chore: Updated README

pontikos-lab · Sep 5, 2024 · 0cffce6 · 0cffce6
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diff --git a/.talismanrc b/.talismanrc
@@ -7,4 +7,6 @@ fileignoreconfig:
     checksum: 00912e74713f45921e593b5f1f98e23b324ab13bd5c9d44edb24c49a08f325b8
   - filename: process_dcm/utils.py
     checksum: fdb35056dbd109dbbac6fd5d3668fbff90ace8f46aa37b787eaa2572c02d0aaf
+  - filename: README.md
+    checksum: 4a9bf4e1400f36c5646be2b85eee66d1681d12e67bd9dce431206d21a7c85f64
 version: ""
diff --git a/README.md b/README.md
@@ -20,26 +20,36 @@ pip install process-dcm
 ```
 
 ```bash
- Usage: process-dcm [OPTIONS] INPUT_DIR
+Usage: process-dcm [OPTIONS] INPUT_DIR
 
  Process DICOM files in subfolders, extract images and metadata using parallel processing.
 
-╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
-│ *    input_dir      TEXT  Input directory containing subfolders with DICOM files. [default: None] [required]                          │
-╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
-╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
-│ --image_format        -f      TEXT     Image format for extracted images (png, jpg, webp). Defaults to: png [default: png]            │
-│ --output_dir          -o      TEXT     Output directory for extracted images and metadata. Defaults to: __input_dir__/exported_data   │
-│                                        Use absolute path if you want to save the output in a specific location.                       │
-│                                        [default: exported_data]                                                                       │
-│ --n_jobs              -j      INTEGER  Number of parallel jobs. Defaults to: 1 [default: 1]                                           │
-│ --overwrite           -w               Overwrite existing images if found.                                                            │
-│ --verbose             -v               Verbose output.                                                                                │
-│ --version             -V               Prints app version                                                                             │
-│ --install-completion                   Install completion for the current shell.                                                      │
-│ --show-completion                      Show completion for the current shell, to copy it or customize the installation.               │
-│ --help                -h               Show this message and exit.                                                                    │
-╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────╮
+│ *    input_dir      TEXT  Input directory containing subfolders with DICOM files. [default: None]   │
+│                           [required]                                                                │
+╰─────────────────────────────────────────────────────────────────────────────────────────────────────╯
+╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────╮
+│ --image_format        -f      TEXT     Image format for extracted images (png, jpg, webp). Defaults │
+│                                        to: png                                                      │
+│                                        [default: png]                                               │
+│ --output_dir          -o      TEXT     Output directory for extracted images and metadata. Defaults │
+│                                        to: exported_data                                            │
+│                                        [default: exported_data]                                     │
+│ --relative            -r               Save extracted data in folders relative to _input_dir_.      │
+│ --n_jobs              -j      INTEGER  Number of parallel jobs. Defaults to: 1 [default: 1]         │
+│ --mapping             -m      TEXT     Path to CSV containing patient_id to study_id mapping. If    │
+│                                        not provided and patient_id is not anonymised, a             │
+│                                        'patient_2_study_id.csv' file will be generated              │
+│ --keep                -k      TEXT     Keep the specified fields (p: patient_key, n: names, d:      │
+│                                        date_of_birth, D: year-only DOB, g: gender)                  │
+│ --overwrite           -w               Overwrite existing images if found.                          │
+│ --verbose             -v               Verbose output.                                              │
+│ --version             -V               Prints app version                                           │
+│ --install-completion                   Install completion for the current shell.                    │
+│ --show-completion                      Show completion for the current shell, to copy it or         │
+│                                        customize the installation.                                  │
+│ --help                -h               Show this message and exit.                                  │
+╰─────────────────────────────────────────────────────────────────────────────────────────────────────╯
 ```
 
 ## For Developers