Add tests and remove reconstruct() (pydicom#61)

docs/changes/v2.0.0.rst

@@ -11,3 +11,4 @@ Changes
 * Switched packaging and build to ``pyproject.toml``
 * Added type hints
 * Added support for version 2 of the pixel data decoding interface
+* Removed ``utils.reconstruct()``

libjpeg/_libjpeg.pyx

@@ -133,44 +133,3 @@ def get_parameters(src: bytes) -> Tuple[int, Dict[str, int]]:
     }
 
     return status, parameters
-
-
-cdef extern from "cmd/reconstruct.hpp":
-    cdef void Reconstruct(
-        const char *inArray,
-        const char *outArray,
-        int colortrafo,
-        const char *alpha,
-        bool upsample,
-    )
-
-
-def reconstruct(
-    fin: bytes,
-    fout: bytes,
-    colourspace: int,
-    falpha: Union[bytes, None],
-    upsample: bool,
-) -> None:
-    """Decode the JPEG file in `fin` and write it to `fout` as PNM.
-
-    Parameters
-    ----------
-    fin : bytes
-        The path to the JPEG file to be decoded.
-    fout : bytes
-        The path to the decoded PNM file.
-    colourspace : int
-        The colourspace transform to apply.
-    falpha : bytes or None
-        The path where any decoded alpha channel data will be written,
-        otherwise ``None`` to not write alpha channel data. Equivalent to the
-        ``-al file`` flag.
-    upsample : bool
-        ``True`` to disable automatic upsampling, equivalent to the ``-U``
-        flag.
-    """
-    if falpha is None:
-        Reconstruct(fin, fout, colourspace, NULL, upsample)
-    else:
-        Reconstruct(fin, fout, colourspace, falpha, upsample)

libjpeg/tests/test_decode.py

@@ -90,6 +90,35 @@ def test_decode_bytes():
     assert 255 == arr[95, 50]
 
 
+def test_decode_binaryio():
+    """Test decode using binaryio."""
+    with open(DIR_10918 / "p1" / "A1.JPG", "rb") as f:
+        arr = decode(f)
+        assert arr.flags.writeable
+        assert "uint8" == arr.dtype
+        assert arr.shape == (257, 255, 4)
+
+
+def test_decode_raises():
+    """Test decode raises if invalid type"""
+    msg = (
+        "Invalid type 'NoneType' - must be the path to a JPEG file, a "
+        "buffer containing the JPEG data or an open JPEG file-like"
+    )
+    with pytest.raises(TypeError, match=msg):
+        decode(None)
+
+
+def test_v1_invalid_photometric_raises():
+    """Test decode_pixel_data raises if invalid photometric interpretation"""
+    msg = (
+        r"The \(0028,0004\) Photometric Interpretation element is missing "
+        "from the dataset"
+    )
+    with pytest.raises(ValueError, match=msg):
+        decode_pixel_data(DIR_10918 / "p1" / "A1.JPG", version=1)
+
+
 # TODO: convert to using straight JPG data
 @pytest.mark.skipif(not HAS_PYDICOM, reason="No pydicom")
 def test_invalid_colourspace_warns():
@@ -261,7 +290,7 @@ def test_v2_non_conformant_raises(self):
         nr_frames = ds.get("NumberOfFrames", 1)
         frame = next(generate_pixel_data_frame(ds.PixelData, nr_frames))
         msg = (
-            r"libjpeg error code '-1038' returned from decode\(\): A "
+            r"libjpeg error code '-1038' returned from Decode\(\): A "
             r"misplaced marker segment was found - scan start must be zero "
             r"and scan stop must be 63 for the sequential operating modes"
         )

libjpeg/tests/test_handler.py

@@ -10,7 +10,8 @@
 except ImportError:
     HAS_PYDICOM = False
 
-from libjpeg import decode
+from libjpeg import decode, decode_pixel_data
+from libjpeg.utils import COLOURSPACE
 from libjpeg.data import get_indexed_datasets
 
 
@@ -39,6 +40,13 @@ def plot(self, arr, index=None, cmap=None):
         plt.show()
 
 
+@pytest.fixture
+def add_invalid_colour():
+    COLOURSPACE["INVALID"] = -1
+    yield
+    del COLOURSPACE["INVALID"]
+
+
 @pytest.mark.skipif(not HAS_PYDICOM, reason="No dependencies")
 class TestLibrary:
     """Tests for libjpeg itself."""
@@ -57,7 +65,7 @@ def test_non_conformant_raises(self):
         with pytest.raises(RuntimeError, match=msg):
             item["ds"].pixel_array
 
-    def test_invalid_colour_transform(self):
+    def test_invalid_colour_transform(self, add_invalid_colour):
         """Test that an invalid colour transform raises an exception."""
         ds_list = get_indexed_datasets("1.2.840.10008.1.2.4.50")
         # Image has invalid Se value in the SOS marker segment
@@ -70,6 +78,13 @@ def test_invalid_colour_transform(self):
         with pytest.raises(RuntimeError, match=msg):
             decode(data, -1)
 
+        with pytest.raises(RuntimeError, match=msg):
+            decode_pixel_data(
+                data,
+                photometric_interpretation="INVALID",
+                version=2,
+            )
+
 
 # ISO/IEC 10918 JPEG
 @pytest.mark.skipif(not HAS_PYDICOM, reason="No dependencies")

libjpeg/tests/test_parameters.py

@@ -12,6 +12,7 @@
 
 from libjpeg import get_parameters
 from libjpeg.data import get_indexed_datasets, JPEG_DIRECTORY
+from libjpeg.utils import LIBJPEG_ERROR_CODES
 
 
 DIR_10918 = os.path.join(JPEG_DIRECTORY, "10918")
@@ -74,6 +75,47 @@ def test_get_parameters_bytes():
     assert info[3] == params["precision"]
 
 
+def test_get_parameters_binary():
+    """Test get_parameters() using binaryio."""
+    with open(os.path.join(DIR_10918, "p1", "A1.JPG"), "rb") as f:
+        params = get_parameters(f)
+
+    info = (257, 255, 4, 8)
+
+    assert (info[0], info[1]) == (params["rows"], params["columns"])
+    assert info[2] == params["nr_components"]
+    assert info[3] == params["precision"]
+
+
+def test_get_parameters_path():
+    """Test get_parameters() using a path."""
+    params = get_parameters(os.path.join(DIR_10918, "p1", "A1.JPG"))
+
+    info = (257, 255, 4, 8)
+
+    assert (info[0], info[1]) == (params["rows"], params["columns"])
+    assert info[2] == params["nr_components"]
+    assert info[3] == params["precision"]
+
+@pytest.fixture
+def remove_error_code():
+    msg = LIBJPEG_ERROR_CODES[-1038]
+    del LIBJPEG_ERROR_CODES[-1038]
+    yield
+    LIBJPEG_ERROR_CODES[-1038] = msg
+
+
+@pytest.mark.skipif(not HAS_PYDICOM, reason="No dependencies")
+def test_get_parameters_unknown_error(remove_error_code):
+    """Test get_parameters() using a path."""
+    msg = (
+        r"Unknown error code '-1038' returned from GetJPEGParameters\(\): "
+        r"unexpected EOF while parsing the image"
+    )
+    with pytest.raises(RuntimeError, match=msg):
+        get_parameters(b"\xFF\xD8\xFF\xD8\x01\x02\x03")
+
+
 @pytest.mark.skipif(not HAS_PYDICOM, reason="No pydicom")
 def test_non_conformant_raises():
     """Test that a non-conformant JPEG image raises an exception."""
@@ -166,13 +208,8 @@ def test_jls_lossless(self, fname, info):
         # info: (rows, columns, spp, bps)
         index = get_indexed_datasets("1.2.840.10008.1.2.4.80")
         ds = index[fname]["ds"]
-
-        print(fname)
-
         frame = next(self.generate_frames(ds))
         params = get_parameters(frame)
-        print(params)
-        print(info)
 
         assert (info[0], info[1]) == (params["rows"], params["columns"])
         assert info[2] == params["nr_components"]
@@ -184,7 +221,6 @@ def test_jls_lossy(self, fname, info):
         # info: (rows, columns, spp, bps)
         index = get_indexed_datasets("1.2.840.10008.1.2.4.81")
         ds = index[fname]["ds"]
-
         frame = next(self.generate_frames(ds))
         params = get_parameters(frame)
 

libjpeg/utils.py

@@ -118,8 +118,9 @@ def decode(
         required_methods = ["read", "tell", "seek"]
         if not all([hasattr(stream, meth) for meth in required_methods]):
             raise TypeError(
-                "The Python object containing the encoded JPEG 2000 data must "
-                "either be bytes or have read(), tell() and seek() methods."
+                f"Invalid type '{type(stream).__name__}' - must be the path "
+                "to a JPEG file, a buffer containing the JPEG data or an open "
+                "JPEG file-like"
             )
         buffer = stream.read()
 
@@ -222,11 +223,11 @@ def decode_pixel_data(
 
     if code in LIBJPEG_ERROR_CODES:
         raise RuntimeError(
-            f"libjpeg error code '{code}' returned from decode(): "
+            f"libjpeg error code '{code}' returned from Decode(): "
             f"{LIBJPEG_ERROR_CODES[code]} - {msg}"
         )
 
-    raise RuntimeError(f"Unknown error code '{code}' returned from decode(): {msg}")
+    raise RuntimeError(f"Unknown error code '{code}' returned from Decode(): {msg}")
 
 
 def get_parameters(
@@ -280,53 +281,5 @@ def get_parameters(
         )
 
     raise RuntimeError(
-        f"Unknown error code '{status}' returned from GetJPEGParameters(): {msg}"
+        f"Unknown error code '{code}' returned from GetJPEGParameters(): {msg}"
     )
-
-
-def reconstruct(
-    fin: Union[str, os.PathLike, bytes],
-    fout: Union[str, os.PathLike, bytes],
-    colourspace: int = 1,
-    falpha: Union[bytes, None] = None,
-    upsample: bool = True,
-) -> None:
-    """Simple wrapper for the libjpeg ``cmd/reconstruct::Reconstruct()``
-    function.
-
-    Parameters
-    ----------
-    fin : bytes
-        The path to the JPEG file to be decoded.
-    fout : bytes
-        The path to the decoded PPM or PGM (if `falpha` is ``True``) file(s).
-    colourspace : int, optional
-        The colourspace transform to apply.
-        | ``0`` : ``JPGFLAG_MATRIX_COLORTRANSFORMATION_NONE``  (``-c`` flag)
-        | ``1`` : ``JPGFLAG_MATRIX_COLORTRANSFORMATION_YCBCR`` (default)
-        | ``2`` : ``JPGFLAG_MATRIX_COLORTRANSFORMATION_LSRCT`` (``-cls`` flag)
-        | ``2`` : ``JPGFLAG_MATRIX_COLORTRANSFORMATION_RCT``
-        | ``3`` : ``JPGFLAG_MATRIX_COLORTRANSFORMATION_FREEFORM``
-        See `here<https://github.com/thorfdbg/libjpeg/blob/87636f3b26b41b85b2fb7355c589a8c456ef808c/interface/parameters.hpp#L381>`_
-        for more information.
-    falpha : bytes, optional
-        The path where any decoded alpha channel data will be written (as a
-        PGM file), otherwise ``None`` (default) to not write alpha channel
-        data. Equivalent to the ``-al file`` flag.
-    upsample : bool, optional
-        ``True`` (default) to disable automatic upsampling, equivalent to
-        the ``-U`` flag.
-    """
-    if isinstance(fin, (str, Path)):
-        fin = str(fin)
-        fin = bytes(fin, "utf-8")
-
-    if isinstance(fout, (str, Path)):
-        fout = str(fout)
-        fout = bytes(fout, "utf-8")
-
-    if falpha and isinstance(falpha, (str, Path)):
-        falpha = str(falpha)
-        falpha = bytes(falpha, "utf-8")
-
-    _libjpeg.reconstruct(fin, fout, colourspace, falpha, upsample)