@pikaa-ai/pikaa 0.2.4 → 0.3.0

package/skills/pydicom/SKILL.md

@@ -0,0 +1,381 @@
+---
+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)

package/skills/pydicom/references/common_tags.md

@@ -0,0 +1,277 @@
+# DICOM data elements, tags, and privacy review
+
+This is a working guide, not a complete DICOM dictionary or an attribute
+confidentiality profile. pydicom 3.0.2 bundles the 2024c public dictionary; use
+the live DICOM PS3.3/PS3.6 and the selected IOD when correctness depends on a
+newer edition.
+
+## Privacy boundary
+
+DICOM metadata and pixels may contain PHI. Do not print a complete `Dataset`,
+serialize the full dataset to JSON, or copy arbitrary values into logs. Tag
+names that appear technical can still identify a person through site-specific
+values, free text, private data, UIDs, dates, devices, or linkage with external
+records.
+
+DICOM PS3.15 Annex E says that applying attribute actions does not guarantee
+that the Information Object is de-identified. A valid workflow must select a
+profile/options for its context and include expert verification and
+re-identification risk review.
+
+## pydicom access model
+
+```python
+from pydicom import dcmread
+from pydicom.tag import Tag
+
+ds = dcmread(
+    "authorized/input.dcm",
+    stop_before_pixels=True,
+    specific_tags=["SOPClassUID", "Modality", "Rows", "Columns"],
+)
+
+modality = ds.get("Modality", "UNSPECIFIED")
+element = ds.get_item(Tag(0x0008, 0x0016))
+```
+
+- Keyword access (`ds.Modality`) returns the value and raises `AttributeError`
+  when absent.
+- `ds.get("Modality", default)` is safer for optional elements.
+- Tag indexing (`ds[0x0008, 0x0016]`) returns a `DataElement`; read `.value`
+  only when authorized.
+- A tag consists of a 16-bit group and 16-bit element.
+- Standard public tags generally use even groups. Private data uses odd groups
+  and private creator blocks.
+- `Dataset` contains `DataElement` objects. A value with VR `SQ` is a
+  `Sequence` of nested `Dataset` items.
+
+## Narrow technical allowlist
+
+The following values are commonly useful for bounded technical inventory.
+They do not make an entire record safe to disclose.
+
+| Tag | Keyword | VR | Technical use |
+|---|---|---|---|
+| (0008,0016) | SOPClassUID | UI | Identifies the standardized SOP Class |
+| (0008,0060) | Modality | CS | Modality code |
+| (0002,0010) | TransferSyntaxUID | UI | File encoding/compression |
+| (0028,0002) | SamplesPerPixel | US | Samples per pixel |
+| (0028,0004) | PhotometricInterpretation | CS | Pixel color/monochrome interpretation |
+| (0028,0006) | PlanarConfiguration | US | Color sample layout |
+| (0028,0008) | NumberOfFrames | IS | Declared frames |
+| (0028,0010) | Rows | US | Rows per frame |
+| (0028,0011) | Columns | US | Columns per frame |
+| (0028,0100) | BitsAllocated | US | Storage bits per sample |
+| (0028,0101) | BitsStored | US | Meaningful bits per sample |
+| (0028,0102) | HighBit | US | Highest stored bit |
+| (0028,0103) | PixelRepresentation | US | Unsigned (0) or signed (1) |
+| (0028,0301) | BurnedInAnnotation | CS | Declared burned-in annotation status |
+| (0028,0302) | RecognizableVisualFeatures | CS | Declared recognizable-feature status |
+| (0028,2110) | LossyImageCompression | CS | Whether lossy compression occurred |
+
+`BurnedInAnnotation=NO` is a declaration, not proof that pixels are clean.
+Absence, `YES`, or another value requires review. Even `NO` does not address
+recognizable facial/anatomic features or matching against source images.
+
+## Instance, relationship, and spatial elements
+
+These values are technically important but can enable linkage or reveal
+individual context. Do not emit them in default reports.
+
+| Tag | Keyword | Privacy/semantic concern |
+|---|---|---|
+| (0008,0018) | SOPInstanceUID | Instance identifier; may support linkage |
+| (0020,000D) | StudyInstanceUID | Study-level linkage |
+| (0020,000E) | SeriesInstanceUID | Series-level linkage |
+| (0020,0052) | FrameOfReferenceUID | Spatial/reference linkage |
+| (0008,1155) | ReferencedSOPInstanceUID | Cross-instance relationship |
+| (0020,0032) | ImagePositionPatient | Patient-coordinate position |
+| (0020,0037) | ImageOrientationPatient | Patient-coordinate orientation |
+| (0028,0030) | PixelSpacing | Physical sample spacing |
+| (0018,0050) | SliceThickness | Nominal reconstructed thickness |
+| (0018,0088) | SpacingBetweenSlices | Center-to-center spacing when defined |
+
+Do not sort a series only by `SliceLocation` or assume `SliceThickness` equals
+inter-slice spacing. Reconstruct geometry from the applicable IOD, orientation,
+position, frame functional groups, and validated series membership.
+
+## Direct and quasi-identifiers
+
+The following examples are not exhaustive. PS3.15 Table E.1-1 and the chosen
+options control action selection, including nested occurrences.
+
+| Tag | Keyword | Typical risk |
+|---|---|---|
+| (0010,0010) | PatientName | Direct identifier |
+| (0010,0020) | PatientID | Direct/local identifier |
+| (0010,0021) | IssuerOfPatientID | Identifier namespace |
+| (0010,0030) | PatientBirthDate | Date/quasi-identifier |
+| (0010,0032) | PatientBirthTime | Time/quasi-identifier |
+| (0010,0040) | PatientSex | Patient characteristic |
+| (0010,1010) | PatientAge | Patient characteristic |
+| (0010,1020) | PatientSize | Patient characteristic |
+| (0010,1030) | PatientWeight | Patient characteristic |
+| (0010,1040) | PatientAddress | Direct identifier |
+| (0010,2154) | PatientTelephoneNumbers | Direct identifier |
+| (0010,4000) | PatientComments | Free text |
+| (0008,0050) | AccessionNumber | Order/study linkage |
+| (0020,0010) | StudyID | Local study identifier |
+| (0040,1001) | RequestedProcedureID | Order linkage |
+| (0040,0009) | ScheduledProcedureStepID | Workflow linkage |
+| (0008,0090) | ReferringPhysicianName | Person identifier |
+| (0008,1050) | PerformingPhysicianName | Person identifier |
+| (0008,1070) | OperatorsName | Person identifier |
+| (0008,0080) | InstitutionName | Organization identifier |
+| (0008,0081) | InstitutionAddress | Organization/location identifier |
+| (0008,1010) | StationName | Device/site identifier |
+| (0018,1000) | DeviceSerialNumber | Device identifier |
+| (0008,1030) | StudyDescription | Potential free text |
+| (0008,103E) | SeriesDescription | Potential free text |
+| (0018,1030) | ProtocolName | Site/user-entered text |
+
+Required IOD type matters. A PS3.15 action can remove (`X`), zero (`Z`),
+replace with a valid dummy value (`D`), replace a UID consistently (`U`), keep
+(`K`), or clean (`C`), with conditional combinations. Blind deletion can make
+an instance non-conformant.
+
+## Dates and times
+
+Common date/time elements include:
+
+| Tag | Keyword | VR |
+|---|---|---|
+| (0008,0012) | InstanceCreationDate | DA |
+| (0008,0013) | InstanceCreationTime | TM |
+| (0008,0020) | StudyDate | DA |
+| (0008,0030) | StudyTime | TM |
+| (0008,0021) | SeriesDate | DA |
+| (0008,0031) | SeriesTime | TM |
+| (0008,0022) | AcquisitionDate | DA |
+| (0008,0032) | AcquisitionTime | TM |
+| (0008,002A) | AcquisitionDateTime | DT |
+| (0008,0023) | ContentDate | DA |
+| (0008,0033) | ContentTime | TM |
+
+VR syntax:
+
+- `DA`: `YYYYMMDD`
+- `TM`: `HHMMSS.FFFFFF` with permitted truncation
+- `DT`: `YYYYMMDDHHMMSS.FFFFFF&ZZXX` with permitted truncation
+
+Date/time handling is not solved by replacing every value with a constant.
+Review:
+
+- whether full dates or modified dates are allowed by the selected PS3.15
+  option;
+- one consistent shift across the intended longitudinal scope;
+- leap days, range limits, partial precision, time zones, and midnight
+  crossings;
+- standalone `TM` values that cannot be shifted safely without a paired date;
+- interval preservation and external event linkage;
+- IOD Type 1/2 requirements and scientific utility.
+
+Record the policy and caveats without logging original values.
+
+## UIDs: replace instance relationships, not semantics
+
+UID VR is `UI`, but not every UID is an identifier to pseudonymize.
+
+Usually structural/semantic and preserved:
+
+- Transfer Syntax UID
+- SOP Class UID and Referenced SOP Class UID
+- coding/context/template UIDs defined by standards
+- implementation UID handling according to rebuilt File Meta Information
+
+Often instance/reference linkage requiring profile-directed, consistent
+replacement:
+
+- Study, Series, SOP Instance, and Frame of Reference UIDs
+- Referenced SOP Instance UIDs in sequences
+- synchronization, concatenation, tracking, specimen, and transaction UIDs
+
+Use one-to-one replacement over the declared scope. A keyed deterministic
+mapping can maintain consistency, but the key/map is sensitive. Replacing UIDs
+does not itself prevent pixel or metadata matching and must not create false
+confidence.
+
+## Sequences and recursive traversal
+
+Identifiers may occur at any nesting depth:
+
+```python
+def visit(dataset):
+    for element in dataset:
+        if element.VR == "SQ":
+            for item in element.value:
+                visit(item)
+        else:
+            review(element.tag, element.keyword, element.VR)
+```
+
+Bound recursion depth and total elements for untrusted files. Do not print
+values from the callback. pydicom's `Dataset.walk()` is also recursive by
+default, and `remove_private_tags()` uses recursive traversal.
+
+## Private data
+
+Private elements use odd group numbers and a private creator block. Their
+semantics are vendor-defined and names may be unknown or non-unique. Access by
+tag or `PrivateBlock`, not by the descriptive display name.
+
+```python
+private_count = sum(1 for element in ds.iterall() if element.tag.is_private)
+```
+
+`Dataset.remove_private_tags()` recursively removes private elements, but:
+
+- private removal alone is not de-identification;
+- standard elements, sequences, pixels, graphics, and overlays still matter;
+- some private elements may be scientifically necessary;
+- the PS3.15 Retain Safe Private Option requires evidence that retained
+  elements are safe and removal/processing of all others.
+
+Default to remove or reject private data. Explicit retention needs a reviewed
+allowlist and provenance.
+
+## Pixel, graphics, and structured content
+
+Potential identifying content is not limited to `(7FE0,0010) PixelData`:
+
+- Float/Double Float Pixel Data
+- overlays in repeating `60xx` groups
+- retired curves in `50xx` groups
+- presentation-state graphics and annotations
+- Structured Report text/content items
+- waveforms, encapsulated documents, spectra, and other bulk content
+- full-face images and recognizable head/neck reconstructions
+
+The PS3.15 Clean Pixel Data, Clean Recognizable Visual Features, Clean
+Graphics, and Clean Structured Content options address different risks.
+Human review may be required, and cleaning can impair utility.
+
+## DICOM JSON
+
+`Dataset.to_json()` and `to_json_dict()` preserve DICOM element content.
+Binary data is either base64 `InlineBinary` or represented by `BulkDataURI`.
+Therefore:
+
+- JSON is not a safe metadata summary;
+- full JSON can contain the same PHI as the source dataset;
+- a bulk-data handler must enforce storage and retrieval authorization;
+- pydicom 3.0.2 documents JSON support as beta.
+
+Use `scripts/extract_metadata.py` for allowlisted aggregate inventory.
+
+## Sources (verified 2026-07-23)
+
+- [pydicom 3.0.2 dataset basics](https://pydicom.github.io/pydicom/stable/tutorials/dataset_basics.html)
+- [pydicom core elements](https://pydicom.github.io/pydicom/stable/guides/user/base_element.html)
+- [pydicom private elements](https://pydicom.github.io/pydicom/stable/guides/user/private_data_elements.html)
+- [pydicom DICOM JSON tutorial](https://pydicom.github.io/pydicom/stable/tutorials/dicom_json.html)
+- [DICOM PS3.3 2026c, Information Object Definitions](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/PS3.3.html)
+- [DICOM PS3.3 Image Pixel Module](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.3.html)
+- [DICOM PS3.5, Data Structures and Encoding](https://dicom.nema.org/medical/dicom/current/output/chtml/part05/PS3.5.html)
+- [DICOM PS3.5 private elements](https://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.8.2.html)
+- [DICOM PS3.6, Data Dictionary](https://dicom.nema.org/medical/dicom/current/output/chtml/part06/PS3.6.html)
+- [DICOM PS3.15 2026c, Annex E confidentiality profiles](https://dicom.nema.org/medical/dicom/current/output/html/part15.html)