
Milestone
Enhance WSIReader usability and perfo...
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WSIReader defaults and tensor conversion drbeh/MONAI
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