--- name: pydicom description: Use pydicom to read, inspect, write, transform, and safely preflight local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compression plugins, frames, private elements, JSON, and bounded de-identification review. license: MIT compatibility: Python 3.10+ with pydicom 3.0.2; optional pinned NumPy, Pillow, and pixel plugins. Helper CLIs are local-only and require authorized data. metadata: version: "1.1" skill-author: "K-Dense Inc." last-reviewed: "2026-07-23" --- # pydicom Use pydicom for DICOM dataset I/O and pixel processing. Version 3.0.2 is the current stable release reviewed here. It fixes CVE-2026-32711, a crafted DICOMDIR path-traversal issue. pydicom 3.0.2 declares Python `>=3.10`; its bundled DICOM dictionary is 2024c, while the live DICOM Standard may be newer. ## Mandatory safety boundary - Work only with local data that the user is authorized to access. - DICOM metadata, file names, private elements, overlays, structured content, and pixels may contain protected health information (PHI). - Never print `Dataset`, export full metadata/JSON, or log element values by default. Use a documented allowlist and aggregate output. - pydicom is a general DICOM framework, not a diagnostic viewer. Pixel output, validation, conversion, and plugin availability are not diagnostic claims. - De-identification is profile-, purpose-, recipient-, jurisdiction-, and threat-context-specific. It requires privacy/DICOM expert verification. - Never claim that a tag-removal script is DICOM PS3.15, HIPAA, GDPR, or other compliance. Preserve originals and audit derived outputs. - Treat deterministic pseudonymization keys and UID maps as re-identification secrets: use least privilege and encrypted/managed secret storage, never commit, sync, log, or share them with derivatives, and define backup, rotation, revocation, and destruction procedures. A leaked key invalidates the intended separation; rotation also changes deterministic mappings. - Set explicit input-file, file-count, frame-count, decoded-byte, and output limits before parsing untrusted or unusually large datasets. ## Installation Create or activate an isolated environment, then install the exact reviewed release: ```bash uv pip install "pydicom==3.0.2" ``` Uncompressed pixel arrays and image rendering: ```bash uv pip install "pydicom==3.0.2" "numpy==2.5.1" "Pillow==12.3.0" ``` Install only the transfer-syntax plugins required by the deployment: ```bash # JPEG/JPEG-LS, JPEG 2000/HTJ2K, and faster RLE through pylibjpeg uv pip install "numpy==2.5.1" "pylibjpeg==2.1.0" \ "pylibjpeg-libjpeg==2.4.0" "pylibjpeg-openjpeg==2.5.0" \ "pylibjpeg-rle==2.2.0" # JPEG-LS encoder/decoder uv pip install "numpy==2.5.1" "pyjpegls==1.5.1" # Alternative decoder with platform-specific wheels uv pip install "python-gdcm==3.2.6" ``` Plugin licenses and wheels differ by package/platform; review them before deployment. Pillow has documented decoding limitations and pydicom cautions that plugin output must be independently checked. Native codec wheels widen the supply-chain and memory-safety boundary. For a controlled deployment, resolve these exact pins on a trusted build host, lock and verify wheel hashes/provenance, mirror approved artifacts internally, scan them, and install with hash enforcement rather than resolving from the public index at runtime. ## Choose the workflow 1. Need an aggregate overview: run `scripts/extract_metadata.py`. 2. Need bounded technical checks: run `scripts/dicom_inventory.py`. 3. Need codec deployment preflight: run `scripts/transfer_syntax_inspector.py`. 4. Need frame/memory planning: run `scripts/pixel_frame_planner.py`. 5. Need one non-diagnostic rendered frame: run `scripts/dicom_to_image.py`. 6. Need a pseudonymized derivative: read the de-identification section, create a site-reviewed action profile, then run `scripts/anonymize_dicom.py` and `scripts/deidentification_audit.py`. 7. Need to check a sensitive UID map: run `scripts/uid_mapping_validator.py`. ## Read datasets safely `dcmread()` returns a `FileDataset`, a `Dataset` subclass with File Format state such as `file_meta`, preamble, and original encoding. ```python from pathlib import Path import pydicom path = Path("authorized/input.dcm") ds = pydicom.dcmread( path, stop_before_pixels=True, specific_tags=[ "SOPClassUID", "Modality", "Rows", "Columns", "NumberOfFrames", ], ) technical = { "sop_class": ds.get("SOPClassUID"), "modality": ds.get("Modality"), "rows": ds.get("Rows"), "columns": ds.get("Columns"), } ``` Use: - `stop_before_pixels=True` for metadata-only work. - `specific_tags=[...]` for a minimum allowlist. - `defer_size="1 MiB"` when a later write must preserve large values. - `force=False` (default). `force=True` only bypasses the File Format header check; it does not prove the bytes are valid DICOM. Do not call `print(ds)`, `repr(ds)`, or iterate values into logs on clinical data. ## Dataset, DataElement, and sequences Access standard elements by keyword and check for absence: ```python modality = ds.get("Modality", "UNSPECIFIED") if "ReferencedImageSequence" in ds: for item in ds.ReferencedImageSequence: referenced_class = item.get("ReferencedSOPClassUID") ``` Tag access, such as `ds[0x0010, 0x0010]`, returns a `DataElement`; its `.value` is separate. `Sequence` behaves like a list of nested `Dataset` items. Privacy actions must recurse through every sequence item, not only the top level. When creating a file, use `FileMetaDataset` for group `0002`, keep dataset and file-meta SOP UIDs consistent, set a Transfer Syntax UID, and write in enforced File Format: ```python from pydicom import dcmwrite from pydicom.dataset import FileDataset, FileMetaDataset from pydicom.uid import CTImageStorage, ExplicitVRLittleEndian, generate_uid meta = FileMetaDataset() meta.MediaStorageSOPClassUID = CTImageStorage meta.MediaStorageSOPInstanceUID = generate_uid() meta.TransferSyntaxUID = ExplicitVRLittleEndian ds = FileDataset(None, {}, file_meta=meta, preamble=b"\0" * 128) ds.SOPClassUID = meta.MediaStorageSOPClassUID ds.SOPInstanceUID = meta.MediaStorageSOPInstanceUID # Add all attributes required by the selected IOD before writing. dcmwrite("new.dcm", ds, enforce_file_format=True, overwrite=False) ``` `write_like_original` is deprecated in pydicom 3.0; use `enforce_file_format`. A successful write is not full PS3.3 IOD conformance. ## UIDs and transfer syntax The File Meta Information Transfer Syntax UID controls dataset encoding and pixel compression: ```python ts = ds.file_meta.TransferSyntaxUID summary = { "uid": str(ts), "name": ts.name, "compressed": ts.is_compressed, "implicit_vr": ts.is_implicit_VR, "little_endian": ts.is_little_endian, } ``` pydicom 3.0 chooses write encoding from the Transfer Syntax UID before legacy dataset flags. Do not replace structural UIDs (Transfer Syntax, SOP Class, or coding-scheme UIDs) during pseudonymization. Instance/reference UID replacement must be one-to-one and consistent across the complete declared scope. Read [references/transfer_syntaxes.md](references/transfer_syntaxes.md) before compression, decompression, or encapsulation. ## Pixel data and frames The stable `pydicom.pixels` API supports path-based, frame-specific decoding: ```python from pydicom.pixels import pixel_array # Reads only the selected frame where the source permits it. frame = pixel_array("authorized/image.dcm", index=0, raw=False) ``` Shape semantics: - grayscale single frame: `(rows, columns)` - grayscale multi-frame: `(frames, rows, columns)` - color single frame: `(rows, columns, samples)` - color multi-frame: `(frames, rows, columns, samples)` `raw=False` converts YCbCr pixel data to RGB when possible; `raw=True` retains the decoded color space after mandatory minimal processing. Use `iter_pixels(path, indices=[...])` for bounded multi-frame iteration. For grayscale display, apply transforms in this order: ```python from pydicom.pixels import apply_modality_lut, apply_voi_lut modality_values = apply_modality_lut(frame, ds) display_values = apply_voi_lut(modality_values, ds, index=0) ``` Modality LUT/rescale and VOI/windowing change display/value semantics. MONOCHROME1 may require presentation inversion. Palette Color requires `apply_color_lut()`. Presentation states and ICC behavior may require a validated viewer. Never use per-frame min/max normalization for quantitative analysis. ## Compression, decompression, and encapsulation - Accessing `pixel_array` decodes as needed but does not change the dataset. - `Dataset.decompress()` changes Pixel Data in place, sets Explicit VR Little Endian, updates image metadata, and generates a new SOP Instance UID by default. - `Dataset.compress(uid)` changes Pixel Data and Transfer Syntax in place and generates a new SOP Instance UID by default. - pydicom 3.0 built-in/found encoders cover RLE Lossless, JPEG-LS, and JPEG 2000 combinations documented in the stable plugin matrix. - Each compressed frame is separately encoded and then encapsulated. Use `encapsulate()` or `encapsulate_extended()` for externally encoded frames. - Read frames with current `pydicom.encaps.generate_frames()` or `get_frame()`; legacy encapsulation generator names are deprecated for pydicom 4. Always inspect capabilities first, limit decoded bytes/frames, and verify pixel correctness independently. Lossy compression acceptability is outside pydicom and the DICOM encoding specification. ## DICOM JSON and private elements `Dataset.to_json()`, `to_json_dict()`, and `Dataset.from_json()` implement the DICOM JSON Model, but pydicom documents JSON support as beta. Full JSON may inline binary data and expose every identifier and pixel payload. Do not emit it as a metadata report. A `BulkDataURI` handler introduces separate storage, authorization, and retrieval obligations. Private elements are not standardized and may contain PHI: ```python # Recursive removal, but not sufficient de-identification by itself. ds.remove_private_tags() ``` Retain private elements only under an explicit reviewed safe-private policy. Read [references/common_tags.md](references/common_tags.md) for tag access, privacy classes, and standard pointers. ## De-identification workflow DICOM PS3.15 Annex E explicitly states that confidentiality profiles do not guarantee removal of all identifying information and do not replace a complete de-identification process. 1. Define purpose, recipients, linkage needs, regulations, threat model, and acceptable re-identification risk. 2. Select the Basic Application Level Confidentiality Profile and needed options (pixel, recognizable visual features, graphics, structured content, descriptors, temporal information, patient characteristics, devices, institutions, UIDs, and safe private data). 3. Preserve source objects unchanged in controlled storage. 4. Apply every action recursively, including nested sequences. 5. Replace instance/reference UIDs consistently across the complete scope; preserve structural UIDs. 6. Decide date/time handling explicitly. A fixed shift can preserve intervals but partial dates, time zones, standalone times, leap days, longitudinal linkage, and external events require reviewed policy. 7. Inspect pixels, overlays, graphics, structured content, and recognizable visual features. Do not infer clean pixels from missing metadata or set `BurnedInAnnotation=NO` without verification. 8. Rebuild File Meta Information and preamble to prevent leakage. 9. Run technical validation and a de-identification audit, then perform expert verification and documented risk review. The bundled script intentionally sets `PatientIdentityRemoved` to `NO` because it cannot establish successful de-identification. ## Helper CLIs All `--help` paths are dependency-free. The tools perform no network access and emit no DICOM values beyond narrow technical allowlists. Bundled content consists of the two linked references, the documented helper scripts, and synthetic tests. The pydicom runtime dependency is installed from the pinned PyPI release. ```bash # Redacted aggregate metadata python scripts/extract_metadata.py authorized/ --recursive # Metadata-only technical inventory python scripts/dicom_inventory.py authorized/ --recursive # Installed codec/plugin capabilities python scripts/transfer_syntax_inspector.py --input authorized/image.dcm # Frame shape, byte, and transform plan python scripts/pixel_frame_planner.py authorized/image.dcm --frames 0,2-4 # One non-diagnostic frame python scripts/dicom_to_image.py authorized/image.dcm frame.png \ --acknowledge-pixel-phi # Create a secret key, then a scoped pseudonymized derivative plus audit python scripts/anonymize_dicom.py --generate-uid-key project.key python scripts/anonymize_dicom.py authorized/in.dcm derived/out.dcm \ --uid-key-file project.key --uid-scope export-v1 \ --audit-report derived/out.audit.json # Audit candidate metadata; no pixel decompression python scripts/deidentification_audit.py derived/out.dcm # Validate an explicitly requested sensitive UID mapping python scripts/uid_mapping_validator.py derived/uid-map.json \ --uid-key-file project.key --uid-scope export-v1 ``` The generated raw key file is a controlled-local convenience and is created with owner-only permissions. For production, materialize key bytes from an approved secret manager into a locked ephemeral file, restrict access to the de-identification service, and securely remove it afterward. Store any optional UID map separately from derivatives; it directly links original and replacement identifiers. ## pydicom 3.0 migration notes - `read_file()` and `write_file()` were removed; use `dcmread()` and `dcmwrite()`. - `write_like_original` is deprecated; use `enforce_file_format`. - `pydicom.pixel_data_handlers` is deprecated for removal in v4; use `pydicom.pixels`. - `Dataset.pixel_array` uses the new pixels backend by default and converts YCbCr to RGB when possible. - `JPEGLossless` now means UID `1.2.840.10008.1.2.4.57`; `JPEGLosslessSV1` is `.70`. - `Dataset.is_little_endian` and `is_implicit_VR` are deprecated for v4. ## Sources (verified 2026-07-23) - [pydicom 3.0.2 on PyPI](https://pypi.org/project/pydicom/) — released 2026-03-19; Python `>=3.10`. - [pydicom releases](https://github.com/pydicom/pydicom/releases) — 3.0.2 and CVE-2026-32711 details. - [Stable release notes](https://pydicom.github.io/pydicom/stable/release_notes/index.html) - [Stable installation guide](https://pydicom.github.io/pydicom/stable/tutorials/installation.html) - [Dataset basics](https://pydicom.github.io/pydicom/stable/tutorials/dataset_basics.html) - [Stable pixel tutorial](https://pydicom.github.io/pydicom/stable/tutorials/pixel_data/introduction.html) - [Stable pixel plugins](https://pydicom.github.io/pydicom/stable/guides/user/image_data_handlers.html) - [Stable compression tutorial](https://pydicom.github.io/pydicom/stable/tutorials/pixel_data/compressing.html) - [Stable DICOM JSON tutorial](https://pydicom.github.io/pydicom/stable/tutorials/dicom_json.html) - [Stable private-element guide](https://pydicom.github.io/pydicom/stable/guides/user/private_data_elements.html) - [Current DICOM Standard](https://www.dicomstandard.org/current) - [DICOM PS3.3](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/PS3.3.html), [PS3.5](https://dicom.nema.org/medical/dicom/current/output/chtml/part05/PS3.5.html), [PS3.6](https://dicom.nema.org/medical/dicom/current/output/chtml/part06/PS3.6.html), and [PS3.15](https://dicom.nema.org/medical/dicom/current/output/html/part15.html)