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Example 2: Defining a Dataset with File Data

 

Example 2: Dataset with File Data

The Data Schema

🛹 Pro-tip: you can skip this step using Auto-Generated Data Schemas if you don't have specific requirements for the dataset schema.

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The Data Schema can be uploaded as a CSV to the Rhino Web UI or added directly to the Rhino Web UI through the built-in Data Schema editor. For this example, we will create this Dataset within the UI and name it SpO2 Schema.

Field Name Image Age Gender SpO2
Identifier        
Description        
Role Input Input Metadata Output
Type Filename Age Enum Percent
Type Parameters     {"choices": ["m", "f", "o"]}  
May Contain PHI? False True False False

 

The Dataset's Tabular Data

🛹 Pro-tip: you can skip providing tabular data if you don't need metadata (e.g., your dataset is a list of files for inference) and want to use all files in the specific folder defined `File Data Path`. See example below.

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The tabular data CSV file is prepared within the institutional firewall from data in clinical systems and then copied via SFTP to the Rhino Client.

Image Age Gender SpO2
males/123.png 52 m 0.97
males/456.png 38 m 0.98
females/789.png 45 f 0.98

For this example: Let’s say this tabular CSV file was copied via SFTP to the following location on your Rhino Client: /rhino_data/uploads/spo2/dataset1.csv

 

The Dataset's DICOM Data

No DICOM data exists in this Dataset

 

The Dataset's File Data

All image files associated with the cases in the tabular data file are queried from the clinical data systems, de-identified, and then copied via SFTP to the Rhino Client.

The Rhino Client expects the files to be located precisely at the relative path that is specified in the tabular data file, where these paths are relative to a base path provided during Dataset import.

For this example, let's say we place our file data in the following locations on our Rhino Client

  • /rhino_data/uploads/image_data/males/123.png
  • /rhino_data/uploads/image_data/males/456.png
  • /rhino_data/uploads/image_data/females/789.png

 

Example 2: Load Specific Files

Dataset Import parameters:

  1. Name: Example 2 Dataset
  2. Description:  Example 2 Dataset
  3. Data Schema: SpO2 Schema v0
  4. Tabular Data File Path: /rhino_data/uploads/spo2/dataset1.csv
  5. DICOM Data Path:
    • Import Method: Filesystem
    • Path: /rhino_data/ (Default Value: Do not change)
  6. File Data Path: /rhino_data/uploads/images
  7. Is Data De-identified?: Yes

Example 2 Simplified: Load All Files Under a Folder

Dataset Import parameters:

  1. Name: Example 2 Dataset
  2. Description:  Example 2 Dataset
  3. Data Schema: SpO2 Schema v0
  4. Tabular Data File Path: `LEAVE EMPTY`
  5. DICOM Data Path:
    • Import Method: Filesystem
    • Path: `LEAVE EMPTY`
  6. File Data Path: /rhino_data/uploads/images
  7. Is Data De-identified?: Yes
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