Added DICOM text SR assets and updated all operator test functions. #201
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
MMelQin
force-pushed
the
mqin/dicom_report
branch
from
47b688f to
cb14410
Compare
Signed-off-by: mmelqin <[email protected]>
MMelQin
force-pushed
the
mqin/dicom_report
branch
from
313cacf to
1f2fa41
Compare
Signed-off-by: mmelqin <[email protected]>
MMelQin
force-pushed
the
mqin/dicom_report
branch
from
963ace4 to
505796f
Compare
Signed-off-by: mmelqin <[email protected]>
Signed-off-by: mmelqin <[email protected]>
… and is handled. Signed-off-by: mmelqin <[email protected]>
MMelQin
force-pushed
the
mqin/dicom_report
branch
from
51c1a84 to
810f632
Compare
Signed-off-by: mmelqin <[email protected]>
Signed-off-by: mmelqin <[email protected]>
Signed-off-by: mmelqin <[email protected]>
|
All checks, except the code coverage one, succeeded. Code coverage is allow to show failure, but both functional and integration testing was performed and succeeded.
So the PR is ready to be merged. |
Signed-off-by: mmelqin <[email protected]>
Signed-off-by: mmelqin <[email protected]>
gigony
approved these changes
Nov 23, 2021
examples/apps/mednist_classifier_monaideploy/mednist_classifier_monaideploy.py
Outdated
Show resolved
Hide resolved
Signed-off-by: mmelqin <[email protected]>
gigony
reviewed
Nov 23, 2021
docs/source/release_notes/v0.2.0.md
Outdated
| ### Series Selection Operator | ||
| This is to support the use case where whole DICOM studies are used as input to an AI inference application even though only specific series are applicable. | ||
|
|
||
| The selection rules are defined in JSON, allowing multiple selections, each with a set of matching conditions. The rules processing engine is implemented in the `DICOMSeriesSelectorOperator`, which itself is regarded as a base class with default implementation. More advanced rules and processing engine can be implemented in derived classes. |
There was a problem hiding this comment.
Suggested change
| The selection rules are defined in JSON, allowing multiple selections, each with a set of matching conditions. The rules processing engine is implemented in the `DICOMSeriesSelectorOperator`, which itself is regarded as a base class with default implementation. More advanced rules and processing engine can be implemented in derived classes. | |
| The selection rules are defined in JSON, allowing multiple selections, each with a set of matching conditions. The rules processing engine is implemented in the `DICOMSeriesSelectorOperator`, which itself is regarded as a base class with the default implementation. More advanced rules and processing engines can be implemented in derived classes. |
There was a problem hiding this comment.
It was meant to say "rules processing engine"
There was a problem hiding this comment.
One second thought, rules can be redefined too, if the base class is not used for the new definition of rules.
docs/source/release_notes/v0.2.0.md
Outdated
| Multiple instances of the series selection operators, each having its own rules, can be chained in a MONAI Deploy application. In part this is made possible by the new App SDK Domain classes which encapsulate the selected series in a DICOM study, and are used as the output of each series selection operator. | ||
|
|
||
| ### DICOM Comprehensive Structured Report Writer | ||
| This is introduced to support generating DICOM SR SOP instances for AI classification result, and as such, the DICOM SR writer is limited to support textual results. |
There was a problem hiding this comment.
Suggested change
| This is introduced to support generating DICOM SR SOP instances for AI classification result, and as such, the DICOM SR writer is limited to support textual results. | |
| This is introduced to support generating DICOM SR SOP instances for the AI classification result, and as such, the DICOM SR writer is limited to support textual results. |
There was a problem hiding this comment.
changed result to results.
docs/source/release_notes/v0.2.0.md
Outdated
| This is introduced to support generating DICOM SR SOP instances for AI classification result, and as such, the DICOM SR writer is limited to support textual results. | ||
|
|
||
| The DICOM SR writer is implemented in `DICOMTextSRWriterOperator`, it | ||
| - loads AI result from in-memory object as well as from file path, with memory taking precedence |
There was a problem hiding this comment.
Suggested change
| - loads AI result from in-memory object as well as from file path, with memory taking precedence | |
| - loads the AI result from the in-memory object as well as from file path, with memory taking precedence |
docs/source/release_notes/v0.2.0.md
Outdated
| The DICOM SR writer is implemented in `DICOMTextSRWriterOperator`, it | ||
| - loads AI result from in-memory object as well as from file path, with memory taking precedence | ||
| - copies applicable DICOM tags from the original DICOM series used as input for the inference application, as well as generating tags anew when there is no DICOM series provided. | ||
| - supports assigning DICOM tags via a dictionary with DICOM keywords and value, so that an application can customize the tags in the DICOM SR instance |
There was a problem hiding this comment.
Suggested change
| - supports assigning DICOM tags via a dictionary with DICOM keywords and value, so that an application can customize the tags in the DICOM SR instance | |
| - supports assigning DICOM tags via a dictionary with DICOM keywords and values, so that an application can customize the tags in the DICOM SR instance |
There was a problem hiding this comment.
value to their respective values, just to be specific.
docs/source/release_notes/v0.2.0.md
Outdated
| ### Updated example applications | ||
| - [The AI Spleen Segmentation](https://github.com/Project-MONAI/monai-deploy-app-sdk/tree/main/examples/apps/ai_spleen_seg_app) application updated to demonstrate the use of series selection rules | ||
| - [The MedNIST Classifier application](https://github.com/Project-MONAI/monai-deploy-app-sdk/tree/main/examples/apps/mednist_classifier_monaideploy) updated to demonstrate the use of DCIOM SR writing (without initial DICOM input) | ||
| - Updated are the main functions of the built-in [operators](https://github.com/Project-MONAI/monai-deploy-app-sdk/tree/main/monai/deploy/operators), which serve as examples on parsing the output objects |
There was a problem hiding this comment.
Suggested change
| - Updated are the main functions of the built-in [operators](https://github.com/Project-MONAI/monai-deploy-app-sdk/tree/main/monai/deploy/operators), which serve as examples on parsing the output objects | |
| - Updated are the main functions of the built-in [operators](https://github.com/Project-MONAI/monai-deploy-app-sdk/tree/main/monai/deploy/operators), which serve as examples of parsing the output objects |
There was a problem hiding this comment.
changed to examples on how to parse, wanted to emphasize the how, as the Domain classes are getting more complex now, mingled with native classes from underlying packages.
Signed-off-by: mmelqin <[email protected]>
Merged
vikashg
pushed a commit
that referenced
this pull request
Nov 25, 2021
…201) * Added DICOM text SR assets and updated all operator test functions. Signed-off-by: mmelqin <[email protected]> * Correcr style checker errors. Signed-off-by: mmelqin <[email protected]> * More style checker fix Signed-off-by: mmelqin <[email protected]> * More style checker fix to add Union[<type>, None] Signed-off-by: mmelqin <[email protected]> * Why the checker is so dumb, None for the typed object should be fine, and is handled. Signed-off-by: mmelqin <[email protected]> * Correct SR class name Signed-off-by: mmelqin <[email protected]> * Integrated DICOM SR Writer Operator to MedNIST classifier example Signed-off-by: mmelqin <[email protected]> * Correct typos in the comments Signed-off-by: mmelqin <[email protected]> * Add release note Signed-off-by: mmelqin <[email protected]> * Added updates to notebooks and fixed issues. Signed-off-by: mmelqin <[email protected]> * Cleaned up comment lines per review comments Signed-off-by: mmelqin <[email protected]> * Updated release_notes index.md, as well as release note itself Signed-off-by: mmelqin <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR intends to add the DICOM text SR related assets as well as updating operator test functions,