Data (Input/Output) Examples
******************************
Example of these files can be found in the /data/_ directory.

.. _/data/ :https://github.com/mousavikahaki/ValidPath/tree/main/data

Here are the input and output examples for each module:

WSI Handler
--------------
	**Input:** Whole Slide Image file (.SVS,DICOM,TIFF)

	Link to the Data File Example: SVSFile_

.. _SVSFile: https://github.com/mousavikahaki/ValidPath/blob/main/data/CMU-1-Small-Region.svs

	Link to the Jupyter Notebook Example Script: WSI_Handler_

.. _WSI_Handler: https://github.com/mousavikahaki/ValidPath/blob/main/01_read_wsi.ipynb
 

	**Output:** Processed file such as sub image region


Annotation Extraction
--------------
	**Input:** Whole Slide Image file (.SVS,DICOM,TIFF) and annotation file (.xml)

	Link to the WSI File Example: SVSFile_
	
	Link to the XML File Example: XMLFile_
	
.. _XMLFile: https://github.com/mousavikahaki/ValidPath/blob/main/data/CMU-1-Small-Region.xml

	Link to the Jupyter Notebook Example Script: AnnotationExtraction_

.. _AnnotationExtraction: https://github.com/mousavikahaki/ValidPath/blob/main/02_annotation_extraction.ipynb
 

	**Output:** Extracted annotation file
	
	Link to the Output Data File Example: Annotation_
	
.. _Annotation: https://github.com/mousavikahaki/ValidPath/tree/main/data/images/CMU-1-Small-Region

Patch Extraction
--------------
	**Input:** Extracted annotation file generated from Annotation Extraction Step

	Link to the Input Data File Example: Annotation_

	Link to the Jupyter Notebook Example Script: PatchExtraction_

.. _PatchExtraction: https://github.com/mousavikahaki/ValidPath/blob/main/03_patch_extraction.ipynb 
 

	**Output:** Extracted Patches
	
	Link to the Output Data File Example: Patches_
	
.. _Patches: https://github.com/mousavikahaki/ValidPath/tree/main/data/ROIs

Annotation File Generator
--------------
	**Input:** Extracted Patches generated from Patch Extraction Step

	Link to the Output Data File Example: Patches_

	Link to the Jupyter Notebook Example Script: AnnotationGenerator_

.. _AnnotationGenerator: https://github.com/mousavikahaki/ValidPath/blob/main/4_annotation_generator.ipynb 
 
	**Output:** Generated Annotation File (.xml)
	
	Link to the Output Data File Example: xml_file_
	
.. _xml_file: https://github.com/mousavikahaki/ValidPath/tree/main/data/AnnGeneration

Performance Assessment 
--------------
	**Input:** Continuous classification scores generated by ML model and the binary truth

	Link to the Output Data File Example: MLResultExample_
	
.. _MLResultExample: https://github.com/mousavikahaki/ValidPath/blob/main/data/ResultsExample.xlsx

	Link to the Jupyter Notebook Example Script: PerformanceAssessment_

.. _PerformanceAssessment: https://github.com/mousavikahaki/ValidPath/blob/main/05_performance_assessment.ipynb 
 
	**Output:** Performance Assessment Results
	
	Example of the results output:


	
.. image:: ../img/assessment_output_example1.png
   :width: 300px
   :align: center
.. image:: ../img/assessment_output_example2.png
   :width: 300px
   :align: center