Add svs mappings

mappings/test_svs_mappings/svs_mappings/device_exposure.md

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+## Table name: device_exposure
+
+### Reading from svs_metadata.csv
+
+![](md_files/image1.png)
+
+| Destination Field | Source field | Logic | Comment field |
+| --- | --- | --- | --- |
+| device_exposure_id |  |  |  |
+| person_id |  |  |  |
+| device_concept_id |  |  |  |
+| device_exposure_start_date |  |  |  |
+| device_exposure_start_datetime |  |  |  |
+| device_exposure_end_date |  |  |  |
+| device_exposure_end_datetime |  |  |  |
+| device_type_concept_id |  |  |  |
+| unique_device_id | aperio.dsr id<br>aperio.scanscope id |  | Scanner details could also map to device_exposure for more detailed implementations.<br>Could be used to represent the scanning device used to capture the image. |
+| production_id |  |  |  |
+| quantity |  |  |  |
+| provider_id | aperio.user |  | Connects the device user to the specific provider involved in capturing the image.<br> |
+| visit_occurrence_id |  |  |  |
+| visit_detail_id |  |  |  |
+| device_source_value |  |  |  |
+| device_source_concept_id |  |  |  |
+| unit_concept_id |  |  |  |
+| unit_source_value |  |  |  |
+| unit_source_concept_id |  |  |  |
+

mappings/test_svs_mappings/svs_mappings/image_feature.md

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+## Table name: image_feature
+
+### Reading from svs_thumbnail.csv
+
+![](md_files/image3.png)
+
+| Destination Field | Source field | Logic | Comment field |
+| --- | --- | --- | --- |
+| feature_id |  |  |  |
+| image_id |  |  |  |
+| feature_type | x<br>y<br>red<br>green<br>blue | Assign feature_type_concept_id = <concept_id_for_X_Coordinate>, where concept ID represents the X-coordinate feature type. Example: 1234567.<br>Assign feature_type_concept_id = <concept_id_for_Y_Coordinate>, where concept ID represents the Y-coordinate feature type. Example: 1234567.<br>Assign feature_type_concept_id = <concept_id_for_Red_Channel_Intensity>, where concept ID represents the Red intensity feature. Example: 2345678.<br>Assign feature_type_concept_id = <concept_id_for_Green_Channel_Intensity>, where concept ID represents the Green intensity feature. Example: 2345679.<br>Assign feature_type_concept_id = <concept_id_for_Blue_Channel_Intensity>, where concept ID represents the Blue intensity feature. Example: 2345680. | Feature Type should represent the type of measurement or attribute you are capturing. This is for X coordinate. (X and Y represent the spatial position of a pixel.)<br>Feature Type should represent the type of measurement or attribute you are capturing. This is for Y coordinate. (X and Y represent the spatial position of a pixel.)<br>The feature is Red channel intensity (feature type)<br>The feature is Green channel intensity (feature type)<br>The feature is Blue channel intensity (feature type)<br> |
+| feature_value | x<br>y<br>blue<br>red<br>green |  | Actual value from the source CSV (e.g., the X-coordinate value itself).<br>Actual value from the source CSV (e.g., the Y-coordinate value itself).<br>The actual value for the Blue channel intensity<br>The actual value for the Red channel intensity<br>The actual value for the Green channel intensity<br> |
+| unit_concept_id |  |  |  |
+| extraction_method |  |  |  |
+| date_of_extraction |  |  |  |
+
+### Reading from svs_image_data.csv
+
+![](md_files/image4.png)
+
+| Destination Field | Source field | Logic | Comment field |
+| --- | --- | --- | --- |
+| feature_id |  |  |  |
+| image_id |  |  |  |
+| feature_type | level<br>width<br>height<br>downsample | Assign feature_type_concept_id = <concept_id_for_level>, where concept ID represents the level feature type. Example: 1234567.<br>Assign feature_type_concept_id = <concept_id_for_width>, where concept ID represents the width feature type. Example: 1234567.<br>Assign feature_type_concept_id = <concept_id_for_width>, where concept ID represents the width feature type. Example: 1234567.<br>Assign feature_type_concept_id = <concept_id_for_downsample>, where concept ID represents the downsample feature type. Example: 1234567. | Level of the image pyramid (used for multi-resolution images).<br>Width of the original image (or downsampled image level).<br>Height of the original image (or downsampled image level).<br>Represents how much the image has been downsampled at each level.<br> |
+| feature_value | downsample<br>height<br>width<br>level |  | The actual downsample value for the image<br>The actual height value of the image<br>The actual width value of the image<br>The actual level value of the image<br> |
+| unit_concept_id |  |  |  |
+| extraction_method |  |  |  |
+| date_of_extraction |  |  |  |
+
+### Reading from svs_metadata.csv
+
+![](md_files/image5.png)
+
+| Destination Field | Source field | Logic | Comment field |
+| --- | --- | --- | --- |
+| feature_id |  |  |  |
+| image_id |  |  |  |
+| feature_type | aperio.appmag<br>aperio.mpp | Assign feature_type_concept_id = <concept_id_for_magnificatione>, where concept ID represents the objective magnification feature type. Example: 123456<br>Assign feature_type_concept_id = <concept_id_for_mpp>, where concept ID represents the microns per pixel feature. Example: 345678. | Describes the image's magnification (e.g., 20x). Concept ID could be for magnification.<br>MPP feature gives the resolution of the image at a pixel level.<br> |
+| feature_value | aperio.appmag<br>aperio.mpp<br>aperio.originalheight<br>aperio.originalwidth |  | Actual value of the image's magnification (e.g., 20x)<br>Actual value of resolution of the image at a pixel level.<br>Original height of the image<br>Original width of image<br> |
+| unit_concept_id |  |  |  |
+| extraction_method |  |  |  |
+| date_of_extraction |  |  |  |
+

mappings/test_svs_mappings/svs_mappings/image_occurrence.md

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+## Table name: image_occurrence
+
+### Reading from svs_metadata.csv
+
+![](md_files/image2.png)
+
+| Destination Field | Source field | Logic | Comment field |
+| --- | --- | --- | --- |
+| image_id | aperio.imageid |  |  |
+| person_id |  |  |  |
+| study_id |  |  |  |
+| modality |  |  |  |
+| body_part_examined |  |  |  |
+| date_of_image | aperio.date |  |  |
+| file_location |  |  |  |
+

mappings/test_svs_mappings/svs_mappings/index.md

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+# Source Data Mapping Approach to CDMv5.4
+
+![](md_files/image6.png)
+
+## Contents
+
+[device_exposure](device_exposure.md)
+
+[image_occurrence](image_occurrence.md)
+
+[image_feature](image_feature.md)
+
+[source_appendix](source_appendix.md)
+

mappings/test_svs_mappings/svs_mappings/source_appendix.md

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+# Appendix: source tables
+
+### Table: svs_image_data.csv
+
+| Field | Type | Most freq. value | Comment |
+| --- | --- | --- | --- |
+| level | INT |  |  |
+| width | INT |  |  |
+| height | INT |  |  |
+| downsample | REAL |  |  |
+
+### Table: svs_thumbnail.csv
+
+| Field | Type | Most freq. value | Comment |
+| --- | --- | --- | --- |
+| x | INT | 110 |  |
+| y | INT | 88 |  |
+| red | INT | 243 |  |
+| green | INT | 243 |  |
+| blue | INT | 242 |  |
+
+### Table: svs_metadata.csv
+
+| Field | Type | Most freq. value | Comment |
+| --- | --- | --- | --- |
+| aperio.appmag | INT |  |  |
+| aperio.dsr id | VARCHAR |  |  |
+| aperio.date | DATE |  | Maps directly to the timestamp for when the image occurrence took place. |
+| aperio.displaycolor | INT |  |  |
+| aperio.exposure scale | REAL |  |  |
+| aperio.exposure time | INT |  |  |
+| aperio.filename | INT |  |  |
+| aperio.focus offset | REAL |  |  |
+| aperio.icc profile | VARCHAR |  |  |
+| aperio.imageid | INT |  | Maps directly to the identifier for the image occurrence. |
+| aperio.left | REAL |  |  |
+| aperio.lineareaxoffset | REAL |  |  |
+| aperio.lineareayoffset | REAL |  |  |
+| aperio.linecameraskew | INT |  |  |
+| aperio.mpp | REAL |  |  |
+| aperio.originalheight | INT |  |  |
+| aperio.originalwidth | INT |  |  |
+| aperio.scanscope id | VARCHAR |  |  |
+| aperio.stripewidth | INT |  |  |
+| aperio.time | VARCHAR |  |  |
+| aperio.time zone | VARCHAR |  |  |
+| aperio.top | REAL |  |  |
+| aperio.user | VARCHAR |  |  |
+| openslide.associated.thumbnail.height | INT |  |  |
+| openslide.associated.thumbnail.width | INT |  |  |
+| openslide.comment | VARCHAR |  |  |
+| 42672x25390 [0 | VARCHAR |  |  |
+| openslide.level-count | INT |  |  |
+| openslide.level[0].downsample | INT |  |  |
+| openslide.level[0].height | INT |  |  |
+| openslide.level[0].tile-height | INT |  |  |
+| openslide.level[0].tile-width | INT |  |  |
+| openslide.level[0].width | INT |  |  |
+| openslide.level[1].downsample | REAL |  |  |
+| openslide.level[1].height | INT |  |  |
+| openslide.level[1].tile-height | INT |  |  |
+| openslide.level[1].tile-width | INT |  |  |
+| openslide.level[1].width | INT |  |  |
+| openslide.level[2].downsample | REAL |  |  |
+| openslide.level[2].height | INT |  |  |
+| openslide.level[2].tile-height | INT |  |  |
+| openslide.level[2].tile-width | INT |  |  |
+| openslide.level[2].width | INT |  |  |
+| openslide.mpp-x | REAL |  |  |
+| openslide.mpp-y | REAL |  |  |
+| openslide.objective-power | INT |  |  |
+| openslide.quickhash-1 | VARCHAR |  |  |
+| openslide.vendor | VARCHAR |  |  |
+| tiff.imagedescription | VARCHAR |  |  |
+| 42672x25390 [0 | VARCHAR |  |  |
+| tiff.resolutionunit | VARCHAR |  |  |
+