dicom-dre 1.0.0.dev3__tar.gz → 1.0.0.dev5__tar.gz

{dicom_dre-1.0.0.dev3 → dicom_dre-1.0.0.dev5}/.gitignore

@@ -40,3 +40,6 @@ coverage.xml
 
 # Local working files
 temp/
+
+# Avoid accidentally committing sensitive or temporary files
+*.dcm

dicom_dre-1.0.0.dev5/CHANGELOG.md

@@ -0,0 +1,56 @@
+# CHANGELOG
+
+<!-- version list -->
+
+## v1.0.0-dev.4 (2026-07-28)
+
+### Bug Fixes
+
+- More public api
+  ([`0dfb8c0`](https://github.com/susom/dicom-dre/commit/0dfb8c0ec19bb5090e9c77348f0dd96ac83978e6))
+
+
+## v1.0.0-dev.3 (2026-07-27)
+
+### Documentation
+
+- Clarify redactor usage
+  ([`77c4871`](https://github.com/susom/dicom-dre/commit/77c4871ff9ba7edcfd8107bcd485f7af40f982f1))
+
+- Clarify with implementation
+  ([`4c8a61d`](https://github.com/susom/dicom-dre/commit/4c8a61db18194d3b2033658db0d9b246a375cb31))
+
+- Consistency
+  ([`5c8f40a`](https://github.com/susom/dicom-dre/commit/5c8f40a2853036c1ce8d6f4b6d25ca53aff3f9ec))
+
+- Misc
+  ([`27a6b3b`](https://github.com/susom/dicom-dre/commit/27a6b3be40d57b646a803add32217ebb26ef5595))
+
+- Misc
+  ([`3be5bb3`](https://github.com/susom/dicom-dre/commit/3be5bb36b0684eca2321d2224700995882ac5e83))
+
+### Features
+
+- Previous should have been a feat, let's bump dev version build
+  ([`317bfcd`](https://github.com/susom/dicom-dre/commit/317bfcde78ee770b6d13e7f0361cf83b2e2f00d9))
+
+
+## v1.0.0-dev.2 (2026-07-24)
+
+### Documentation
+
+- Initial rewrite from source repo
+  ([`80e26c9`](https://github.com/susom/dicom-dre/commit/80e26c99e5f270528dfa2ddb8551b0baf3fdc7b7))
+
+- Scaffolding
+  ([`c1db56a`](https://github.com/susom/dicom-dre/commit/c1db56a224050b8704f82ac99b857d6c0c43690f))
+
+### Performance Improvements
+
+- Redactor caching
+  ([`ce14989`](https://github.com/susom/dicom-dre/commit/ce14989512d0d688d6b726444c84f91cafc28757))
+
+
+## v1.0.0-dev.1 (2026-07-24)
+
+- Initial Release

{dicom_dre-1.0.0.dev3 → dicom_dre-1.0.0.dev5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dicom-dre
-Version: 1.0.0.dev3
+Version: 1.0.0.dev5
 Summary: DICOM De-identification & Redaction Engine
 Project-URL: repository, https://github.com/susom/dicom-dre
 Author-email: Stanford <people@stanford.edu>
@@ -121,6 +121,26 @@ dicom-dre deidentify a.dcm b.dcm dir/ -o out/ \
 Sources are read but never modified. The command exits non-zero if any instance
 is `QUARANTINED`; `FILTERED` instances are a normal outcome.
 
+### JPEG DCT accelerator status
+
+JPEG DCT-domain blanking uses an optional compiled C extension that is roughly
+300x faster than the pure-Python fallback. Confirm it is active:
+
+```bash
+dicom-dre accelerator-status
+```
+
+The command prints `JPEG DCT C accelerator: ACTIVE` and exits `0` when the
+extension is loaded, or reports the pure-Python fallback and exits `1`
+otherwise. The same state is available in Python via
+`dicom_dre.jpeg_dct_accelerator_available()`:
+
+```python
+from dicom_dre import jpeg_dct_accelerator_available
+
+assert jpeg_dct_accelerator_available(), "JPEG DCT C accelerator is not compiled"
+```
+
 ### Profiles
 
 Select a de-identification profile with `--profile`:

{dicom_dre-1.0.0.dev3 → dicom_dre-1.0.0.dev5}/README.md

@@ -96,6 +96,26 @@ dicom-dre deidentify a.dcm b.dcm dir/ -o out/ \
 Sources are read but never modified. The command exits non-zero if any instance
 is `QUARANTINED`; `FILTERED` instances are a normal outcome.
 
+### JPEG DCT accelerator status
+
+JPEG DCT-domain blanking uses an optional compiled C extension that is roughly
+300x faster than the pure-Python fallback. Confirm it is active:
+
+```bash
+dicom-dre accelerator-status
+```
+
+The command prints `JPEG DCT C accelerator: ACTIVE` and exits `0` when the
+extension is loaded, or reports the pure-Python fallback and exits `1`
+otherwise. The same state is available in Python via
+`dicom_dre.jpeg_dct_accelerator_available()`:
+
+```python
+from dicom_dre import jpeg_dct_accelerator_available
+
+assert jpeg_dct_accelerator_available(), "JPEG DCT C accelerator is not compiled"
+```
+
 ### Profiles
 
 Select a de-identification profile with `--profile`:

{dicom_dre-1.0.0.dev3 → dicom_dre-1.0.0.dev5}/docs/guides/cli.md

@@ -91,3 +91,31 @@ dicom-dre deidentify studies/ -o out/ -r \
     -p PATIENT_ID=TEST -p ACCESSION_NUMBER=TESTING \
     -j 8
 ```
+
+## Checking the JPEG DCT accelerator
+
+JPEG DCT-domain blanking uses an optional compiled C extension
+(`_jpeg_dct_accel`) that is roughly 300x faster than the pure-Python fallback.
+The `dicom-dre accelerator-status` command reports whether that extension is
+active, so operators can confirm the fast path in CI and health checks.
+
+```bash
+dicom-dre accelerator-status
+```
+
+It prints one line and sets the exit code:
+
+- `JPEG DCT C accelerator: ACTIVE` — exit code `0`.
+- `JPEG DCT C accelerator: NOT AVAILABLE (using pure-Python fallback, ~300x slower)`
+  — exit code `1`.
+
+The same state is available from Python through
+[`dicom_dre.jpeg_dct_accelerator_available`](../reference/api.md):
+
+```python
+from dicom_dre import jpeg_dct_accelerator_available
+
+if not jpeg_dct_accelerator_available():
+    raise SystemExit("JPEG DCT C accelerator is not compiled")
+```
+

{dicom_dre-1.0.0.dev3 → dicom_dre-1.0.0.dev5}/src/dicom_dre/__init__.py

@@ -20,14 +20,19 @@ from dicom_dre.catalog import DeviceCatalog
 from dicom_dre.catalog import DicomTags
 from dicom_dre.catalog import Variant
 from dicom_dre.default_catalog import get_default_catalog
+from dicom_dre.jpeg_dct_scrubber import jpeg_dct_accelerator_available
+from dicom_dre.jpeg_dct_scrubber import jpeg_dct_accelerator_info
 from dicom_dre.parameters import DeidParameters
 from dicom_dre.pipeline import deidentify_file
 from dicom_dre.profile import DeidProfile
+from dicom_dre.profile import correct_implicit_vr_elements
 from dicom_dre.profiles import default_profile
 from dicom_dre.profiles import lds_no_dob_profile
 from dicom_dre.profiles import lds_profile
 from dicom_dre.profiles import pixels_only_profile
 from dicom_dre.profiles.builder import build_profile
+from dicom_dre.profiles.default import DATE_TAGS
+from dicom_dre.profiles.default import UID_TAGS
 from dicom_dre.result import BatchItemResult
 from dicom_dre.result import DeidentifyResult
 from dicom_dre.result import Outcome
@@ -45,6 +50,7 @@ except ImportError:  # pragma: no cover - version file generated at build time
 __all__ = [
     "BatchItemResult",
     "CatalogDecision",
+    "DATE_TAGS",
     "DeidParameters",
     "DeidProfile",
     "DeidentifyResult",
@@ -56,14 +62,18 @@ __all__ = [
     "ProfileSpec",
     "ScrubRegion",
     "TextRedactor",
+    "UID_TAGS",
     "Variant",
     "__version__",
     "build_profile",
+    "correct_implicit_vr_elements",
     "deidentify_file",
     "deidentify_paths",
     "default_profile",
     "get_default_catalog",
     "get_text_redactor",
+    "jpeg_dct_accelerator_available",
+    "jpeg_dct_accelerator_info",
     "lds_no_dob_profile",
     "lds_profile",
     "pixels_only_profile",

{dicom_dre-1.0.0.dev3 → dicom_dre-1.0.0.dev5}/src/dicom_dre/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '1.0.0.dev3'
-__version_tuple__ = version_tuple = (1, 0, 0, 'dev3')
+__version__ = version = '1.0.0.dev5'
+__version_tuple__ = version_tuple = (1, 0, 0, 'dev5')
 
 __commit_id__ = commit_id = None

{dicom_dre-1.0.0.dev3 → dicom_dre-1.0.0.dev5}/src/dicom_dre/cli.py

@@ -17,6 +17,7 @@ import click
 
 from dicom_dre import __version__
 from dicom_dre import deidentify_paths
+from dicom_dre import jpeg_dct_accelerator_available
 from dicom_dre.batch import OutputPathCollisionError
 from dicom_dre.batch import ProfileSpec
 from dicom_dre.parameters import DeidParameters
@@ -220,6 +221,21 @@ def deidentify(
         raise SystemExit(1)
 
 
+@cli.command(name="accelerator-status", short_help="Report JPEG DCT C accelerator status.")
+def accelerator_status() -> None:
+    """Report whether the JPEG DCT C accelerator is active.
+
+    Prints a human-readable status line and sets the process exit code: ``0``
+    when the accelerator is active, ``1`` when the pure-Python fallback is in
+    use. Usable in CI and health checks.
+    """
+    if jpeg_dct_accelerator_available():
+        click.echo("JPEG DCT C accelerator: ACTIVE")
+        return
+    click.echo("JPEG DCT C accelerator: NOT AVAILABLE (using pure-Python fallback, ~300x slower)")
+    raise SystemExit(1)
+
+
 def _resolve_allowlist_path(allowlist: str) -> Path:
     """Resolve an allowlist filename or absolute path to a concrete Path.
 

{dicom_dre-1.0.0.dev3 → dicom_dre-1.0.0.dev5}/src/dicom_dre/jpeg_dct_scrubber.py

@@ -68,6 +68,7 @@ Acknowledgements:
 import io
 import logging
 import struct
+import sys
 import warnings
 from typing import TYPE_CHECKING
 
@@ -103,6 +104,39 @@ except ImportError:
     )
 
 
+def jpeg_dct_accelerator_available() -> bool:
+    """Report whether the JPEG DCT C accelerator is active.
+
+    Returns the effective runtime state used by the scrubber to select the fast
+    path. When ``False`` the pure-Python entropy codec fallback is used, which
+    is roughly 300x slower.
+
+    This function is import-safe and side-effect-free: it does not raise and
+    does not re-emit the missing-extension warning.
+
+    Returns:
+        ``True`` if the compiled ``_jpeg_dct_accel`` extension is loaded and in
+        use, ``False`` if the pure-Python fallback is active.
+    """
+    return _HAS_C_ACCEL
+
+
+def jpeg_dct_accelerator_info() -> dict[str, object]:
+    """Return diagnostic details about the JPEG DCT C accelerator.
+
+    Returns:
+        A mapping with at least the key ``"available"`` (``bool``). When the
+        accelerator is loaded, ``"path"`` holds the extension module file path
+        if it can be determined.
+    """
+    info: dict[str, object] = {"available": _HAS_C_ACCEL}
+    if _HAS_C_ACCEL:
+        module_file = getattr(sys.modules.get("dicom_dre._jpeg_dct_accel"), "__file__", None)
+        if module_file is not None:
+            info["path"] = module_file
+    return info
+
+
 # JPEG markers
 SOI = 0xFFD8
 EOI = 0xFFD9

{dicom_dre-1.0.0.dev3 → dicom_dre-1.0.0.dev5}/src/dicom_dre/profile.py

@@ -71,7 +71,7 @@ class DeidProfile:
         self._apply_global_rules(ds)
         self._emit_deid_method_code_sequence(ds)
         _remove_group_length_tags(ds)
-        _correct_implicit_vr_elements(ds)
+        correct_implicit_vr_elements(ds)
 
     def _validate_jitter(self, params: DeidParameters) -> None:
         """Reject a jitter inconsistent with this profile's date policy.
@@ -329,7 +329,7 @@ def _remove_group_length_tags(ds: Dataset) -> None:
 _STRING_VRS = frozenset({"CS", "DS", "IS", "LO", "SH", "PN", "UI", "AE", "AS", "DA", "DT", "TM", "LT", "ST", "UT"})
 
 
-def _correct_implicit_vr_elements(ds: Dataset) -> None:
+def correct_implicit_vr_elements(ds: Dataset) -> None:
     """Correct VRs for elements pydicom decoded as OB or UN inside sequences.
 
     Some DICOM files use implicit VR encoding inside explicit VR sequences.
@@ -348,7 +348,7 @@ def _correct_implicit_vr_elements(ds: Dataset) -> None:
 
         if vr == "SQ" and elem.value:
             for item in elem.value:
-                _correct_implicit_vr_elements(item)
+                correct_implicit_vr_elements(item)
             continue
 
         if vr not in ("OB", "UN"):
@@ -387,3 +387,8 @@ def _correct_implicit_vr_elements(ds: Dataset) -> None:
         elif correct_vr == "SS" and len(raw_val) == 2:
             elem.VR = correct_vr
             elem.value = struct.unpack("<h", raw_val)[0]
+
+
+# Backward-compatible alias for the former private name. Internal callers and
+# existing imports continue to resolve to the public function object.
+_correct_implicit_vr_elements = correct_implicit_vr_elements

{dicom_dre-1.0.0.dev3 → dicom_dre-1.0.0.dev5}/tests/unit/test_cli.py

@@ -309,3 +309,28 @@ def test_redactor_allow_token(tmp_path: Path) -> None:
     assert "Added 1 token" in result.output
     contents = allowlist.read_text(encoding="utf-8")
     assert "abdomen" in contents, "New token should be written to the allowlist"
+
+
+def test_accelerator_status_active(monkeypatch) -> None:
+    """The command reports ACTIVE and exits 0 when the accelerator is present."""
+    from dicom_dre import cli as cli_module
+
+    monkeypatch.setattr(cli_module, "jpeg_dct_accelerator_available", lambda: True)
+    runner = CliRunner()
+    result = runner.invoke(cli, ["accelerator-status"])
+
+    assert result.exit_code == 0, f"Expected exit code 0 when active, got {result.exit_code}: {result.output}"
+    assert "JPEG DCT C accelerator: ACTIVE" in result.output, f"Expected ACTIVE line, got: {result.output!r}"
+
+
+def test_accelerator_status_fallback(monkeypatch) -> None:
+    """The command reports the fallback and exits non-zero when absent."""
+    from dicom_dre import cli as cli_module
+
+    monkeypatch.setattr(cli_module, "jpeg_dct_accelerator_available", lambda: False)
+    runner = CliRunner()
+    result = runner.invoke(cli, ["accelerator-status"])
+
+    assert result.exit_code == 1, f"Expected exit code 1 on fallback, got {result.exit_code}: {result.output}"
+    assert "NOT AVAILABLE" in result.output, f"Expected NOT AVAILABLE, got: {result.output!r}"
+    assert "pure-Python fallback" in result.output, f"Expected fallback note, got: {result.output!r}"

dicom_dre-1.0.0.dev5/tests/unit/test_public_api.py

@@ -0,0 +1,94 @@
+"""Tests for the stable top-level public API exports."""
+
+import dicom_dre
+
+
+def test_public_names_importable_from_package_root():
+    """The three promoted symbols are importable from the package root."""
+    from dicom_dre import DATE_TAGS
+    from dicom_dre import UID_TAGS
+    from dicom_dre import correct_implicit_vr_elements
+
+    assert callable(correct_implicit_vr_elements)
+    assert isinstance(DATE_TAGS, frozenset)
+    assert isinstance(UID_TAGS, frozenset)
+
+
+def test_tag_set_membership_unchanged():
+    """DATE_TAGS and UID_TAGS retain their published sizes."""
+    assert len(dicom_dre.DATE_TAGS) == 28
+    assert len(dicom_dre.UID_TAGS) == 35
+
+
+def test_private_alias_identity_holds():
+    """The underscore alias resolves to the same public function object."""
+    assert dicom_dre.correct_implicit_vr_elements is dicom_dre.profile._correct_implicit_vr_elements
+
+
+def test_public_names_in_all():
+    """All three names are advertised in the package __all__."""
+    assert "DATE_TAGS" in dicom_dre.__all__
+    assert "UID_TAGS" in dicom_dre.__all__
+    assert "correct_implicit_vr_elements" in dicom_dre.__all__
+
+
+def test_accelerator_functions_in_all():
+    """The accelerator status helpers are advertised in __all__."""
+    assert "jpeg_dct_accelerator_available" in dicom_dre.__all__, "jpeg_dct_accelerator_available should be in __all__"
+    assert "jpeg_dct_accelerator_info" in dicom_dre.__all__, "jpeg_dct_accelerator_info should be in __all__"
+
+
+def test_accelerator_available_importable_from_root():
+    """jpeg_dct_accelerator_available is importable from the package root."""
+    from dicom_dre import jpeg_dct_accelerator_available
+
+    assert isinstance(jpeg_dct_accelerator_available(), bool), (
+        f"Expected bool, got {type(jpeg_dct_accelerator_available())}"
+    )
+
+
+def test_accelerator_available_reflects_runtime_flag():
+    """The function returns the effective runtime accelerator flag."""
+    from dicom_dre import jpeg_dct_accelerator_available
+    from dicom_dre import jpeg_dct_scrubber
+
+    assert jpeg_dct_accelerator_available() is jpeg_dct_scrubber._HAS_C_ACCEL, (
+        "Function should return the same value the scrubber uses (_HAS_C_ACCEL)"
+    )
+
+
+def test_accelerator_available_true(monkeypatch):
+    """When the extension flag is set, the function reports True."""
+    from dicom_dre import jpeg_dct_accelerator_available
+    from dicom_dre import jpeg_dct_scrubber
+
+    monkeypatch.setattr(jpeg_dct_scrubber, "_HAS_C_ACCEL", True)
+    assert jpeg_dct_accelerator_available() is True, "Expected True when _HAS_C_ACCEL is True"
+
+
+def test_accelerator_available_false(monkeypatch):
+    """When the extension flag is unset, the function reports False."""
+    from dicom_dre import jpeg_dct_accelerator_available
+    from dicom_dre import jpeg_dct_scrubber
+
+    monkeypatch.setattr(jpeg_dct_scrubber, "_HAS_C_ACCEL", False)
+    assert jpeg_dct_accelerator_available() is False, "Expected False when _HAS_C_ACCEL is False"
+
+
+def test_accelerator_info_available_key():
+    """jpeg_dct_accelerator_info reports a boolean availability key."""
+    from dicom_dre import jpeg_dct_accelerator_info
+
+    info = jpeg_dct_accelerator_info()
+    assert isinstance(info["available"], bool), f"Expected bool for 'available', got {type(info['available'])}"
+
+
+def test_accelerator_info_absent_has_no_path(monkeypatch):
+    """When the accelerator is absent, no extension path is reported."""
+    from dicom_dre import jpeg_dct_accelerator_info
+    from dicom_dre import jpeg_dct_scrubber
+
+    monkeypatch.setattr(jpeg_dct_scrubber, "_HAS_C_ACCEL", False)
+    info = jpeg_dct_accelerator_info()
+    assert info["available"] is False, "Expected available False when _HAS_C_ACCEL is False"
+    assert "path" not in info, f"Expected no 'path' key when absent, got {info}"

dicom_dre-1.0.0.dev3/CHANGELOG.md

@@ -1,23 +0,0 @@
-# CHANGELOG
-
-<!-- version list -->
-
-## v1.0.0-dev.2 (2026-07-24)
-
-### Documentation
-
-- Initial rewrite from source repo
-  ([`80e26c9`](https://github.com/susom/dicom-dre/commit/80e26c99e5f270528dfa2ddb8551b0baf3fdc7b7))
-
-- Scaffolding
-  ([`c1db56a`](https://github.com/susom/dicom-dre/commit/c1db56a224050b8704f82ac99b857d6c0c43690f))
-
-### Performance Improvements
-
-- Redactor caching
-  ([`ce14989`](https://github.com/susom/dicom-dre/commit/ce14989512d0d688d6b726444c84f91cafc28757))
-
-
-## v1.0.0-dev.1 (2026-07-24)
-
-- Initial Release